so.owl
type: Ontology
IAO format-version: 1.2
IAO date: 14:04:2011 13:58
IAO auto-generated-by: OBO-Edit 2.1-beta10
IAO remark: autogenerated-by\: DAG-Edit version 1.417\nsaved-by\: eilbeck\ndate\: Tue May 11 15\:18\:44 PDT 2004\nversion\: $Revision\: 1.45 $
IAO saved-by: kareneilbeck
IAO default-namespace: sequence

adjacent_to
type: ObjectProperty
IAO_0000115: A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence. X adjacent_to Y iff X and Y share a boundary but do not overlap.
IAO subset: SOFA
IAO id: adjacent_to

Axiom
annotated target: A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence. X adjacent_to Y iff X and Y share a boundary but do not overlap.
IAO xref: PMID:20226267
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: adjacent_to

associated_with
type: ObjectProperty
comment: This relationship is vague and up for discussion.
IAO id: associated_with

complete_evidence_for_feature
type: ObjectProperty
type: TransitiveProperty
IAO_0000115: B is complete_evidence_for_feature A if the extent (5' and 3' boundaries) and internal boundaries of B fully support the extent and internal boundaries of A.
comment: If A is a feature with multiple regions such as a multi exon transcript, the supporting EST evidence is complete if each of the regions is supported by an equivalent region in B. Also there must be no extra regions in B that are not represented in A. This relationship was requested by jeltje on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222.
IAO id: complete_evidence_for_feature
sub property of: evidence_for_feature

Axiom
annotated target: B is complete_evidence_for_feature A if the extent (5' and 3' boundaries) and internal boundaries of B fully support the extent and internal boundaries of A.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: complete_evidence_for_feature

connects_on
type: ObjectProperty
comment: Example: A splice_junction connects_on exon, exon, mature_transcript.
IAO creation date: Thu Oct 14 01:38:51 PDT 2010
IAO_0000115: X connects_on Y, Z, R iff whenever Z is on a R, X is adjacent to a Y and adjacent to a Z.
IAO id: connects_on
IAO created by: kareneilbeck

Axiom
IAO xref: PMID:20226267
annotated target: X connects_on Y, Z, R iff whenever Z is on a R, X is adjacent to a Y and adjacent to a Z.
annotated property: IAO_0000115
annotated source: connects_on

contained_by
type: ObjectProperty
type: TransitiveProperty
comment: The inverse is contains. Example: intein contained_by immature_peptide_region.
IAO creation date: Thu Oct 14 01:26:16 PDT 2010
IAO_0000115: X contained_by Y iff X starts after start of Y and X ends before end of Y.
IAO id: contained_by
IAO created by: kareneilbeck

Axiom
IAO xref: PMID:20226267
annotated target: X contained_by Y iff X starts after start of Y and X ends before end of Y.
annotated property: IAO_0000115
annotated source: contained_by

contains
type: ObjectProperty
type: TransitiveProperty
comment: Example: pre_miRNA contains miRNA_loop.
IAO_0000115: The inverse of contained_by.
IAO creation date: Thu Oct 14 01:32:15 PDT 2010
IAO id: contains
IAO created by: kareneilbeck

Axiom
IAO xref: PMID:20226267
annotated target: The inverse of contained_by.
annotated property: IAO_0000115
annotated source: contains

derives_from
type: ObjectProperty
type: TransitiveProperty
IAO subset: SOFA
IAO id: derives_from

disconnected_from
type: ObjectProperty
comment: Example: intron disconnected from exon \{on primary_transcript}.
IAO creation date: Thu Oct 14 01:42:10 PDT 2010
IAO_0000115: X is disconnected_from Y iff it is not the case that X overlaps Y.
IAO id: disconnected_from
IAO created by: kareneilbeck

Axiom
IAO xref: PMID:20226267
annotated target: X is disconnected_from Y iff it is not the case that X overlaps Y.
annotated property: IAO_0000115
annotated source: disconnected_from

edited_from
type: ObjectProperty
IAO creation date: Wed Aug 19 02:19:45 PDT 2009
IAO id: edited_from
IAO created by: kareneilbeck

edited_to
type: ObjectProperty
IAO creation date: Wed Aug 19 02:19:11 PDT 2009
IAO id: edited_to
IAO created by: kareneilbeck

evidence_for_feature
type: ObjectProperty
type: TransitiveProperty
IAO_0000115: B is evidence_for_feature A, if an instance of B supports the existence of A.
comment: This relationship was requested by nlw on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222.
IAO id: evidence_for_feature

Axiom
annotated target: B is evidence_for_feature A, if an instance of B supports the existence of A.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: evidence_for_feature

exemplar_of
type: ObjectProperty
comment: Tracker id: 2594157.
IAO_0000115: X is exemplar of Y if X is the best evidence for Y.
IAO id: exemplar_of

Axiom
IAO xref: SO:ke
annotated target: X is exemplar of Y if X is the best evidence for Y.
annotated property: IAO_0000115
annotated source: exemplar_of

finished_by
type: ObjectProperty
comment: Example CDS finished_by stop_codon.
IAO creation date: Thu Oct 14 01:45:45 PDT 2010
IAO_0000115: Xy is finished_by Y if Y part of X, and X and Y share a 3' boundary.
IAO id: finished_by
IAO created by: kareneilbeck

Axiom
IAO xref: PMID:20226267
annotated target: Xy is finished_by Y if Y part of X, and X and Y share a 3' boundary.
annotated property: IAO_0000115
annotated source: finished_by

finishes
type: ObjectProperty
comment: Example: stop_codon finishes CDS.
IAO creation date: Thu Oct 14 02:17:53 PDT 2010
IAO_0000115: X finishes Y if X is part_of Y and X and Y share a 3' or C terminal boundary.
IAO id: finishes
IAO created by: kareneilbeck

Axiom
IAO xref: PMID:20226267
annotated target: X finishes Y if X is part_of Y and X and Y share a 3' or C terminal boundary.
annotated property: IAO_0000115
annotated source: finishes

genome_of
type: ObjectProperty
IAO id: genome_of

guided_by
type: ObjectProperty
IAO creation date: Wed Aug 19 02:27:04 PDT 2009
IAO id: guided_by
IAO created by: kareneilbeck

guides
type: ObjectProperty
IAO creation date: Wed Aug 19 02:27:24 PDT 2009
IAO id: guides
IAO created by: kareneilbeck

has_integral_part
type: ObjectProperty
comment: Example: mRNA has_integral_part CDS.
IAO creation date: Wed Aug 19 00:01:46 PDT 2009
IAO_0000115: X has_integral_part Y if and only if: X has_part Y and Y part_of X.
IAO id: has_integral_part
IAO created by: kareneilbeck
sub property of: has_part

Axiom
annotated target: X has_integral_part Y if and only if: X has_part Y and Y part_of X.
IAO xref: http://precedings.nature.com/documents/3495/version/1
annotated property: IAO_0000115
annotated source: has_integral_part

has_origin
type: ObjectProperty
IAO id: has_origin

has_part
type: ObjectProperty
comment: Example: operon has_part gene.
IAO_0000115: Inverse of part_of.
IAO id: has_part

Axiom
annotated target: Inverse of part_of.
IAO xref: http://precedings.nature.com/documents/3495/version/1
annotated property: IAO_0000115
annotated source: has_part

has_quality
type: ObjectProperty
comment: The relationship between a feature and an attribute.
IAO id: has_quality

homologous_to
type: ObjectProperty
type: SymmetricProperty
IAO subset: SOFA
IAO id: homologous_to
sub property of: similar_to

integral_part_of
type: ObjectProperty
comment: Example: exon integral_part_of transcript.
IAO creation date: Wed Aug 19 00:03:28 PDT 2009
IAO_0000115: X integral_part_of Y if and only if: X part_of Y and Y has_part X.
IAO id: integral_part_of
IAO created by: kareneilbeck
sub property of: part_of

Axiom
annotated target: X integral_part_of Y if and only if: X part_of Y and Y has_part X.
IAO xref: http://precedings.nature.com/documents/3495/version/1
annotated property: IAO_0000115
annotated source: integral_part_of

is_consecutive_sequence_of
type: ObjectProperty
comment: Example: region is consecutive_sequence of base.
IAO_0000115: R is_consecutive_sequence_of R iff every instance of R is equivalent to a collection of instances of U:u1, u2, un, such that no pair of ux uy is overlapping and for all ux, it is adjacent to ux-1 and ux+1, with the exception of the initial and terminal u1,and un (which may be identical).
IAO creation date: Thu Oct 14 02:19:48 PDT 2010
IAO id: is_consecutive_sequence_of
IAO created by: kareneilbeck

Axiom
IAO xref: PMID:20226267
annotated target: R is_consecutive_sequence_of R iff every instance of R is equivalent to a collection of instances of U:u1, u2, un, such that no pair of ux uy is overlapping and for all ux, it is adjacent to ux-1 and ux+1, with the exception of the initial and terminal u1,and un (which may be identical).
annotated property: IAO_0000115
annotated source: is_consecutive_sequence_of

maximally_overlaps
type: ObjectProperty
IAO_0000115: A maximally_overlaps X iff all parts of A (including A itself) overlap both A and Y.
comment: Example: non_coding_region_of_exon maximally_overlaps the intersections of exon and UTR.
IAO creation date: Thu Oct 14 01:34:48 PDT 2010
IAO created by: kareneilbeck
IAO id: maximally_overlaps

Axiom
annotated target: A maximally_overlaps X iff all parts of A (including A itself) overlap both A and Y.
IAO xref: PMID:20226267
annotated property: IAO_0000115
annotated source: maximally_overlaps

member_of
type: ObjectProperty
type: TransitiveProperty
comment: A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444.
IAO subset: SOFA
IAO id: member_of

non_functional_homolog_of
type: ObjectProperty
IAO_0000115: A relationship between a pseudogenic feature and its functional ancestor.
IAO subset: SOFA
IAO id: non_functional_homolog_of
sub property of: homologous_to

Axiom
annotated target: A relationship between a pseudogenic feature and its functional ancestor.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: non_functional_homolog_of

orthologous_to
type: ObjectProperty
type: SymmetricProperty
IAO subset: SOFA
IAO id: orthologous_to
sub property of: homologous_to

overlaps
type: ObjectProperty
comment: Example: coding_exon overlaps CDS.
IAO creation date: Thu Oct 14 01:33:15 PDT 2010
IAO_0000115: X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y.
IAO created by: kareneilbeck
IAO id: overlaps

Axiom
IAO xref: PMID:20226267
annotated target: X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y.
annotated property: IAO_0000115
annotated source: overlaps

paralogous_to
type: ObjectProperty
type: SymmetricProperty
IAO subset: SOFA
IAO id: paralogous_to
sub property of: homologous_to

part_of
type: ObjectProperty
type: TransitiveProperty
comment: Example: amino_acid part_of polypeptide.
IAO subset: SOFA
IAO_0000115: X part_of Y if X is a subregion of Y.
IAO id: part_of

Axiom
annotated target: X part_of Y if X is a subregion of Y.
IAO xref: http://precedings.nature.com/documents/3495/version/1
annotated property: IAO_0000115
annotated source: part_of

partial_evidence_for_feature
type: ObjectProperty
IAO_0000115: B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A.
IAO id: partial_evidence_for_feature
sub property of: evidence_for_feature

Axiom
annotated target: B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: partial_evidence_for_feature

position_of
type: ObjectProperty
IAO id: position_of

processed_from
type: ObjectProperty
comment: Example: miRNA processed_from miRNA_primary_transcript.
IAO_0000115: Inverse of processed_into.
IAO creation date: Wed Aug 19 00:14:00 PDT 2009
IAO created by: kareneilbeck
IAO id: processed_from

Axiom
annotated target: Inverse of processed_into.
IAO xref: http://precedings.nature.com/documents/3495/version/1
annotated property: IAO_0000115
annotated source: processed_from

processed_into
type: ObjectProperty
comment: Example: miRNA_primary_transcript processed into miRNA.
IAO creation date: Wed Aug 19 00:15:02 PDT 2009
IAO_0000115: X is processed_into Y if a region X is modified to create Y.
IAO created by: kareneilbeck
IAO id: processed_into

Axiom
annotated target: X is processed_into Y if a region X is modified to create Y.
IAO xref: http://precedings.nature.com/documents/3495/version/1
annotated property: IAO_0000115
annotated source: processed_into

recombined_from
type: ObjectProperty
IAO creation date: Wed Aug 19 02:21:03 PDT 2009
IAO created by: kareneilbeck
IAO id: recombined_from

recombined_to
type: ObjectProperty
IAO creation date: Wed Aug 19 02:20:07 PDT 2009
IAO created by: kareneilbeck
IAO id: recombined_to

sequence_of
type: ObjectProperty
IAO id: sequence_of

similar_to
type: ObjectProperty
type: SymmetricProperty
IAO subset: SOFA
IAO id: similar_to

started_by
type: ObjectProperty
comment: Example: CDS started_by start_codon.
IAO creation date: Thu Oct 14 01:43:55 PDT 2010
IAO_0000115: X is strted_by Y if Y is part_of X and X and Y share a 5' boundary.
IAO created by: kareneilbeck
IAO id: started_by

Axiom
IAO xref: PMID:20226267
annotated target: X is strted_by Y if Y is part_of X and X and Y share a 5' boundary.
annotated property: IAO_0000115
annotated source: started_by

starts
type: ObjectProperty
comment: Example: start_codon starts CDS.
IAO creation date: Thu Oct 14 01:47:53 PDT 2010
IAO_0000115: X starts Y if X is part of Y, and A and Y share a 5' or N-terminal boundary.
IAO created by: kareneilbeck
IAO id: starts

Axiom
IAO xref: PMID:20226267
annotated target: X starts Y if X is part of Y, and A and Y share a 5' or N-terminal boundary.
annotated property: IAO_0000115
annotated source: starts

trans_spliced_from
type: ObjectProperty
IAO creation date: Wed Aug 19 02:22:14 PDT 2009
IAO created by: kareneilbeck
IAO id: trans_spliced_from

trans_spliced_to
type: ObjectProperty
IAO creation date: Wed Aug 19 02:22:00 PDT 2009
IAO created by: kareneilbeck
IAO id: trans_spliced_to

transcribed_from
type: ObjectProperty
comment: Example: primary_transcript transcribed_from gene.
IAO creation date: Wed Aug 19 00:05:39 PDT 2009
IAO_0000115: X is transcribed_from Y if X is synthesized from template Y.
IAO created by: kareneilbeck
IAO id: transcribed_from

Axiom
annotated target: X is transcribed_from Y if X is synthesized from template Y.
IAO xref: http://precedings.nature.com/documents/3495/version/1
annotated property: IAO_0000115
annotated source: transcribed_from

transcribed_to
type: ObjectProperty
comment: Example: gene transcribed_to primary_transcript.
IAO_0000115: Inverse of transcribed_from.
IAO creation date: Wed Aug 19 00:08:24 PDT 2009
IAO created by: kareneilbeck
IAO id: transcribed_to

Axiom
annotated target: Inverse of transcribed_from.
IAO xref: http://precedings.nature.com/documents/3495/version/1
annotated property: IAO_0000115
annotated source: transcribed_to

translates_to
type: ObjectProperty
comment: Example: codon translates_to amino_acid.
IAO_0000115: Inverse of translation _of.
IAO creation date: Wed Aug 19 00:11:53 PDT 2009
IAO created by: kareneilbeck
IAO id: translates_to

Axiom
annotated target: Inverse of translation _of.
IAO xref: http://precedings.nature.com/documents/3495/version/1
annotated property: IAO_0000115
annotated source: translates_to

translation_of
type: ObjectProperty
comment: Example: Polypeptide translation_of CDS.
IAO creation date: Wed Aug 19 00:09:59 PDT 2009
IAO_0000115: X is translation of Y if X is translated by ribosome to create Y.
IAO created by: kareneilbeck
IAO id: translation_of

Axiom
annotated target: X is translation of Y if X is translated by ribosome to create Y.
IAO xref: http://precedings.nature.com/documents/3495/version/1
annotated property: IAO_0000115
annotated source: translation_of

variant_of
type: ObjectProperty
IAO_0000115: A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A.
comment: Added to SO during the immunology workshop, June 2007. This relationship was approved by Barry Smith.
IAO id: variant_of

Axiom
annotated target: A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A.
IAO xref: SO:immuno_workshop
annotated property: IAO_0000115
annotated source: variant_of

Sequence_Ontology
type: Class
IAO id: SO:0000000
IAO subset: SOFA
deprecated: true

region
type: Class
subclass of: sequence_feature
disjoint with: junction
IAO_0000115: A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
IAO id: SO:0000001
IAO subset: SOFA
IAO_0000118: sequence

Axiom
annotated target: A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: region

Axiom
IAO scope: EXACT
annotated target: sequence
annotated property: IAO_0000118
annotated source: region

sequence_secondary_structure
type: Class
subclass of: SO_0001411
IAO_0000115: A folded sequence.
IAO id: SO:0000002
IAO_0000118: sequence secondary structure

Axiom
annotated target: A folded sequence.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: sequence_secondary_structure

Axiom
IAO scope: EXACT
annotated target: sequence secondary structure
annotated property: IAO_0000118
annotated source: sequence_secondary_structure

G_quartet
type: Class
subclass of: sequence_secondary_structure
IAO_0000118: G quartet
IAO_0000118: G tetrad
IAO_0000118: G-quadruplex
IAO_0000118: G-quartet
IAO_0000115: G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet.
IAO_0000118: G-tetrad
IAO_0000118: G_quadruplex
IAO id: SO:0000003
IAO_0000118: guanine tetrad
IAO xref: http://en.wikipedia.org/wiki/G-quadruplex

Axiom
IAO scope: EXACT
annotated target: G quartet
annotated property: IAO_0000118
annotated source: G_quartet

Axiom
IAO scope: EXACT
annotated target: G-tetrad
annotated property: IAO_0000118
annotated source: G_quartet

Axiom
IAO scope: EXACT
annotated target: G tetrad
annotated property: IAO_0000118
annotated source: G_quartet

Axiom
IAO scope: EXACT
annotated target: guanine tetrad
annotated property: IAO_0000118
annotated source: G_quartet

Axiom
IAO scope: EXACT
annotated target: G_quadruplex
annotated property: IAO_0000118
annotated source: G_quartet

Axiom
annotated target: G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet.
IAO xref: http://www.ncbi.nlm.nih.gov/pubmed/7919797
annotated property: IAO_0000115
annotated source: G_quartet

Axiom
IAO scope: EXACT
annotated target: G-quadruplex
annotated property: IAO_0000118
annotated source: G_quartet

Axiom
IAO scope: EXACT
annotated target: G-quartet
annotated property: IAO_0000118
annotated source: G_quartet

interior_coding_exon
type: Class
subclass of: coding_exon
IAO id: SO:0000004
IAO subset: SOFA
IAO_0000118: interior coding exon

Axiom
IAO scope: EXACT
annotated target: interior coding exon
annotated property: IAO_0000118
annotated source: interior_coding_exon

satellite_DNA
type: Class
subclass of: tandem_repeat
IAO id: SO:0000005
IAO subset: SOFA
IAO_0000115: The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA.
IAO xref: http://en.wikipedia.org/wiki/Satellite_DNA
IAO_0000118: satellite DNA

Axiom
IAO scope: EXACT
annotated target: satellite DNA
annotated property: IAO_0000118
annotated source: satellite_DNA

Axiom
annotated target: The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA.
IAO xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
annotated property: IAO_0000115
annotated source: satellite_DNA

PCR_product
type: Class
subclass of: reagent
IAO_0000115: A region amplified by a PCR reaction.
IAO_0000118: PCR product
IAO id: SO:0000006
IAO subset: SOFA
comment: This term is mapped to MGED. This term is now located in OBI, with the following ID OBI_0000406.
IAO_0000118: amplicon
IAO xref: http://en.wikipedia.org/wiki/RAPD

Axiom
IAO scope: RELATED
annotated target: amplicon
annotated property: IAO_0000118
annotated source: PCR_product

Axiom
annotated target: A region amplified by a PCR reaction.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: PCR_product

Axiom
IAO scope: EXACT
annotated target: PCR product
annotated property: IAO_0000118
annotated source: PCR_product

read_pair
type: Class
subclass of: read
subclass of: Restriction
  on property: part_of
  some values from: SO_0001790
subclass of: Restriction
  on property: part_of
  some values from: contig
IAO_0000115: One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert.
IAO id: SO:0000007
IAO subset: SOFA
IAO_0000118: mate pair
IAO_0000118: read-pair

Axiom
IAO scope: EXACT
annotated target: mate pair
annotated property: IAO_0000118
annotated source: read_pair

Axiom
annotated target: One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert.
IAO xref: SO:ls
annotated property: IAO_0000115
annotated source: read_pair

Axiom
IAO scope: EXACT
annotated target: read-pair
annotated property: IAO_0000118
annotated source: read_pair

gene_sensu_your_favorite_organism
type: Class
IAO id: SO:0000008
deprecated: true

gene_class
type: Class
IAO id: SO:0000009
deprecated: true

protein_coding
type: Class
subclass of: gene_attribute
IAO id: SO:0000010
IAO_0000118: protein-coding

Axiom
IAO scope: EXACT
annotated target: protein-coding
annotated property: IAO_0000118
annotated source: protein_coding

non_protein_coding
type: Class
subclass of: gene_attribute
IAO id: SO:0000011
IAO_0000118: non protein-coding

Axiom
IAO scope: EXACT
annotated target: non protein-coding
annotated property: IAO_0000118
annotated source: non_protein_coding

scRNA_primary_transcript
type: Class
subclass of: nc_primary_transcript
IAO id: SO:0000012
IAO_0000115: The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a eukaryote.
IAO_0000118: scRNA primary transcript
IAO_0000118: scRNA transcript
IAO_0000118: small cytoplasmic RNA
IAO_0000118: small cytoplasmic RNA transcript
IAO_0000118: small_cytoplasmic_RNA

Axiom
IAO scope: RELATED
annotated target: small cytoplasmic RNA
annotated property: IAO_0000118
annotated source: scRNA_primary_transcript

Axiom
IAO scope: EXACT
annotated target: small cytoplasmic RNA transcript
annotated property: IAO_0000118
annotated source: scRNA_primary_transcript

Axiom
IAO scope: EXACT
annotated target: scRNA transcript
annotated property: IAO_0000118
annotated source: scRNA_primary_transcript

Axiom
IAO scope: RELATED
annotated target: small_cytoplasmic_RNA
annotated property: IAO_0000118
annotated source: scRNA_primary_transcript

Axiom
annotated target: The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a eukaryote.
IAO xref: http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html
annotated property: IAO_0000115
annotated source: scRNA_primary_transcript

Axiom
IAO scope: EXACT
annotated target: scRNA primary transcript
annotated property: IAO_0000118
annotated source: scRNA_primary_transcript

scRNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: scRNA_primary_transcript
IAO_0000115: Any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote.
IAO id: SO:0000013
IAO subset: SOFA
IAO_0000118: small cytoplasmic RNA

Axiom
IAO scope: EXACT
annotated target: small cytoplasmic RNA
annotated property: IAO_0000118
annotated source: scRNA

Axiom
annotated target: Any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote.
IAO xref: http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html
annotated property: IAO_0000115
annotated source: scRNA

INR_motif
type: Class
subclass of: SO_0001660
subclass of: Restriction
  on property: part_of
  some values from: SO_0001669
IAO_0000115: A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element.
comment: Binds TAF1, TAF2.
IAO_0000118: DMp2
IAO_0000118: INR motif
IAO id: SO:0000014
IAO_0000118: initiator
IAO_0000118: initiator motif

Axiom
annotated target: DMp2
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: INR_motif

Axiom
annotated target: A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element.
IAO xref: PMID:12651739
IAO xref: PMID:16858867
annotated property: IAO_0000115
annotated source: INR_motif

Axiom
IAO scope: EXACT
annotated target: INR motif
annotated property: IAO_0000118
annotated source: INR_motif

Axiom
IAO scope: EXACT
annotated target: initiator
annotated property: IAO_0000118
annotated source: INR_motif

Axiom
IAO scope: EXACT
annotated target: initiator motif
annotated property: IAO_0000118
annotated source: INR_motif

DPE_motif
type: Class
subclass of: SO_0001660
subclass of: Restriction
  on property: part_of
  some values from: SO_0001669
IAO_0000115: A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C).
comment: Binds TAF6, TAF9.
IAO_0000118: CRWMGCGWKCGCTTS
IAO_0000118: DPE motif
IAO id: SO:0000015
IAO_0000118: downstream core promoter element

Axiom
annotated target: DPE motif
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DPE_motif

Axiom
IAO scope: EXACT
annotated target: downstream core promoter element
annotated property: IAO_0000118
annotated source: DPE_motif

Axiom
annotated target: CRWMGCGWKCGCTTS
IAO scope: NARROW
annotated property: IAO_0000118
annotated source: DPE_motif

Axiom
annotated target: A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C).
IAO xref: PMID:12651739\:12537576
IAO xref: PMID:16858867
annotated property: IAO_0000115
annotated source: DPE_motif

BREu_motif
type: Class
subclass of: SO_0001660
subclass of: Restriction
  on property: part_of
  some values from: SO_0001669
IAO_0000115: A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB.
IAO_0000118: B-recognition element
IAO_0000118: BRE motif
IAO_0000118: BREu
IAO_0000118: BREu motif
comment: Binds TFIIB.
IAO id: SO:0000016
IAO_0000118: TFIIB recognition element
IAO_0000118: transcription factor B-recognition element

Axiom
annotated target: BREu motif
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: BREu_motif

Axiom
annotated target: BRE motif
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: BREu_motif

Axiom
IAO scope: EXACT
annotated target: transcription factor B-recognition element
annotated property: IAO_0000118
annotated source: BREu_motif

Axiom
annotated target: BREu
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: BREu_motif

Axiom
IAO scope: RELATED
annotated target: TFIIB recognition element
annotated property: IAO_0000118
annotated source: BREu_motif

Axiom
annotated target: A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB.
IAO xref: PMID:12651739
IAO xref: PMID:16858867
annotated property: IAO_0000115
annotated source: BREu_motif

Axiom
annotated target: B-recognition element
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: BREu_motif

PSE_motif
type: Class
subclass of: DNA_motif
subclass of: Restriction
  on property: part_of
  some values from: promoter
IAO_0000115: A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G).
IAO_0000118: PSE motif
IAO id: SO:0000017
IAO_0000118: proximal sequence element

Axiom
annotated target: A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G).
IAO xref: PMID:12651739
annotated property: IAO_0000115
annotated source: PSE_motif

Axiom
IAO scope: EXACT
annotated target: proximal sequence element
annotated property: IAO_0000118
annotated source: PSE_motif

Axiom
IAO scope: EXACT
annotated target: PSE motif
annotated property: IAO_0000118
annotated source: PSE_motif

linkage_group
type: Class
subclass of: SO_0001411
IAO_0000115: A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned.
IAO id: SO:0000018
IAO xref: http://en.wikipedia.org/wiki/Linkage_group
IAO_0000118: linkage group

Axiom
IAO scope: EXACT
annotated target: linkage group
annotated property: IAO_0000118
annotated source: linkage_group

Axiom
annotated target: A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned.
IAO xref: ISBN:038752046
annotated property: IAO_0000115
annotated source: linkage_group

RNA_internal_loop
type: Class
subclass of: RNA_motif
IAO_0000115: A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge.
IAO_0000118: RNA internal loop
IAO id: SO:0000020

Axiom
IAO scope: EXACT
annotated target: RNA internal loop
annotated property: IAO_0000118
annotated source: RNA_internal_loop

Axiom
annotated target: A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: RNA_internal_loop

asymmetric_RNA_internal_loop
type: Class
subclass of: RNA_internal_loop
IAO_0000115: An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand.
IAO id: SO:0000021
IAO_0000118: asymmetric RNA internal loop

Axiom
annotated target: An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: asymmetric_RNA_internal_loop

Axiom
IAO scope: EXACT
annotated target: asymmetric RNA internal loop
annotated property: IAO_0000118
annotated source: asymmetric_RNA_internal_loop

A_minor_RNA_motif
type: Class
subclass of: RNA_motif
IAO_0000118: A minor RNA motif
IAO_0000115: A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix.
IAO id: SO:0000022

Axiom
annotated target: A minor RNA motif
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: A_minor_RNA_motif

Axiom
annotated target: A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: A_minor_RNA_motif

K_turn_RNA_motif
type: Class
subclass of: asymmetric_RNA_internal_loop
IAO_0000118: K turn RNA motif
IAO_0000118: K-turn
IAO id: SO:0000023
IAO_0000115: The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices.
IAO xref: http://en.wikipedia.org/wiki/K-turn
IAO_0000118: kink turn
IAO_0000118: kink-turn motif

Axiom
IAO scope: EXACT
annotated target: K-turn
annotated property: IAO_0000118
annotated source: K_turn_RNA_motif

Axiom
IAO scope: EXACT
annotated target: kink-turn motif
annotated property: IAO_0000118
annotated source: K_turn_RNA_motif

Axiom
IAO scope: EXACT
annotated target: kink turn
annotated property: IAO_0000118
annotated source: K_turn_RNA_motif

Axiom
IAO scope: EXACT
annotated target: K turn RNA motif
annotated property: IAO_0000118
annotated source: K_turn_RNA_motif

Axiom
IAO xref: SO:ke
annotated target: The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices.
annotated property: IAO_0000115
annotated source: K_turn_RNA_motif

sarcin_like_RNA_motif
type: Class
subclass of: asymmetric_RNA_internal_loop
IAO_0000115: A loop in ribosomal RNA containing the sites of attack for ricin and sarcin.
IAO id: SO:0000024
IAO_0000118: sarcin like RNA motif
IAO_0000118: sarcin/ricin RNA domain
IAO_0000118: sarcin/ricin domain
IAO_0000118: sarcin/ricin loop

Axiom
IAO scope: EXACT
annotated target: sarcin/ricin domain
annotated property: IAO_0000118
annotated source: sarcin_like_RNA_motif

Axiom
IAO scope: EXACT
annotated target: sarcin/ricin RNA domain
annotated property: IAO_0000118
annotated source: sarcin_like_RNA_motif

Axiom
IAO scope: EXACT
annotated target: sarcin like RNA motif
annotated property: IAO_0000118
annotated source: sarcin_like_RNA_motif

Axiom
annotated target: A loop in ribosomal RNA containing the sites of attack for ricin and sarcin.
IAO xref: http://www.ncbi.nlm.nih.gov/pubmed/7897662
annotated property: IAO_0000115
annotated source: sarcin_like_RNA_motif

Axiom
IAO scope: EXACT
annotated target: sarcin/ricin loop
annotated property: IAO_0000118
annotated source: sarcin_like_RNA_motif

symmetric_RNA_internal_loop
type: Class
subclass of: RNA_internal_loop
IAO_0000118: A-minor RNA motif
IAO_0000115: An internal RNA loop where the extent of the loop on both stands is the same size.
IAO id: SO:0000025

Axiom
annotated target: A-minor RNA motif
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: symmetric_RNA_internal_loop

Axiom
annotated target: An internal RNA loop where the extent of the loop on both stands is the same size.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: symmetric_RNA_internal_loop

RNA_junction_loop
type: Class
subclass of: RNA_motif
IAO_0000118: RNA junction loop
IAO id: SO:0000026

Axiom
IAO scope: EXACT
annotated target: RNA junction loop
annotated property: IAO_0000118
annotated source: RNA_junction_loop

RNA_hook_turn
type: Class
subclass of: RNA_junction_loop
IAO_0000118: RNA hook turn
IAO id: SO:0000027
IAO_0000118: hook turn
IAO_0000118: hook-turn motif

Axiom
IAO scope: EXACT
annotated target: hook-turn motif
annotated property: IAO_0000118
annotated source: RNA_hook_turn

Axiom
IAO scope: EXACT
annotated target: RNA hook turn
annotated property: IAO_0000118
annotated source: RNA_hook_turn

Axiom
IAO scope: RELATED
annotated target: hook turn
annotated property: IAO_0000118
annotated source: RNA_hook_turn

base_pair
type: Class
subclass of: sequence_secondary_structure
IAO id: SO:0000028
IAO_0000118: base pair
IAO xref: http://en.wikipedia.org/wiki/Base_pair

Axiom
IAO scope: EXACT
annotated target: base pair
annotated property: IAO_0000118
annotated source: base_pair

WC_base_pair
type: Class
subclass of: base_pair
IAO id: SO:0000029
IAO_0000115: The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation.
IAO_0000118: WC base pair
IAO_0000118: Watson Crick base pair
IAO_0000118: Watson-Crick base pair
IAO_0000118: Watson-Crick pair
IAO_0000118: canonical base pair

Axiom
IAO scope: EXACT
annotated target: Watson-Crick pair
annotated property: IAO_0000118
annotated source: WC_base_pair

Axiom
IAO scope: EXACT
annotated target: Watson Crick base pair
annotated property: IAO_0000118
annotated source: WC_base_pair

Axiom
IAO xref: PMID:12177293
annotated target: The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation.
annotated property: IAO_0000115
annotated source: WC_base_pair

Axiom
IAO scope: EXACT
annotated target: canonical base pair
annotated property: IAO_0000118
annotated source: WC_base_pair

Axiom
IAO scope: EXACT
annotated target: WC base pair
annotated property: IAO_0000118
annotated source: WC_base_pair

Axiom
IAO scope: RELATED
annotated target: Watson-Crick base pair
annotated property: IAO_0000118
annotated source: WC_base_pair

sugar_edge_base_pair
type: Class
subclass of: base_pair
IAO_0000115: A type of non-canonical base-pairing.
IAO id: SO:0000030
IAO_0000118: sugar edge base pair

Axiom
annotated target: A type of non-canonical base-pairing.
IAO xref: PMID:12177293
annotated property: IAO_0000115
annotated source: sugar_edge_base_pair

Axiom
IAO scope: EXACT
annotated target: sugar edge base pair
annotated property: IAO_0000118
annotated source: sugar_edge_base_pair

aptamer
type: Class
subclass of: oligo
IAO_0000115: DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules.
IAO id: SO:0000031
IAO xref: http://en.wikipedia.org/wiki/Aptamer

Axiom
annotated target: DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules.
IAO xref: http://aptamer.icmb.utexas.edu
annotated property: IAO_0000115
annotated source: aptamer

DNA_aptamer
type: Class
subclass of: aptamer
IAO_0000118: DNA aptamer
IAO_0000115: DNA molecules that have been selected from random pools based on their ability to bind other molecules.
IAO id: SO:0000032

Axiom
annotated target: DNA aptamer
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DNA_aptamer

Axiom
annotated target: DNA molecules that have been selected from random pools based on their ability to bind other molecules.
IAO xref: http:aptamer.icmb.utexas.edu
annotated property: IAO_0000115
annotated source: DNA_aptamer

RNA_aptamer
type: Class
subclass of: aptamer
IAO_0000118: RNA aptamer
IAO_0000115: RNA molecules that have been selected from random pools based on their ability to bind other molecules.
IAO id: SO:0000033

Axiom
IAO scope: EXACT
annotated target: RNA aptamer
annotated property: IAO_0000118
annotated source: RNA_aptamer

Axiom
annotated target: RNA molecules that have been selected from random pools based on their ability to bind other molecules.
IAO xref: http://aptamer.icmb.utexas.edu
annotated property: IAO_0000115
annotated source: RNA_aptamer

morpholino_oligo
type: Class
equivalent class: Class
  intersection of: synthetic_oligo
  intersection of: Restriction
    on property: has_quality
    some values from: morpholino_backbone
subclass of: synthetic_oligo
IAO_0000115: Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino.
IAO id: SO:0000034
IAO_0000118: morphant
IAO_0000118: morpholino
IAO_0000118: morpholino oligo

Axiom
IAO scope: EXACT
annotated target: morpholino oligo
annotated property: IAO_0000118
annotated source: morpholino_oligo

Axiom
annotated target: Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino.
IAO xref: http://www.gene-tools.com/
annotated property: IAO_0000115
annotated source: morpholino_oligo

Axiom
IAO scope: EXACT
annotated target: morpholino
annotated property: IAO_0000118
annotated source: morpholino_oligo

Axiom
IAO scope: BROAD
annotated target: morphant
annotated property: IAO_0000118
annotated source: morpholino_oligo

riboswitch
type: Class
subclass of: mRNA_region
subclass of: Restriction
  on property: part_of
  some values from: mRNA
IAO_0000115: A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites.
IAO id: SO:0000035
IAO xref: http://en.wikipedia.org/wiki/Riboswitch
IAO_0000118: riboswitch RNA

Axiom
annotated target: A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites.
IAO xref: PMID:2820954
annotated property: IAO_0000115
annotated source: riboswitch

Axiom
IAO scope: EXACT
annotated target: riboswitch RNA
annotated property: IAO_0000118
annotated source: riboswitch

matrix_attachment_site
type: Class
subclass of: chromosomal_regulatory_element
IAO_0000115: A DNA region that is required for the binding of chromatin to the nuclear matrix.
IAO_0000118: MAR
IAO_0000118: S/MAR
IAO_0000118: S/MAR element
IAO_0000118: SMAR
IAO id: SO:0000036
IAO xref: http://en.wikipedia.org/wiki/Matrix_attachment_site
IAO_0000118: matrix association region
IAO_0000118: matrix attachment region
IAO_0000118: matrix attachment site
IAO_0000118: nuclear matrix association region
IAO_0000118: nuclear matrix attachment site
IAO_0000118: scaffold attachment site
IAO_0000118: scaffold matrix attachment region

Axiom
annotated target: A DNA region that is required for the binding of chromatin to the nuclear matrix.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: matrix_attachment_site

Axiom
IAO scope: RELATED
annotated target: S/MAR element
annotated property: IAO_0000118
annotated source: matrix_attachment_site

Axiom
IAO scope: EXACT
annotated target: MAR
annotated property: IAO_0000118
annotated source: matrix_attachment_site

Axiom
IAO scope: EXACT
annotated target: matrix attachment site
annotated property: IAO_0000118
annotated source: matrix_attachment_site

Axiom
IAO scope: EXACT
annotated target: scaffold matrix attachment region
annotated property: IAO_0000118
annotated source: matrix_attachment_site

Axiom
IAO scope: EXACT
annotated target: SMAR
annotated property: IAO_0000118
annotated source: matrix_attachment_site

Axiom
IAO scope: EXACT
annotated target: matrix association region
annotated property: IAO_0000118
annotated source: matrix_attachment_site

Axiom
IAO scope: EXACT
annotated target: nuclear matrix association region
annotated property: IAO_0000118
annotated source: matrix_attachment_site

Axiom
IAO scope: EXACT
annotated target: matrix attachment region
annotated property: IAO_0000118
annotated source: matrix_attachment_site

Axiom
IAO scope: EXACT
annotated target: scaffold attachment site
annotated property: IAO_0000118
annotated source: matrix_attachment_site

Axiom
IAO scope: EXACT
annotated target: S/MAR
annotated property: IAO_0000118
annotated source: matrix_attachment_site

Axiom
IAO scope: EXACT
annotated target: nuclear matrix attachment site
annotated property: IAO_0000118
annotated source: matrix_attachment_site

locus_control_region
type: Class
subclass of: CRM
IAO_0000115: A DNA region that includes DNAse hypersensitive sites located 5' to a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene.
IAO_0000118: LCR
IAO id: SO:0000037
IAO xref: http://en.wikipedia.org/wiki/Locus_control_region
IAO_0000118: locus control element
IAO_0000118: locus control region

Axiom
IAO scope: RELATED
annotated target: locus control element
annotated property: IAO_0000118
annotated source: locus_control_region

Axiom
IAO scope: EXACT
annotated target: locus control region
annotated property: IAO_0000118
annotated source: locus_control_region

Axiom
IAO scope: EXACT
annotated target: LCR
annotated property: IAO_0000118
annotated source: locus_control_region

Axiom
annotated target: A DNA region that includes DNAse hypersensitive sites located 5' to a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: locus_control_region

match_set
type: Class
IAO_0000115: A collection of match parts.
IAO id: SO:0000038
IAO subset: SOFA
deprecated: true

Axiom
annotated target: A collection of match parts.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: match_set

match_part
type: Class
subclass of: SO_0001410
subclass of: Restriction
  on property: part_of
  some values from: match
IAO_0000115: A part of a match, for example an hsp from blast is a match_part.
IAO id: SO:0000039
IAO subset: SOFA
IAO_0000118: match part

Axiom
annotated target: A part of a match, for example an hsp from blast is a match_part.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: match_part

Axiom
IAO scope: EXACT
annotated target: match part
annotated property: IAO_0000118
annotated source: match_part

genomic_clone
type: Class
equivalent class: Class
  intersection of: clone
  intersection of: Restriction
    on property: has_quality
    some values from: genomic_DNA
subclass of: clone
IAO_0000115: A clone of a DNA region of a genome.
IAO id: SO:0000040
IAO_0000118: genomic clone

Axiom
annotated target: A clone of a DNA region of a genome.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: genomic_clone

Axiom
IAO scope: EXACT
annotated target: genomic clone
annotated property: IAO_0000118
annotated source: genomic_clone

sequence_operation
type: Class
IAO_0000115: An operation that can be applied to a sequence, that results in a change.
IAO id: SO:0000041
IAO_0000118: sequence operation
deprecated: true

Axiom
annotated target: An operation that can be applied to a sequence, that results in a change.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: sequence_operation

Axiom
IAO scope: EXACT
annotated target: sequence operation
annotated property: IAO_0000118
annotated source: sequence_operation

pseudogene_attribute
type: Class
IAO_0000115: An attribute of a pseudogene (SO:0000336).
IAO id: SO:0000042
IAO_0000118: pseudogene attribute
deprecated: true

Axiom
IAO scope: EXACT
annotated target: pseudogene attribute
annotated property: IAO_0000118
annotated source: pseudogene_attribute

Axiom
annotated target: An attribute of a pseudogene (SO:0000336).
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: pseudogene_attribute

processed_pseudogene
type: Class
subclass of: pseudogene
IAO_0000115: A pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promoters, but often including a polyA tail.
comment: Please not the synonym R psi M uses the spelled out form of the greek letter.
IAO_0000118: R psi G
IAO id: SO:0000043
IAO_0000118: processed pseudogene
IAO_0000118: pseudogene by reverse transcription
IAO_0000118: retropseudogene

Axiom
IAO scope: EXACT
annotated target: processed pseudogene
annotated property: IAO_0000118
annotated source: processed_pseudogene

Axiom
IAO scope: EXACT
annotated target: retropseudogene
annotated property: IAO_0000118
annotated source: processed_pseudogene

Axiom
IAO scope: RELATED
annotated target: pseudogene by reverse transcription
annotated property: IAO_0000118
annotated source: processed_pseudogene

Axiom
annotated target: A pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promoters, but often including a polyA tail.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: processed_pseudogene

Axiom
annotated target: R psi G
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: processed_pseudogene

pseudogene_by_unequal_crossing_over
type: Class
subclass of: SO_0001760
IAO_0000115: A pseudogene caused by unequal crossing over at recombination.
IAO id: SO:0000044
IAO_0000118: pseudogene by unequal crossing over

Axiom
IAO scope: EXACT
annotated target: pseudogene by unequal crossing over
annotated property: IAO_0000118
annotated source: pseudogene_by_unequal_crossing_over

Axiom
annotated target: A pseudogene caused by unequal crossing over at recombination.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: pseudogene_by_unequal_crossing_over

delete
type: Class
IAO id: SO:0000045
IAO_0000115: To remove a subsection of sequence.
deprecated: true

Axiom
IAO xref: SO:ke
annotated target: To remove a subsection of sequence.
annotated property: IAO_0000115
annotated source: delete

insert
type: Class
IAO id: SO:0000046
IAO_0000115: To insert a subsection of sequence.
deprecated: true

Axiom
IAO xref: SO:ke
annotated target: To insert a subsection of sequence.
annotated property: IAO_0000115
annotated source: insert

invert
type: Class
IAO id: SO:0000047
IAO_0000115: To invert a subsection of sequence.
deprecated: true

Axiom
IAO xref: SO:ke
annotated target: To invert a subsection of sequence.
annotated property: IAO_0000115
annotated source: invert

substitute
type: Class
IAO id: SO:0000048
IAO_0000115: To substitute a subsection of sequence for another.
deprecated: true

Axiom
IAO xref: SO:ke
annotated target: To substitute a subsection of sequence for another.
annotated property: IAO_0000115
annotated source: substitute

translocate
type: Class
IAO id: SO:0000049
IAO_0000115: To translocate a subsection of sequence.
deprecated: true

Axiom
IAO xref: SO:ke
annotated target: To translocate a subsection of sequence.
annotated property: IAO_0000115
annotated source: translocate

gene_part
type: Class
IAO_0000115: A part of a gene, that has no other route in the ontology back to region. This concept is necessary for logical inference as these parts must have the properties of region. It also allows us to associate all the parts of genes with a gene.
IAO id: SO:0000050
IAO subset: SOFA
deprecated: true

Axiom
annotated target: A part of a gene, that has no other route in the ontology back to region. This concept is necessary for logical inference as these parts must have the properties of region. It also allows us to associate all the parts of genes with a gene.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: gene_part

probe
type: Class
subclass of: oligo
IAO_0000115: A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid.
IAO id: SO:0000051
IAO xref: http://en.wikipedia.org/wiki/Hybridization_probe

Axiom
annotated target: A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: probe

assortment_derived_deficiency
type: Class
IAO id: SO:0000052
IAO_0000118: assortment-derived_deficiency
deprecated: true

Axiom
IAO scope: RELATED
annotated target: assortment-derived_deficiency
annotated property: IAO_0000118
annotated source: assortment_derived_deficiency

sequence_variant_affecting_regulatory_region
type: Class
IAO_0000115: A sequence_variant_effect which changes the regulatory region of a gene.
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
IAO id: SO:0000053
IAO_0100001: SO:0001556
IAO_0000118: mutation affecting regulatory region
IAO_0000118: sequence variant affecting regulatory region
deprecated: true

Axiom
IAO scope: RELATED
annotated target: mutation affecting regulatory region
annotated property: IAO_0000118
annotated source: sequence_variant_affecting_regulatory_region

Axiom
IAO scope: EXACT
annotated target: sequence variant affecting regulatory region
annotated property: IAO_0000118
annotated source: sequence_variant_affecting_regulatory_region

Axiom
annotated target: A sequence_variant_effect which changes the regulatory region of a gene.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: sequence_variant_affecting_regulatory_region

aneuploid
type: Class
subclass of: SO_1000182
IAO_0000115: A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number.
IAO id: SO:0000054
IAO xref: http://en.wikipedia.org/wiki/Aneuploid

Axiom
annotated target: A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: aneuploid

hyperploid
type: Class
subclass of: aneuploid
IAO_0000115: A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present.
IAO id: SO:0000055
IAO xref: http://en.wikipedia.org/wiki/Hyperploid

Axiom
annotated target: A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: hyperploid

hypoploid
type: Class
subclass of: aneuploid
IAO_0000115: A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing.
IAO id: SO:0000056
IAO xref: http://en.wikipedia.org/wiki/Hypoploid

Axiom
annotated target: A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: hypoploid

operator
type: Class
subclass of: gene_group_regulatory_region
IAO_0000115: A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon.
IAO id: SO:0000057
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/Operator_(biology)#Operator
IAO_0000118: operator segment

Axiom
annotated target: A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: operator

Axiom
IAO scope: EXACT
annotated target: operator segment
annotated property: IAO_0000118
annotated source: operator

assortment_derived_aneuploid
type: Class
IAO id: SO:0000058
IAO_0000118: assortment-derived_aneuploid
deprecated: true

Axiom
IAO scope: RELATED
annotated target: assortment-derived_aneuploid
annotated property: IAO_0000118
annotated source: assortment_derived_aneuploid

nuclease_binding_site
type: Class
subclass of: SO_0001654
IAO_0000115: A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease.
IAO id: SO:0000059
IAO subset: SOFA
IAO_0000118: nuclease binding site

Axiom
IAO scope: EXACT
annotated target: nuclease binding site
annotated property: IAO_0000118
annotated source: nuclease_binding_site

Axiom
annotated target: A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease.
IAO xref: SO:cb
annotated property: IAO_0000115
annotated source: nuclease_binding_site

compound_chromosome_arm
type: Class
subclass of: SO_1000042
comment: FLAG - this term is should probably be a part of rather than an is_a.
IAO id: SO:0000060
IAO_0000118: compound chromosome arm

Axiom
IAO scope: EXACT
annotated target: compound chromosome arm
annotated property: IAO_0000118
annotated source: compound_chromosome_arm

restriction_enzyme_binding_site
type: Class
subclass of: nuclease_binding_site
IAO_0000115: A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme.
comment: A region of a molecule that binds to a restriction enzyme.
IAO id: SO:0000061
IAO_0000118: restriction endonuclease binding site
IAO_0000118: restriction enzyme binding site

Axiom
IAO scope: EXACT
annotated target: restriction endonuclease binding site
annotated property: IAO_0000118
annotated source: restriction_enzyme_binding_site

Axiom
IAO scope: EXACT
annotated target: restriction enzyme binding site
annotated property: IAO_0000118
annotated source: restriction_enzyme_binding_site

Axiom
annotated target: A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme.
IAO xref: SO:cb
annotated property: IAO_0000115
annotated source: restriction_enzyme_binding_site

deficient_intrachromosomal_transposition
type: Class
equivalent class: Class
  intersection of: SO_1000041
  intersection of: Restriction
    on property: has_part
    some values from: deletion
subclass of: SO_1000029
subclass of: SO_1000041
IAO_0000115: An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining.
IAO id: SO:0000062
IAO_0000118: deficient intrachromosomal transposition

Axiom
IAO scope: EXACT
annotated target: deficient intrachromosomal transposition
annotated property: IAO_0000118
annotated source: deficient_intrachromosomal_transposition

Axiom
annotated target: An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining.
IAO xref: FB:reference_manual
annotated property: IAO_0000115
annotated source: deficient_intrachromosomal_transposition

deficient_interchromosomal_transposition
type: Class
subclass of: SO_1000155
IAO_0000115: An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining.
IAO id: SO:0000063
IAO_0000118: deficient interchromosomal transposition

Axiom
annotated target: An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: deficient_interchromosomal_transposition

Axiom
IAO scope: EXACT
annotated target: deficient interchromosomal transposition
annotated property: IAO_0000118
annotated source: deficient_interchromosomal_transposition

gene_by_transcript_attribute
type: Class
IAO id: SO:0000064
comment: This classes of attributes was added by MA to allow the broad description of genes based on qualities of the transcript(s). A product of SO meeting 2004.
deprecated: true

free_chromosome_arm
type: Class
subclass of: SO_1000183
IAO_0000115: A chromosome structure variation whereby an arm exists as an individual chromosome element.
IAO id: SO:0000065
IAO_0000118: free chromosome arm

Axiom
IAO scope: EXACT
annotated target: free chromosome arm
annotated property: IAO_0000118
annotated source: free_chromosome_arm

Axiom
annotated target: A chromosome structure variation whereby an arm exists as an individual chromosome element.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: free_chromosome_arm

gene_by_polyadenylation_attribute
type: Class
IAO id: SO:0000066
deprecated: true

gene_to_gene_feature
type: Class
subclass of: gene_attribute
IAO id: SO:0000067
IAO_0000118: gene to gene feature

Axiom
IAO scope: EXACT
annotated target: gene to gene feature
annotated property: IAO_0000118
annotated source: gene_to_gene_feature

overlapping
type: Class
subclass of: gene_to_gene_feature
IAO_0000115: An attribute describing a gene that has a sequence that overlaps the sequence of another gene.
IAO id: SO:0000068

Axiom
annotated target: An attribute describing a gene that has a sequence that overlaps the sequence of another gene.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: overlapping

inside_intron
type: Class
subclass of: overlapping
IAO_0000115: An attribute to describe a gene when it is located within the intron of another gene.
IAO id: SO:0000069
IAO_0000118: inside intron

Axiom
IAO scope: EXACT
annotated target: inside intron
annotated property: IAO_0000118
annotated source: inside_intron

Axiom
annotated target: An attribute to describe a gene when it is located within the intron of another gene.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: inside_intron

inside_intron_antiparallel
type: Class
subclass of: inside_intron
IAO_0000115: An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand.
IAO id: SO:0000070
IAO_0000118: inside intron antiparallel

Axiom
IAO scope: EXACT
annotated target: inside intron antiparallel
annotated property: IAO_0000118
annotated source: inside_intron_antiparallel

Axiom
annotated target: An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: inside_intron_antiparallel

inside_intron_parallel
type: Class
subclass of: inside_intron
IAO_0000115: An attribute to describe a gene when it is located within the intron of another gene and on the same strand.
IAO id: SO:0000071
IAO_0000118: inside intron parallel

Axiom
IAO scope: EXACT
annotated target: inside intron parallel
annotated property: IAO_0000118
annotated source: inside_intron_parallel

Axiom
annotated target: An attribute to describe a gene when it is located within the intron of another gene and on the same strand.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: inside_intron_parallel

end_overlapping_gene
type: Class
IAO id: SO:0000072
deprecated: true

five_prime_three_prime_overlap
type: Class
subclass of: overlapping
IAO_0000115: An attribute to describe a gene when the five prime region overlaps with another gene's 3' region.
IAO id: SO:0000073
IAO_0000118: five prime-three prime overlap

Axiom
IAO scope: EXACT
annotated target: five prime-three prime overlap
annotated property: IAO_0000118
annotated source: five_prime_three_prime_overlap

Axiom
annotated target: An attribute to describe a gene when the five prime region overlaps with another gene's 3' region.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: five_prime_three_prime_overlap

five_prime_five_prime_overlap
type: Class
subclass of: overlapping
IAO_0000115: An attribute to describe a gene when the five prime region overlaps with another gene's five prime region.
IAO id: SO:0000074
IAO_0000118: five prime-five prime overlap

Axiom
IAO scope: EXACT
annotated target: five prime-five prime overlap
annotated property: IAO_0000118
annotated source: five_prime_five_prime_overlap

Axiom
annotated target: An attribute to describe a gene when the five prime region overlaps with another gene's five prime region.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: five_prime_five_prime_overlap

three_prime_three_prime_overlap
type: Class
subclass of: overlapping
IAO_0000115: An attribute to describe a gene when the 3' region overlaps with another gene's 3' region.
IAO id: SO:0000075
IAO_0000118: three prime-three prime overlap

Axiom
IAO scope: EXACT
annotated target: three prime-three prime overlap
annotated property: IAO_0000118
annotated source: three_prime_three_prime_overlap

Axiom
annotated target: An attribute to describe a gene when the 3' region overlaps with another gene's 3' region.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: three_prime_three_prime_overlap

three_prime_five_prime_overlap
type: Class
subclass of: overlapping
IAO_0000118: 5' 3' overlap
IAO_0000115: An attribute to describe a gene when the 3' region overlaps with another gene's 5' region.
IAO id: SO:0000076
IAO_0000118: three prime five prime overlap

Axiom
IAO scope: EXACT
annotated target: three prime five prime overlap
annotated property: IAO_0000118
annotated source: three_prime_five_prime_overlap

Axiom
annotated target: An attribute to describe a gene when the 3' region overlaps with another gene's 5' region.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: three_prime_five_prime_overlap

Axiom
annotated target: 5' 3' overlap
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: three_prime_five_prime_overlap

antisense
type: Class
subclass of: overlapping
IAO_0000115: A region sequence that is complementary to a sequence of messenger RNA.
IAO id: SO:0000077
IAO xref: http://en.wikipedia.org/wiki/Antisense

Axiom
annotated target: A region sequence that is complementary to a sequence of messenger RNA.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: antisense

polycistronic_transcript
type: Class
equivalent class: Class
  intersection of: transcript
  intersection of: Restriction
    on property: has_quality
    some values from: polycistronic
subclass of: transcript
IAO_0000115: A transcript that is polycistronic.
IAO id: SO:0000078
IAO_0000118: polycistronic transcript

Axiom
IAO scope: EXACT
annotated target: polycistronic transcript
annotated property: IAO_0000118
annotated source: polycistronic_transcript

Axiom
annotated target: A transcript that is polycistronic.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: polycistronic_transcript

dicistronic_transcript
type: Class
equivalent class: Class
  intersection of: transcript
  intersection of: Restriction
    on property: has_quality
    some values from: dicistronic
subclass of: polycistronic_transcript
IAO_0000115: A transcript that is dicistronic.
IAO id: SO:0000079
IAO_0000118: dicistronic transcript

Axiom
IAO scope: EXACT
annotated target: dicistronic transcript
annotated property: IAO_0000118
annotated source: dicistronic_transcript

Axiom
annotated target: A transcript that is dicistronic.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: dicistronic_transcript

operon_member
type: Class
subclass of: gene_array_member
IAO id: SO:0000080
IAO_0000118: operon member

Axiom
IAO scope: EXACT
annotated target: operon member
annotated property: IAO_0000118
annotated source: operon_member

gene_array_member
type: Class
subclass of: gene_attribute
IAO id: SO:0000081
IAO_0000118: gene array member

Axiom
IAO scope: EXACT
annotated target: gene array member
annotated property: IAO_0000118
annotated source: gene_array_member

processed_transcript_attribute
type: Class
IAO id: SO:0000082
deprecated: true

macronuclear_sequence
type: Class
subclass of: organelle_sequence
IAO id: SO:0000083
IAO_0000118: macronuclear sequence

Axiom
IAO scope: EXACT
annotated target: macronuclear sequence
annotated property: IAO_0000118
annotated source: macronuclear_sequence

micronuclear_sequence
type: Class
subclass of: organelle_sequence
IAO id: SO:0000084
IAO_0000118: micronuclear sequence

Axiom
IAO scope: EXACT
annotated target: micronuclear sequence
annotated property: IAO_0000118
annotated source: micronuclear_sequence

gene_by_genome_location
type: Class
IAO id: SO:0000085
deprecated: true

gene_by_organelle_of_genome
type: Class
IAO id: SO:0000086
deprecated: true

nuclear_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_origin
    some values from: nuclear_sequence
subclass of: gene
IAO_0000115: A gene from nuclear sequence.
IAO id: SO:0000087
IAO xref: http://en.wikipedia.org/wiki/Nuclear_gene
IAO_0000118: nuclear gene

Axiom
IAO scope: EXACT
annotated target: nuclear gene
annotated property: IAO_0000118
annotated source: nuclear_gene

Axiom
annotated target: A gene from nuclear sequence.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: nuclear_gene

mt_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_origin
    some values from: mitochondrial_sequence
subclass of: gene
IAO_0000115: A gene located in mitochondrial sequence.
IAO id: SO:0000088
IAO xref: http://en.wikipedia.org/wiki/Mitochondrial_gene
IAO_0000118: mitochondrial gene
IAO_0000118: mt gene

Axiom
IAO scope: EXACT
annotated target: mt gene
annotated property: IAO_0000118
annotated source: mt_gene

Axiom
IAO scope: EXACT
annotated target: mitochondrial gene
annotated property: IAO_0000118
annotated source: mt_gene

Axiom
annotated target: A gene located in mitochondrial sequence.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: mt_gene

kinetoplast_gene
type: Class
equivalent class: Class
  intersection of: mt_gene
  intersection of: Restriction
    on property: has_origin
    some values from: kinetoplast
subclass of: mt_gene
IAO_0000115: A gene located in kinetoplast sequence.
IAO id: SO:0000089
IAO_0000118: kinetoplast gene

Axiom
IAO scope: EXACT
annotated target: kinetoplast gene
annotated property: IAO_0000118
annotated source: kinetoplast_gene

Axiom
annotated target: A gene located in kinetoplast sequence.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: kinetoplast_gene

plastid_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_origin
    some values from: plastid_sequence
subclass of: gene
IAO_0000115: A gene from plastid sequence.
IAO id: SO:0000090
IAO_0000118: plastid gene

Axiom
annotated target: A gene from plastid sequence.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: plastid_gene

Axiom
IAO scope: EXACT
annotated target: plastid gene
annotated property: IAO_0000118
annotated source: plastid_gene

apicoplast_gene
type: Class
equivalent class: Class
  intersection of: plastid_gene
  intersection of: Restriction
    on property: has_origin
    some values from: apicoplast_sequence
subclass of: plastid_gene
IAO_0000115: A gene from apicoplast sequence.
IAO id: SO:0000091
IAO_0000118: apicoplast gene

Axiom
annotated target: A gene from apicoplast sequence.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: apicoplast_gene

Axiom
IAO scope: EXACT
annotated target: apicoplast gene
annotated property: IAO_0000118
annotated source: apicoplast_gene

ct_gene
type: Class
equivalent class: Class
  intersection of: plastid_gene
  intersection of: Restriction
    on property: has_origin
    some values from: chloroplast_sequence
subclass of: plastid_gene
IAO_0000115: A gene from chloroplast sequence.
IAO id: SO:0000092
IAO_0000118: chloroplast gene
IAO_0000118: ct gene

Axiom
IAO scope: EXACT
annotated target: chloroplast gene
annotated property: IAO_0000118
annotated source: ct_gene

Axiom
IAO scope: EXACT
annotated target: ct gene
annotated property: IAO_0000118
annotated source: ct_gene

Axiom
annotated target: A gene from chloroplast sequence.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: ct_gene

chromoplast_gene
type: Class
equivalent class: Class
  intersection of: plastid_gene
  intersection of: Restriction
    on property: has_origin
    some values from: chromoplast_sequence
subclass of: plastid_gene
IAO_0000115: A gene from chromoplast_sequence.
IAO id: SO:0000093
IAO_0000118: chromoplast gene

Axiom
IAO scope: EXACT
annotated target: chromoplast gene
annotated property: IAO_0000118
annotated source: chromoplast_gene

Axiom
annotated target: A gene from chromoplast_sequence.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: chromoplast_gene

cyanelle_gene
type: Class
equivalent class: Class
  intersection of: plastid_gene
  intersection of: Restriction
    on property: has_origin
    some values from: cyanelle_sequence
subclass of: plastid_gene
IAO_0000115: A gene from cyanelle sequence.
IAO id: SO:0000094
IAO_0000118: cyanelle gene

Axiom
annotated target: A gene from cyanelle sequence.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: cyanelle_gene

Axiom
IAO scope: EXACT
annotated target: cyanelle gene
annotated property: IAO_0000118
annotated source: cyanelle_gene

leucoplast_gene
type: Class
equivalent class: Class
  intersection of: plastid_gene
  intersection of: Restriction
    on property: has_origin
    some values from: leucoplast_sequence
subclass of: plastid_gene
IAO_0000115: A plastid gene from leucoplast sequence.
IAO id: SO:0000095
IAO_0000118: leucoplast gene

Axiom
annotated target: A plastid gene from leucoplast sequence.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: leucoplast_gene

Axiom
IAO scope: EXACT
annotated target: leucoplast gene
annotated property: IAO_0000118
annotated source: leucoplast_gene

proplastid_gene
type: Class
equivalent class: Class
  intersection of: plastid_gene
  intersection of: Restriction
    on property: has_origin
    some values from: proplastid_sequence
subclass of: plastid_gene
IAO_0000115: A gene from proplastid sequence.
IAO id: SO:0000096
IAO_0000118: proplastid gene

Axiom
IAO scope: EXACT
annotated target: proplastid gene
annotated property: IAO_0000118
annotated source: proplastid_gene

Axiom
annotated target: A gene from proplastid sequence.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: proplastid_gene

nucleomorph_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_origin
    some values from: nucleomorphic_sequence
subclass of: gene
IAO_0000115: A gene from nucleomorph sequence.
IAO id: SO:0000097
IAO_0000118: nucleomorph gene

Axiom
annotated target: A gene from nucleomorph sequence.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: nucleomorph_gene

Axiom
IAO scope: EXACT
annotated target: nucleomorph gene
annotated property: IAO_0000118
annotated source: nucleomorph_gene

plasmid_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_origin
    some values from: plasmid_location
subclass of: gene
IAO_0000115: A gene from plasmid sequence.
IAO id: SO:0000098
IAO_0000118: plasmid gene

Axiom
IAO scope: EXACT
annotated target: plasmid gene
annotated property: IAO_0000118
annotated source: plasmid_gene

Axiom
annotated target: A gene from plasmid sequence.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: plasmid_gene

proviral_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_origin
    some values from: proviral_location
subclass of: gene
IAO_0000115: A gene from proviral sequence.
IAO id: SO:0000099
IAO_0000118: proviral gene

Axiom
annotated target: A gene from proviral sequence.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: proviral_gene

Axiom
IAO scope: EXACT
annotated target: proviral gene
annotated property: IAO_0000118
annotated source: proviral_gene

endogenous_retroviral_gene
type: Class
equivalent class: Class
  intersection of: proviral_gene
  intersection of: Restriction
    on property: has_origin
    some values from: endogenous_retroviral_sequence
subclass of: proviral_gene
IAO_0000115: A proviral gene with origin endogenous retrovirus.
IAO id: SO:0000100
IAO_0000118: endogenous retroviral gene

Axiom
IAO scope: EXACT
annotated target: endogenous retroviral gene
annotated property: IAO_0000118
annotated source: endogenous_retroviral_gene

Axiom
annotated target: A proviral gene with origin endogenous retrovirus.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: endogenous_retroviral_gene

transposable_element
type: Class
subclass of: integrated_mobile_genetic_element
IAO_0000115: A transposon or insertion sequence. An element that can insert in a variety of DNA sequences.
IAO id: SO:0000101
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/Transposable_element
IAO_0000118: transposable element
IAO_0000118: transposon

Axiom
annotated target: A transposon or insertion sequence. An element that can insert in a variety of DNA sequences.
IAO xref: http://www.sci.sdsu.edu/~smaloy/Glossary/T.html
annotated property: IAO_0000115
annotated source: transposable_element

Axiom
IAO scope: EXACT
annotated target: transposon
annotated property: IAO_0000118
annotated source: transposable_element

Axiom
IAO scope: EXACT
annotated target: transposable element
annotated property: IAO_0000118
annotated source: transposable_element

expressed_sequence_match
type: Class
subclass of: nucleotide_match
IAO_0000115: A match to an EST or cDNA sequence.
IAO id: SO:0000102
IAO subset: SOFA
IAO_0000118: expressed sequence match

Axiom
IAO scope: EXACT
annotated target: expressed sequence match
annotated property: IAO_0000118
annotated source: expressed_sequence_match

Axiom
annotated target: A match to an EST or cDNA sequence.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: expressed_sequence_match

clone_insert_end
type: Class
subclass of: junction
subclass of: Restriction
  on property: part_of
  some values from: clone_insert
IAO id: SO:0000103
IAO subset: SOFA
IAO_0000115: The end of the clone insert.
IAO_0000118: clone insert end

Axiom
IAO xref: SO:ke
annotated target: The end of the clone insert.
annotated property: IAO_0000115
annotated source: clone_insert_end

Axiom
IAO scope: EXACT
annotated target: clone insert end
annotated property: IAO_0000118
annotated source: clone_insert_end

polypeptide
type: Class
subclass of: SO_0001411
subclass of: Restriction
  on property: derives_from
  some values from: CDS
IAO_0000115: A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation.
IAO id: SO:0000104
IAO alt id: SO:0000358
IAO subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The term 'protein' was merged with 'polypeptide'. Although 'protein' was a sequence_attribute and therefore meant to describe the quality rather than an actual feature, it was being used erroneously. It is replaced by 'peptidyl' as the polymer attribute.
IAO xref: http://en.wikipedia.org/wiki/Polypeptide
IAO_0000118: protein

Axiom
annotated target: A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: polypeptide

Axiom
IAO scope: EXACT
annotated target: protein
annotated property: IAO_0000118
annotated source: polypeptide

chromosome_arm
type: Class
subclass of: chromosome_part
IAO_0000115: A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere.
IAO id: SO:0000105
IAO_0000118: chromosome arm

Axiom
annotated target: A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere.
IAO xref: http://www.medterms.com/script/main/art.asp
annotated property: IAO_0000115
annotated source: chromosome_arm

Axiom
IAO scope: EXACT
annotated target: chromosome arm
annotated property: IAO_0000118
annotated source: chromosome_arm

non_capped_primary_transcript
type: Class
IAO id: SO:0000106
deprecated: true

sequencing_primer
type: Class
subclass of: primer
IAO id: SO:0000107
IAO_0000118: sequencing primer

Axiom
IAO scope: EXACT
annotated target: sequencing primer
annotated property: IAO_0000118
annotated source: sequencing_primer

mRNA_with_frameshift
type: Class
equivalent class: Class
  intersection of: mRNA
  intersection of: Restriction
    on property: has_quality
    some values from: frameshift
subclass of: mRNA
IAO_0000115: An mRNA with a frameshift.
IAO id: SO:0000108
IAO_0000118: frameshifted mRNA
IAO_0000118: mRNA with frameshift

Axiom
IAO scope: EXACT
annotated target: mRNA with frameshift
annotated property: IAO_0000118
annotated source: mRNA_with_frameshift

Axiom
annotated target: An mRNA with a frameshift.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: mRNA_with_frameshift

Axiom
IAO scope: EXACT
annotated target: frameshifted mRNA
annotated property: IAO_0000118
annotated source: mRNA_with_frameshift

sequence_variant_obs
type: Class
IAO_0000115: A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.
IAO id: SO:0000109
IAO subset: SOFA
IAO_0000118: mutation
deprecated: true

Axiom
IAO scope: RELATED
annotated target: mutation
annotated property: IAO_0000118
annotated source: sequence_variant_obs

Axiom
annotated target: A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: sequence_variant_obs

sequence_feature
type: Class
disjoint with: chromosome_variation
disjoint with: sequence_attribute
IAO_0000115: An extent of biological sequence.
IAO id: SO:0000110
IAO subset: SOFA
IAO_0000118: located sequence feature
IAO_0000118: located_sequence_feature
IAO_0000118: sequence feature

Axiom
IAO scope: EXACT
annotated target: sequence feature
annotated property: IAO_0000118
annotated source: sequence_feature

Axiom
IAO scope: RELATED
annotated target: located sequence feature
annotated property: IAO_0000118
annotated source: sequence_feature

Axiom
annotated target: An extent of biological sequence.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: sequence_feature

Axiom
IAO scope: EXACT
annotated target: located_sequence_feature
annotated property: IAO_0000118
annotated source: sequence_feature

transposable_element_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: part_of
    some values from: transposable_element
subclass of: gene
subclass of: Restriction
  on property: part_of
  some values from: transposable_element
IAO_0000115: A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast.
IAO id: SO:0000111
IAO_0000118: transposable element gene

Axiom
annotated target: A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: transposable_element_gene

Axiom
IAO scope: EXACT
annotated target: transposable element gene
annotated property: IAO_0000118
annotated source: transposable_element_gene

primer
type: Class
subclass of: ss_oligo
IAO_0000115: A short preexisting polynucleotide chain to which new deoxyribonucleotides can be added by DNA polymerase.
IAO_0000118: DNA primer
IAO id: SO:0000112
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/Primer_(molecular_biology)
IAO_0000118: primer oligonucleotide
IAO_0000118: primer polynucleotide
IAO_0000118: primer sequence

Axiom
IAO scope: EXACT
annotated target: primer sequence
annotated property: IAO_0000118
annotated source: primer

Axiom
annotated target: A short preexisting polynucleotide chain to which new deoxyribonucleotides can be added by DNA polymerase.
IAO xref: http://www.ornl.gov/TechResources/Human_Genome/publicat/primer2001/glossary.html
annotated property: IAO_0000115
annotated source: primer

Axiom
IAO scope: EXACT
annotated target: primer oligonucleotide
annotated property: IAO_0000118
annotated source: primer

Axiom
IAO scope: EXACT
annotated target: primer polynucleotide
annotated property: IAO_0000118
annotated source: primer

Axiom
annotated target: DNA primer
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: primer

proviral_region
type: Class
subclass of: integrated_mobile_genetic_element
IAO_0000115: A viral sequence which has integrated into a host genome.
IAO id: SO:0000113
IAO subset: SOFA
IAO_0000118: proviral region
IAO_0000118: proviral sequence

Axiom
IAO scope: EXACT
annotated target: proviral region
annotated property: IAO_0000118
annotated source: proviral_region

Axiom
IAO scope: RELATED
annotated target: proviral sequence
annotated property: IAO_0000118
annotated source: proviral_region

Axiom
annotated target: A viral sequence which has integrated into a host genome.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: proviral_region

methylated_C
type: Class
subclass of: methylated_base_feature
IAO_0000115: A methylated deoxy-cytosine.
IAO id: SO:0000114
IAO subset: SOFA
IAO_0000118: methylated C
IAO_0000118: methylated cytosine
IAO_0000118: methylated cytosine base
IAO_0000118: methylated cytosine residue

Axiom
IAO scope: EXACT
annotated target: methylated C
annotated property: IAO_0000118
annotated source: methylated_C

Axiom
IAO scope: EXACT
annotated target: methylated cytosine residue
annotated property: IAO_0000118
annotated source: methylated_C

Axiom
IAO scope: EXACT
annotated target: methylated cytosine
annotated property: IAO_0000118
annotated source: methylated_C

Axiom
annotated target: A methylated deoxy-cytosine.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: methylated_C

Axiom
IAO scope: EXACT
annotated target: methylated cytosine base
annotated property: IAO_0000118
annotated source: methylated_C

transcript_feature
type: Class
IAO id: SO:0000115
deprecated: true

edited
type: Class
subclass of: transcript_attribute
IAO_0000115: An attribute describing a sequence that is modified by editing.
IAO id: SO:0000116

Axiom
annotated target: An attribute describing a sequence that is modified by editing.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: edited

transcript_with_readthrough_stop_codon
type: Class
IAO id: SO:0000117
deprecated: true

transcript_with_translational_frameshift
type: Class
equivalent class: Class
  intersection of: transcript
  intersection of: Restriction
    on property: has_quality
    some values from: translationally_frameshifted
subclass of: transcript
IAO_0000115: A transcript with a translational frameshift.
IAO id: SO:0000118
IAO_0000118: transcript with translational frameshift

Axiom
annotated target: A transcript with a translational frameshift.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: transcript_with_translational_frameshift

Axiom
IAO scope: EXACT
annotated target: transcript with translational frameshift
annotated property: IAO_0000118
annotated source: transcript_with_translational_frameshift

regulated
type: Class
subclass of: gene_attribute
IAO_0000115: An attribute to describe a sequence that is regulated.
IAO id: SO:0000119

Axiom
annotated target: An attribute to describe a sequence that is regulated.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: regulated

protein_coding_primary_transcript
type: Class
subclass of: primary_transcript
IAO_0000115: A primary transcript that, at least in part, encodes one or more proteins.
comment: May contain introns.
IAO id: SO:0000120
IAO subset: SOFA
IAO_0000118: pre mRNA
IAO_0000118: protein coding primary transcript

Axiom
IAO scope: RELATED
annotated target: pre mRNA
annotated property: IAO_0000118
annotated source: protein_coding_primary_transcript

Axiom
annotated target: A primary transcript that, at least in part, encodes one or more proteins.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: protein_coding_primary_transcript

Axiom
IAO scope: EXACT
annotated target: protein coding primary transcript
annotated property: IAO_0000118
annotated source: protein_coding_primary_transcript

forward_primer
type: Class
equivalent class: Class
  intersection of: primer
  intersection of: Restriction
    on property: has_quality
    some values from: forward
subclass of: primer
IAO_0000115: A single stranded oligo used for polymerase chain reaction.
IAO_0000118: DNA forward primer
IAO id: SO:0000121
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
IAO_0000118: forward DNA primer
IAO_0000118: forward primer
IAO_0000118: forward primer oligo
IAO_0000118: forward primer oligonucleotide
IAO_0000118: forward primer polynucleotide
IAO_0000118: forward primer sequence

Axiom
IAO scope: EXACT
annotated target: forward primer oligonucleotide
annotated property: IAO_0000118
annotated source: forward_primer

Axiom
IAO scope: EXACT
annotated target: forward primer sequence
annotated property: IAO_0000118
annotated source: forward_primer

Axiom
IAO scope: EXACT
annotated target: forward primer
annotated property: IAO_0000118
annotated source: forward_primer

Axiom
annotated target: DNA forward primer
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: forward_primer

Axiom
IAO scope: EXACT
annotated target: forward primer polynucleotide
annotated property: IAO_0000118
annotated source: forward_primer

Axiom
annotated target: A single stranded oligo used for polymerase chain reaction.
IAO xref: http://mged.sourceforge.net/ontologies/MGEDontology.php
annotated property: IAO_0000115
annotated source: forward_primer

Axiom
IAO scope: EXACT
annotated target: forward primer oligo
annotated property: IAO_0000118
annotated source: forward_primer

Axiom
IAO scope: EXACT
annotated target: forward DNA primer
annotated property: IAO_0000118
annotated source: forward_primer

RNA_sequence_secondary_structure
type: Class
subclass of: sequence_secondary_structure
IAO_0000115: A folded RNA sequence.
IAO_0000118: RNA sequence secondary structure
IAO id: SO:0000122

Axiom
annotated target: A folded RNA sequence.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: RNA_sequence_secondary_structure

Axiom
IAO scope: EXACT
annotated target: RNA sequence secondary structure
annotated property: IAO_0000118
annotated source: RNA_sequence_secondary_structure

transcriptionally_regulated
type: Class
subclass of: regulated
IAO_0000115: An attribute describing a gene that is regulated at transcription.
comment: By:<protein_id>.
IAO id: SO:0000123
IAO_0000118: transcriptionally regulated

Axiom
annotated target: An attribute describing a gene that is regulated at transcription.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: transcriptionally_regulated

Axiom
IAO scope: EXACT
annotated target: transcriptionally regulated
annotated property: IAO_0000118
annotated source: transcriptionally_regulated

transcriptionally_constitutive
type: Class
subclass of: transcriptionally_regulated
IAO_0000115: Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate.
IAO id: SO:0000124
IAO_0000118: transcriptionally constitutive

Axiom
IAO scope: EXACT
annotated target: transcriptionally constitutive
annotated property: IAO_0000118
annotated source: transcriptionally_constitutive

Axiom
annotated target: Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: transcriptionally_constitutive

transcriptionally_induced
type: Class
subclass of: transcriptionally_regulated
IAO_0000115: An inducer molecule is required for transcription to occur.
IAO id: SO:0000125
IAO_0000118: transcriptionally induced

Axiom
IAO scope: EXACT
annotated target: transcriptionally induced
annotated property: IAO_0000118
annotated source: transcriptionally_induced

Axiom
annotated target: An inducer molecule is required for transcription to occur.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: transcriptionally_induced

transcriptionally_repressed
type: Class
subclass of: transcriptionally_regulated
IAO_0000115: A repressor molecule is required for transcription to stop.
IAO id: SO:0000126
IAO_0000118: transcriptionally repressed

Axiom
IAO scope: EXACT
annotated target: transcriptionally repressed
annotated property: IAO_0000118
annotated source: transcriptionally_repressed

Axiom
annotated target: A repressor molecule is required for transcription to stop.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: transcriptionally_repressed

silenced_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: silenced
subclass of: gene
IAO_0000115: A gene that is silenced.
IAO id: SO:0000127
IAO_0000118: silenced gene

Axiom
IAO scope: EXACT
annotated target: silenced gene
annotated property: IAO_0000118
annotated source: silenced_gene

Axiom
annotated target: A gene that is silenced.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: silenced_gene

gene_silenced_by_DNA_modification
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: silenced_by_DNA_modification
subclass of: silenced_gene
IAO_0000115: A gene that is silenced by DNA modification.
IAO id: SO:0000128
IAO_0000118: gene silenced by DNA modification

Axiom
annotated target: A gene that is silenced by DNA modification.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: gene_silenced_by_DNA_modification

Axiom
IAO scope: EXACT
annotated target: gene silenced by DNA modification
annotated property: IAO_0000118
annotated source: gene_silenced_by_DNA_modification

gene_silenced_by_DNA_methylation
type: Class
equivalent class: Class
  intersection of: gene_silenced_by_DNA_modification
  intersection of: Restriction
    on property: has_quality
    some values from: silenced_by_DNA_methylation
subclass of: gene_silenced_by_DNA_modification
IAO_0000115: A gene that is silenced by DNA methylation.
IAO id: SO:0000129
IAO_0000118: gene silenced by DNA methylation
IAO_0000118: methylation-silenced gene

Axiom
IAO scope: EXACT
annotated target: methylation-silenced gene
annotated property: IAO_0000118
annotated source: gene_silenced_by_DNA_methylation

Axiom
IAO scope: EXACT
annotated target: gene silenced by DNA methylation
annotated property: IAO_0000118
annotated source: gene_silenced_by_DNA_methylation

Axiom
annotated target: A gene that is silenced by DNA methylation.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: gene_silenced_by_DNA_methylation

post_translationally_regulated
type: Class
subclass of: regulated
IAO_0000115: An attribute describing a gene that is regulated after it has been translated.
IAO id: SO:0000130
IAO_0000118: post translationally regulated
IAO_0000118: post-translationally regulated

Axiom
IAO scope: EXACT
annotated target: post translationally regulated
annotated property: IAO_0000118
annotated source: post_translationally_regulated

Axiom
annotated target: An attribute describing a gene that is regulated after it has been translated.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: post_translationally_regulated

Axiom
IAO scope: EXACT
annotated target: post-translationally regulated
annotated property: IAO_0000118
annotated source: post_translationally_regulated

translationally_regulated
type: Class
subclass of: regulated
IAO_0000115: An attribute describing a gene that is regulated as it is translated.
IAO id: SO:0000131
IAO_0000118: translationally regulated

Axiom
IAO scope: EXACT
annotated target: translationally regulated
annotated property: IAO_0000118
annotated source: translationally_regulated

Axiom
annotated target: An attribute describing a gene that is regulated as it is translated.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: translationally_regulated

reverse_primer
type: Class
equivalent class: Class
  intersection of: primer
  intersection of: Restriction
    on property: has_quality
    some values from: reverse
subclass of: primer
IAO_0000115: A single stranded oligo used for polymerase chain reaction.
IAO_0000118: DNA reverse primer
IAO id: SO:0000132
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
IAO_0000118: reverse DNA primer
IAO_0000118: reverse primer
IAO_0000118: reverse primer oligo
IAO_0000118: reverse primer oligonucleotide
IAO_0000118: reverse primer sequence

Axiom
IAO scope: EXACT
annotated target: reverse DNA primer
annotated property: IAO_0000118
annotated source: reverse_primer

Axiom
IAO scope: EXACT
annotated target: reverse primer
annotated property: IAO_0000118
annotated source: reverse_primer

Axiom
IAO scope: EXACT
annotated target: reverse primer oligo
annotated property: IAO_0000118
annotated source: reverse_primer

Axiom
IAO scope: EXACT
annotated target: reverse primer sequence
annotated property: IAO_0000118
annotated source: reverse_primer

Axiom
IAO scope: EXACT
annotated target: reverse primer oligonucleotide
annotated property: IAO_0000118
annotated source: reverse_primer

Axiom
annotated target: DNA reverse primer
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: reverse_primer

Axiom
annotated target: A single stranded oligo used for polymerase chain reaction.
IAO xref: http://mged.sourceforge.net/ontologies/MGEDontology.php
annotated property: IAO_0000115
annotated source: reverse_primer

epigenetically_modified
type: Class
subclass of: gene_attribute
IAO id: SO:0000133
IAO_0000115: This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones.
IAO_0000118: epigenetically modified

Axiom
IAO scope: EXACT
annotated target: epigenetically modified
annotated property: IAO_0000118
annotated source: epigenetically_modified

Axiom
IAO xref: SO:ke
annotated target: This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones.
annotated property: IAO_0000115
annotated source: epigenetically_modified

imprinted
type: Class
subclass of: regulated
subclass of: epigenetically_modified
IAO_0000115: Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin.
IAO id: SO:0000134
IAO xref: http:http\://en.wikipedia.org/wiki/Genomic_imprinting

Axiom
annotated target: Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: imprinted

maternally_imprinted
type: Class
subclass of: imprinted
IAO id: SO:0000135
IAO_0000115: The maternal copy of the gene is modified, rendering it transcriptionally silent.
IAO_0000118: maternally imprinted

Axiom
IAO xref: SO:ke
annotated target: The maternal copy of the gene is modified, rendering it transcriptionally silent.
annotated property: IAO_0000115
annotated source: maternally_imprinted

Axiom
IAO scope: EXACT
annotated target: maternally imprinted
annotated property: IAO_0000118
annotated source: maternally_imprinted

paternally_imprinted
type: Class
subclass of: imprinted
IAO id: SO:0000136
IAO_0000115: The paternal copy of the gene is modified, rendering it transcriptionally silent.
IAO_0000118: paternally imprinted

Axiom
IAO scope: EXACT
annotated target: paternally imprinted
annotated property: IAO_0000118
annotated source: paternally_imprinted

Axiom
IAO xref: SO:ke
annotated target: The paternal copy of the gene is modified, rendering it transcriptionally silent.
annotated property: IAO_0000115
annotated source: paternally_imprinted

allelically_excluded
type: Class
subclass of: epigenetically_modified
IAO_0000115: Allelic exclusion is a process occurring in diploid organisms, where a gene is inactivated and not expressed in that cell.
comment: Examples are x-inactivation and immunoglobulin formation.
IAO id: SO:0000137
IAO_0000118: allelically excluded

Axiom
annotated target: Allelic exclusion is a process occurring in diploid organisms, where a gene is inactivated and not expressed in that cell.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: allelically_excluded

Axiom
IAO scope: EXACT
annotated target: allelically excluded
annotated property: IAO_0000118
annotated source: allelically_excluded

gene_rearranged_at_DNA_level
type: Class
equivalent class: Class
  intersection of: epigenetically_modified_gene
  intersection of: Restriction
    on property: has_quality
    some values from: rearranged_at_DNA_level
subclass of: epigenetically_modified_gene
IAO_0000115: An epigenetically modified gene, rearranged at the DNA level.
IAO id: SO:0000138
IAO_0000118: gene rearranged at DNA level

Axiom
annotated target: An epigenetically modified gene, rearranged at the DNA level.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: gene_rearranged_at_DNA_level

Axiom
IAO scope: EXACT
annotated target: gene rearranged at DNA level
annotated property: IAO_0000118
annotated source: gene_rearranged_at_DNA_level

ribosome_entry_site
type: Class
subclass of: mRNA_region
IAO_0000115: Region in mRNA where ribosome assembles.
IAO id: SO:0000139
IAO subset: SOFA
IAO_0000118: ribosome entry site

Axiom
IAO scope: EXACT
annotated target: ribosome entry site
annotated property: IAO_0000118
annotated source: ribosome_entry_site

Axiom
annotated target: Region in mRNA where ribosome assembles.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: ribosome_entry_site

attenuator
type: Class
subclass of: SO_0001680
subclass of: Restriction
  on property: part_of
  some values from: mRNA
IAO_0000115: A sequence segment located within the five prime end of an mRNA that causes premature termination of translation.
IAO id: SO:0000140
IAO subset: SOFA
IAO_0000118: attenuator sequence
IAO xref: http://en.wikipedia.org/wiki/Attenuator

Axiom
annotated target: A sequence segment located within the five prime end of an mRNA that causes premature termination of translation.
IAO xref: SO:as
annotated property: IAO_0000115
annotated source: attenuator

Axiom
IAO scope: EXACT
annotated target: attenuator sequence
annotated property: IAO_0000118
annotated source: attenuator

terminator
type: Class
subclass of: SO_0001679
subclass of: Restriction
  on property: part_of
  some values from: transcript
IAO id: SO:0000141
IAO subset: SOFA
IAO_0000115: The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription.
IAO xref: http://en.wikipedia.org/wiki/Terminator_(genetics)
IAO_0000118: terminator sequence

Axiom
annotated target: The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription.
IAO xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
annotated property: IAO_0000115
annotated source: terminator

Axiom
IAO scope: EXACT
annotated target: terminator sequence
annotated property: IAO_0000118
annotated source: terminator

DNA_sequence_secondary_structure
type: Class
subclass of: sequence_secondary_structure
IAO_0000115: A folded DNA sequence.
IAO_0000118: DNA sequence secondary structure
IAO id: SO:0000142

Axiom
annotated target: DNA sequence secondary structure
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DNA_sequence_secondary_structure

Axiom
annotated target: A folded DNA sequence.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: DNA_sequence_secondary_structure

assembly_component
type: Class
subclass of: SO_0001410
IAO_0000115: A region of known length which may be used to manufacture a longer region.
IAO id: SO:0000143
IAO subset: SOFA
IAO_0000118: assembly component

Axiom
IAO scope: EXACT
annotated target: assembly component
annotated property: IAO_0000118
annotated source: assembly_component

Axiom
annotated target: A region of known length which may be used to manufacture a longer region.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: assembly_component

primary_transcript_attribute
type: Class
IAO id: SO:0000144
deprecated: true

recoded_codon
type: Class
subclass of: codon
IAO_0000115: A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough.
IAO id: SO:0000145
IAO_0000118: recoded codon

Axiom
annotated target: A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: recoded_codon

Axiom
IAO scope: EXACT
annotated target: recoded codon
annotated property: IAO_0000118
annotated source: recoded_codon

capped
type: Class
subclass of: transcript_attribute
IAO_0000115: An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end.
IAO id: SO:0000146

Axiom
annotated target: An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: capped

exon
type: Class
subclass of: transcript_region
IAO_0000115: A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing.
IAO id: SO:0000147
IAO subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
IAO xref: http://en.wikipedia.org/wiki/Exon

Axiom
annotated target: A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: exon

supercontig
type: Class
subclass of: sequence_assembly
subclass of: Restriction
  on property: part_of
  some values from: ultracontig
IAO_0000115: One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's.
IAO id: SO:0000148
IAO subset: SOFA
IAO_0000118: scaffold

Axiom
annotated target: One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's.
IAO xref: SO:ls
annotated property: IAO_0000115
annotated source: supercontig

Axiom
IAO scope: RELATED
annotated target: scaffold
annotated property: IAO_0000118
annotated source: supercontig

contig
type: Class
subclass of: assembly_component
subclass of: sequence_assembly
subclass of: Restriction
  on property: part_of
  some values from: supercontig
IAO_0000115: A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases.
IAO id: SO:0000149
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/Contig

Axiom
annotated target: A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases.
IAO xref: SO:ls
annotated property: IAO_0000115
annotated source: contig

read
type: Class
subclass of: assembly_component
subclass of: Restriction
  on property: part_of
  some values from: contig
IAO_0000115: A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine.
IAO id: SO:0000150
IAO subset: SOFA

Axiom
annotated target: A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine.
IAO xref: SO:rd
annotated property: IAO_0000115
annotated source: read

clone
type: Class
subclass of: reagent
IAO_0000115: A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism.
IAO id: SO:0000151
IAO subset: SOFA
IAO xref: http:http\://en.wikipedia.org/wiki/Clone_(genetics)

Axiom
annotated target: A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: clone

YAC
type: Class
subclass of: vector_replicon
IAO id: SO:0000152
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
IAO_0000115: Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells.
IAO_0000118: yeast artificial chromosome

Axiom
IAO xref: SO:ma
annotated target: Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells.
annotated property: IAO_0000115
annotated source: YAC

Axiom
IAO scope: EXACT
annotated target: yeast artificial chromosome
annotated property: IAO_0000118
annotated source: YAC

BAC
type: Class
subclass of: vector_replicon
IAO_0000115: Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host.
IAO id: SO:0000153
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
IAO_0000118: bacterial artificial chromosome

Axiom
IAO scope: EXACT
annotated target: bacterial artificial chromosome
annotated property: IAO_0000118
annotated source: BAC

Axiom
annotated target: Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: BAC

PAC
type: Class
subclass of: vector_replicon
IAO_0000118: P1
IAO_0000118: P1 artificial chromosome
IAO id: SO:0000154
IAO_0000115: The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells.
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Drosophila melanogaster PACs carry an average insert size of 80 kb. The library represents a 6-fold coverage of the genome.
IAO xref: http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome

Axiom
IAO scope: EXACT
annotated target: P1 artificial chromosome
annotated property: IAO_0000118
annotated source: PAC

Axiom
IAO scope: EXACT
annotated target: P1
annotated property: IAO_0000118
annotated source: PAC

Axiom
annotated target: The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells.
IAO xref: http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome
annotated property: IAO_0000115
annotated source: PAC

plasmid
type: Class
subclass of: replicon
IAO_0000115: A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism.
IAO id: SO:0000155
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
IAO_0000118: plasmid sequence

Axiom
annotated target: A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: plasmid

Axiom
IAO scope: EXACT
annotated target: plasmid sequence
annotated property: IAO_0000118
annotated source: plasmid

cosmid
type: Class
subclass of: vector_replicon
IAO_0000115: A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites.
comment: Paper: vans GA et al. High efficiency vectors for cosmid microcloning and genomic analysis. Gene 1989; 79(1):9-20. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
IAO id: SO:0000156
IAO_0000118: cosmid vector
IAO xref: http://en.wikipedia.org/wiki/Cosmid

Axiom
annotated target: A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: cosmid

Axiom
IAO scope: EXACT
annotated target: cosmid vector
annotated property: IAO_0000118
annotated source: cosmid

phagemid
type: Class
subclass of: vector_replicon
IAO_0000115: A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with \"helper\" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids.
IAO id: SO:0000157
IAO xref: http://en.wikipedia.org/wiki/Phagemid
IAO_0000118: phagemid vector

Axiom
annotated target: A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with \"helper\" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: phagemid

Axiom
IAO scope: RELATED
annotated target: phagemid vector
annotated property: IAO_0000118
annotated source: phagemid

fosmid
type: Class
subclass of: vector_replicon
IAO_0000115: A cloning vector that utilizes the E. coli F factor.
comment: Birren BW et al. A human chromosome 22 fosmid resource: mapping and analysis of 96 clones. Genomics 1996.
IAO id: SO:0000158
IAO_0000118: fosmid vector
IAO xref: http://en.wikipedia.org/wiki/Fosmid

Axiom
annotated target: A cloning vector that utilizes the E. coli F factor.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: fosmid

Axiom
IAO scope: RELATED
annotated target: fosmid vector
annotated property: IAO_0000118
annotated source: fosmid

deletion
type: Class
subclass of: sequence_alteration
subclass of: SO_0001411
IAO id: SO:0000159
IAO alt id: SO:1000033
IAO subset: SOFA
IAO_0000115: The point at which one or more contiguous nucleotides were excised.
IAO_0000118: deleted_sequence
IAO xref: http://en.wikipedia.org/wiki/Nucleotide_deletion
IAO_0000118: nucleotide deletion
IAO_0000118: nucleotide_deletion

Axiom
IAO scope: EXACT
annotated target: nucleotide deletion
annotated property: IAO_0000118
annotated source: deletion

Axiom
IAO scope: EXACT
annotated target: deleted_sequence
annotated property: IAO_0000118
annotated source: deletion

Axiom
IAO xref: SO:ke
annotated target: The point at which one or more contiguous nucleotides were excised.
annotated property: IAO_0000115
annotated source: deletion

Axiom
IAO scope: EXACT
annotated target: nucleotide_deletion
annotated property: IAO_0000118
annotated source: deletion

lambda_clone
type: Class
IAO_0000115: A linear clone derived from lambda bacteriophage. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome.
IAO id: SO:0000160
deprecated: true

Axiom
annotated target: A linear clone derived from lambda bacteriophage. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome.
IAO xref: ISBN:0-1767-2380-8
annotated property: IAO_0000115
annotated source: lambda_clone

methylated_A
type: Class
subclass of: methylated_base_feature
IAO_0000115: A modified RNA base in which adenine has been methylated.
IAO id: SO:0000161
IAO subset: SOFA
IAO_0000118: methylated A
IAO_0000118: methylated adenine
IAO_0000118: methylated adenine base
IAO_0000118: methylated adenine residue

Axiom
IAO scope: EXACT
annotated target: methylated adenine base
annotated property: IAO_0000118
annotated source: methylated_A

Axiom
IAO scope: EXACT
annotated target: methylated adenine residue
annotated property: IAO_0000118
annotated source: methylated_A

Axiom
IAO scope: EXACT
annotated target: methylated A
annotated property: IAO_0000118
annotated source: methylated_A

Axiom
IAO scope: EXACT
annotated target: methylated adenine
annotated property: IAO_0000118
annotated source: methylated_A

Axiom
annotated target: A modified RNA base in which adenine has been methylated.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: methylated_A

splice_site
type: Class
subclass of: primary_transcript_region
IAO_0000115: Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction.
IAO id: SO:0000162
IAO subset: SOFA
comment: With spliceosomal introns, the splice sites bind the spliceosomal machinery.
IAO xref: http://en.wikipedia.org/wiki/Splice_site
IAO_0000118: splice site

Axiom
annotated target: Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction.
IAO xref: SO:cjm
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: splice_site

Axiom
IAO scope: EXACT
annotated target: splice site
annotated property: IAO_0000118
annotated source: splice_site

five_prime_cis_splice_site
type: Class
subclass of: SO_0001419
IAO_0000118: 5' splice site
IAO_0000115: Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron.
IAO id: SO:0000163
IAO subset: SOFA
IAO_0000118: donor
IAO_0000118: donor splice site
IAO_0000118: five prime splice site
IAO_0000118: splice donor site

Axiom
IAO scope: EXACT
annotated target: five prime splice site
annotated property: IAO_0000118
annotated source: five_prime_cis_splice_site

Axiom
IAO scope: EXACT
annotated target: donor splice site
annotated property: IAO_0000118
annotated source: five_prime_cis_splice_site

Axiom
annotated target: Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron.
IAO xref: SO:cjm
IAO xref: SO:ke
IAO xref: http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html
annotated property: IAO_0000115
annotated source: five_prime_cis_splice_site

Axiom
IAO scope: EXACT
annotated target: splice donor site
annotated property: IAO_0000118
annotated source: five_prime_cis_splice_site

Axiom
IAO scope: RELATED
annotated target: donor
annotated property: IAO_0000118
annotated source: five_prime_cis_splice_site

Axiom
annotated target: 5' splice site
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: five_prime_cis_splice_site

three_prime_cis_splice_site
type: Class
subclass of: SO_0001419
IAO_0000118: 3' splice site
IAO_0000115: Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron.
IAO id: SO:0000164
IAO subset: SOFA
IAO_0000118: acceptor
IAO_0000118: acceptor splice site
IAO_0000118: splice acceptor site
IAO_0000118: three prime splice site

Axiom
IAO scope: RELATED
annotated target: acceptor
annotated property: IAO_0000118
annotated source: three_prime_cis_splice_site

Axiom
IAO scope: EXACT
annotated target: three prime splice site
annotated property: IAO_0000118
annotated source: three_prime_cis_splice_site

Axiom
IAO scope: EXACT
annotated target: acceptor splice site
annotated property: IAO_0000118
annotated source: three_prime_cis_splice_site

Axiom
annotated target: Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron.
IAO xref: SO:cjm
IAO xref: SO:ke
IAO xref: http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html
annotated property: IAO_0000115
annotated source: three_prime_cis_splice_site

Axiom
annotated target: 3' splice site
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: three_prime_cis_splice_site

Axiom
IAO scope: EXACT
annotated target: splice acceptor site
annotated property: IAO_0000118
annotated source: three_prime_cis_splice_site

enhancer
type: Class
subclass of: CRM
IAO_0000115: A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter.
comment: An enhancer may participate in an enhanceosome GO:0034206. A protein-DNA complex formed by the association of a distinct set of general and specific transcription factors with a region of enhancer DNA. The cooperative assembly of an enhanceosome confers specificity of transcriptional regulation. This comment is a place holder should we start to make cross products with GO.
IAO id: SO:0000165
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/Enhancer_(genetics)

Axiom
annotated target: A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter.
IAO xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
annotated property: IAO_0000115
annotated source: enhancer

enhancer_bound_by_factor
type: Class
equivalent class: Class
  intersection of: enhancer
  intersection of: Restriction
    on property: has_quality
    some values from: bound_by_factor
subclass of: enhancer
IAO_0000115: An enhancer bound by a factor.
IAO id: SO:0000166
IAO_0000118: enhancer bound by factor

Axiom
annotated target: An enhancer bound by a factor.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: enhancer_bound_by_factor

Axiom
IAO scope: EXACT
annotated target: enhancer bound by factor
annotated property: IAO_0000118
annotated source: enhancer_bound_by_factor

promoter
type: Class
subclass of: transcriptional_cis_regulatory_region
IAO_0000115: A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery.
IAO id: SO:0000167
IAO subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The region on a DNA molecule involved in RNA polymerase binding to initiate transcription.
IAO xref: http://en.wikipedia.org/wiki/Promoter
IAO_0000118: promoter sequence

Axiom
IAO scope: EXACT
annotated target: promoter sequence
annotated property: IAO_0000118
annotated source: promoter

Axiom
annotated target: A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery.
IAO xref: SO:regcreative
annotated property: IAO_0000115
annotated source: promoter

restriction_enzyme_cut_site
type: Class
IAO_0000115: A specific nucleotide sequence of DNA at or near which a particular restriction enzyme cuts the DNA.
IAO id: SO:0000168
deprecated: true

Axiom
annotated target: A specific nucleotide sequence of DNA at or near which a particular restriction enzyme cuts the DNA.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: restriction_enzyme_cut_site

RNApol_I_promoter
type: Class
subclass of: RNA_polymerase_promoter
IAO_0000115: A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription.
IAO_0000118: RNA polymerase A promoter
IAO_0000118: RNApol I promoter
IAO id: SO:0000169
IAO_0000118: pol I promoter
IAO_0000118: polymerase I promoter

Axiom
IAO scope: EXACT
annotated target: RNA polymerase A promoter
annotated property: IAO_0000118
annotated source: RNApol_I_promoter

Axiom
IAO scope: EXACT
annotated target: polymerase I promoter
annotated property: IAO_0000118
annotated source: RNApol_I_promoter

Axiom
IAO scope: EXACT
annotated target: RNApol I promoter
annotated property: IAO_0000118
annotated source: RNApol_I_promoter

Axiom
annotated target: A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: RNApol_I_promoter

Axiom
IAO scope: EXACT
annotated target: pol I promoter
annotated property: IAO_0000118
annotated source: RNApol_I_promoter

RNApol_II_promoter
type: Class
subclass of: RNA_polymerase_promoter
IAO_0000115: A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription.
IAO_0000118: RNA polymerase B promoter
IAO_0000118: RNApol II promoter
IAO id: SO:0000170
IAO_0000118: pol II promoter
IAO_0000118: polymerase II promoter

Axiom
IAO scope: EXACT
annotated target: RNA polymerase B promoter
annotated property: IAO_0000118
annotated source: RNApol_II_promoter

Axiom
IAO scope: EXACT
annotated target: polymerase II promoter
annotated property: IAO_0000118
annotated source: RNApol_II_promoter

Axiom
annotated target: A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: RNApol_II_promoter

Axiom
IAO scope: EXACT
annotated target: RNApol II promoter
annotated property: IAO_0000118
annotated source: RNApol_II_promoter

Axiom
IAO scope: RELATED
annotated target: pol II promoter
annotated property: IAO_0000118
annotated source: RNApol_II_promoter

RNApol_III_promoter
type: Class
subclass of: RNA_polymerase_promoter
IAO_0000115: A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription.
IAO_0000118: RNA polymerase C promoter
IAO_0000118: RNApol III promoter
IAO id: SO:0000171
IAO_0000118: pol III promoter
IAO_0000118: polymerase III promoter

Axiom
IAO scope: EXACT
annotated target: polymerase III promoter
annotated property: IAO_0000118
annotated source: RNApol_III_promoter

Axiom
IAO scope: EXACT
annotated target: RNA polymerase C promoter
annotated property: IAO_0000118
annotated source: RNApol_III_promoter

Axiom
annotated target: A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: RNApol_III_promoter

Axiom
IAO scope: EXACT
annotated target: pol III promoter
annotated property: IAO_0000118
annotated source: RNApol_III_promoter

Axiom
IAO scope: EXACT
annotated target: RNApol III promoter
annotated property: IAO_0000118
annotated source: RNApol_III_promoter

CAAT_signal
type: Class
subclass of: DNA_motif
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_promoter
IAO_0000118: CAAT box
IAO_0000118: CAAT signal
IAO_0000118: CAAT-box
IAO_0000115: Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT.
IAO id: SO:0000172
IAO xref: http://en.wikipedia.org/wiki/CAAT_box

Axiom
annotated target: Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT.
IAO xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
annotated property: IAO_0000115
annotated source: CAAT_signal

Axiom
annotated target: CAAT-box
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: CAAT_signal

Axiom
annotated target: CAAT signal
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: CAAT_signal

Axiom
annotated target: CAAT box
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: CAAT_signal

GC_rich_promoter_region
type: Class
subclass of: SO_0001659
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_promoter
IAO_0000115: A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG.
IAO_0000118: GC rich promoter region
IAO_0000118: GC-rich region
IAO id: SO:0000173

Axiom
IAO scope: EXACT
annotated target: GC-rich region
annotated property: IAO_0000118
annotated source: GC_rich_promoter_region

Axiom
IAO scope: EXACT
annotated target: GC rich promoter region
annotated property: IAO_0000118
annotated source: GC_rich_promoter_region

Axiom
annotated target: A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG.
IAO xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
annotated property: IAO_0000115
annotated source: GC_rich_promoter_region

TATA_box
type: Class
subclass of: SO_0001660
IAO_0000115: A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T).
comment: Binds TBP.
IAO_0000118: Goldstein-Hogness box
IAO id: SO:0000174
IAO_0000118: TATA box
IAO xref: http://en.wikipedia.org/wiki/TATA_box

Axiom
IAO scope: EXACT
annotated target: Goldstein-Hogness box
annotated property: IAO_0000118
annotated source: TATA_box

Axiom
IAO scope: EXACT
annotated target: TATA box
annotated property: IAO_0000118
annotated source: TATA_box

Axiom
annotated target: A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T).
IAO xref: PMID:16858867
IAO xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
annotated property: IAO_0000115
annotated source: TATA_box

minus_10_signal
type: Class
subclass of: DNA_motif
subclass of: Restriction
  on property: part_of
  some values from: SO_0001671
IAO_0000118: -10 signal
IAO_0000115: A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70.
IAO_0000118: Pribnow Schaller box
IAO_0000118: Pribnow box
IAO_0000118: Pribnow-Schaller box
IAO id: SO:0000175
IAO xref: http://en.wikipedia.org/wiki/Pribnow_box
IAO_0000118: minus 10 signal

Axiom
annotated target: -10 signal
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: minus_10_signal

Axiom
IAO scope: EXACT
annotated target: Pribnow Schaller box
annotated property: IAO_0000118
annotated source: minus_10_signal

Axiom
IAO scope: EXACT
annotated target: Pribnow-Schaller box
annotated property: IAO_0000118
annotated source: minus_10_signal

Axiom
IAO scope: EXACT
annotated target: minus 10 signal
annotated property: IAO_0000118
annotated source: minus_10_signal

Axiom
IAO scope: EXACT
annotated target: Pribnow box
annotated property: IAO_0000118
annotated source: minus_10_signal

Axiom
annotated target: A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70.
IAO xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
annotated property: IAO_0000115
annotated source: minus_10_signal

minus_35_signal
type: Class
subclass of: DNA_motif
subclass of: Restriction
  on property: part_of
  some values from: SO_0001671
IAO_0000118: -35 signal
IAO_0000115: A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70.
IAO id: SO:0000176
IAO_0000118: minus 35 signal

Axiom
annotated target: -35 signal
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: minus_35_signal

Axiom
annotated target: A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70.
IAO xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
annotated property: IAO_0000115
annotated source: minus_35_signal

Axiom
IAO scope: EXACT
annotated target: minus 35 signal
annotated property: IAO_0000118
annotated source: minus_35_signal

cross_genome_match
type: Class
subclass of: nucleotide_match
IAO_0000115: A nucleotide match against a sequence from another organism.
IAO id: SO:0000177
IAO subset: SOFA
IAO_0000118: cross genome match

Axiom
annotated target: A nucleotide match against a sequence from another organism.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: cross_genome_match

Axiom
IAO scope: EXACT
annotated target: cross genome match
annotated property: IAO_0000118
annotated source: cross_genome_match

operon
type: Class
subclass of: SO_0005855
IAO_0000115: A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region.
IAO id: SO:0000178
IAO subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
IAO xref: http://en.wikipedia.org/wiki/Operon

Axiom
annotated target: A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: operon

clone_insert_start
type: Class
subclass of: junction
subclass of: Restriction
  on property: part_of
  some values from: clone_insert
IAO id: SO:0000179
IAO subset: SOFA
IAO_0000115: The start of the clone insert.
IAO_0000118: clone insert start

Axiom
IAO xref: SO:ke
annotated target: The start of the clone insert.
annotated property: IAO_0000115
annotated source: clone_insert_start

Axiom
IAO scope: EXACT
annotated target: clone insert start
annotated property: IAO_0000118
annotated source: clone_insert_start

retrotransposon
type: Class
subclass of: transposable_element
IAO_0000115: A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase.
IAO id: SO:0000180
IAO_0000118: class I
IAO_0000118: class I transposon
IAO xref: http://en.wikipedia.org/wiki/Retrotransposon
IAO_0000118: retrotransposon element

Axiom
IAO scope: RELATED
annotated target: class I
annotated property: IAO_0000118
annotated source: retrotransposon

Axiom
annotated target: A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase.
IAO xref: http://www.dddmag.com/Glossary.aspx#r
annotated property: IAO_0000115
annotated source: retrotransposon

Axiom
IAO scope: EXACT
annotated target: class I transposon
annotated property: IAO_0000118
annotated source: retrotransposon

Axiom
IAO scope: EXACT
annotated target: retrotransposon element
annotated property: IAO_0000118
annotated source: retrotransposon

translated_nucleotide_match
type: Class
subclass of: nucleotide_match
IAO_0000115: A match against a translated sequence.
IAO id: SO:0000181
IAO subset: SOFA
IAO_0000118: translated nucleotide match

Axiom
annotated target: A match against a translated sequence.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: translated_nucleotide_match

Axiom
IAO scope: EXACT
annotated target: translated nucleotide match
annotated property: IAO_0000118
annotated source: translated_nucleotide_match

DNA_transposon
type: Class
subclass of: transposable_element
IAO_0000115: A transposon where the mechanism of transposition is via a DNA intermediate.
IAO_0000118: DNA transposon
IAO id: SO:0000182
IAO_0000118: class II
IAO_0000118: class II transposon

Axiom
IAO scope: EXACT
annotated target: class II transposon
annotated property: IAO_0000118
annotated source: DNA_transposon

Axiom
IAO scope: RELATED
annotated target: class II
annotated property: IAO_0000118
annotated source: DNA_transposon

Axiom
annotated target: DNA transposon
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DNA_transposon

Axiom
annotated target: A transposon where the mechanism of transposition is via a DNA intermediate.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: DNA_transposon

non_transcribed_region
type: Class
subclass of: gene_component_region
IAO_0000115: A region of the gene which is not transcribed.
IAO id: SO:0000183
IAO subset: SOFA
IAO_0000118: non transcribed region
IAO_0000118: non-transcribed sequence
IAO_0000118: nontranscribed region
IAO_0000118: nontranscribed sequence

Axiom
IAO scope: EXACT
annotated target: nontranscribed sequence
annotated property: IAO_0000118
annotated source: non_transcribed_region

Axiom
IAO scope: EXACT
annotated target: non transcribed region
annotated property: IAO_0000118
annotated source: non_transcribed_region

Axiom
IAO scope: EXACT
annotated target: nontranscribed region
annotated property: IAO_0000118
annotated source: non_transcribed_region

Axiom
IAO scope: EXACT
annotated target: non-transcribed sequence
annotated property: IAO_0000118
annotated source: non_transcribed_region

Axiom
annotated target: A region of the gene which is not transcribed.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: non_transcribed_region

U2_intron
type: Class
subclass of: spliceosomal_intron
IAO_0000115: A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs.
comment: May have either GT-AG or AT-AG 5' and 3' boundaries.
IAO id: SO:0000184
IAO_0000118: U2 intron

Axiom
IAO scope: EXACT
annotated target: U2 intron
annotated property: IAO_0000118
annotated source: U2_intron

Axiom
annotated target: A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs.
IAO xref: PMID:9428511
annotated property: IAO_0000115
annotated source: U2_intron

primary_transcript
type: Class
subclass of: transcript
IAO_0000115: A transcript that in its initial state requires modification to be functional.
IAO id: SO:0000185
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/Primary_transcript
IAO_0000118: precursor RNA
IAO_0000118: primary transcript

Axiom
IAO scope: EXACT
annotated target: precursor RNA
annotated property: IAO_0000118
annotated source: primary_transcript

Axiom
annotated target: A transcript that in its initial state requires modification to be functional.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: primary_transcript

Axiom
IAO scope: EXACT
annotated target: primary transcript
annotated property: IAO_0000118
annotated source: primary_transcript

LTR_retrotransposon
type: Class
subclass of: retrotransposon
IAO_0000115: A retrotransposon flanked by long terminal repeat sequences.
IAO_0000118: LTR retrotransposon
IAO id: SO:0000186
IAO_0000118: long terminal repeat retrotransposon

Axiom
annotated target: A retrotransposon flanked by long terminal repeat sequences.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: LTR_retrotransposon

Axiom
IAO scope: EXACT
annotated target: LTR retrotransposon
annotated property: IAO_0000118
annotated source: LTR_retrotransposon

Axiom
IAO scope: EXACT
annotated target: long terminal repeat retrotransposon
annotated property: IAO_0000118
annotated source: LTR_retrotransposon

repeat_family
type: Class
IAO_0000115: A group of characterized repeat sequences.
IAO id: SO:0000187
IAO subset: SOFA
deprecated: true

Axiom
annotated target: A group of characterized repeat sequences.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: repeat_family

intron
type: Class
subclass of: primary_transcript_region
IAO_0000115: A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it.
IAO id: SO:0000188
IAO subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
IAO xref: http://en.wikipedia.org/wiki/Intron

Axiom
annotated target: A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it.
IAO xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
annotated property: IAO_0000115
annotated source: intron

non_LTR_retrotransposon
type: Class
subclass of: retrotransposon
IAO_0000115: A retrotransposon without long terminal repeat sequences.
IAO id: SO:0000189
IAO_0000118: non LTR retrotransposon

Axiom
annotated target: A retrotransposon without long terminal repeat sequences.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: non_LTR_retrotransposon

Axiom
IAO scope: EXACT
annotated target: non LTR retrotransposon
annotated property: IAO_0000118
annotated source: non_LTR_retrotransposon

five_prime_intron
type: Class
subclass of: intron
IAO_0000118: 5' intron
IAO_0000118: 5' intron sequence
IAO id: SO:0000190
IAO_0000118: five prime intron

Axiom
IAO scope: EXACT
annotated target: five prime intron
annotated property: IAO_0000118
annotated source: five_prime_intron

Axiom
annotated target: 5' intron sequence
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: five_prime_intron

Axiom
annotated target: 5' intron
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: five_prime_intron

interior_intron
type: Class
subclass of: intron
IAO id: SO:0000191
IAO_0000118: interior intron

Axiom
IAO scope: EXACT
annotated target: interior intron
annotated property: IAO_0000118
annotated source: interior_intron

three_prime_intron
type: Class
subclass of: intron
IAO_0000118: 3' intron
IAO_0000118: 3' intron sequence
IAO id: SO:0000192
IAO_0000118: three prime intron

Axiom
annotated target: 3' intron
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: three_prime_intron

Axiom
IAO scope: EXACT
annotated target: three prime intron
annotated property: IAO_0000118
annotated source: three_prime_intron

Axiom
annotated target: 3' intron sequence
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: three_prime_intron

RFLP_fragment
type: Class
subclass of: restriction_fragment
IAO_0000115: A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme.
IAO_0000118: RFLP
IAO_0000118: RFLP fragment
IAO id: SO:0000193
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism
IAO_0000118: restriction fragment length polymorphism

Axiom
IAO scope: EXACT
annotated target: RFLP fragment
annotated property: IAO_0000118
annotated source: RFLP_fragment

Axiom
IAO scope: EXACT
annotated target: RFLP
annotated property: IAO_0000118
annotated source: RFLP_fragment

Axiom
IAO scope: EXACT
annotated target: restriction fragment length polymorphism
annotated property: IAO_0000118
annotated source: RFLP_fragment

Axiom
annotated target: A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme.
IAO xref: GOC:pj
annotated property: IAO_0000115
annotated source: RFLP_fragment

LINE_element
type: Class
subclass of: non_LTR_retrotransposon
IAO_0000115: A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats.
IAO_0000118: LINE
IAO_0000118: LINE element
IAO_0000118: Long interspersed element
IAO_0000118: Long interspersed nuclear element
IAO id: SO:0000194

Axiom
IAO scope: EXACT
annotated target: Long interspersed nuclear element
annotated property: IAO_0000118
annotated source: LINE_element

Axiom
IAO scope: EXACT
annotated target: Long interspersed element
annotated property: IAO_0000118
annotated source: LINE_element

Axiom
IAO scope: EXACT
annotated target: LINE element
annotated property: IAO_0000118
annotated source: LINE_element

Axiom
IAO scope: EXACT
annotated target: LINE
annotated property: IAO_0000118
annotated source: LINE_element

Axiom
annotated target: A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats.
IAO xref: http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html
annotated property: IAO_0000115
annotated source: LINE_element

coding_exon
type: Class
subclass of: exon
IAO_0000115: An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon).
IAO id: SO:0000195
IAO subset: SOFA
IAO_0000118: coding exon

Axiom
IAO scope: EXACT
annotated target: coding exon
annotated property: IAO_0000118
annotated source: coding_exon

Axiom
annotated target: An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon).
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: coding_exon

five_prime_coding_exon_coding_region
type: Class
subclass of: coding_region_of_exon
subclass of: Restriction
  on property: part_of
  some values from: five_prime_coding_exon
IAO id: SO:0000196
IAO subset: SOFA
IAO_0000115: The sequence of the five_prime_coding_exon that codes for protein.
IAO_0000118: five prime exon coding region

Axiom
IAO xref: SO:cjm
annotated target: The sequence of the five_prime_coding_exon that codes for protein.
annotated property: IAO_0000115
annotated source: five_prime_coding_exon_coding_region

Axiom
IAO scope: EXACT
annotated target: five prime exon coding region
annotated property: IAO_0000118
annotated source: five_prime_coding_exon_coding_region

three_prime_coding_exon_coding_region
type: Class
subclass of: coding_region_of_exon
subclass of: Restriction
  on property: part_of
  some values from: three_prime_coding_exon
IAO id: SO:0000197
IAO subset: SOFA
IAO_0000115: The sequence of the three_prime_coding_exon that codes for protein.
IAO_0000118: three prime exon coding region

Axiom
IAO scope: EXACT
annotated target: three prime exon coding region
annotated property: IAO_0000118
annotated source: three_prime_coding_exon_coding_region

Axiom
IAO xref: SO:cjm
annotated target: The sequence of the three_prime_coding_exon that codes for protein.
annotated property: IAO_0000115
annotated source: three_prime_coding_exon_coding_region

noncoding_exon
type: Class
subclass of: exon
IAO_0000115: An exon that does not contain any codons.
IAO id: SO:0000198
IAO subset: SOFA
IAO_0000118: noncoding exon

Axiom
annotated target: An exon that does not contain any codons.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: noncoding_exon

Axiom
IAO scope: EXACT
annotated target: noncoding exon
annotated property: IAO_0000118
annotated source: noncoding_exon

translocation
type: Class
subclass of: sequence_alteration
IAO_0000115: A region of nucleotide sequence that has translocated to a new position.
IAO subset: DBVAR
IAO id: SO:0000199
IAO_0000118: transchr
IAO_0000118: translocated sequence

Axiom
IAO scope: RELATED
IAO xref: http://www.ncbi.nlm.nih.gov/dbvar/
annotated target: transchr
annotated property: IAO_0000118
annotated source: translocation

Axiom
annotated target: A region of nucleotide sequence that has translocated to a new position.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: translocation

Axiom
IAO scope: EXACT
annotated target: translocated sequence
annotated property: IAO_0000118
annotated source: translocation

five_prime_coding_exon
type: Class
subclass of: coding_exon
IAO_0000118: 5' coding exon
IAO id: SO:0000200
IAO subset: SOFA
IAO_0000115: The 5' most coding exon.
IAO_0000118: five prime coding exon

Axiom
annotated target: 5' coding exon
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: five_prime_coding_exon

Axiom
IAO xref: SO:ke
annotated target: The 5' most coding exon.
annotated property: IAO_0000115
annotated source: five_prime_coding_exon

Axiom
IAO scope: EXACT
annotated target: five prime coding exon
annotated property: IAO_0000118
annotated source: five_prime_coding_exon

interior_exon
type: Class
subclass of: exon
IAO_0000115: An exon that is bounded by 5' and 3' splice sites.
IAO id: SO:0000201
IAO_0000118: interior exon

Axiom
IAO scope: EXACT
annotated target: interior exon
annotated property: IAO_0000118
annotated source: interior_exon

Axiom
annotated target: An exon that is bounded by 5' and 3' splice sites.
IAO xref: PMID:10373547
annotated property: IAO_0000115
annotated source: interior_exon

three_prime_coding_exon
type: Class
subclass of: coding_exon
IAO_0000118: 3' coding exon
IAO id: SO:0000202
IAO_0000115: The coding exon that is most 3-prime on a given transcript.
IAO_0000118: three prime coding exon

Axiom
annotated target: 3' coding exon
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: three_prime_coding_exon

Axiom
IAO scope: EXACT
annotated target: three prime coding exon
annotated property: IAO_0000118
annotated source: three_prime_coding_exon

Axiom
IAO xref: SO:ma
annotated target: The coding exon that is most 3-prime on a given transcript.
annotated property: IAO_0000115
annotated source: three_prime_coding_exon

UTR
type: Class
subclass of: mRNA_region
IAO_0000115: Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated.
IAO id: SO:0000203
IAO subset: SOFA
IAO_0000118: untranslated region

Axiom
IAO scope: EXACT
annotated target: untranslated region
annotated property: IAO_0000118
annotated source: UTR

Axiom
annotated target: Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: UTR

five_prime_UTR
type: Class
subclass of: UTR
IAO_0000118: 5' UTR
IAO_0000115: A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein.
IAO id: SO:0000204
IAO subset: SOFA
IAO_0000118: five prime UTR
IAO_0000118: five_prime_untranslated_region
IAO xref: http://en.wikipedia.org/wiki/5'_UTR

Axiom
annotated target: A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein.
IAO xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
annotated property: IAO_0000115
annotated source: five_prime_UTR

Axiom
IAO scope: EXACT
annotated target: five prime UTR
annotated property: IAO_0000118
annotated source: five_prime_UTR

Axiom
annotated target: 5' UTR
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: five_prime_UTR

Axiom
IAO scope: EXACT
annotated target: five_prime_untranslated_region
annotated property: IAO_0000118
annotated source: five_prime_UTR

three_prime_UTR
type: Class
subclass of: UTR
IAO_0000115: A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein.
IAO id: SO:0000205
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/Three_prime_untranslated_region
IAO_0000118: three prime UTR
IAO_0000118: three prime untranslated region

Axiom
annotated target: A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein.
IAO xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
annotated property: IAO_0000115
annotated source: three_prime_UTR

Axiom
IAO scope: EXACT
annotated target: three prime UTR
annotated property: IAO_0000118
annotated source: three_prime_UTR

Axiom
IAO scope: EXACT
annotated target: three prime untranslated region
annotated property: IAO_0000118
annotated source: three_prime_UTR

SINE_element
type: Class
subclass of: non_LTR_retrotransposon
IAO_0000115: A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element.
IAO_0000118: SINE element
IAO id: SO:0000206
IAO_0000118: Short interspersed element
IAO_0000118: Short interspersed nuclear element
IAO xref: http://en.wikipedia.org/wiki/Short_interspersed_nuclear_element

Axiom
IAO scope: EXACT
annotated target: Short interspersed element
annotated property: IAO_0000118
annotated source: SINE_element

Axiom
annotated target: A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: SINE_element

Axiom
IAO scope: EXACT
annotated target: Short interspersed nuclear element
annotated property: IAO_0000118
annotated source: SINE_element

Axiom
IAO scope: EXACT
annotated target: SINE element
annotated property: IAO_0000118
annotated source: SINE_element

simple_sequence_length_variation
type: Class
subclass of: sequence_length_variation
IAO id: SO:0000207
IAO_0000118: SSLP
IAO_0000118: simple sequence length polymorphism
IAO_0000118: simple sequence length variation

Axiom
IAO scope: RELATED
annotated target: simple sequence length polymorphism
annotated property: IAO_0000118
annotated source: simple_sequence_length_variation

Axiom
IAO scope: RELATED
annotated target: SSLP
annotated property: IAO_0000118
annotated source: simple_sequence_length_variation

Axiom
IAO scope: EXACT
annotated target: simple sequence length variation
annotated property: IAO_0000118
annotated source: simple_sequence_length_variation

terminal_inverted_repeat_element
type: Class
subclass of: DNA_transposon
IAO_0000115: A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long.
IAO id: SO:0000208
IAO_0000118: TIR element
IAO_0000118: terminal inverted repeat element

Axiom
annotated target: A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long.
IAO xref: http://www.genetics.org/cgi/reprint/156/4/1983.pdf
annotated property: IAO_0000115
annotated source: terminal_inverted_repeat_element

Axiom
IAO scope: EXACT
annotated target: terminal inverted repeat element
annotated property: IAO_0000118
annotated source: terminal_inverted_repeat_element

Axiom
IAO scope: EXACT
annotated target: TIR element
annotated property: IAO_0000118
annotated source: terminal_inverted_repeat_element

rRNA_primary_transcript
type: Class
subclass of: nc_primary_transcript
IAO_0000115: A primary transcript encoding a ribosomal RNA.
IAO id: SO:0000209
IAO subset: SOFA
IAO_0000118: rRNA primary transcript
IAO_0000118: ribosomal RNA primary transcript

Axiom
IAO scope: EXACT
annotated target: rRNA primary transcript
annotated property: IAO_0000118
annotated source: rRNA_primary_transcript

Axiom
annotated target: A primary transcript encoding a ribosomal RNA.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: rRNA_primary_transcript

Axiom
IAO scope: EXACT
annotated target: ribosomal RNA primary transcript
annotated property: IAO_0000118
annotated source: rRNA_primary_transcript

tRNA_primary_transcript
type: Class
subclass of: nc_primary_transcript
IAO_0000115: A primary transcript encoding a transfer RNA (SO:0000253).
IAO id: SO:0000210
IAO_0000118: tRNA primary transcript

Axiom
annotated target: A primary transcript encoding a transfer RNA (SO:0000253).
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: tRNA_primary_transcript

Axiom
IAO scope: EXACT
annotated target: tRNA primary transcript
annotated property: IAO_0000118
annotated source: tRNA_primary_transcript

alanine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
IAO_0000115: A primary transcript encoding alanyl tRNA.
IAO id: SO:0000211
IAO_0000118: alanine tRNA primary transcript

Axiom
annotated target: A primary transcript encoding alanyl tRNA.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: alanine_tRNA_primary_transcript

Axiom
IAO scope: EXACT
annotated target: alanine tRNA primary transcript
annotated property: IAO_0000118
annotated source: alanine_tRNA_primary_transcript

arginine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
IAO_0000115: A primary transcript encoding arginyl tRNA (SO:0000255).
IAO id: SO:0000212
IAO_0000118: arginine tRNA primary transcript

Axiom
annotated target: A primary transcript encoding arginyl tRNA (SO:0000255).
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: arginine_tRNA_primary_transcript

Axiom
IAO scope: EXACT
annotated target: arginine tRNA primary transcript
annotated property: IAO_0000118
annotated source: arginine_tRNA_primary_transcript

asparagine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
IAO_0000115: A primary transcript encoding asparaginyl tRNA (SO:0000256).
IAO id: SO:0000213
IAO_0000118: asparagine tRNA primary transcript

Axiom
IAO scope: EXACT
annotated target: asparagine tRNA primary transcript
annotated property: IAO_0000118
annotated source: asparagine_tRNA_primary_transcript

Axiom
annotated target: A primary transcript encoding asparaginyl tRNA (SO:0000256).
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: asparagine_tRNA_primary_transcript

aspartic_acid_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
IAO_0000115: A primary transcript encoding aspartyl tRNA (SO:0000257).
IAO id: SO:0000214
IAO_0000118: aspartic acid tRNA primary transcript

Axiom
IAO scope: EXACT
annotated target: aspartic acid tRNA primary transcript
annotated property: IAO_0000118
annotated source: aspartic_acid_tRNA_primary_transcript

Axiom
annotated target: A primary transcript encoding aspartyl tRNA (SO:0000257).
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: aspartic_acid_tRNA_primary_transcript

cysteine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
IAO_0000115: A primary transcript encoding cysteinyl tRNA (SO:0000258).
IAO id: SO:0000215
IAO_0000118: cysteine tRNA primary transcript

Axiom
annotated target: A primary transcript encoding cysteinyl tRNA (SO:0000258).
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: cysteine_tRNA_primary_transcript

Axiom
IAO scope: EXACT
annotated target: cysteine tRNA primary transcript
annotated property: IAO_0000118
annotated source: cysteine_tRNA_primary_transcript

glutamic_acid_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
IAO_0000115: A primary transcript encoding glutaminyl tRNA (SO:0000260).
IAO id: SO:0000216
IAO_0000118: glutamic acid tRNA primary transcript

Axiom
IAO scope: EXACT
annotated target: glutamic acid tRNA primary transcript
annotated property: IAO_0000118
annotated source: glutamic_acid_tRNA_primary_transcript

Axiom
annotated target: A primary transcript encoding glutaminyl tRNA (SO:0000260).
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: glutamic_acid_tRNA_primary_transcript

glutamine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
IAO_0000115: A primary transcript encoding glutamyl tRNA (SO:0000260).
IAO id: SO:0000217
IAO_0000118: glutamine tRNA primary transcript

Axiom
annotated target: A primary transcript encoding glutamyl tRNA (SO:0000260).
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: glutamine_tRNA_primary_transcript

Axiom
IAO scope: EXACT
annotated target: glutamine tRNA primary transcript
annotated property: IAO_0000118
annotated source: glutamine_tRNA_primary_transcript

glycine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
IAO_0000115: A primary transcript encoding glycyl tRNA (SO:0000263).
IAO id: SO:0000218
IAO_0000118: glycine tRNA primary transcript

Axiom
annotated target: A primary transcript encoding glycyl tRNA (SO:0000263).
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: glycine_tRNA_primary_transcript

Axiom
IAO scope: EXACT
annotated target: glycine tRNA primary transcript
annotated property: IAO_0000118
annotated source: glycine_tRNA_primary_transcript

histidine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
IAO_0000115: A primary transcript encoding histidyl tRNA (SO:0000262).
IAO id: SO:0000219
IAO_0000118: histidine tRNA primary transcript

Axiom
annotated target: A primary transcript encoding histidyl tRNA (SO:0000262).
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: histidine_tRNA_primary_transcript

Axiom
IAO scope: EXACT
annotated target: histidine tRNA primary transcript
annotated property: IAO_0000118
annotated source: histidine_tRNA_primary_transcript

isoleucine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
IAO_0000115: A primary transcript encoding isoleucyl tRNA (SO:0000263).
IAO id: SO:0000220
IAO_0000118: isoleucine tRNA primary transcript

Axiom
annotated target: A primary transcript encoding isoleucyl tRNA (SO:0000263).
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: isoleucine_tRNA_primary_transcript

Axiom
IAO scope: EXACT
annotated target: isoleucine tRNA primary transcript
annotated property: IAO_0000118
annotated source: isoleucine_tRNA_primary_transcript

leucine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
IAO_0000115: A primary transcript encoding leucyl tRNA (SO:0000264).
IAO id: SO:0000221
IAO_0000118: leucine tRNA primary transcript

Axiom
annotated target: A primary transcript encoding leucyl tRNA (SO:0000264).
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: leucine_tRNA_primary_transcript

Axiom
IAO scope: EXACT
annotated target: leucine tRNA primary transcript
annotated property: IAO_0000118
annotated source: leucine_tRNA_primary_transcript

lysine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
IAO_0000115: A primary transcript encoding lysyl tRNA (SO:0000265).
IAO id: SO:0000222
IAO_0000118: lysine tRNA primary transcript

Axiom
annotated target: A primary transcript encoding lysyl tRNA (SO:0000265).
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: lysine_tRNA_primary_transcript

Axiom
IAO scope: EXACT
annotated target: lysine tRNA primary transcript
annotated property: IAO_0000118
annotated source: lysine_tRNA_primary_transcript

methionine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
IAO_0000115: A primary transcript encoding methionyl tRNA (SO:0000266).
IAO id: SO:0000223
IAO_0000118: methionine tRNA primary transcript

Axiom
annotated target: A primary transcript encoding methionyl tRNA (SO:0000266).
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: methionine_tRNA_primary_transcript

Axiom
IAO scope: EXACT
annotated target: methionine tRNA primary transcript
annotated property: IAO_0000118
annotated source: methionine_tRNA_primary_transcript

phenylalanine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
IAO_0000115: A primary transcript encoding phenylalanyl tRNA (SO:0000267).
IAO id: SO:0000224
IAO_0000118: phenylalanine tRNA primary transcript

Axiom
annotated target: A primary transcript encoding phenylalanyl tRNA (SO:0000267).
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: phenylalanine_tRNA_primary_transcript

Axiom
IAO scope: EXACT
annotated target: phenylalanine tRNA primary transcript
annotated property: IAO_0000118
annotated source: phenylalanine_tRNA_primary_transcript

proline_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
IAO_0000115: A primary transcript encoding prolyl tRNA (SO:0000268).
IAO id: SO:0000225
IAO_0000118: proline tRNA primary transcript

Axiom
IAO scope: EXACT
annotated target: proline tRNA primary transcript
annotated property: IAO_0000118
annotated source: proline_tRNA_primary_transcript

Axiom
annotated target: A primary transcript encoding prolyl tRNA (SO:0000268).
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: proline_tRNA_primary_transcript

serine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
IAO_0000115: A primary transcript encoding seryl tRNA (SO:000269).
IAO id: SO:0000226
IAO_0000118: serine tRNA primary transcript

Axiom
IAO scope: EXACT
annotated target: serine tRNA primary transcript
annotated property: IAO_0000118
annotated source: serine_tRNA_primary_transcript

Axiom
annotated target: A primary transcript encoding seryl tRNA (SO:000269).
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: serine_tRNA_primary_transcript

threonine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
IAO_0000115: A primary transcript encoding threonyl tRNA (SO:000270).
IAO id: SO:0000227
IAO_0000118: threonine tRNA primary transcript

Axiom
annotated target: A primary transcript encoding threonyl tRNA (SO:000270).
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: threonine_tRNA_primary_transcript

Axiom
IAO scope: EXACT
annotated target: threonine tRNA primary transcript
annotated property: IAO_0000118
annotated source: threonine_tRNA_primary_transcript

tryptophan_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
IAO_0000115: A primary transcript encoding tryptophanyl tRNA (SO:000271).
IAO id: SO:0000228
IAO_0000118: tryptophan tRNA primary transcript

Axiom
annotated target: A primary transcript encoding tryptophanyl tRNA (SO:000271).
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: tryptophan_tRNA_primary_transcript

Axiom
IAO scope: EXACT
annotated target: tryptophan tRNA primary transcript
annotated property: IAO_0000118
annotated source: tryptophan_tRNA_primary_transcript

tyrosine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
IAO_0000115: A primary transcript encoding tyrosyl tRNA (SO:000272).
IAO id: SO:0000229
IAO_0000118: tyrosine tRNA primary transcript

Axiom
annotated target: A primary transcript encoding tyrosyl tRNA (SO:000272).
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: tyrosine_tRNA_primary_transcript

Axiom
IAO scope: EXACT
annotated target: tyrosine tRNA primary transcript
annotated property: IAO_0000118
annotated source: tyrosine_tRNA_primary_transcript

valine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
IAO_0000115: A primary transcript encoding valyl tRNA (SO:000273).
IAO id: SO:0000230
IAO_0000118: valine tRNA primary transcript

Axiom
annotated target: A primary transcript encoding valyl tRNA (SO:000273).
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: valine_tRNA_primary_transcript

Axiom
IAO scope: EXACT
annotated target: valine tRNA primary transcript
annotated property: IAO_0000118
annotated source: valine_tRNA_primary_transcript

snRNA_primary_transcript
type: Class
subclass of: nc_primary_transcript
IAO_0000115: A primary transcript encoding a small nuclear RNA (SO:0000274).
IAO id: SO:0000231
IAO_0000118: snRNA primary transcript

Axiom
IAO scope: EXACT
annotated target: snRNA primary transcript
annotated property: IAO_0000118
annotated source: snRNA_primary_transcript

Axiom
annotated target: A primary transcript encoding a small nuclear RNA (SO:0000274).
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: snRNA_primary_transcript

snoRNA_primary_transcript
type: Class
subclass of: nc_primary_transcript
IAO_0000115: A primary transcript encoding a small nucleolar mRNA (SO:0000275).
IAO id: SO:0000232
IAO_0000118: snoRNA primary transcript

Axiom
IAO scope: EXACT
annotated target: snoRNA primary transcript
annotated property: IAO_0000118
annotated source: snoRNA_primary_transcript

Axiom
annotated target: A primary transcript encoding a small nucleolar mRNA (SO:0000275).
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: snoRNA_primary_transcript

mature_transcript
type: Class
subclass of: transcript
subclass of: Restriction
  on property: derives_from
  some values from: primary_transcript
comment: A processed transcript cannot contain introns.
IAO_0000115: A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified.
IAO id: SO:0000233
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/Mature_transcript
IAO_0000118: mature transcript

Axiom
IAO scope: EXACT
annotated target: mature transcript
annotated property: IAO_0000118
annotated source: mature_transcript

Axiom
annotated target: A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: mature_transcript

mRNA
type: Class
subclass of: mature_transcript
comment: An mRNA does not contain introns as it is a processed_transcript. The equivalent kind of primary_transcript is protein_coding_primary_transcript (SO:0000120) which may contain introns. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
IAO_0000115: Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns.
IAO id: SO:0000234
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/MRNA
IAO_0000118: messenger RNA

Axiom
IAO scope: EXACT
annotated target: messenger RNA
annotated property: IAO_0000118
annotated source: mRNA

Axiom
annotated target: Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: mRNA

TF_binding_site
type: Class
subclass of: SO_0001654
subclass of: SO_0001679
IAO_0000115: A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667].
IAO id: SO:0000235
IAO subset: SOFA
IAO_0000118: TF binding site
IAO_0000118: transcription factor binding site

Axiom
IAO scope: EXACT
annotated target: TF binding site
annotated property: IAO_0000118
annotated source: TF_binding_site

Axiom
annotated target: A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667].
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: TF_binding_site

Axiom
IAO scope: EXACT
annotated target: transcription factor binding site
annotated property: IAO_0000118
annotated source: TF_binding_site

ORF
type: Class
subclass of: reading_frame
IAO id: SO:0000236
IAO subset: SOFA
comment: The definition was modified by Rama. ORF is defined by the sequence, whereas the CDS is defined according to whether a polypeptide is made. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
IAO_0000115: The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER.
IAO_0000118: open reading frame

Axiom
IAO xref: SGD:rb
IAO xref: SO:ma
annotated target: The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER.
annotated property: IAO_0000115
annotated source: ORF

Axiom
IAO scope: EXACT
annotated target: open reading frame
annotated property: IAO_0000118
annotated source: ORF

transcript_attribute
type: Class
subclass of: feature_attribute
IAO id: SO:0000237
IAO_0000118: transcript attribute

Axiom
IAO scope: EXACT
annotated target: transcript attribute
annotated property: IAO_0000118
annotated source: transcript_attribute

foldback_element
type: Class
subclass of: DNA_transposon
IAO_0000115: A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats.
IAO_0000118: LVR element
IAO id: SO:0000238
IAO_0000118: foldback element
IAO_0000118: long inverted repeat element

Axiom
IAO scope: RELATED
annotated target: long inverted repeat element
annotated property: IAO_0000118
annotated source: foldback_element

Axiom
annotated target: LVR element
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: foldback_element

Axiom
annotated target: A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats.
IAO xref: http://www.genetics.org/cgi/reprint/156/4/1983.pdf
annotated property: IAO_0000115
annotated source: foldback_element

Axiom
IAO scope: EXACT
annotated target: foldback element
annotated property: IAO_0000118
annotated source: foldback_element

flanking_region
type: Class
subclass of: SO_0001412
IAO id: SO:0000239
IAO subset: SOFA
IAO_0000115: The sequences extending on either side of a specific region.
IAO_0000118: flanking region

Axiom
IAO xref: SO:ke
annotated target: The sequences extending on either side of a specific region.
annotated property: IAO_0000115
annotated source: flanking_region

Axiom
IAO scope: EXACT
annotated target: flanking region
annotated property: IAO_0000118
annotated source: flanking_region

chromosome_variation
type: Class
subclass of: SO_0001507
subclass of: Restriction
  on property: part_of
  some values from: SO_0001524
disjoint with: sequence_attribute
IAO id: SO:0000240
IAO_0000118: chromosome variation

Axiom
IAO scope: EXACT
annotated target: chromosome variation
annotated property: IAO_0000118
annotated source: chromosome_variation

internal_UTR
type: Class
subclass of: UTR
IAO_0000115: A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal.
IAO id: SO:0000241
IAO_0000118: internal UTR

Axiom
IAO scope: EXACT
annotated target: internal UTR
annotated property: IAO_0000118
annotated source: internal_UTR

Axiom
annotated target: A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal.
IAO xref: SO:cjm
annotated property: IAO_0000115
annotated source: internal_UTR

untranslated_region_polycistronic_mRNA
type: Class
subclass of: UTR
IAO id: SO:0000242
IAO_0000115: The untranslated sequence separating the 'cistrons' of multicistronic mRNA.
IAO_0000118: untranslated region polycistronic mRNA

Axiom
IAO scope: EXACT
annotated target: untranslated region polycistronic mRNA
annotated property: IAO_0000118
annotated source: untranslated_region_polycistronic_mRNA

Axiom
IAO xref: SO:ke
annotated target: The untranslated sequence separating the 'cistrons' of multicistronic mRNA.
annotated property: IAO_0000115
annotated source: untranslated_region_polycistronic_mRNA

internal_ribosome_entry_site
type: Class
subclass of: ribosome_entry_site
IAO_0000118: IRES
IAO id: SO:0000243
IAO_0000115: Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation.
IAO xref: http://en.wikipedia.org/wiki/Internal_ribosome_entry_site
IAO_0000118: internal ribosomal entry sequence
IAO_0000118: internal ribosomal entry site
IAO_0000118: internal ribosome entry sequence
IAO_0000118: internal ribosome entry site

Axiom
IAO scope: EXACT
annotated target: internal ribosome entry site
annotated property: IAO_0000118
annotated source: internal_ribosome_entry_site

Axiom
IAO xref: SO:ke
annotated target: Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation.
annotated property: IAO_0000115
annotated source: internal_ribosome_entry_site

Axiom
IAO scope: EXACT
annotated target: internal ribosomal entry sequence
annotated property: IAO_0000118
annotated source: internal_ribosome_entry_site

Axiom
IAO scope: EXACT
annotated target: internal ribosomal entry site
annotated property: IAO_0000118
annotated source: internal_ribosome_entry_site

Axiom
IAO scope: RELATED
annotated target: internal ribosome entry sequence
annotated property: IAO_0000118
annotated source: internal_ribosome_entry_site

Axiom
IAO scope: EXACT
annotated target: IRES
annotated property: IAO_0000118
annotated source: internal_ribosome_entry_site

four_cutter_restriction_site
type: Class
IAO_0000118: 4-cutter_restriction_site
IAO id: SO:0000244
IAO_0000118: four-cutter_restriction_sit
deprecated: true

Axiom
annotated target: 4-cutter_restriction_site
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: four_cutter_restriction_site

Axiom
IAO scope: RELATED
annotated target: four-cutter_restriction_sit
annotated property: IAO_0000118
annotated source: four_cutter_restriction_site

mRNA_by_polyadenylation_status
type: Class
IAO id: SO:0000245
deprecated: true

polyadenylated
type: Class
subclass of: mRNA_attribute
IAO_0000115: A attribute describing the addition of a poly A tail to the 3' end of a mRNA molecule.
IAO id: SO:0000246

Axiom
annotated target: A attribute describing the addition of a poly A tail to the 3' end of a mRNA molecule.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: polyadenylated

mRNA_not_polyadenylated
type: Class
IAO id: SO:0000247
deprecated: true

sequence_length_variation
type: Class
subclass of: SO_1000002
IAO id: SO:0000248
IAO_0000118: sequence length variation

Axiom
IAO scope: EXACT
annotated target: sequence length variation
annotated property: IAO_0000118
annotated source: sequence_length_variation

six_cutter_restriction_site
type: Class
IAO_0000118: 6-cutter_restriction_site
IAO id: SO:0000249
IAO_0000118: six-cutter_restriction_site
deprecated: true

Axiom
annotated target: 6-cutter_restriction_site
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: six_cutter_restriction_site

Axiom
IAO scope: RELATED
annotated target: six-cutter_restriction_site
annotated property: IAO_0000118
annotated source: six_cutter_restriction_site

modified_RNA_base_feature
type: Class
subclass of: base
IAO_0000115: A post_transcriptionally modified base.
IAO id: SO:0000250
IAO_0000118: modified RNA base feature

Axiom
annotated target: A post_transcriptionally modified base.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: modified_RNA_base_feature

Axiom
IAO scope: EXACT
annotated target: modified RNA base feature
annotated property: IAO_0000118
annotated source: modified_RNA_base_feature

eight_cutter_restriction_site
type: Class
IAO_0000118: 8-cutter_restriction_site
IAO id: SO:0000251
IAO_0000118: eight-cutter_restriction_site
deprecated: true

Axiom
IAO scope: RELATED
annotated target: eight-cutter_restriction_site
annotated property: IAO_0000118
annotated source: eight_cutter_restriction_site

Axiom
annotated target: 8-cutter_restriction_site
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: eight_cutter_restriction_site

rRNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: rRNA_primary_transcript
IAO_0000115: RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity.
IAO id: SO:0000252
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/RRNA
IAO_0000118: ribosomal RNA
IAO_0000118: ribosomal ribonucleic acid

Axiom
IAO scope: EXACT
annotated target: ribosomal ribonucleic acid
annotated property: IAO_0000118
annotated source: rRNA

Axiom
IAO scope: EXACT
annotated target: ribosomal RNA
annotated property: IAO_0000118
annotated source: rRNA

Axiom
IAO xref: ISBN:0198506732
annotated target: RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity.
IAO xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
annotated property: IAO_0000115
annotated source: rRNA

tRNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: tRNA_primary_transcript
IAO id: SO:0000253
IAO subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
IAO_0000115: Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position.
IAO xref: http://en.wikipedia.org/wiki/TRNA
IAO_0000118: transfer RNA
IAO_0000118: transfer ribonucleic acid

Axiom
IAO scope: RELATED
annotated target: transfer ribonucleic acid
annotated property: IAO_0000118
annotated source: tRNA

Axiom
IAO xref: ISBN:0198506732
annotated target: Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position.
IAO xref: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc
annotated property: IAO_0000115
annotated source: tRNA

Axiom
IAO scope: RELATED
annotated target: transfer RNA
annotated property: IAO_0000118
annotated source: tRNA

alanyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: alanine_tRNA_primary_transcript
IAO_0000115: A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region.
IAO id: SO:0000254
IAO_0000118: alanyl tRNA
IAO_0000118: alanyl-transfer RNA
IAO_0000118: alanyl-transfer ribonucleic acid

Axiom
IAO scope: EXACT
annotated target: alanyl tRNA
annotated property: IAO_0000118
annotated source: alanyl_tRNA

Axiom
IAO scope: EXACT
annotated target: alanyl-transfer RNA
annotated property: IAO_0000118
annotated source: alanyl_tRNA

Axiom
annotated target: A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: alanyl_tRNA

Axiom
IAO scope: EXACT
annotated target: alanyl-transfer ribonucleic acid
annotated property: IAO_0000118
annotated source: alanyl_tRNA

rRNA_small_subunit_primary_transcript
type: Class
subclass of: rRNA_primary_transcript
IAO_0000115: A primary transcript encoding a small ribosomal subunit RNA.
IAO id: SO:0000255
IAO_0000118: rRNA small subunit primary transcript

Axiom
annotated target: A primary transcript encoding a small ribosomal subunit RNA.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: rRNA_small_subunit_primary_transcript

Axiom
IAO scope: EXACT
annotated target: rRNA small subunit primary transcript
annotated property: IAO_0000118
annotated source: rRNA_small_subunit_primary_transcript

asparaginyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: asparagine_tRNA_primary_transcript
IAO_0000115: A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region.
IAO id: SO:0000256
IAO_0000118: asparaginyl tRNA
IAO_0000118: asparaginyl-transfer RNA
IAO_0000118: asparaginyl-transfer ribonucleic acid

Axiom
IAO scope: EXACT
annotated target: asparaginyl tRNA
annotated property: IAO_0000118
annotated source: asparaginyl_tRNA

Axiom
annotated target: A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: asparaginyl_tRNA

Axiom
IAO scope: EXACT
annotated target: asparaginyl-transfer RNA
annotated property: IAO_0000118
annotated source: asparaginyl_tRNA

Axiom
IAO scope: EXACT
annotated target: asparaginyl-transfer ribonucleic acid
annotated property: IAO_0000118
annotated source: asparaginyl_tRNA

aspartyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: aspartic_acid_tRNA_primary_transcript
IAO_0000115: A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region.
IAO id: SO:0000257
IAO_0000118: aspartyl tRNA
IAO_0000118: aspartyl-transfer RNA
IAO_0000118: aspartyl-transfer ribonucleic acid

Axiom
IAO scope: EXACT
annotated target: aspartyl tRNA
annotated property: IAO_0000118
annotated source: aspartyl_tRNA

Axiom
IAO scope: EXACT
annotated target: aspartyl-transfer RNA
annotated property: IAO_0000118
annotated source: aspartyl_tRNA

Axiom
annotated target: A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: aspartyl_tRNA

Axiom
IAO scope: EXACT
annotated target: aspartyl-transfer ribonucleic acid
annotated property: IAO_0000118
annotated source: aspartyl_tRNA

cysteinyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: cysteine_tRNA_primary_transcript
IAO_0000115: A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region.
IAO id: SO:0000258
IAO_0000118: cysteinyl tRNA
IAO_0000118: cysteinyl-transfer RNA
IAO_0000118: cysteinyl-transfer ribonucleic acid

Axiom
annotated target: A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: cysteinyl_tRNA

Axiom
IAO scope: EXACT
annotated target: cysteinyl tRNA
annotated property: IAO_0000118
annotated source: cysteinyl_tRNA

Axiom
IAO scope: EXACT
annotated target: cysteinyl-transfer ribonucleic acid
annotated property: IAO_0000118
annotated source: cysteinyl_tRNA

Axiom
IAO scope: EXACT
annotated target: cysteinyl-transfer RNA
annotated property: IAO_0000118
annotated source: cysteinyl_tRNA

glutaminyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: glutamic_acid_tRNA_primary_transcript
IAO_0000115: A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region.
IAO id: SO:0000259
IAO_0000118: glutaminyl tRNA
IAO_0000118: glutaminyl-transfer RNA
IAO_0000118: glutaminyl-transfer ribonucleic acid

Axiom
IAO scope: EXACT
annotated target: glutaminyl-transfer ribonucleic acid
annotated property: IAO_0000118
annotated source: glutaminyl_tRNA

Axiom
IAO scope: EXACT
annotated target: glutaminyl tRNA
annotated property: IAO_0000118
annotated source: glutaminyl_tRNA

Axiom
annotated target: A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: glutaminyl_tRNA

Axiom
IAO scope: EXACT
annotated target: glutaminyl-transfer RNA
annotated property: IAO_0000118
annotated source: glutaminyl_tRNA

glutamyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: glutamine_tRNA_primary_transcript
IAO_0000115: A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region.
IAO id: SO:0000260
IAO_0000118: glutamyl tRNA
IAO_0000118: glutamyl-transfer RNA
IAO_0000118: glutamyl-transfer ribonucleic acid

Axiom
IAO scope: RELATED
annotated target: glutamyl-transfer RNA
annotated property: IAO_0000118
annotated source: glutamyl_tRNA

Axiom
IAO scope: EXACT
annotated target: glutamyl tRNA
annotated property: IAO_0000118
annotated source: glutamyl_tRNA

Axiom
IAO scope: EXACT
annotated target: glutamyl-transfer ribonucleic acid
annotated property: IAO_0000118
annotated source: glutamyl_tRNA

Axiom
annotated target: A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: glutamyl_tRNA

glycyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: glycine_tRNA_primary_transcript
IAO_0000115: A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region.
IAO id: SO:0000261
IAO_0000118: glycyl tRNA
IAO_0000118: glycyl-transfer RNA
IAO_0000118: glycyl-transfer ribonucleic acid

Axiom
IAO scope: RELATED
annotated target: glycyl-transfer ribonucleic acid
annotated property: IAO_0000118
annotated source: glycyl_tRNA

Axiom
IAO scope: EXACT
annotated target: glycyl tRNA
annotated property: IAO_0000118
annotated source: glycyl_tRNA

Axiom
annotated target: A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: glycyl_tRNA

Axiom
IAO scope: RELATED
annotated target: glycyl-transfer RNA
annotated property: IAO_0000118
annotated source: glycyl_tRNA

histidyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: histidine_tRNA_primary_transcript
IAO_0000115: A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region.
IAO id: SO:0000262
IAO_0000118: histidyl tRNA
IAO_0000118: histidyl-transfer RNA
IAO_0000118: histidyl-transfer ribonucleic acid

Axiom
IAO scope: EXACT
annotated target: histidyl tRNA
annotated property: IAO_0000118
annotated source: histidyl_tRNA

Axiom
annotated target: A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: histidyl_tRNA

Axiom
IAO scope: EXACT
annotated target: histidyl-transfer ribonucleic acid
annotated property: IAO_0000118
annotated source: histidyl_tRNA

Axiom
IAO scope: EXACT
annotated target: histidyl-transfer RNA
annotated property: IAO_0000118
annotated source: histidyl_tRNA

isoleucyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: isoleucine_tRNA_primary_transcript
IAO_0000115: A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region.
IAO id: SO:0000263
IAO_0000118: isoleucyl tRNA
IAO_0000118: isoleucyl-transfer RNA
IAO_0000118: isoleucyl-transfer ribonucleic acid

Axiom
IAO scope: EXACT
annotated target: isoleucyl-transfer ribonucleic acid
annotated property: IAO_0000118
annotated source: isoleucyl_tRNA

Axiom
IAO scope: EXACT
annotated target: isoleucyl-transfer RNA
annotated property: IAO_0000118
annotated source: isoleucyl_tRNA

Axiom
IAO scope: EXACT
annotated target: isoleucyl tRNA
annotated property: IAO_0000118
annotated source: isoleucyl_tRNA

Axiom
annotated target: A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: isoleucyl_tRNA

leucyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: leucine_tRNA_primary_transcript
IAO_0000115: A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region.
IAO id: SO:0000264
IAO_0000118: leucyl tRNA
IAO_0000118: leucyl-transfer RNA
IAO_0000118: leucyl-transfer ribonucleic acid

Axiom
annotated target: A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: leucyl_tRNA

Axiom
IAO scope: EXACT
annotated target: leucyl-transfer ribonucleic acid
annotated property: IAO_0000118
annotated source: leucyl_tRNA

Axiom
IAO scope: EXACT
annotated target: leucyl tRNA
annotated property: IAO_0000118
annotated source: leucyl_tRNA

Axiom
IAO scope: EXACT
annotated target: leucyl-transfer RNA
annotated property: IAO_0000118
annotated source: leucyl_tRNA

lysyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: lysine_tRNA_primary_transcript
IAO_0000115: A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region.
IAO id: SO:0000265
IAO_0000118: lysyl tRNA
IAO_0000118: lysyl-transfer RNA
IAO_0000118: lysyl-transfer ribonucleic acid

Axiom
IAO scope: EXACT
annotated target: lysyl tRNA
annotated property: IAO_0000118
annotated source: lysyl_tRNA

Axiom
IAO scope: EXACT
annotated target: lysyl-transfer RNA
annotated property: IAO_0000118
annotated source: lysyl_tRNA

Axiom
annotated target: A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: lysyl_tRNA

Axiom
IAO scope: EXACT
annotated target: lysyl-transfer ribonucleic acid
annotated property: IAO_0000118
annotated source: lysyl_tRNA

methionyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: methionine_tRNA_primary_transcript
IAO_0000115: A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region.
IAO id: SO:0000266
IAO_0000118: methionyl tRNA
IAO_0000118: methionyl-transfer RNA
IAO_0000118: methionyl-transfer ribonucleic acid

Axiom
IAO scope: EXACT
annotated target: methionyl-transfer ribonucleic acid
annotated property: IAO_0000118
annotated source: methionyl_tRNA

Axiom
annotated target: A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: methionyl_tRNA

Axiom
IAO scope: EXACT
annotated target: methionyl-transfer RNA
annotated property: IAO_0000118
annotated source: methionyl_tRNA

Axiom
IAO scope: EXACT
annotated target: methionyl tRNA
annotated property: IAO_0000118
annotated source: methionyl_tRNA

phenylalanyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: phenylalanine_tRNA_primary_transcript
IAO_0000115: A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region.
IAO id: SO:0000267
IAO_0000118: phenylalanyl tRNA
IAO_0000118: phenylalanyl-transfer RNA
IAO_0000118: phenylalanyl-transfer ribonucleic acid

Axiom
IAO scope: EXACT
annotated target: phenylalanyl-transfer RNA
annotated property: IAO_0000118
annotated source: phenylalanyl_tRNA

Axiom
IAO scope: EXACT
annotated target: phenylalanyl-transfer ribonucleic acid
annotated property: IAO_0000118
annotated source: phenylalanyl_tRNA

Axiom
IAO scope: EXACT
annotated target: phenylalanyl tRNA
annotated property: IAO_0000118
annotated source: phenylalanyl_tRNA

Axiom
annotated target: A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: phenylalanyl_tRNA

prolyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: proline_tRNA_primary_transcript
IAO_0000115: A tRNA sequence that has a proline anticodon, and a 3' proline binding region.
IAO id: SO:0000268
IAO_0000118: prolyl tRNA
IAO_0000118: prolyl-transfer RNA
IAO_0000118: prolyl-transfer ribonucleic acid

Axiom
IAO scope: EXACT
annotated target: prolyl tRNA
annotated property: IAO_0000118
annotated source: prolyl_tRNA

Axiom
IAO scope: EXACT
annotated target: prolyl-transfer ribonucleic acid
annotated property: IAO_0000118
annotated source: prolyl_tRNA

Axiom
annotated target: A tRNA sequence that has a proline anticodon, and a 3' proline binding region.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: prolyl_tRNA

Axiom
IAO scope: EXACT
annotated target: prolyl-transfer RNA
annotated property: IAO_0000118
annotated source: prolyl_tRNA

seryl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: serine_tRNA_primary_transcript
IAO_0000115: A tRNA sequence that has a serine anticodon, and a 3' serine binding region.
IAO id: SO:0000269
IAO_0000118: seryl tRNA
IAO_0000118: seryl-transfer RNA
IAO_0000118: seryl-transfer ribonucleic acid

Axiom
annotated target: A tRNA sequence that has a serine anticodon, and a 3' serine binding region.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: seryl_tRNA

Axiom
IAO scope: RELATED
annotated target: seryl-transfer ribonucleic acid
annotated property: IAO_0000118
annotated source: seryl_tRNA

Axiom
IAO scope: EXACT
annotated target: seryl tRNA
annotated property: IAO_0000118
annotated source: seryl_tRNA

Axiom
IAO scope: EXACT
annotated target: seryl-transfer RNA
annotated property: IAO_0000118
annotated source: seryl_tRNA

threonyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: threonine_tRNA_primary_transcript
IAO_0000115: A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region.
IAO id: SO:0000270
IAO_0000118: threonyl tRNA
IAO_0000118: threonyl-transfer RNA
IAO_0000118: threonyl-transfer ribonucleic acid

Axiom
IAO scope: EXACT
annotated target: threonyl-transfer ribonucleic acid
annotated property: IAO_0000118
annotated source: threonyl_tRNA

Axiom
annotated target: A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: threonyl_tRNA

Axiom
IAO scope: RELATED
annotated target: threonyl-transfer RNA
annotated property: IAO_0000118
annotated source: threonyl_tRNA

Axiom
IAO scope: EXACT
annotated target: threonyl tRNA
annotated property: IAO_0000118
annotated source: threonyl_tRNA

tryptophanyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: tryptophan_tRNA_primary_transcript
IAO_0000115: A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region.
IAO id: SO:0000271
IAO_0000118: tryptophanyl tRNA
IAO_0000118: tryptophanyl-transfer RNA
IAO_0000118: tryptophanyl-transfer ribonucleic acid

Axiom
IAO scope: EXACT
annotated target: tryptophanyl-transfer RNA
annotated property: IAO_0000118
annotated source: tryptophanyl_tRNA

Axiom
annotated target: A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: tryptophanyl_tRNA

Axiom
IAO scope: EXACT
annotated target: tryptophanyl tRNA
annotated property: IAO_0000118
annotated source: tryptophanyl_tRNA

Axiom
IAO scope: EXACT
annotated target: tryptophanyl-transfer ribonucleic acid
annotated property: IAO_0000118
annotated source: tryptophanyl_tRNA

tyrosyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: tyrosine_tRNA_primary_transcript
IAO_0000115: A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region.
IAO id: SO:0000272
IAO_0000118: tyrosyl tRNA
IAO_0000118: tyrosyl-transfer RNA
IAO_0000118: tyrosyl-transfer ribonucleic acid

Axiom
IAO scope: EXACT
annotated target: tyrosyl-transfer ribonucleic acid
annotated property: IAO_0000118
annotated source: tyrosyl_tRNA

Axiom
IAO scope: RELATED
annotated target: tyrosyl-transfer RNA
annotated property: IAO_0000118
annotated source: tyrosyl_tRNA

Axiom
annotated target: A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: tyrosyl_tRNA

Axiom
IAO scope: EXACT
annotated target: tyrosyl tRNA
annotated property: IAO_0000118
annotated source: tyrosyl_tRNA

valyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: valine_tRNA_primary_transcript
IAO_0000115: A tRNA sequence that has a valine anticodon, and a 3' valine binding region.
IAO id: SO:0000273
IAO_0000118: valyl tRNA
IAO_0000118: valyl-transfer RNA
IAO_0000118: valyl-transfer ribonucleic acid

Axiom
annotated target: A tRNA sequence that has a valine anticodon, and a 3' valine binding region.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: valyl_tRNA

Axiom
IAO scope: EXACT
annotated target: valyl-transfer ribonucleic acid
annotated property: IAO_0000118
annotated source: valyl_tRNA

Axiom
IAO scope: EXACT
annotated target: valyl tRNA
annotated property: IAO_0000118
annotated source: valyl_tRNA

Axiom
IAO scope: RELATED
annotated target: valyl-transfer RNA
annotated property: IAO_0000118
annotated source: valyl_tRNA

snRNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: snRNA_primary_transcript
IAO_0000115: A small nuclear RNA molecule involved in pre-mRNA splicing and processing.
IAO id: SO:0000274
IAO subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
IAO xref: http://en.wikipedia.org/wiki/SnRNA
IAO_0000118: small nuclear RNA

Axiom
IAO scope: EXACT
annotated target: small nuclear RNA
annotated property: IAO_0000118
annotated source: snRNA

Axiom
annotated target: A small nuclear RNA molecule involved in pre-mRNA splicing and processing.
IAO xref: PMID:11733745
IAO xref: WB:ems
IAO xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
annotated property: IAO_0000115
annotated source: snRNA

snoRNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: snoRNA_primary_transcript
IAO_0000115: A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA.
IAO id: SO:0000275
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/SnoRNA
IAO_0000118: small nucleolar RNA

Axiom
annotated target: A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA.
IAO xref: GOC:kgc
annotated property: IAO_0000115
annotated source: snoRNA

Axiom
IAO scope: EXACT
annotated target: small nucleolar RNA
annotated property: IAO_0000118
annotated source: snoRNA

miRNA
type: Class
subclass of: small_regulatory_ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: miRNA_primary_transcript
IAO id: SO:0000276
IAO subset: SOFA
IAO_0000115: Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors.
IAO xref: http://en.wikipedia.org/wiki/MiRNA
IAO_0000118: micro RNA
IAO_0000118: microRNA

Axiom
IAO scope: EXACT
annotated target: micro RNA
annotated property: IAO_0000118
annotated source: miRNA

Axiom
IAO xref: PMID:12592000
annotated target: Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors.
annotated property: IAO_0000115
annotated source: miRNA

Axiom
IAO scope: EXACT
annotated target: microRNA
annotated property: IAO_0000118
annotated source: miRNA

bound_by_factor
type: Class
subclass of: feature_attribute
IAO_0000115: An attribute describing a sequence that is bound by another molecule.
comment: Formerly called transcript_by_bound_factor.
IAO id: SO:0000277
IAO_0000118: bound by factor

Axiom
annotated target: An attribute describing a sequence that is bound by another molecule.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: bound_by_factor

Axiom
IAO scope: EXACT
annotated target: bound by factor
annotated property: IAO_0000118
annotated source: bound_by_factor

transcript_bound_by_nucleic_acid
type: Class
equivalent class: Class
  intersection of: transcript
  intersection of: Restriction
    on property: has_quality
    some values from: bound_by_nucleic_acid
subclass of: transcript
IAO_0000115: A transcript that is bound by a nucleic acid.
comment: Formerly called transcript_by_bound_nucleic_acid.
IAO id: SO:0000278
IAO_0000118: transcript bound by nucleic acid

Axiom
annotated target: A transcript that is bound by a nucleic acid.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: transcript_bound_by_nucleic_acid

Axiom
IAO scope: EXACT
annotated target: transcript bound by nucleic acid
annotated property: IAO_0000118
annotated source: transcript_bound_by_nucleic_acid

transcript_bound_by_protein
type: Class
equivalent class: Class
  intersection of: transcript
  intersection of: Restriction
    on property: has_quality
    some values from: bound_by_protein
subclass of: transcript
IAO_0000115: A transcript that is bound by a protein.
comment: Formerly called transcript_by_bound_protein.
IAO id: SO:0000279
IAO_0000118: transcript bound by protein

Axiom
IAO scope: EXACT
annotated target: transcript bound by protein
annotated property: IAO_0000118
annotated source: transcript_bound_by_protein

Axiom
annotated target: A transcript that is bound by a protein.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: transcript_bound_by_protein

engineered_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: engineered
subclass of: gene
subclass of: engineered_region
IAO_0000115: A gene that is engineered.
IAO id: SO:0000280
IAO_0000118: engineered gene

Axiom
IAO scope: EXACT
annotated target: engineered gene
annotated property: IAO_0000118
annotated source: engineered_gene

Axiom
annotated target: A gene that is engineered.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: engineered_gene

engineered_foreign_gene
type: Class
equivalent class: Class
  intersection of: engineered_gene
  intersection of: Restriction
    on property: has_quality
    some values from: engineered
  intersection of: Restriction
    on property: has_quality
    some values from: foreign
subclass of: engineered_gene
subclass of: foreign_gene
subclass of: engineered_foreign_region
IAO_0000115: A gene that is engineered and foreign.
IAO id: SO:0000281
IAO_0000118: engineered foreign gene

Axiom
IAO scope: EXACT
annotated target: engineered foreign gene
annotated property: IAO_0000118
annotated source: engineered_foreign_gene

Axiom
annotated target: A gene that is engineered and foreign.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: engineered_foreign_gene

mRNA_with_minus_1_frameshift
type: Class
equivalent class: Class
  intersection of: mRNA_with_frameshift
  intersection of: Restriction
    on property: has_quality
    some values from: minus_1_frameshift
subclass of: mRNA_with_frameshift
IAO_0000115: An mRNA with a minus 1 frameshift.
IAO id: SO:0000282
IAO_0000118: mRNA with minus 1 frameshift

Axiom
annotated target: An mRNA with a minus 1 frameshift.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: mRNA_with_minus_1_frameshift

Axiom
IAO scope: EXACT
annotated target: mRNA with minus 1 frameshift
annotated property: IAO_0000118
annotated source: mRNA_with_minus_1_frameshift

engineered_foreign_transposable_element_gene
type: Class
equivalent class: Class
  intersection of: transposable_element_gene
  intersection of: Restriction
    on property: has_quality
    some values from: engineered
  intersection of: Restriction
    on property: has_quality
    some values from: foreign
subclass of: transposable_element_gene
subclass of: engineered_foreign_gene
IAO_0000115: A transposable_element that is engineered and foreign.
IAO id: SO:0000283
IAO_0000118: engineered foreign transposable element gene

Axiom
annotated target: A transposable_element that is engineered and foreign.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: engineered_foreign_transposable_element_gene

Axiom
IAO scope: EXACT
annotated target: engineered foreign transposable element gene
annotated property: IAO_0000118
annotated source: engineered_foreign_transposable_element_gene

type_I_enzyme_restriction_site
type: Class
IAO id: SO:0000284
IAO_0000115: The recognition site is bipartite and interrupted.
deprecated: true

Axiom
annotated target: The recognition site is bipartite and interrupted.
IAO xref: http://www.promega.com
annotated property: IAO_0000115
annotated source: type_I_enzyme_restriction_site

foreign_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: foreign
subclass of: gene
IAO_0000115: A gene that is foreign.
IAO id: SO:0000285
IAO_0000118: foreign gene

Axiom
annotated target: A gene that is foreign.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: foreign_gene

Axiom
IAO scope: EXACT
annotated target: foreign gene
annotated property: IAO_0000118
annotated source: foreign_gene

long_terminal_repeat
type: Class
subclass of: repeat_region
subclass of: Restriction
  on property: part_of
  some values from: LTR_retrotransposon
IAO_0000115: A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses.
IAO_0000118: LTR
IAO id: SO:0000286
IAO_0000118: direct terminal repeat
IAO xref: http://en.wikipedia.org/wiki/Long_terminal_repeat
IAO_0000118: long terminal repeat

Axiom
annotated target: A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses.
IAO xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
annotated property: IAO_0000115
annotated source: long_terminal_repeat

Axiom
IAO scope: EXACT
annotated target: LTR
annotated property: IAO_0000118
annotated source: long_terminal_repeat

Axiom
IAO scope: RELATED
annotated target: direct terminal repeat
annotated property: IAO_0000118
annotated source: long_terminal_repeat

Axiom
IAO scope: EXACT
annotated target: long terminal repeat
annotated property: IAO_0000118
annotated source: long_terminal_repeat

fusion_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: fusion
subclass of: gene
IAO_0000115: A gene that is a fusion.
IAO id: SO:0000287
IAO_0000118: fusion gene
IAO xref: http://en.wikipedia.org/wiki/Fusion_gene

Axiom
annotated target: A gene that is a fusion.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: fusion_gene

Axiom
IAO scope: EXACT
annotated target: fusion gene
annotated property: IAO_0000118
annotated source: fusion_gene

engineered_fusion_gene
type: Class
equivalent class: Class
  intersection of: fusion_gene
  intersection of: Restriction
    on property: has_quality
    some values from: engineered
subclass of: engineered_gene
subclass of: fusion_gene
IAO_0000115: A fusion gene that is engineered.
IAO id: SO:0000288
IAO_0000118: engineered fusion gene

Axiom
IAO scope: EXACT
annotated target: engineered fusion gene
annotated property: IAO_0000118
annotated source: engineered_fusion_gene

Axiom
annotated target: A fusion gene that is engineered.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: engineered_fusion_gene

microsatellite
type: Class
subclass of: satellite_DNA
IAO_0000115: A repeat_region containing repeat_units (2 to 4 bp) that is repeated multiple times in tandem.
IAO id: SO:0000289
IAO subset: SOFA
IAO_0000118: VNTR
IAO xref: http://en.wikipedia.org/wiki/Microsatellite
IAO_0000118: microsatellite locus
IAO_0000118: microsatellite marker

Axiom
IAO scope: EXACT
annotated target: microsatellite marker
annotated property: IAO_0000118
annotated source: microsatellite

Axiom
IAO scope: EXACT
annotated target: VNTR
annotated property: IAO_0000118
annotated source: microsatellite

Axiom
annotated target: A repeat_region containing repeat_units (2 to 4 bp) that is repeated multiple times in tandem.
IAO xref: http://www.informatics.jax.org/silver/glossary.shtml
annotated property: IAO_0000115
annotated source: microsatellite

Axiom
IAO scope: EXACT
annotated target: microsatellite locus
annotated property: IAO_0000118
annotated source: microsatellite

dinucleotide_repeat_microsatellite_feature
type: Class
subclass of: microsatellite
IAO id: SO:0000290
IAO_0000118: dinucleotide repeat microsatellite
IAO_0000118: dinucleotide repeat microsatellite feature
IAO_0000118: dinucleotide repeat microsatellite locus
IAO_0000118: dinucleotide repeat microsatellite marker

Axiom
IAO scope: EXACT
annotated target: dinucleotide repeat microsatellite locus
annotated property: IAO_0000118
annotated source: dinucleotide_repeat_microsatellite_feature

Axiom
IAO scope: EXACT
annotated target: dinucleotide repeat microsatellite
annotated property: IAO_0000118
annotated source: dinucleotide_repeat_microsatellite_feature

Axiom
IAO scope: EXACT
annotated target: dinucleotide repeat microsatellite marker
annotated property: IAO_0000118
annotated source: dinucleotide_repeat_microsatellite_feature

Axiom
IAO scope: EXACT
annotated target: dinucleotide repeat microsatellite feature
annotated property: IAO_0000118
annotated source: dinucleotide_repeat_microsatellite_feature

trinucleotide_repeat_microsatellite_feature
type: Class
subclass of: microsatellite
IAO id: SO:0000291
IAO_0000118: dinucleotide repeat microsatellite marker
IAO_0000118: rinucleotide repeat microsatellite
IAO_0000118: trinucleotide repeat microsatellite feature
IAO_0000118: trinucleotide repeat microsatellite locus

Axiom
IAO scope: RELATED
annotated target: dinucleotide repeat microsatellite marker
annotated property: IAO_0000118
annotated source: trinucleotide_repeat_microsatellite_feature

Axiom
IAO scope: EXACT
annotated target: rinucleotide repeat microsatellite
annotated property: IAO_0000118
annotated source: trinucleotide_repeat_microsatellite_feature

Axiom
IAO scope: EXACT
annotated target: trinucleotide repeat microsatellite feature
annotated property: IAO_0000118
annotated source: trinucleotide_repeat_microsatellite_feature

Axiom
IAO scope: EXACT
annotated target: trinucleotide repeat microsatellite locus
annotated property: IAO_0000118
annotated source: trinucleotide_repeat_microsatellite_feature

repetitive_element
type: Class
IAO id: SO:0000292
deprecated: true

engineered_foreign_repetitive_element
type: Class
equivalent class: Class
  intersection of: repeat_region
  intersection of: Restriction
    on property: has_quality
    some values from: engineered
  intersection of: Restriction
    on property: has_quality
    some values from: foreign
subclass of: repeat_region
subclass of: engineered_foreign_region
IAO_0000115: A repetitive element that is engineered and foreign.
IAO id: SO:0000293
IAO_0000118: engineered foreign repetitive element

Axiom
annotated target: A repetitive element that is engineered and foreign.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: engineered_foreign_repetitive_element

Axiom
IAO scope: EXACT
annotated target: engineered foreign repetitive element
annotated property: IAO_0000118
annotated source: engineered_foreign_repetitive_element

inverted_repeat
type: Class
subclass of: repeat_region
IAO id: SO:0000294
IAO subset: SOFA
IAO_0000115: The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC.
IAO xref: http://en.wikipedia.org/wiki/Inverted_repeat
IAO_0000118: inverted repeat
IAO_0000118: inverted repeat sequence

Axiom
IAO scope: EXACT
annotated target: inverted repeat sequence
annotated property: IAO_0000118
annotated source: inverted_repeat

Axiom
IAO xref: SO:ke
annotated target: The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC.
annotated property: IAO_0000115
annotated source: inverted_repeat

Axiom
IAO scope: EXACT
annotated target: inverted repeat
annotated property: IAO_0000118
annotated source: inverted_repeat

U12_intron
type: Class
subclass of: spliceosomal_intron
IAO_0000115: A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs.
comment: May have either GT-AC or AT-AC 5' and 3' boundaries.
IAO id: SO:0000295
IAO_0000118: U12 intron
IAO_0000118: U12-dependent intron

Axiom
annotated target: A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs.
IAO xref: PMID:9428511
annotated property: IAO_0000115
annotated source: U12_intron

Axiom
IAO scope: EXACT
annotated target: U12-dependent intron
annotated property: IAO_0000118
annotated source: U12_intron

Axiom
IAO scope: EXACT
annotated target: U12 intron
annotated property: IAO_0000118
annotated source: U12_intron

origin_of_replication
type: Class
subclass of: SO_0001411
subclass of: Restriction
  on property: part_of
  some values from: replicon
IAO id: SO:0000296
IAO subset: SOFA
IAO_0000115: The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies.
IAO xref: http://en.wikipedia.org/wiki/Origin_of_replication
IAO_0000118: ori
IAO_0000118: origin of replication

Axiom
IAO scope: EXACT
annotated target: origin of replication
annotated property: IAO_0000118
annotated source: origin_of_replication

Axiom
IAO scope: EXACT
annotated target: ori
annotated property: IAO_0000118
annotated source: origin_of_replication

Axiom
annotated target: The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies.
IAO xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
annotated property: IAO_0000115
annotated source: origin_of_replication

D_loop
type: Class
subclass of: origin_of_replication
IAO_0000118: D-loop
IAO_0000115: Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein.
IAO id: SO:0000297
IAO_0000118: displacement loop
IAO xref: http://en.wikipedia.org/wiki/D_loop

Axiom
annotated target: Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein.
IAO xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
annotated property: IAO_0000115
annotated source: D_loop

Axiom
IAO scope: RELATED
annotated target: displacement loop
annotated property: IAO_0000118
annotated source: D_loop

Axiom
annotated target: D-loop
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: D_loop

recombination_feature
type: Class
subclass of: SO_0001411
IAO id: SO:0000298
IAO_0000118: recombination feature

Axiom
IAO scope: EXACT
annotated target: recombination feature
annotated property: IAO_0000118
annotated source: recombination_feature

specific_recombination_site
type: Class
subclass of: sequence_rearrangement_feature
IAO id: SO:0000299
IAO_0000118: specific recombination site

Axiom
IAO scope: EXACT
annotated target: specific recombination site
annotated property: IAO_0000118
annotated source: specific_recombination_site

recombination_feature_of_rearranged_gene
type: Class
subclass of: specific_recombination_site
IAO id: SO:0000300
IAO_0000118: recombination feature of rearranged gene

Axiom
IAO scope: EXACT
annotated target: recombination feature of rearranged gene
annotated property: IAO_0000118
annotated source: recombination_feature_of_rearranged_gene

vertebrate_immune_system_gene_recombination_feature
type: Class
subclass of: recombination_feature_of_rearranged_gene
IAO id: SO:0000301
IAO_0000118: vertebrate immune system gene recombination feature

Axiom
IAO scope: EXACT
annotated target: vertebrate immune system gene recombination feature
annotated property: IAO_0000118
annotated source: vertebrate_immune_system_gene_recombination_feature

J_gene_recombination_feature
type: Class
subclass of: vertebrate_immune_system_gene_recombination_signal_feature
IAO_0000118: J gene recombination feature
IAO_0000118: J-RS
IAO_0000115: Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence.
IAO id: SO:0000302

Axiom
IAO scope: EXACT
annotated target: J gene recombination feature
annotated property: IAO_0000118
annotated source: J_gene_recombination_feature

Axiom
IAO scope: EXACT
annotated target: J-RS
annotated property: IAO_0000118
annotated source: J_gene_recombination_feature

Axiom
annotated target: Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: J_gene_recombination_feature

clip
type: Class
subclass of: primary_transcript_region
IAO_0000115: Part of the primary transcript that is clipped off during processing.
IAO id: SO:0000303
IAO subset: SOFA

Axiom
annotated target: Part of the primary transcript that is clipped off during processing.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: clip

type_II_enzyme_restriction_site
type: Class
IAO id: SO:0000304
IAO_0000115: The recognition site is either palindromic, partially palindromic or an interrupted palindrome. Cleavage occurs within the recognition site.
deprecated: true

Axiom
annotated target: The recognition site is either palindromic, partially palindromic or an interrupted palindrome. Cleavage occurs within the recognition site.
IAO xref: http://www.promega.com
annotated property: IAO_0000115
annotated source: type_II_enzyme_restriction_site

modified_base
type: Class
subclass of: SO_0001720
IAO_0000115: A modified nucleotide, i.e. a nucleotide other than A, T, C. G.
comment: Modified base:<modified_base>.
IAO id: SO:0000305
IAO subset: SOFA
IAO_0000118: modified base site

Axiom
annotated target: A modified nucleotide, i.e. a nucleotide other than A, T, C. G.
IAO xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
annotated property: IAO_0000115
annotated source: modified_base

Axiom
IAO scope: EXACT
annotated target: modified base site
annotated property: IAO_0000118
annotated source: modified_base

methylated_base_feature
type: Class
subclass of: modified_base
IAO_0000115: A nucleotide modified by methylation.
IAO id: SO:0000306
IAO subset: SOFA
IAO_0000118: methylated base feature

Axiom
annotated target: A nucleotide modified by methylation.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: methylated_base_feature

Axiom
IAO scope: EXACT
annotated target: methylated base feature
annotated property: IAO_0000118
annotated source: methylated_base_feature

CpG_island
type: Class
subclass of: SO_0001411
IAO_0000118: CG island
IAO_0000118: CpG island
IAO_0000115: Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes.
IAO id: SO:0000307
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/CpG_island

Axiom
annotated target: CG island
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: CpG_island

Axiom
annotated target: Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes.
IAO xref: SO:rd
annotated property: IAO_0000115
annotated source: CpG_island

Axiom
annotated target: CpG island
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: CpG_island

sequence_feature_locating_method
type: Class
IAO id: SO:0000308
deprecated: true

computed_feature
type: Class
IAO id: SO:0000309
deprecated: true

predicted_ab_initio_computation
type: Class
IAO id: SO:0000310
deprecated: true

computed_feature_by_similarity
type: Class
IAO_0000115: .
IAO id: SO:0000311
comment: similar to:<sequence_id>
deprecated: true

Axiom
annotated target: .
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: computed_feature_by_similarity

experimentally_determined
type: Class
subclass of: validated
IAO_0000115: Attribute to describe a feature that has been experimentally verified.
IAO id: SO:0000312
IAO_0000118: experimentally determined

Axiom
IAO scope: EXACT
annotated target: experimentally determined
annotated property: IAO_0000118
annotated source: experimentally_determined

Axiom
annotated target: Attribute to describe a feature that has been experimentally verified.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: experimentally_determined

stem_loop
type: Class
subclass of: RNA_sequence_secondary_structure
IAO_0000115: A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences.
IAO_0000118: RNA_hairpin_loop
IAO alt id: SO:0000019
IAO id: SO:0000313
IAO xref: http://en.wikipedia.org/wiki/Stem_loop
IAO_0000118: stem loop
IAO_0000118: stem-loop

Axiom
annotated target: A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences.
IAO xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
annotated property: IAO_0000115
annotated source: stem_loop

Axiom
IAO scope: EXACT
annotated target: stem loop
annotated property: IAO_0000118
annotated source: stem_loop

Axiom
IAO scope: EXACT
annotated target: RNA_hairpin_loop
annotated property: IAO_0000118
annotated source: stem_loop

Axiom
IAO scope: EXACT
annotated target: stem-loop
annotated property: IAO_0000118
annotated source: stem_loop

direct_repeat
type: Class
subclass of: repeat_region
IAO_0000115: A repeat where the same sequence is repeated in the same direction. Example: GCTGA-----GCTGA.
IAO id: SO:0000314
IAO subset: SOFA
IAO_0000118: direct repeat
IAO xref: http://en.wikipedia.org/wiki/Direct_repeat

Axiom
annotated target: A repeat where the same sequence is repeated in the same direction. Example: GCTGA-----GCTGA.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: direct_repeat

Axiom
IAO scope: EXACT
annotated target: direct repeat
annotated property: IAO_0000118
annotated source: direct_repeat

TSS
type: Class
subclass of: primary_transcript_region
IAO id: SO:0000315
IAO subset: SOFA
IAO_0000115: The first base where RNA polymerase begins to synthesize the RNA transcript.
IAO_0000118: transcription start site

Axiom
IAO xref: SO:ke
annotated target: The first base where RNA polymerase begins to synthesize the RNA transcript.
annotated property: IAO_0000115
annotated source: TSS

Axiom
IAO scope: EXACT
annotated target: transcription start site
annotated property: IAO_0000118
annotated source: TSS

CDS
type: Class
subclass of: mRNA_region
IAO_0000115: A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.
IAO id: SO:0000316
IAO subset: SOFA
IAO_0000118: coding sequence

Axiom
annotated target: A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: CDS

Axiom
IAO scope: EXACT
annotated target: coding sequence
annotated property: IAO_0000118
annotated source: CDS

cDNA_clone
type: Class
equivalent class: Class
  intersection of: clone
  intersection of: Restriction
    on property: has_quality
    some values from: cDNA
subclass of: clone
IAO_0000115: Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host.
IAO id: SO:0000317
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
IAO_0000118: cDNA clone

Axiom
annotated target: Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host.
IAO xref: http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html
annotated property: IAO_0000115
annotated source: cDNA_clone

Axiom
IAO scope: EXACT
annotated target: cDNA clone
annotated property: IAO_0000118
annotated source: cDNA_clone

start_codon
type: Class
subclass of: codon
IAO_0000115: First codon to be translated by a ribosome.
IAO id: SO:0000318
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/Start_codon
IAO_0000118: initiation codon
IAO_0000118: start codon

Axiom
IAO scope: EXACT
annotated target: initiation codon
annotated property: IAO_0000118
annotated source: start_codon

Axiom
annotated target: First codon to be translated by a ribosome.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: start_codon

Axiom
IAO scope: EXACT
annotated target: start codon
annotated property: IAO_0000118
annotated source: start_codon

stop_codon
type: Class
subclass of: codon
IAO_0000115: In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis.
IAO id: SO:0000319
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/Stop_codon
IAO_0000118: stop codon

Axiom
annotated target: In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: stop_codon

Axiom
IAO scope: EXACT
annotated target: stop codon
annotated property: IAO_0000118
annotated source: stop_codon

intronic_splice_enhancer
type: Class
subclass of: splice_enhancer
subclass of: spliceosomal_intron_region
IAO id: SO:0000320
IAO_0000115: Sequences within the intron that modulate splice site selection for some introns.
IAO_0000118: intronic splice enhancer

Axiom
IAO scope: EXACT
annotated target: intronic splice enhancer
annotated property: IAO_0000118
annotated source: intronic_splice_enhancer

Axiom
IAO xref: SO:ke
annotated target: Sequences within the intron that modulate splice site selection for some introns.
annotated property: IAO_0000115
annotated source: intronic_splice_enhancer

mRNA_with_plus_1_frameshift
type: Class
equivalent class: Class
  intersection of: mRNA_with_frameshift
  intersection of: Restriction
    on property: has_quality
    some values from: plus_1_frameshift
subclass of: mRNA_with_frameshift
IAO_0000115: An mRNA with a plus 1 frameshift.
IAO id: SO:0000321
IAO_0000118: mRNA with plus 1 frameshift

Axiom
IAO scope: EXACT
annotated target: mRNA with plus 1 frameshift
annotated property: IAO_0000118
annotated source: mRNA_with_plus_1_frameshift

Axiom
annotated target: An mRNA with a plus 1 frameshift.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: mRNA_with_plus_1_frameshift

nuclease_hypersensitive_site
type: Class
subclass of: nuclease_sensitive_site
IAO id: SO:0000322
IAO_0000118: nuclease hypersensitive site

Axiom
IAO scope: EXACT
annotated target: nuclease hypersensitive site
annotated property: IAO_0000118
annotated source: nuclease_hypersensitive_site

coding_start
type: Class
subclass of: CDS_region
IAO id: SO:0000323
IAO_0000115: The first base to be translated into protein.
IAO_0000118: coding start
IAO_0000118: translation initiation site
IAO_0000118: translation start

Axiom
IAO scope: EXACT
annotated target: coding start
annotated property: IAO_0000118
annotated source: coding_start

Axiom
IAO xref: SO:ke
annotated target: The first base to be translated into protein.
annotated property: IAO_0000115
annotated source: coding_start

Axiom
IAO scope: RELATED
annotated target: translation start
annotated property: IAO_0000118
annotated source: coding_start

Axiom
IAO scope: EXACT
annotated target: translation initiation site
annotated property: IAO_0000118
annotated source: coding_start

tag
type: Class
subclass of: oligo
IAO_0000115: A nucleotide sequence that may be used to identify a larger sequence.
IAO id: SO:0000324
IAO subset: SOFA

Axiom
annotated target: A nucleotide sequence that may be used to identify a larger sequence.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: tag

rRNA_large_subunit_primary_transcript
type: Class
subclass of: rRNA_primary_transcript
IAO_0000115: A primary transcript encoding a large ribosomal subunit RNA.
IAO id: SO:0000325
IAO subset: SOFA
IAO_0000118: rRNA large subunit primary transcript

Axiom
IAO scope: EXACT
annotated target: rRNA large subunit primary transcript
annotated property: IAO_0000118
annotated source: rRNA_large_subunit_primary_transcript

Axiom
annotated target: A primary transcript encoding a large ribosomal subunit RNA.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: rRNA_large_subunit_primary_transcript

SAGE_tag
type: Class
subclass of: tag
IAO_0000115: A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts.
IAO_0000118: SAGE tag
IAO id: SO:0000326
IAO subset: SOFA

Axiom
annotated target: A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts.
IAO xref: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi
annotated property: IAO_0000115
annotated source: SAGE_tag

Axiom
IAO scope: EXACT
annotated target: SAGE tag
annotated property: IAO_0000118
annotated source: SAGE_tag

coding_end
type: Class
subclass of: CDS_region
IAO id: SO:0000327
IAO_0000115: The last base to be translated into protein. It does not include the stop codon.
IAO_0000118: coding end
IAO_0000118: translation termination site
IAO_0000118: translation_end

Axiom
IAO scope: EXACT
annotated target: coding end
annotated property: IAO_0000118
annotated source: coding_end

Axiom
IAO xref: SO:ke
annotated target: The last base to be translated into protein. It does not include the stop codon.
annotated property: IAO_0000115
annotated source: coding_end

Axiom
IAO scope: EXACT
annotated target: translation termination site
annotated property: IAO_0000118
annotated source: coding_end

Axiom
IAO scope: EXACT
annotated target: translation_end
annotated property: IAO_0000118
annotated source: coding_end

microarray_oligo
type: Class
subclass of: probe
IAO id: SO:0000328
IAO_0000118: microarray oligo
IAO_0000118: microarray oligonucleotide

Axiom
IAO scope: EXACT
annotated target: microarray oligonucleotide
annotated property: IAO_0000118
annotated source: microarray_oligo

Axiom
IAO scope: EXACT
annotated target: microarray oligo
annotated property: IAO_0000118
annotated source: microarray_oligo

mRNA_with_plus_2_frameshift
type: Class
equivalent class: Class
  intersection of: mRNA_with_frameshift
  intersection of: Restriction
    on property: has_quality
    some values from: plus_2_framshift
subclass of: mRNA_with_frameshift
IAO_0000115: An mRNA with a plus 2 frameshift.
IAO id: SO:0000329
IAO_0000118: mRNA with plus 2 frameshift

Axiom
IAO scope: EXACT
annotated target: mRNA with plus 2 frameshift
annotated property: IAO_0000118
annotated source: mRNA_with_plus_2_frameshift

Axiom
annotated target: An mRNA with a plus 2 frameshift.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: mRNA_with_plus_2_frameshift

conserved_region
type: Class
subclass of: SO_0001410
IAO_0000115: Region of sequence similarity by descent from a common ancestor.
IAO id: SO:0000330
IAO subset: SOFA
IAO_0000118: conserved region
IAO xref: http://en.wikipedia.org/wiki/Conserved_region

Axiom
IAO scope: EXACT
annotated target: conserved region
annotated property: IAO_0000118
annotated source: conserved_region

Axiom
annotated target: Region of sequence similarity by descent from a common ancestor.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: conserved_region

STS
type: Class
subclass of: tag
IAO id: SO:0000331
IAO subset: SOFA
IAO_0000115: Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known.
IAO_0000118: sequence tag site

Axiom
annotated target: Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known.
IAO xref: http://www.biospace.com
annotated property: IAO_0000115
annotated source: STS

Axiom
IAO scope: EXACT
annotated target: sequence tag site
annotated property: IAO_0000118
annotated source: STS

coding_conserved_region
type: Class
subclass of: conserved_region
IAO_0000115: Coding region of sequence similarity by descent from a common ancestor.
IAO id: SO:0000332
IAO subset: SOFA
IAO_0000118: coding conserved region

Axiom
IAO scope: EXACT
annotated target: coding conserved region
annotated property: IAO_0000118
annotated source: coding_conserved_region

Axiom
annotated target: Coding region of sequence similarity by descent from a common ancestor.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: coding_conserved_region

exon_junction
type: Class
subclass of: junction
subclass of: Restriction
  on property: part_of
  some values from: mature_transcript
IAO id: SO:0000333
IAO subset: SOFA
IAO_0000115: The boundary between two exons in a processed transcript.
IAO_0000118: exon junction

Axiom
IAO scope: EXACT
annotated target: exon junction
annotated property: IAO_0000118
annotated source: exon_junction

Axiom
IAO xref: SO:ke
annotated target: The boundary between two exons in a processed transcript.
annotated property: IAO_0000115
annotated source: exon_junction

nc_conserved_region
type: Class
subclass of: conserved_region
IAO_0000115: Non-coding region of sequence similarity by descent from a common ancestor.
IAO id: SO:0000334
IAO subset: SOFA
IAO_0000118: nc conserved region
IAO_0000118: noncoding conserved region

Axiom
IAO scope: EXACT
annotated target: noncoding conserved region
annotated property: IAO_0000118
annotated source: nc_conserved_region

Axiom
IAO scope: EXACT
annotated target: nc conserved region
annotated property: IAO_0000118
annotated source: nc_conserved_region

Axiom
annotated target: Non-coding region of sequence similarity by descent from a common ancestor.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: nc_conserved_region

mRNA_with_minus_2_frameshift
type: Class
equivalent class: Class
  intersection of: mRNA_with_frameshift
  intersection of: Restriction
    on property: has_quality
    some values from: minus_2_frameshift
subclass of: mRNA_with_frameshift
IAO_0000115: A mRNA with a minus 2 frameshift.
IAO id: SO:0000335
IAO_0000118: mRNA with minus 2 frameshift

Axiom
annotated target: A mRNA with a minus 2 frameshift.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: mRNA_with_minus_2_frameshift

Axiom
IAO scope: EXACT
annotated target: mRNA with minus 2 frameshift
annotated property: IAO_0000118
annotated source: mRNA_with_minus_2_frameshift

pseudogene
type: Class
subclass of: SO_0001411
subclass of: Restriction
  on property: non_functional_homolog_of
  some values from: gene
IAO_0000115: A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \"normal\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \"normal\" paralog).
IAO id: SO:0000336
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/Pseudogene

Axiom
annotated target: A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \"normal\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \"normal\" paralog).
IAO xref: http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html
annotated property: IAO_0000115
annotated source: pseudogene

RNAi_reagent
type: Class
subclass of: ds_oligo
IAO_0000115: A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference.
IAO_0000118: RNAi reagent
IAO id: SO:0000337
IAO subset: SOFA

Axiom
IAO scope: EXACT
annotated target: RNAi reagent
annotated property: IAO_0000118
annotated source: RNAi_reagent

Axiom
annotated target: A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference.
IAO xref: SO:rd
annotated property: IAO_0000115
annotated source: RNAi_reagent

MITE
type: Class
subclass of: terminal_inverted_repeat_element
IAO_0000115: A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins.
IAO id: SO:0000338
IAO_0000118: miniature inverted repeat transposable element

Axiom
IAO scope: EXACT
annotated target: miniature inverted repeat transposable element
annotated property: IAO_0000118
annotated source: MITE

Axiom
annotated target: A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins.
IAO xref: http://www.pnas.org/cgi/content/full/97/18/10083
annotated property: IAO_0000115
annotated source: MITE

recombination_hotspot
type: Class
subclass of: recombination_feature
IAO_0000115: A region in a genome which promotes recombination.
IAO id: SO:0000339
IAO xref: http://en.wikipedia.org/wiki/Recombination_hotspot
IAO_0000118: recombination hotspot

Axiom
IAO scope: EXACT
annotated target: recombination hotspot
annotated property: IAO_0000118
annotated source: recombination_hotspot

Axiom
annotated target: A region in a genome which promotes recombination.
IAO xref: SO:rd
annotated property: IAO_0000115
annotated source: recombination_hotspot

chromosome
type: Class
subclass of: replicon
IAO id: SO:0000340
IAO subset: SOFA
IAO_0000115: Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication.
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
IAO xref: http://en.wikipedia.org/wiki/Chromosome

Axiom
IAO xref: SO:ma
annotated target: Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication.
annotated property: IAO_0000115
annotated source: chromosome

chromosome_band
type: Class
subclass of: chromosome_part
IAO_0000115: A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark.
IAO id: SO:0000341
IAO subset: SOFA
IAO_0000118: chromosome band
IAO_0000118: cytoband
IAO_0000118: cytological band
IAO xref: http://en.wikipedia.org/wiki/Cytological_band

Axiom
IAO scope: EXACT
annotated target: cytological band
annotated property: IAO_0000118
annotated source: chromosome_band

Axiom
annotated target: A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: chromosome_band

Axiom
IAO scope: EXACT
annotated target: cytoband
annotated property: IAO_0000118
annotated source: chromosome_band

Axiom
IAO scope: EXACT
annotated target: chromosome band
annotated property: IAO_0000118
annotated source: chromosome_band

site_specific_recombination_target_region
type: Class
subclass of: specific_recombination_site
IAO id: SO:0000342
IAO_0000118: site specific recombination target region

Axiom
IAO scope: EXACT
annotated target: site specific recombination target region
annotated property: IAO_0000118
annotated source: site_specific_recombination_target_region

match
type: Class
subclass of: SO_0001410
IAO_0000115: A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4.
IAO id: SO:0000343
IAO subset: SOFA

Axiom
annotated target: A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: match

splice_enhancer
type: Class
subclass of: splicing_regulatory_region
IAO_0000115: Region of a transcript that regulates splicing.
IAO id: SO:0000344
IAO subset: SOFA
IAO_0000118: splice enhancer

Axiom
annotated target: Region of a transcript that regulates splicing.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: splice_enhancer

Axiom
IAO scope: EXACT
annotated target: splice enhancer
annotated property: IAO_0000118
annotated source: splice_enhancer

EST
type: Class
subclass of: tag
subclass of: Restriction
  on property: derives_from
  some values from: mRNA
IAO_0000115: A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long.
IAO id: SO:0000345
IAO subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
IAO_0000118: expressed sequence tag

Axiom
annotated target: A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: EST

Axiom
IAO scope: EXACT
annotated target: expressed sequence tag
annotated property: IAO_0000118
annotated source: EST

loxP_site
type: Class
subclass of: resolution_site
IAO_0000118: Cre-recombination target region
IAO id: SO:0000346
IAO_0000118: loxP site

Axiom
annotated target: Cre-recombination target region
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: loxP_site

Axiom
IAO scope: EXACT
annotated target: loxP site
annotated property: IAO_0000118
annotated source: loxP_site

nucleotide_match
type: Class
subclass of: match
IAO_0000115: A match against a nucleotide sequence.
IAO id: SO:0000347
IAO subset: SOFA
IAO_0000118: nucleotide match

Axiom
annotated target: A match against a nucleotide sequence.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: nucleotide_match

Axiom
IAO scope: EXACT
annotated target: nucleotide match
annotated property: IAO_0000118
annotated source: nucleotide_match

nucleic_acid
type: Class
subclass of: polymer_attribute
IAO_0000115: An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone.
IAO id: SO:0000348
IAO xref: http://en.wikipedia.org/wiki/Nucleic_acid
IAO_0000118: nucleic acid

Axiom
IAO scope: EXACT
annotated target: nucleic acid
annotated property: IAO_0000118
annotated source: nucleic_acid

Axiom
annotated target: An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone.
IAO xref: CHEBI:33696
IAO xref: RSC:cb
annotated property: IAO_0000115
annotated source: nucleic_acid

protein_match
type: Class
subclass of: match
IAO_0000115: A match against a protein sequence.
IAO id: SO:0000349
IAO subset: SOFA
IAO_0000118: protein match

Axiom
annotated target: A match against a protein sequence.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: protein_match

Axiom
IAO scope: EXACT
annotated target: protein match
annotated property: IAO_0000118
annotated source: protein_match

FRT_site
type: Class
subclass of: inversion_site
IAO_0000115: An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid.
IAO_0000118: FLP recombination target region
IAO_0000118: FRT site
IAO id: SO:0000350

Axiom
annotated target: An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: FRT_site

Axiom
IAO scope: EXACT
annotated target: FRT site
annotated property: IAO_0000118
annotated source: FRT_site

Axiom
IAO scope: EXACT
annotated target: FLP recombination target region
annotated property: IAO_0000118
annotated source: FRT_site

synthetic_sequence
type: Class
subclass of: polymer_attribute
IAO_0000115: An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence.
IAO id: SO:0000351
IAO_0000118: synthetic sequence

Axiom
annotated target: An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: synthetic_sequence

Axiom
IAO scope: EXACT
annotated target: synthetic sequence
annotated property: IAO_0000118
annotated source: synthetic_sequence

DNA
type: Class
subclass of: nucleic_acid
IAO_0000115: An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone.
IAO id: SO:0000352

Axiom
annotated target: An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone.
IAO xref: RSC:cb
annotated property: IAO_0000115
annotated source: DNA

sequence_assembly
type: Class
subclass of: assembly
IAO_0000115: A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences.
IAO id: SO:0000353
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/Sequence_assembly
IAO_0000118: sequence assembly

Axiom
IAO scope: EXACT
annotated target: sequence assembly
annotated property: IAO_0000118
annotated source: sequence_assembly

Axiom
annotated target: A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: sequence_assembly

group_1_intron_homing_endonuclease_target_region
type: Class
subclass of: nuclease_sensitive_site
IAO_0000115: A region of intronic nucleotide sequence targeted by a nuclease enzyme.
IAO id: SO:0000354
IAO_0000118: group 1 intron homing endonuclease target region

Axiom
IAO scope: EXACT
annotated target: group 1 intron homing endonuclease target region
annotated property: IAO_0000118
annotated source: group_1_intron_homing_endonuclease_target_region

Axiom
annotated target: A region of intronic nucleotide sequence targeted by a nuclease enzyme.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: group_1_intron_homing_endonuclease_target_region

haplotype_block
type: Class
subclass of: recombination_feature
IAO_0000115: A region of the genome which is co-inherited as the result of the lack of historic recombination within it.
IAO id: SO:0000355
IAO_0000118: haplotype block

Axiom
annotated target: A region of the genome which is co-inherited as the result of the lack of historic recombination within it.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: haplotype_block

Axiom
IAO scope: EXACT
annotated target: haplotype block
annotated property: IAO_0000118
annotated source: haplotype_block

RNA
type: Class
subclass of: nucleic_acid
IAO_0000115: An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone.
IAO id: SO:0000356
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.

Axiom
annotated target: An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone.
IAO xref: RSC:cb
annotated property: IAO_0000115
annotated source: RNA

flanked
type: Class
subclass of: feature_attribute
IAO_0000115: An attribute describing a region that is bounded either side by a particular kind of region.
IAO id: SO:0000357

Axiom
annotated target: An attribute describing a region that is bounded either side by a particular kind of region.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: flanked

floxed
type: Class
subclass of: flanked
IAO_0000115: An attribute describing sequence that is flanked by Lox-P sites.
IAO id: SO:0000359
IAO xref: http://en.wikipedia.org/wiki/Floxed

Axiom
annotated target: An attribute describing sequence that is flanked by Lox-P sites.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: floxed

codon
type: Class
subclass of: CDS_region
IAO_0000115: A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS.
IAO id: SO:0000360
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/Codon

Axiom
annotated target: A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS.
IAO xref: SO:ke
IAO xref: http://www.everythingbio.com/glos/definition.php
annotated property: IAO_0000115
annotated source: codon

FRT_flanked
type: Class
subclass of: flanked
IAO_0000115: An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT.
IAO_0000118: FRT flanked
IAO id: SO:0000361

Axiom
IAO scope: EXACT
annotated target: FRT flanked
annotated property: IAO_0000118
annotated source: FRT_flanked

Axiom
annotated target: An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: FRT_flanked

invalidated_by_chimeric_cDNA
type: Class
subclass of: invalidated
IAO_0000115: A cDNA clone constructed from more than one mRNA. Usually an experimental artifact.
IAO id: SO:0000362
IAO_0000118: invalidated by chimeric cDNA

Axiom
annotated target: A cDNA clone constructed from more than one mRNA. Usually an experimental artifact.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: invalidated_by_chimeric_cDNA

Axiom
IAO scope: EXACT
annotated target: invalidated by chimeric cDNA
annotated property: IAO_0000118
annotated source: invalidated_by_chimeric_cDNA

floxed_gene
type: Class
equivalent class: Class
  intersection of: transgene
  intersection of: Restriction
    on property: has_quality
    some values from: floxed
subclass of: transgene
IAO_0000115: A transgene that is floxed.
IAO id: SO:0000363
IAO_0000118: floxed gene

Axiom
IAO scope: EXACT
annotated target: floxed gene
annotated property: IAO_0000118
annotated source: floxed_gene

Axiom
annotated target: A transgene that is floxed.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: floxed_gene

transposable_element_flanking_region
type: Class
subclass of: flanking_region
IAO id: SO:0000364
IAO_0000115: The region of sequence surrounding a transposable element.
IAO_0000118: transposable element flanking region

Axiom
IAO xref: SO:ke
annotated target: The region of sequence surrounding a transposable element.
annotated property: IAO_0000115
annotated source: transposable_element_flanking_region

Axiom
IAO scope: EXACT
annotated target: transposable element flanking region
annotated property: IAO_0000118
annotated source: transposable_element_flanking_region

integron
type: Class
subclass of: integrated_mobile_genetic_element
IAO_0000115: A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site.
IAO id: SO:0000365
IAO xref: http://en.wikipedia.org/wiki/Integron

Axiom
annotated target: A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site.
IAO xref: SO:as
annotated property: IAO_0000115
annotated source: integron

insertion_site
type: Class
subclass of: junction
IAO id: SO:0000366
IAO subset: SOFA
IAO_0000115: The junction where an insertion occurred.
IAO_0000118: insertion site

Axiom
IAO scope: EXACT
annotated target: insertion site
annotated property: IAO_0000118
annotated source: insertion_site

Axiom
IAO xref: SO:ke
annotated target: The junction where an insertion occurred.
annotated property: IAO_0000115
annotated source: insertion_site

attI_site
type: Class
subclass of: integration_excision_site
subclass of: Restriction
  on property: part_of
  some values from: integron
IAO_0000115: A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place.
IAO id: SO:0000367
IAO_0000118: attI site

Axiom
annotated target: A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place.
IAO xref: SO:as
annotated property: IAO_0000115
annotated source: attI_site

Axiom
IAO scope: EXACT
annotated target: attI site
annotated property: IAO_0000118
annotated source: attI_site

transposable_element_insertion_site
type: Class
subclass of: insertion_site
IAO id: SO:0000368
IAO subset: SOFA
IAO_0000115: The junction in a genome where a transposable_element has inserted.
IAO_0000118: transposable element insertion site

Axiom
IAO xref: SO:ke
annotated target: The junction in a genome where a transposable_element has inserted.
annotated property: IAO_0000115
annotated source: transposable_element_insertion_site

Axiom
IAO scope: EXACT
annotated target: transposable element insertion site
annotated property: IAO_0000118
annotated source: transposable_element_insertion_site

integrase_coding_region
type: Class
IAO id: SO:0000369
deprecated: true

small_regulatory_ncRNA
type: Class
subclass of: ncRNA
IAO_0000115: A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression.
IAO id: SO:0000370
IAO subset: SOFA
IAO_0000118: small regulatory ncRNA

Axiom
annotated target: A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: small_regulatory_ncRNA

Axiom
IAO scope: EXACT
annotated target: small regulatory ncRNA
annotated property: IAO_0000118
annotated source: small_regulatory_ncRNA

conjugative_transposon
type: Class
subclass of: DNA_transposon
IAO_0000115: A transposon that encodes function required for conjugation.
IAO id: SO:0000371
IAO_0000118: conjugative transposon

Axiom
IAO scope: EXACT
annotated target: conjugative transposon
annotated property: IAO_0000118
annotated source: conjugative_transposon

Axiom
annotated target: A transposon that encodes function required for conjugation.
IAO xref: http://www.sci.sdsu.edu/~smaloy/Glossary/C.html
annotated property: IAO_0000115
annotated source: conjugative_transposon

enzymatic_RNA
type: Class
equivalent class: Class
  intersection of: transcript
  intersection of: Restriction
    on property: has_quality
    some values from: enzymatic
subclass of: transcript
IAO_0000115: An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein.
IAO id: SO:0000372
IAO subset: SOFA
comment: This was moved to be a child of transcript (SO:0000673) because some enzymatic RNA regions are part of primary transcripts and some are part of processed transcripts.
IAO_0000118: enzymatic RNA

Axiom
IAO scope: EXACT
annotated target: enzymatic RNA
annotated property: IAO_0000118
annotated source: enzymatic_RNA

Axiom
annotated target: An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein.
IAO xref: RSC:cb
annotated property: IAO_0000115
annotated source: enzymatic_RNA

recombinationally_inverted_gene
type: Class
equivalent class: Class
  intersection of: recombinationally_rearranged_gene
  intersection of: Restriction
    on property: has_quality
    some values from: SO_1000036
subclass of: recombinationally_rearranged_gene
IAO_0000115: A recombinationally rearranged gene by inversion.
IAO id: SO:0000373
IAO_0000118: recombinationally inverted gene

Axiom
annotated target: A recombinationally rearranged gene by inversion.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: recombinationally_inverted_gene

Axiom
IAO scope: EXACT
annotated target: recombinationally inverted gene
annotated property: IAO_0000118
annotated source: recombinationally_inverted_gene

ribozyme
type: Class
equivalent class: Class
  intersection of: enzymatic_RNA
  intersection of: Restriction
    on property: has_quality
    some values from: ribozymic
subclass of: enzymatic_RNA
IAO_0000115: An RNA with catalytic activity.
IAO id: SO:0000374
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/Ribozyme

Axiom
annotated target: An RNA with catalytic activity.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: ribozyme

rRNA_5_8S
type: Class
subclass of: large_subunit_rRNA
IAO_0000118: 5.8S LSU rRNA
IAO_0000118: 5.8S rRNA
IAO_0000118: 5.8S ribosomal RNA
IAO_0000115: 5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea.
IAO id: SO:0000375
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA
IAO_0000118: rRNA 5 8S

Axiom
annotated target: 5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea.
IAO xref: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc
annotated property: IAO_0000115
annotated source: rRNA_5_8S

Axiom
annotated target: 5.8S rRNA
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: rRNA_5_8S

Axiom
IAO scope: EXACT
annotated target: rRNA 5 8S
annotated property: IAO_0000118
annotated source: rRNA_5_8S

Axiom
annotated target: 5.8S ribosomal RNA
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: rRNA_5_8S

Axiom
annotated target: 5.8S LSU rRNA
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: rRNA_5_8S

RNA_6S
type: Class
subclass of: small_regulatory_ncRNA
IAO_0000118: 6S RNA
IAO_0000115: A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase.
IAO_0000118: RNA 6S
IAO id: SO:0000376
IAO xref: http://en.wikipedia.org/wiki/6S_RNA

Axiom
IAO scope: EXACT
annotated target: RNA 6S
annotated property: IAO_0000118
annotated source: RNA_6S

Axiom
annotated target: 6S RNA
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: RNA_6S

Axiom
annotated target: A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase.
IAO xref: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc
annotated property: IAO_0000115
annotated source: RNA_6S

CsrB_RsmB_RNA
type: Class
subclass of: small_regulatory_ncRNA
IAO_0000115: An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family.
IAO_0000118: CsrB RsmB RNA
IAO_0000118: CsrB-RsmB RNA
IAO id: SO:0000377

Axiom
annotated target: An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family.
IAO xref: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc
annotated property: IAO_0000115
annotated source: CsrB_RsmB_RNA

Axiom
annotated target: CsrB RsmB RNA
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: CsrB_RsmB_RNA

Axiom
annotated target: CsrB-RsmB RNA
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: CsrB_RsmB_RNA

DsrA_RNA
type: Class
subclass of: small_regulatory_ncRNA
IAO_0000118: DsrA RNA
IAO_0000115: DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation.
IAO id: SO:0000378
IAO xref: http://en.wikipedia.org/wiki/DsrA_RNA

Axiom
annotated target: DsrA RNA
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DsrA_RNA

Axiom
annotated target: DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation.
IAO xref: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc
annotated property: IAO_0000115
annotated source: DsrA_RNA

GcvB_RNA
type: Class
subclass of: DsrA_RNA
IAO_0000115: A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli.
IAO_0000118: GcvB RNA
IAO id: SO:0000379
IAO xref: http://en.wikipedia.org/wiki/GcvB_RNA

Axiom
annotated target: A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli.
IAO xref: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc
annotated property: IAO_0000115
annotated source: GcvB_RNA

Axiom
IAO scope: EXACT
annotated target: GcvB RNA
annotated property: IAO_0000118
annotated source: GcvB_RNA

hammerhead_ribozyme
type: Class
equivalent class: Class
  intersection of: RNA_motif
  intersection of: Restriction
    on property: has_quality
    some values from: ribozymic
subclass of: RNA_motif
IAO_0000115: A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs.
IAO id: SO:0000380
IAO subset: SOFA
IAO_0000118: hammerhead ribozyme
IAO xref: http://en.wikipedia.org/wiki/Hammerhead_ribozyme

Axiom
annotated target: A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs.
IAO xref: http://rnaworld.bio.ku.edu/class/RNA/RNA00/RNA_World_3.html
annotated property: IAO_0000115
annotated source: hammerhead_ribozyme

Axiom
IAO scope: EXACT
annotated target: hammerhead ribozyme
annotated property: IAO_0000118
annotated source: hammerhead_ribozyme

group_IIA_intron
type: Class
subclass of: group_II_intron
IAO id: SO:0000381
IAO_0000118: group IIA intron

Axiom
IAO scope: EXACT
annotated target: group IIA intron
annotated property: IAO_0000118
annotated source: group_IIA_intron

group_IIB_intron
type: Class
subclass of: group_II_intron
IAO id: SO:0000382
IAO_0000118: group IIB intron

Axiom
IAO scope: EXACT
annotated target: group IIB intron
annotated property: IAO_0000118
annotated source: group_IIB_intron

MicF_RNA
type: Class
subclass of: antisense_RNA
IAO_0000115: A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message.
IAO_0000118: MicF RNA
IAO id: SO:0000383
IAO xref: http://en.wikipedia.org/wiki/MicF_RNA

Axiom
IAO scope: EXACT
annotated target: MicF RNA
annotated property: IAO_0000118
annotated source: MicF_RNA

Axiom
annotated target: A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message.
IAO xref: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc
annotated property: IAO_0000115
annotated source: MicF_RNA

OxyS_RNA
type: Class
subclass of: small_regulatory_ncRNA
IAO_0000115: A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages.
IAO_0000118: OxyS RNA
IAO id: SO:0000384
IAO xref: http://en.wikipedia.org/wiki/OxyS_RNA

Axiom
IAO scope: EXACT
annotated target: OxyS RNA
annotated property: IAO_0000118
annotated source: OxyS_RNA

Axiom
annotated target: A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages.
IAO xref: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc
annotated property: IAO_0000115
annotated source: OxyS_RNA

RNase_MRP_RNA
type: Class
subclass of: ncRNA
IAO_0000118: RNase MRP RNA
IAO id: SO:0000385
IAO subset: SOFA
IAO_0000115: The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs.

Axiom
annotated target: The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs.
IAO xref: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc
annotated property: IAO_0000115
annotated source: RNase_MRP_RNA

Axiom
IAO scope: EXACT
annotated target: RNase MRP RNA
annotated property: IAO_0000118
annotated source: RNase_MRP_RNA

RNase_P_RNA
type: Class
subclass of: ncRNA
IAO_0000118: RNase P RNA
IAO id: SO:0000386
IAO subset: SOFA
IAO_0000115: The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs.

Axiom
annotated target: The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs.
IAO xref: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc
annotated property: IAO_0000115
annotated source: RNase_P_RNA

Axiom
IAO scope: EXACT
annotated target: RNase P RNA
annotated property: IAO_0000118
annotated source: RNase_P_RNA

RprA_RNA
type: Class
subclass of: small_regulatory_ncRNA
IAO_0000118: RprA RNA
IAO id: SO:0000387
IAO_0000115: Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential.
IAO xref: http://en.wikipedia.org/wiki/RprA_RNA

Axiom
annotated target: Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential.
IAO xref: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc
annotated property: IAO_0000115
annotated source: RprA_RNA

Axiom
IAO scope: EXACT
annotated target: RprA RNA
annotated property: IAO_0000118
annotated source: RprA_RNA

RRE_RNA
type: Class
subclass of: small_regulatory_ncRNA
IAO_0000118: RRE RNA
IAO id: SO:0000388
IAO_0000115: The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins.

Axiom
IAO scope: EXACT
annotated target: RRE RNA
annotated property: IAO_0000118
annotated source: RRE_RNA

Axiom
annotated target: The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins.
IAO xref: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc
annotated property: IAO_0000115
annotated source: RRE_RNA

spot_42_RNA
type: Class
subclass of: small_regulatory_ncRNA
IAO_0000115: A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels.
IAO id: SO:0000389
IAO xref: http://en.wikipedia.org/wiki/Spot_42_RNA
IAO_0000118: spot-42 RNA

Axiom
IAO scope: EXACT
annotated target: spot-42 RNA
annotated property: IAO_0000118
annotated source: spot_42_RNA

Axiom
annotated target: A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels.
IAO xref: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc
annotated property: IAO_0000115
annotated source: spot_42_RNA

telomerase_RNA
type: Class
subclass of: ncRNA
IAO id: SO:0000390
IAO subset: SOFA
IAO_0000115: The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA.
IAO xref: http://en.wikipedia.org/wiki/Telomerase_RNA
IAO_0000118: telomerase RNA

Axiom
annotated target: The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA.
IAO xref: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc
annotated property: IAO_0000115
annotated source: telomerase_RNA

Axiom
IAO scope: EXACT
annotated target: telomerase RNA
annotated property: IAO_0000118
annotated source: telomerase_RNA

U1_snRNA
type: Class
subclass of: snRNA
IAO id: SO:0000391
IAO subset: SOFA
IAO_0000115: U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV.
IAO_0000118: U1 small nuclear RNA
IAO_0000118: U1 snRNA
IAO xref: http://en.wikipedia.org/wiki/U1_snRNA
IAO_0000118: small nuclear RNA U1
IAO_0000118: snRNA U1

Axiom
IAO scope: EXACT
annotated target: U1 snRNA
annotated property: IAO_0000118
annotated source: U1_snRNA

Axiom
IAO scope: EXACT
IAO xref: RSC:cb
annotated target: small nuclear RNA U1
annotated property: IAO_0000118
annotated source: U1_snRNA

Axiom
IAO scope: EXACT
IAO xref: RSC:cb
annotated target: U1 small nuclear RNA
annotated property: IAO_0000118
annotated source: U1_snRNA

Axiom
annotated target: U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV.
IAO xref: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc
annotated property: IAO_0000115
annotated source: U1_snRNA

Axiom
IAO scope: EXACT
IAO xref: RSC:cb
annotated target: snRNA U1
annotated property: IAO_0000118
annotated source: U1_snRNA

U2_snRNA
type: Class
subclass of: snRNA
IAO id: SO:0000392
IAO subset: SOFA
IAO_0000115: U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing.
IAO_0000118: U2 small nuclear RNA
IAO_0000118: U2 snRNA
IAO xref: http://en.wikipedia.org/wiki/U2_snRNA
IAO_0000118: small nuclear RNA U2
IAO_0000118: snRNA U2

Axiom
IAO scope: EXACT
annotated target: U2 snRNA
annotated property: IAO_0000118
annotated source: U2_snRNA

Axiom
IAO scope: EXACT
IAO xref: RSC:CB
annotated target: small nuclear RNA U2
annotated property: IAO_0000118
annotated source: U2_snRNA

Axiom
IAO scope: EXACT
IAO xref: RSC:CB
annotated target: U2 small nuclear RNA
annotated property: IAO_0000118
annotated source: U2_snRNA

Axiom
IAO scope: EXACT
IAO xref: RSC:CB
annotated target: snRNA U2
annotated property: IAO_0000118
annotated source: U2_snRNA

Axiom
annotated target: U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing.
IAO xref: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc
annotated property: IAO_0000115
annotated source: U2_snRNA

U4_snRNA
type: Class
subclass of: snRNA
IAO id: SO:0000393
IAO subset: SOFA
IAO_0000118: U4 small nuclear RNA
IAO_0000115: U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6.
IAO_0000118: U4 snRNA
IAO xref: http://en.wikipedia.org/wiki/U4_snRNA
IAO_0000118: small nuclear RNA U4
IAO_0000118: snRNA U4

Axiom
IAO scope: EXACT
IAO xref: RSC:cb
annotated target: U4 small nuclear RNA
annotated property: IAO_0000118
annotated source: U4_snRNA

Axiom
IAO scope: EXACT
IAO xref: RSC:cb
annotated target: snRNA U4
annotated property: IAO_0000118
annotated source: U4_snRNA

Axiom
annotated target: U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6.
IAO xref: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc
annotated property: IAO_0000115
annotated source: U4_snRNA

Axiom
IAO scope: EXACT
annotated target: U4 snRNA
annotated property: IAO_0000118
annotated source: U4_snRNA

Axiom
IAO scope: EXACT
IAO xref: RSC:cb
annotated target: small nuclear RNA U4
annotated property: IAO_0000118
annotated source: U4_snRNA

U4atac_snRNA
type: Class
subclass of: snRNA
IAO_0000115: An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397).
IAO id: SO:0000394
IAO subset: SOFA
IAO_0000118: U4atac small nuclear RNA
IAO_0000118: U4atac snRNA
IAO_0000118: small nuclear RNA U4atac
IAO_0000118: snRNA U4atac

Axiom
IAO scope: EXACT
IAO xref: RSC:cb
annotated target: snRNA U4atac
annotated property: IAO_0000118
annotated source: U4atac_snRNA

Axiom
annotated target: An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397).
IAO xref: PMID:=12409455
annotated property: IAO_0000115
annotated source: U4atac_snRNA

Axiom
IAO scope: EXACT
annotated target: U4atac snRNA
annotated property: IAO_0000118
annotated source: U4atac_snRNA

Axiom
IAO scope: EXACT
IAO xref: RSC:cb
annotated target: small nuclear RNA U4atac
annotated property: IAO_0000118
annotated source: U4atac_snRNA

Axiom
IAO scope: EXACT
IAO xref: RSC:cb
annotated target: U4atac small nuclear RNA
annotated property: IAO_0000118
annotated source: U4atac_snRNA

U5_snRNA
type: Class
subclass of: snRNA
IAO id: SO:0000395
IAO subset: SOFA
IAO_0000115: U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation.
IAO_0000118: U5 small nuclear RNA
IAO_0000118: U5 snRNA
IAO xref: http://en.wikipedia.org/wiki/U5_snRNA
IAO_0000118: small nuclear RNA U5
IAO_0000118: snRNA U5

Axiom
IAO scope: EXACT
IAO xref: RSC:cb
annotated target: small nuclear RNA U5
annotated property: IAO_0000118
annotated source: U5_snRNA

Axiom
IAO scope: EXACT
annotated target: U5 snRNA
annotated property: IAO_0000118
annotated source: U5_snRNA

Axiom
annotated target: U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation.
IAO xref: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc
annotated property: IAO_0000115
annotated source: U5_snRNA

Axiom
IAO scope: EXACT
IAO xref: RSC:cb
annotated target: U5 small nuclear RNA
annotated property: IAO_0000118
annotated source: U5_snRNA

Axiom
IAO scope: EXACT
IAO xref: RSC:cb
annotated target: snRNA U5
annotated property: IAO_0000118
annotated source: U5_snRNA

U6_snRNA
type: Class
subclass of: snRNA
IAO id: SO:0000396
IAO subset: SOFA
IAO_0000118: U6 small nuclear RNA
IAO_0000118: U6 snRNA
IAO_0000115: U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA.
IAO xref: http://en.wikipedia.org/wiki/U6_snRNA
IAO_0000118: small nuclear RNA U6
IAO_0000118: snRNA U6

Axiom
IAO scope: EXACT
annotated target: U6 snRNA
annotated property: IAO_0000118
annotated source: U6_snRNA

Axiom
IAO scope: EXACT
IAO xref: RSC:cb
annotated target: small nuclear RNA U6
annotated property: IAO_0000118
annotated source: U6_snRNA

Axiom
IAO scope: EXACT
IAO xref: RSC:cb
annotated target: snRNA U6
annotated property: IAO_0000118
annotated source: U6_snRNA

Axiom
annotated target: U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA.
IAO xref: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc
annotated property: IAO_0000115
annotated source: U6_snRNA

Axiom
IAO scope: EXACT
IAO xref: RSC:cb
annotated target: U6 small nuclear RNA
annotated property: IAO_0000118
annotated source: U6_snRNA

U6atac_snRNA
type: Class
subclass of: snRNA
IAO id: SO:0000397
IAO subset: SOFA
IAO_0000118: U6atac small nuclear RNA
IAO_0000118: U6atac snRNA
IAO_0000115: U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394).
IAO_0000118: snRNA U6atac

Axiom
annotated target: U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394).
IAO xref: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi
annotated property: IAO_0000115
annotated source: U6atac_snRNA

Axiom
IAO scope: EXACT
IAO xref: RSC:cb
annotated target: U6atac small nuclear RNA
annotated property: IAO_0000118
annotated source: U6atac_snRNA

Axiom
IAO scope: EXACT
IAO xref: RSC:cb
annotated target: U6atac snRNA
annotated property: IAO_0000118
annotated source: U6atac_snRNA

Axiom
IAO scope: EXACT
IAO xref: RSC:cb
annotated target: snRNA U6atac
annotated property: IAO_0000118
annotated source: U6atac_snRNA

U11_snRNA
type: Class
subclass of: snRNA
IAO id: SO:0000398
IAO subset: SOFA
IAO_0000118: U11 small nuclear RNA
IAO_0000118: U11 snRNA
IAO_0000115: U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence.
IAO xref: http://en.wikipedia.org/wiki/U11_snRNA
IAO_0000118: small nuclear RNA U11
IAO_0000118: snRNA U11

Axiom
IAO xref: PMID:9622129
annotated target: U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence.
annotated property: IAO_0000115
annotated source: U11_snRNA

Axiom
IAO scope: EXACT
IAO xref: RSC:cb
annotated target: snRNA U11
annotated property: IAO_0000118
annotated source: U11_snRNA

Axiom
IAO scope: EXACT
annotated target: U11 snRNA
annotated property: IAO_0000118
annotated source: U11_snRNA

Axiom
IAO scope: EXACT
IAO xref: RSC:cb
annotated target: small nuclear RNA U11
annotated property: IAO_0000118
annotated source: U11_snRNA

Axiom
IAO scope: EXACT
IAO xref: RSC:cb
annotated target: U11 small nuclear RNA
annotated property: IAO_0000118
annotated source: U11_snRNA

U12_snRNA
type: Class
subclass of: snRNA
IAO id: SO:0000399
IAO subset: SOFA
IAO_0000115: The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns.
IAO_0000118: U12 small nuclear RNA
IAO_0000118: U12 snRNA
IAO xref: http://en.wikipedia.org/wiki/U12_snRNA
IAO_0000118: small nuclear RNA U12
IAO_0000118: snRNA U12

Axiom
IAO scope: EXACT
annotated target: U12 snRNA
annotated property: IAO_0000118
annotated source: U12_snRNA

Axiom
IAO scope: EXACT
IAO xref: RSC:cb
annotated target: U12 small nuclear RNA
annotated property: IAO_0000118
annotated source: U12_snRNA

Axiom
IAO scope: EXACT
IAO xref: RSC:cb
annotated target: small nuclear RNA U12
annotated property: IAO_0000118
annotated source: U12_snRNA

Axiom
IAO scope: EXACT
IAO xref: RSC:cb
annotated target: snRNA U12
annotated property: IAO_0000118
annotated source: U12_snRNA

Axiom
annotated target: The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns.
IAO xref: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc
annotated property: IAO_0000115
annotated source: U12_snRNA

sequence_attribute
type: Class
IAO_0000115: An attribute describes a quality of sequence.
IAO id: SO:0000400
IAO_0000118: sequence attribute

Axiom
annotated target: An attribute describes a quality of sequence.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: sequence_attribute

Axiom
IAO scope: EXACT
annotated target: sequence attribute
annotated property: IAO_0000118
annotated source: sequence_attribute

gene_attribute
type: Class
subclass of: feature_attribute
IAO id: SO:0000401
IAO_0000118: gene attribute

Axiom
IAO scope: EXACT
annotated target: gene attribute
annotated property: IAO_0000118
annotated source: gene_attribute

enhancer_attribute
type: Class
IAO id: SO:0000402
deprecated: true

U14_snoRNA
type: Class
subclass of: C_D_box_snoRNA
subclass of: Restriction
  on property: derives_from
  some values from: SO_0005837
comment: An evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA.
IAO id: SO:0000403
IAO alt id: SO:0005839
IAO subset: SOFA
IAO_0000118: U14 small nucleolar RNA
IAO_0000115: U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates.
IAO_0000118: U14 snoRNA
IAO_0000118: small nucleolar RNA U14
IAO_0000118: snoRNA U14

Axiom
IAO scope: EXACT
annotated target: U14 small nucleolar RNA
annotated property: IAO_0000118
annotated source: U14_snoRNA

Axiom
IAO scope: EXACT
annotated target: small nucleolar RNA U14
annotated property: IAO_0000118
annotated source: U14_snoRNA

Axiom
IAO scope: EXACT
annotated target: snoRNA U14
annotated property: IAO_0000118
annotated source: U14_snoRNA

Axiom
IAO xref: PMID:2551119
annotated target: U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates.
IAO xref: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc
annotated property: IAO_0000115
annotated source: U14_snoRNA

Axiom
IAO scope: EXACT
annotated target: U14 snoRNA
annotated property: IAO_0000118
annotated source: U14_snoRNA

vault_RNA
type: Class
subclass of: ncRNA
IAO_0000115: A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance.
IAO id: SO:0000404
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/Vault_RNA
IAO_0000118: vault RNA

Axiom
IAO scope: EXACT
annotated target: vault RNA
annotated property: IAO_0000118
annotated source: vault_RNA

Axiom
annotated target: A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance.
IAO xref: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc
annotated property: IAO_0000115
annotated source: vault_RNA

Y_RNA
type: Class
subclass of: ncRNA
IAO id: SO:0000405
IAO subset: SOFA
IAO_0000118: Y RNA
IAO_0000115: Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin.
IAO xref: http://en.wikipedia.org/wiki/Y_RNA

Axiom
IAO scope: EXACT
annotated target: Y RNA
annotated property: IAO_0000118
annotated source: Y_RNA

Axiom
annotated target: Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin.
IAO xref: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc
annotated property: IAO_0000115
annotated source: Y_RNA

twintron
type: Class
subclass of: intron
IAO_0000115: An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed.
IAO id: SO:0000406
IAO xref: http://en.wikipedia.org/wiki/Twintron

Axiom
annotated target: An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed.
IAO xref: PMID:1899376
IAO xref: PMID:7823908
annotated property: IAO_0000115
annotated source: twintron

rRNA_18S
type: Class
subclass of: small_subunit_rRNA
IAO_0000118: 18S rRNA
IAO_0000118: 18S ribosomal RNA
IAO_0000115: A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome.
IAO id: SO:0000407
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/18S_ribosomal_RNA
IAO_0000118: rRNA 18S

Axiom
annotated target: 18S ribosomal RNA
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: rRNA_18S

Axiom
IAO scope: EXACT
annotated target: rRNA 18S
annotated property: IAO_0000118
annotated source: rRNA_18S

Axiom
annotated target: A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: rRNA_18S

Axiom
annotated target: 18S rRNA
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: rRNA_18S

site
type: Class
IAO id: SO:0000408
IAO_0000115: The interbase position where something (eg an aberration) occurred.
deprecated: true

Axiom
IAO xref: SO:ke
annotated target: The interbase position where something (eg an aberration) occurred.
annotated property: IAO_0000115
annotated source: site

binding_site
type: Class
subclass of: SO_0001411
IAO_0000115: A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids.
IAO alt id: BS:00033
IAO id: SO:0000409
IAO subset: SOFA
comment: See GO:0005488 : binding.
IAO_0000118: binding_or_interaction_site
IAO subset: biosapiens
IAO xref: http://en.wikipedia.org/wiki/Binding_site
IAO_0000118: site

Axiom
annotated target: A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids.
IAO xref: EBIBS:GAR
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: binding_site

Axiom
IAO scope: RELATED
annotated target: site
annotated property: IAO_0000118
annotated source: binding_site

Axiom
IAO scope: EXACT
annotated target: binding_or_interaction_site
annotated property: IAO_0000118
annotated source: binding_site

protein_binding_site
type: Class
subclass of: binding_site
IAO_0000115: A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules.
IAO id: SO:0000410
IAO subset: SOFA
comment: See GO:0042277 : peptide binding.
IAO_0000118: protein binding site

Axiom
annotated target: A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: protein_binding_site

Axiom
IAO scope: EXACT
annotated target: protein binding site
annotated property: IAO_0000118
annotated source: protein_binding_site

rescue_region
type: Class
equivalent class: Class
  intersection of: reagent
  intersection of: Restriction
    on property: has_quality
    some values from: rescue
subclass of: reagent
IAO_0000115: A region that rescues.
IAO id: SO:0000411
IAO_0000118: rescue fragment
IAO_0000118: rescue region
IAO_0000118: rescue segment

Axiom
annotated target: A region that rescues.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: rescue_region

Axiom
IAO scope: EXACT
annotated target: rescue fragment
annotated property: IAO_0000118
annotated source: rescue_region

Axiom
IAO scope: EXACT
annotated target: rescue region
annotated property: IAO_0000118
annotated source: rescue_region

Axiom
IAO scope: RELATED
annotated target: rescue segment
annotated property: IAO_0000118
annotated source: rescue_region

restriction_fragment
type: Class
subclass of: assembly_component
IAO_0000115: A region of polynucleotide sequence produced by digestion with a restriction endonuclease.
IAO id: SO:0000412
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/Restriction_fragment
IAO_0000118: restriction fragment

Axiom
annotated target: A region of polynucleotide sequence produced by digestion with a restriction endonuclease.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: restriction_fragment

Axiom
IAO scope: EXACT
annotated target: restriction fragment
annotated property: IAO_0000118
annotated source: restriction_fragment

sequence_difference
type: Class
subclass of: remark
IAO_0000115: A region where the sequence differs from that of a specified sequence.
IAO id: SO:0000413
IAO subset: SOFA
IAO_0000118: sequence difference

Axiom
IAO scope: EXACT
annotated target: sequence difference
annotated property: IAO_0000118
annotated source: sequence_difference

Axiom
annotated target: A region where the sequence differs from that of a specified sequence.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: sequence_difference

invalidated_by_genomic_contamination
type: Class
subclass of: invalidated
IAO_0000115: An attribute to describe a feature that is invalidated due to genomic contamination.
IAO id: SO:0000414
IAO_0000118: invalidated by genomic contamination

Axiom
annotated target: An attribute to describe a feature that is invalidated due to genomic contamination.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: invalidated_by_genomic_contamination

Axiom
IAO scope: EXACT
annotated target: invalidated by genomic contamination
annotated property: IAO_0000118
annotated source: invalidated_by_genomic_contamination

invalidated_by_genomic_polyA_primed_cDNA
type: Class
subclass of: invalidated
IAO_0000115: An attribute to describe a feature that is invalidated due to polyA priming.
IAO id: SO:0000415
IAO_0000118: invalidated by genomic polyA primed cDNA

Axiom
IAO scope: EXACT
annotated target: invalidated by genomic polyA primed cDNA
annotated property: IAO_0000118
annotated source: invalidated_by_genomic_polyA_primed_cDNA

Axiom
annotated target: An attribute to describe a feature that is invalidated due to polyA priming.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: invalidated_by_genomic_polyA_primed_cDNA

invalidated_by_partial_processing
type: Class
subclass of: invalidated
IAO_0000115: An attribute to describe a feature that is invalidated due to partial processing.
IAO id: SO:0000416
IAO_0000118: invalidated by partial processing

Axiom
IAO scope: EXACT
annotated target: invalidated by partial processing
annotated property: IAO_0000118
annotated source: invalidated_by_partial_processing

Axiom
annotated target: An attribute to describe a feature that is invalidated due to partial processing.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: invalidated_by_partial_processing

polypeptide_domain
type: Class
subclass of: polypeptide_structural_region
subclass of: SO_0100021
IAO_0000115: A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution.
IAO alt id: BS:00012
IAO alt id: BS:00134
IAO_0000118: DNA_bind
comment: Range. Old definition from before biosapiens: A region of a single polypeptide chain that folds into an independent unit and exhibits biological activity. A polypeptide chain may have multiple domains.
IAO id: SO:0000417
IAO alt id: SO:0001069
IAO subset: biosapiens
IAO_0000118: ca_bind
IAO_0000118: domain
IAO_0000118: np_bind
IAO_0000118: polypeptide domain
IAO_0000118: polypeptide_structural_domain
IAO_0000118: structural domain
IAO_0000118: zn_fing

Axiom
IAO type: BS
annotated target: DNA_bind
IAO scope: RELATED
IAO xref: uniprot:feature_type
annotated property: IAO_0000118
annotated source: polypeptide_domain

Axiom
IAO scope: BROAD
IAO type: BS
annotated target: domain
IAO xref: uniprot:feature_type
annotated property: IAO_0000118
annotated source: polypeptide_domain

Axiom
IAO type: BS
IAO scope: RELATED
IAO xref: uniprot:feature_type
annotated target: zn_fing
annotated property: IAO_0000118
annotated source: polypeptide_domain

Axiom
annotated target: A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution.
IAO xref: EBIBS:GAR
annotated property: IAO_0000115
annotated source: polypeptide_domain

Axiom
IAO type: BS
IAO scope: EXACT
annotated target: polypeptide_structural_domain
annotated property: IAO_0000118
annotated source: polypeptide_domain

Axiom
IAO type: BS
IAO scope: RELATED
annotated target: ca_bind
IAO xref: uniprot:feature_type
annotated property: IAO_0000118
annotated source: polypeptide_domain

Axiom
IAO scope: BROAD
IAO type: BS
annotated target: structural domain
annotated property: IAO_0000118
annotated source: polypeptide_domain

Axiom
IAO type: BS
IAO scope: RELATED
annotated target: np_bind
IAO xref: uniprot:feature_type
annotated property: IAO_0000118
annotated source: polypeptide_domain

Axiom
IAO scope: EXACT
annotated target: polypeptide domain
annotated property: IAO_0000118
annotated source: polypeptide_domain

signal_peptide
type: Class
subclass of: SO_0001527
subclass of: Restriction
  on property: part_of
  some values from: propeptide
IAO alt id: BS:00159
comment: Old def before biosapiens:The sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane leader sequence.
IAO id: SO:0000418
IAO subset: SOFA
IAO_0000115: The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components.
IAO subset: biosapiens
IAO xref: http://en.wikipedia.org/wiki/Signal_peptide
IAO_0000118: signal
IAO_0000118: signal peptide
IAO_0000118: signal peptide coding sequence

Axiom
annotated target: The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components.
IAO xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
annotated property: IAO_0000115
annotated source: signal_peptide

Axiom
IAO scope: EXACT
annotated target: signal peptide coding sequence
annotated property: IAO_0000118
annotated source: signal_peptide

Axiom
IAO scope: EXACT
annotated target: signal peptide
annotated property: IAO_0000118
annotated source: signal_peptide

Axiom
IAO scope: RELATED
annotated target: signal
IAO xref: uniprot:feature_type
annotated property: IAO_0000118
annotated source: signal_peptide

mature_protein_region
type: Class
subclass of: polypeptide_region
subclass of: Restriction
  on property: part_of
  some values from: immature_peptide_region
IAO alt id: BS:00149
IAO id: SO:0000419
IAO subset: SOFA
IAO_0000115: The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide.
comment: This term mature peptide, merged with the biosapiens term mature protein region and took that to be the new name. Old def: The coding sequence for the mature or final peptide or protein product following post-translational modification.
IAO subset: biosapiens
IAO_0000118: chain
IAO_0000118: mature peptide
IAO_0000118: mature protein region

Axiom
IAO scope: RELATED
annotated target: chain
IAO xref: uniprot:feature_type
annotated property: IAO_0000118
annotated source: mature_protein_region

Axiom
IAO scope: EXACT
annotated target: mature protein region
annotated property: IAO_0000118
annotated source: mature_protein_region

Axiom
IAO scope: RELATED
annotated target: mature peptide
annotated property: IAO_0000118
annotated source: mature_protein_region

Axiom
IAO xref: EBIBS:GAR
IAO xref: SO:cb
annotated target: The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide.
IAO xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
annotated property: IAO_0000115
annotated source: mature_protein_region

five_prime_terminal_inverted_repeat
type: Class
subclass of: terminal_inverted_repeat
IAO_0000118: 5' TIR
IAO id: SO:0000420
IAO_0000118: five prime terminal inverted repeat

Axiom
annotated target: 5' TIR
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: five_prime_terminal_inverted_repeat

Axiom
IAO scope: EXACT
annotated target: five prime terminal inverted repeat
annotated property: IAO_0000118
annotated source: five_prime_terminal_inverted_repeat

three_prime_terminal_inverted_repeat
type: Class
subclass of: terminal_inverted_repeat
IAO_0000118: 3' TIR
IAO id: SO:0000421
IAO_0000118: three prime terminal inverted repeat

Axiom
annotated target: 3' TIR
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: three_prime_terminal_inverted_repeat

Axiom
IAO scope: EXACT
annotated target: three prime terminal inverted repeat
annotated property: IAO_0000118
annotated source: three_prime_terminal_inverted_repeat

U5_LTR_region
type: Class
subclass of: LTR_component
IAO id: SO:0000422
IAO_0000118: U5 LTR region
IAO_0000118: U5 long terminal repeat region

Axiom
IAO scope: EXACT
annotated target: U5 long terminal repeat region
annotated property: IAO_0000118
annotated source: U5_LTR_region

Axiom
IAO scope: EXACT
annotated target: U5 LTR region
annotated property: IAO_0000118
annotated source: U5_LTR_region

R_LTR_region
type: Class
subclass of: LTR_component
IAO_0000118: R LTR region
IAO_0000118: R long terminal repeat region
IAO id: SO:0000423

Axiom
IAO scope: EXACT
annotated target: R LTR region
annotated property: IAO_0000118
annotated source: R_LTR_region

Axiom
IAO scope: EXACT
annotated target: R long terminal repeat region
annotated property: IAO_0000118
annotated source: R_LTR_region

U3_LTR_region
type: Class
subclass of: LTR_component
IAO id: SO:0000424
IAO_0000118: U3 LTR region
IAO_0000118: U3 long terminal repeat region

Axiom
IAO scope: EXACT
annotated target: U3 long terminal repeat region
annotated property: IAO_0000118
annotated source: U3_LTR_region

Axiom
IAO scope: EXACT
annotated target: U3 LTR region
annotated property: IAO_0000118
annotated source: U3_LTR_region

five_prime_LTR
type: Class
subclass of: long_terminal_repeat
IAO_0000118: 5' LTR
IAO_0000118: 5' long terminal repeat
IAO id: SO:0000425
IAO_0000118: five prime LTR

Axiom
annotated target: 5' LTR
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: five_prime_LTR

Axiom
IAO scope: EXACT
annotated target: five prime LTR
annotated property: IAO_0000118
annotated source: five_prime_LTR

Axiom
annotated target: 5' long terminal repeat
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: five_prime_LTR

three_prime_LTR
type: Class
subclass of: long_terminal_repeat
IAO_0000118: 3' LTR
IAO_0000118: 3' long terminal repeat
IAO id: SO:0000426
IAO_0000118: three prime LTR

Axiom
annotated target: 3' LTR
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: three_prime_LTR

Axiom
annotated target: 3' long terminal repeat
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: three_prime_LTR

Axiom
IAO scope: EXACT
annotated target: three prime LTR
annotated property: IAO_0000118
annotated source: three_prime_LTR

R_five_prime_LTR_region
type: Class
subclass of: R_LTR_region
subclass of: five_prime_LTR_component
IAO_0000118: R 5' long term repeat region
IAO_0000118: R five prime LTR region
IAO id: SO:0000427

Axiom
IAO scope: EXACT
annotated target: R 5' long term repeat region
annotated property: IAO_0000118
annotated source: R_five_prime_LTR_region

Axiom
IAO scope: EXACT
annotated target: R five prime LTR region
annotated property: IAO_0000118
annotated source: R_five_prime_LTR_region

U5_five_prime_LTR_region
type: Class
subclass of: U5_LTR_region
subclass of: five_prime_LTR_component
IAO id: SO:0000428
IAO_0000118: U5 5' long terminal repeat region
IAO_0000118: U5 five prime LTR region

Axiom
IAO scope: EXACT
annotated target: U5 5' long terminal repeat region
annotated property: IAO_0000118
annotated source: U5_five_prime_LTR_region

Axiom
IAO scope: EXACT
annotated target: U5 five prime LTR region
annotated property: IAO_0000118
annotated source: U5_five_prime_LTR_region

U3_five_prime_LTR_region
type: Class
subclass of: U3_LTR_region
subclass of: five_prime_LTR_component
IAO id: SO:0000429
IAO_0000118: U3 5' long term repeat region
IAO_0000118: U3 five prime LTR region

Axiom
IAO scope: EXACT
annotated target: U3 five prime LTR region
annotated property: IAO_0000118
annotated source: U3_five_prime_LTR_region

Axiom
IAO scope: EXACT
annotated target: U3 5' long term repeat region
annotated property: IAO_0000118
annotated source: U3_five_prime_LTR_region

R_three_prime_LTR_region
type: Class
subclass of: three_prime_LTR_component
IAO_0000118: R 3' long terminal repeat region
IAO_0000118: R three prime LTR region
IAO id: SO:0000430

Axiom
IAO scope: EXACT
annotated target: R 3' long terminal repeat region
annotated property: IAO_0000118
annotated source: R_three_prime_LTR_region

Axiom
IAO scope: EXACT
annotated target: R three prime LTR region
annotated property: IAO_0000118
annotated source: R_three_prime_LTR_region

U3_three_prime_LTR_region
type: Class
subclass of: three_prime_LTR_component
IAO id: SO:0000431
IAO_0000118: U3 3' long terminal repeat region
IAO_0000118: U3 three prime LTR region

Axiom
IAO scope: EXACT
annotated target: U3 three prime LTR region
annotated property: IAO_0000118
annotated source: U3_three_prime_LTR_region

Axiom
IAO scope: EXACT
annotated target: U3 3' long terminal repeat region
annotated property: IAO_0000118
annotated source: U3_three_prime_LTR_region

U5_three_prime_LTR_region
type: Class
subclass of: three_prime_LTR_component
IAO id: SO:0000432
IAO_0000118: U5 3' long terminal repeat region
IAO_0000118: U5 three prime LTR region

Axiom
IAO scope: EXACT
annotated target: U5 3' long terminal repeat region
annotated property: IAO_0000118
annotated source: U5_three_prime_LTR_region

Axiom
IAO scope: EXACT
annotated target: U5 three prime LTR region
annotated property: IAO_0000118
annotated source: U5_three_prime_LTR_region

non_LTR_retrotransposon_polymeric_tract
type: Class
subclass of: repeat_region
subclass of: repeat_component
subclass of: Restriction
  on property: part_of
  some values from: non_LTR_retrotransposon
IAO_0000115: A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon.
IAO id: SO:0000433
IAO_0000118: non LTR retrotransposon polymeric tract

Axiom
annotated target: A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: non_LTR_retrotransposon_polymeric_tract

Axiom
IAO scope: EXACT
annotated target: non LTR retrotransposon polymeric tract
annotated property: IAO_0000118
annotated source: non_LTR_retrotransposon_polymeric_tract

target_site_duplication
type: Class
equivalent class: Class
  intersection of: direct_repeat
  intersection of: Restriction
    on property: derives_from
    some values from: transposable_element
subclass of: direct_repeat
subclass of: Restriction
  on property: derives_from
  some values from: transposable_element
IAO_0000115: A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion.
IAO id: SO:0000434
IAO_0000118: target site duplication

Axiom
annotated target: A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion.
IAO xref: http://www.koko.gov.my/CocoaBioTech/Glossaryt.html
annotated property: IAO_0000115
annotated source: target_site_duplication

Axiom
IAO scope: EXACT
annotated target: target site duplication
annotated property: IAO_0000118
annotated source: target_site_duplication

RR_tract
type: Class
subclass of: conserved_region
subclass of: Restriction
  on property: part_of
  some values from: LTR_retrotransposon
IAO_0000115: A polypurine tract within an LTR_retrotransposon.
IAO_0000118: LTR retrotransposon poly purine tract
IAO_0000118: RR tract
IAO id: SO:0000435

Axiom
annotated target: LTR retrotransposon poly purine tract
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: RR_tract

Axiom
IAO scope: EXACT
annotated target: RR tract
annotated property: IAO_0000118
annotated source: RR_tract

Axiom
annotated target: A polypurine tract within an LTR_retrotransposon.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: RR_tract

ARS
type: Class
subclass of: origin_of_replication
IAO_0000115: A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host.
IAO id: SO:0000436
IAO subset: SOFA
IAO_0000118: autonomously replicating sequence

Axiom
IAO scope: EXACT
annotated target: autonomously replicating sequence
annotated property: IAO_0000118
annotated source: ARS

Axiom
annotated target: A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: ARS

assortment_derived_duplication
type: Class
IAO id: SO:0000437
deprecated: true

gene_not_polyadenylated
type: Class
IAO id: SO:0000438
deprecated: true

inverted_ring_chromosome
type: Class
subclass of: SO_1000030
subclass of: SO_1000045
IAO id: SO:0000439
IAO_0000118: inverted ring chromosome

Axiom
IAO scope: EXACT
annotated target: inverted ring chromosome
annotated property: IAO_0000118
annotated source: inverted_ring_chromosome

vector_replicon
type: Class
subclass of: replicon
subclass of: Restriction
  on property: part_of
  some values from: clone
IAO_0000115: A replicon that has been modified to act as a vector for foreign sequence.
IAO id: SO:0000440
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
IAO xref: http://en.wikipedia.org/wiki/Vector_(molecular_biology)
IAO_0000118: vector
IAO_0000118: vector replicon

Axiom
IAO scope: EXACT
annotated target: vector replicon
annotated property: IAO_0000118
annotated source: vector_replicon

Axiom
annotated target: A replicon that has been modified to act as a vector for foreign sequence.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: vector_replicon

Axiom
IAO scope: EXACT
annotated target: vector
annotated property: IAO_0000118
annotated source: vector_replicon

ss_oligo
type: Class
subclass of: oligo
IAO_0000115: A single stranded oligonucleotide.
IAO id: SO:0000441
IAO subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
IAO_0000118: single strand oligo
IAO_0000118: single strand oligonucleotide
IAO_0000118: single stranded oligonucleotide
IAO_0000118: ss oligo
IAO_0000118: ss oligonucleotide

Axiom
IAO scope: EXACT
annotated target: ss oligonucleotide
annotated property: IAO_0000118
annotated source: ss_oligo

Axiom
annotated target: A single stranded oligonucleotide.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: ss_oligo

Axiom
IAO scope: EXACT
annotated target: ss oligo
annotated property: IAO_0000118
annotated source: ss_oligo

Axiom
IAO scope: EXACT
annotated target: single strand oligo
annotated property: IAO_0000118
annotated source: ss_oligo

Axiom
IAO scope: EXACT
annotated target: single strand oligonucleotide
annotated property: IAO_0000118
annotated source: ss_oligo

Axiom
IAO scope: EXACT
annotated target: single stranded oligonucleotide
annotated property: IAO_0000118
annotated source: ss_oligo

ds_oligo
type: Class
subclass of: oligo
IAO_0000115: A double stranded oligonucleotide.
IAO id: SO:0000442
IAO subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
IAO_0000118: double stranded oligonucleotide
IAO_0000118: ds oligo
IAO_0000118: ds-oligonucleotide

Axiom
IAO scope: EXACT
annotated target: ds-oligonucleotide
annotated property: IAO_0000118
annotated source: ds_oligo

Axiom
IAO scope: EXACT
annotated target: double stranded oligonucleotide
annotated property: IAO_0000118
annotated source: ds_oligo

Axiom
IAO scope: EXACT
annotated target: ds oligo
annotated property: IAO_0000118
annotated source: ds_oligo

Axiom
annotated target: A double stranded oligonucleotide.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: ds_oligo

polymer_attribute
type: Class
subclass of: sequence_attribute
IAO_0000115: An attribute to describe the kind of biological sequence.
IAO id: SO:0000443
IAO_0000118: polymer attribute

Axiom
annotated target: An attribute to describe the kind of biological sequence.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: polymer_attribute

Axiom
IAO scope: EXACT
annotated target: polymer attribute
annotated property: IAO_0000118
annotated source: polymer_attribute

three_prime_noncoding_exon
type: Class
subclass of: noncoding_exon
IAO_0000115: Non-coding exon in the 3' UTR.
IAO id: SO:0000444
IAO_0000118: three prime noncoding exon

Axiom
annotated target: Non-coding exon in the 3' UTR.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: three_prime_noncoding_exon

Axiom
IAO scope: EXACT
annotated target: three prime noncoding exon
annotated property: IAO_0000118
annotated source: three_prime_noncoding_exon

five_prime_noncoding_exon
type: Class
subclass of: noncoding_exon
IAO_0000118: 5' nc exon
IAO_0000118: 5' non coding exon
IAO_0000115: Non-coding exon in the 5' UTR.
IAO id: SO:0000445
IAO_0000118: five prime noncoding exon

Axiom
annotated target: 5' nc exon
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: five_prime_noncoding_exon

Axiom
annotated target: Non-coding exon in the 5' UTR.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: five_prime_noncoding_exon

Axiom
annotated target: 5' non coding exon
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: five_prime_noncoding_exon

Axiom
IAO scope: EXACT
annotated target: five prime noncoding exon
annotated property: IAO_0000118
annotated source: five_prime_noncoding_exon

UTR_intron
type: Class
subclass of: intron
IAO_0000115: Intron located in the untranslated region.
IAO id: SO:0000446
IAO_0000118: UTR intron

Axiom
annotated target: Intron located in the untranslated region.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: UTR_intron

Axiom
IAO scope: EXACT
annotated target: UTR intron
annotated property: IAO_0000118
annotated source: UTR_intron

five_prime_UTR_intron
type: Class
subclass of: UTR_intron
IAO_0000115: An intron located in the 5' UTR.
IAO id: SO:0000447
IAO_0000118: five prime UTR intron

Axiom
annotated target: An intron located in the 5' UTR.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: five_prime_UTR_intron

Axiom
IAO scope: EXACT
annotated target: five prime UTR intron
annotated property: IAO_0000118
annotated source: five_prime_UTR_intron

three_prime_UTR_intron
type: Class
subclass of: UTR_intron
IAO_0000115: An intron located in the 3' UTR.
IAO id: SO:0000448
IAO_0000118: three prime UTR intron

Axiom
annotated target: An intron located in the 3' UTR.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: three_prime_UTR_intron

Axiom
IAO scope: EXACT
annotated target: three prime UTR intron
annotated property: IAO_0000118
annotated source: three_prime_UTR_intron

random_sequence
type: Class
subclass of: synthetic_sequence
IAO_0000115: A sequence of nucleotides or amino acids which, by design, has a \"random\" order of components, given a predetermined input frequency of these components.
IAO id: SO:0000449
IAO_0000118: random sequence

Axiom
IAO scope: EXACT
annotated target: random sequence
annotated property: IAO_0000118
annotated source: random_sequence

Axiom
annotated target: A sequence of nucleotides or amino acids which, by design, has a \"random\" order of components, given a predetermined input frequency of these components.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: random_sequence

interband
type: Class
subclass of: chromosome_part
IAO_0000115: A light region between two darkly staining bands in a polytene chromosome.
IAO id: SO:0000450
IAO_0000118: chromosome interband

Axiom
IAO scope: RELATED
annotated target: chromosome interband
annotated property: IAO_0000118
annotated source: interband

Axiom
annotated target: A light region between two darkly staining bands in a polytene chromosome.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: interband

gene_with_polyadenylated_mRNA
type: Class
equivalent class: Class
  intersection of: protein_coding_gene
  intersection of: Restriction
    on property: transcribed_to
    some values from: polyadenylated_mRNA
subclass of: protein_coding_gene
IAO_0000115: A gene that encodes a polyadenylated mRNA.
IAO id: SO:0000451
IAO_0000118: gene with polyadenylated mRNA

Axiom
annotated target: A gene that encodes a polyadenylated mRNA.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: gene_with_polyadenylated_mRNA

Axiom
IAO scope: EXACT
annotated target: gene with polyadenylated mRNA
annotated property: IAO_0000118
annotated source: gene_with_polyadenylated_mRNA

transgene_attribute
type: Class
IAO id: SO:0000452
deprecated: true

chromosomal_transposition
type: Class
subclass of: SO_1000183
IAO_0000115: A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type.
IAO id: SO:0000453
IAO_0000118: chromosomal transposition
IAO_0000118: transposition

Axiom
IAO scope: NARROW
annotated target: transposition
annotated property: IAO_0000118
annotated source: chromosomal_transposition

Axiom
IAO scope: EXACT
annotated target: chromosomal transposition
annotated property: IAO_0000118
annotated source: chromosomal_transposition

Axiom
annotated target: A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type.
IAO xref: FB:reference_manual
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: chromosomal_transposition

rasiRNA
type: Class
subclass of: ncRNA
IAO_0000115: A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements.
IAO id: SO:0000454
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/RasiRNA
IAO_0000118: repeat associated small interfering RNA

Axiom
annotated target: A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements.
IAO xref: http://www.developmentalcell.com/content/article/abstract
annotated property: IAO_0000115
annotated source: rasiRNA

Axiom
IAO scope: EXACT
annotated target: repeat associated small interfering RNA
annotated property: IAO_0000118
annotated source: rasiRNA

gene_with_mRNA_with_frameshift
type: Class
equivalent class: Class
  intersection of: protein_coding_gene
  intersection of: Restriction
    on property: has_quality
    some values from: frameshift
subclass of: protein_coding_gene
IAO_0000115: A gene that encodes an mRNA with a frameshift.
IAO id: SO:0000455
IAO_0000118: gene with mRNA with frameshift

Axiom
annotated target: A gene that encodes an mRNA with a frameshift.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: gene_with_mRNA_with_frameshift

Axiom
IAO scope: EXACT
annotated target: gene with mRNA with frameshift
annotated property: IAO_0000118
annotated source: gene_with_mRNA_with_frameshift

recombinationally_rearranged_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: recombinationally_rearranged
subclass of: gene
IAO_0000115: A gene that is recombinationally rearranged.
IAO id: SO:0000456
IAO_0000118: recombinationally rearranged gene

Axiom
annotated target: A gene that is recombinationally rearranged.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: recombinationally_rearranged_gene

Axiom
IAO scope: EXACT
annotated target: recombinationally rearranged gene
annotated property: IAO_0000118
annotated source: recombinationally_rearranged_gene

interchromosomal_duplication
type: Class
subclass of: SO_1000037
IAO_0000115: A chromosome duplication involving an insertion from another chromosome.
IAO id: SO:0000457
IAO_0000118: interchromosomal duplication

Axiom
IAO scope: EXACT
annotated target: interchromosomal duplication
annotated property: IAO_0000118
annotated source: interchromosomal_duplication

Axiom
annotated target: A chromosome duplication involving an insertion from another chromosome.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: interchromosomal_duplication

D_gene
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_segment
IAO_0000118: D gene
IAO_0000118: D-GENE
IAO_0000115: Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment.
IAO id: SO:0000458

Axiom
annotated target: D gene
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: D_gene

Axiom
annotated target: D-GENE
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: D_gene

Axiom
annotated target: Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: D_gene

gene_with_trans_spliced_transcript
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: transcribed_to
    some values from: trans_spliced_transcript
subclass of: gene
IAO_0000115: A gene with a transcript that is trans-spliced.
IAO id: SO:0000459
IAO_0000118: gene with trans spliced transcript

Axiom
annotated target: A gene with a transcript that is trans-spliced.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: gene_with_trans_spliced_transcript

Axiom
IAO scope: EXACT
annotated target: gene with trans spliced transcript
annotated property: IAO_0000118
annotated source: gene_with_trans_spliced_transcript

vertebrate_immunoglobulin_T_cell_receptor_segment
type: Class
subclass of: vertebrate_immune_system_gene_recombination_feature
comment: I am using the term segment instead of gene here to avoid confusion with the region 'gene'.
IAO id: SO:0000460
IAO_0000118: vertebrate immunoglobulin T cell receptor segment
IAO_0000118: vertebrate_immunoglobulin/T-cell receptor gene

Axiom
IAO scope: EXACT
annotated target: vertebrate immunoglobulin T cell receptor segment
annotated property: IAO_0000118
annotated source: vertebrate_immunoglobulin_T_cell_receptor_segment

Axiom
IAO scope: EXACT
annotated target: vertebrate_immunoglobulin/T-cell receptor gene
annotated property: IAO_0000118
annotated source: vertebrate_immunoglobulin_T_cell_receptor_segment

inversion_derived_bipartite_deficiency
type: Class
subclass of: SO_1000029
IAO_0000115: A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion.
IAO id: SO:0000461
IAO_0000118: inversion derived bipartite deficiency

Axiom
IAO scope: EXACT
annotated target: inversion derived bipartite deficiency
annotated property: IAO_0000118
annotated source: inversion_derived_bipartite_deficiency

Axiom
annotated target: A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion.
IAO xref: FB:km
annotated property: IAO_0000115
annotated source: inversion_derived_bipartite_deficiency

pseudogenic_region
type: Class
subclass of: SO_0001411
IAO_0000115: A non-functional descendent of a functional entity.
IAO id: SO:0000462
IAO subset: SOFA
IAO_0000118: pseudogenic region

Axiom
annotated target: A non-functional descendent of a functional entity.
IAO xref: SO:cjm
annotated property: IAO_0000115
annotated source: pseudogenic_region

Axiom
IAO scope: EXACT
annotated target: pseudogenic region
annotated property: IAO_0000118
annotated source: pseudogenic_region

encodes_alternately_spliced_transcripts
type: Class
subclass of: gene_attribute
IAO_0000115: A gene that encodes more than one transcript.
IAO id: SO:0000463
IAO_0000118: encodes alternately spliced transcripts

Axiom
annotated target: A gene that encodes more than one transcript.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: encodes_alternately_spliced_transcripts

Axiom
IAO scope: EXACT
annotated target: encodes alternately spliced transcripts
annotated property: IAO_0000118
annotated source: encodes_alternately_spliced_transcripts

decayed_exon
type: Class
subclass of: pseudogenic_region
subclass of: Restriction
  on property: non_functional_homolog_of
  some values from: exon
IAO_0000115: A non-functional descendant of an exon.
IAO id: SO:0000464
IAO subset: SOFA
IAO_0000118: decayed exon

Axiom
annotated target: A non-functional descendant of an exon.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: decayed_exon

Axiom
IAO scope: EXACT
annotated target: decayed exon
annotated property: IAO_0000118
annotated source: decayed_exon

inversion_derived_deficiency_plus_duplication
type: Class
subclass of: SO_1000029
subclass of: SO_1000038
IAO_0000115: A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion.
IAO id: SO:0000465
IAO_0000118: inversion derived deficiency plus duplication

Axiom
annotated target: A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion.
IAO xref: FB:km
annotated property: IAO_0000115
annotated source: inversion_derived_deficiency_plus_duplication

Axiom
IAO scope: EXACT
annotated target: inversion derived deficiency plus duplication
annotated property: IAO_0000118
annotated source: inversion_derived_deficiency_plus_duplication

V_gene
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_segment
IAO_0000115: Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR.
IAO id: SO:0000466
IAO_0000118: V gene
IAO_0000118: V-GENE
IAO_0000118: variable_gene

Axiom
IAO scope: EXACT
annotated target: V gene
annotated property: IAO_0000118
annotated source: V_gene

Axiom
IAO scope: EXACT
annotated target: variable_gene
annotated property: IAO_0000118
annotated source: V_gene

Axiom
annotated target: Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: V_gene

Axiom
IAO scope: EXACT
annotated target: V-GENE
annotated property: IAO_0000118
annotated source: V_gene

post_translationally_regulated_by_protein_stability
type: Class
subclass of: post_translationally_regulated
IAO_0000115: An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein.
IAO id: SO:0000467
IAO_0000118: post translationally regulated by protein stability
IAO_0000118: post-translationally regulated by protein stability

Axiom
IAO scope: EXACT
annotated target: post-translationally regulated by protein stability
annotated property: IAO_0000118
annotated source: post_translationally_regulated_by_protein_stability

Axiom
annotated target: An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: post_translationally_regulated_by_protein_stability

Axiom
IAO scope: EXACT
annotated target: post translationally regulated by protein stability
annotated property: IAO_0000118
annotated source: post_translationally_regulated_by_protein_stability

golden_path_fragment
type: Class
subclass of: assembly_component
subclass of: Restriction
  on property: part_of
  some values from: golden_path
IAO_0000115: One of the pieces of sequence that make up a golden path.
IAO id: SO:0000468
IAO subset: SOFA
IAO_0000118: golden path fragment

Axiom
IAO scope: EXACT
annotated target: golden path fragment
annotated property: IAO_0000118
annotated source: golden_path_fragment

Axiom
annotated target: One of the pieces of sequence that make up a golden path.
IAO xref: SO:rd
annotated property: IAO_0000115
annotated source: golden_path_fragment

post_translationally_regulated_by_protein_modification
type: Class
subclass of: post_translationally_regulated
IAO_0000115: An attribute describing a gene sequence where the resulting protein is modified to regulate it.
IAO id: SO:0000469
IAO_0000118: post translationally regulated by protein modification
IAO_0000118: post-translationally regulated by protein modification

Axiom
annotated target: An attribute describing a gene sequence where the resulting protein is modified to regulate it.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: post_translationally_regulated_by_protein_modification

Axiom
IAO scope: EXACT
annotated target: post-translationally regulated by protein modification
annotated property: IAO_0000118
annotated source: post_translationally_regulated_by_protein_modification

Axiom
IAO scope: EXACT
annotated target: post translationally regulated by protein modification
annotated property: IAO_0000118
annotated source: post_translationally_regulated_by_protein_modification

J_gene
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_segment
IAO_0000115: Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment.
IAO_0000118: J gene
IAO_0000118: J-GENE
IAO id: SO:0000470

Axiom
IAO scope: EXACT
annotated target: J-GENE
annotated property: IAO_0000118
annotated source: J_gene

Axiom
annotated target: Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: J_gene

Axiom
IAO scope: EXACT
annotated target: J gene
annotated property: IAO_0000118
annotated source: J_gene

autoregulated
type: Class
subclass of: transcriptionally_regulated
IAO id: SO:0000471
IAO_0000115: The gene product is involved in its own transcriptional regulation.

Axiom
IAO xref: SO:ke
annotated target: The gene product is involved in its own transcriptional regulation.
annotated property: IAO_0000115
annotated source: autoregulated

tiling_path
type: Class
subclass of: sequence_assembly
IAO_0000115: A set of regions which overlap with minimal polymorphism to form a linear sequence.
IAO id: SO:0000472
IAO subset: SOFA
IAO_0000118: tiling path

Axiom
IAO scope: EXACT
annotated target: tiling path
annotated property: IAO_0000118
annotated source: tiling_path

Axiom
annotated target: A set of regions which overlap with minimal polymorphism to form a linear sequence.
IAO xref: SO:cjm
annotated property: IAO_0000115
annotated source: tiling_path

negatively_autoregulated
type: Class
subclass of: transcriptionally_repressed
subclass of: autoregulated
IAO id: SO:0000473
IAO_0000115: The gene product is involved in its own transcriptional regulation where it decreases transcription.
IAO_0000118: negatively autoregulated

Axiom
IAO xref: SO:ke
annotated target: The gene product is involved in its own transcriptional regulation where it decreases transcription.
annotated property: IAO_0000115
annotated source: negatively_autoregulated

Axiom
IAO scope: EXACT
annotated target: negatively autoregulated
annotated property: IAO_0000118
annotated source: negatively_autoregulated

tiling_path_fragment
type: Class
subclass of: assembly_component
subclass of: Restriction
  on property: part_of
  some values from: tiling_path
IAO_0000115: A piece of sequence that makes up a tiling_path (SO:0000472).
IAO id: SO:0000474
IAO subset: SOFA
IAO_0000118: tiling path fragment

Axiom
IAO scope: EXACT
annotated target: tiling path fragment
annotated property: IAO_0000118
annotated source: tiling_path_fragment

Axiom
annotated target: A piece of sequence that makes up a tiling_path (SO:0000472).
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: tiling_path_fragment

positively_autoregulated
type: Class
subclass of: transcriptionally_induced
subclass of: autoregulated
IAO id: SO:0000475
IAO_0000115: The gene product is involved in its own transcriptional regulation, where it increases transcription.
IAO_0000118: positively autoregulated

Axiom
IAO xref: SO:ke
annotated target: The gene product is involved in its own transcriptional regulation, where it increases transcription.
annotated property: IAO_0000115
annotated source: positively_autoregulated

Axiom
IAO scope: EXACT
annotated target: positively autoregulated
annotated property: IAO_0000118
annotated source: positively_autoregulated

contig_read
type: Class
subclass of: read
IAO_0000115: A DNA sequencer read which is part of a contig.
IAO id: SO:0000476
IAO_0000118: contig read

Axiom
IAO scope: EXACT
annotated target: contig read
annotated property: IAO_0000118
annotated source: contig_read

Axiom
annotated target: A DNA sequencer read which is part of a contig.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: contig_read

polycistronic_gene
type: Class
IAO_0000115: A gene that is polycistronic.
IAO id: SO:0000477
deprecated: true

Axiom
annotated target: A gene that is polycistronic.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: polycistronic_gene

C_gene
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_segment
IAO_0000118: C gene
IAO_0000118: C_GENE
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205).
IAO id: SO:0000478
IAO_0000118: constant gene

Axiom
annotated target: C gene
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: C_gene

Axiom
IAO scope: EXACT
annotated target: constant gene
annotated property: IAO_0000118
annotated source: C_gene

Axiom
annotated target: C_GENE
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: C_gene

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205).
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: C_gene

trans_spliced_transcript
type: Class
equivalent class: Class
  intersection of: transcript
  intersection of: Restriction
    on property: has_quality
    some values from: trans_spliced
subclass of: transcript
IAO_0000115: A transcript that is trans-spliced.
IAO id: SO:0000479
IAO_0000118: trans spliced transcript
IAO_0000118: trans-spliced transcript

Axiom
annotated target: A transcript that is trans-spliced.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: trans_spliced_transcript

Axiom
IAO scope: EXACT
annotated target: trans-spliced transcript
annotated property: IAO_0000118
annotated source: trans_spliced_transcript

Axiom
IAO scope: EXACT
annotated target: trans spliced transcript
annotated property: IAO_0000118
annotated source: trans_spliced_transcript

tiling_path_clone
type: Class
subclass of: clone
subclass of: tiling_path_fragment
IAO_0000115: A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly.
IAO id: SO:0000480
IAO_0000118: tiling path clone

Axiom
IAO scope: EXACT
annotated target: tiling path clone
annotated property: IAO_0000118
annotated source: tiling_path_clone

Axiom
annotated target: A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: tiling_path_clone

terminal_inverted_repeat
type: Class
subclass of: inverted_repeat
subclass of: Restriction
  on property: part_of
  some values from: terminal_inverted_repeat_element
IAO_0000115: An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon.
IAO id: SO:0000481
IAO_0000118: TIR
IAO_0000118: terminal inverted repeat

Axiom
annotated target: An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: terminal_inverted_repeat

Axiom
IAO scope: EXACT
annotated target: TIR
annotated property: IAO_0000118
annotated source: terminal_inverted_repeat

Axiom
IAO scope: EXACT
annotated target: terminal inverted repeat
annotated property: IAO_0000118
annotated source: terminal_inverted_repeat

vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
type: Class
subclass of: vertebrate_immune_system_gene_recombination_feature
IAO id: SO:0000482
IAO_0000118: vertebrate immunoglobulin T cell receptor gene cluster
IAO_0000118: vertebrate_immunoglobulin/T-cell receptor gene cluster

Axiom
IAO scope: EXACT
annotated target: vertebrate immunoglobulin T cell receptor gene cluster
annotated property: IAO_0000118
annotated source: vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

Axiom
IAO scope: EXACT
annotated target: vertebrate_immunoglobulin/T-cell receptor gene cluster
annotated property: IAO_0000118
annotated source: vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

nc_primary_transcript
type: Class
subclass of: primary_transcript
IAO_0000115: A primary transcript that is never translated into a protein.
IAO id: SO:0000483
IAO subset: SOFA
IAO_0000118: nc primary transcript
IAO_0000118: noncoding primary transcript

Axiom
IAO scope: EXACT
annotated target: noncoding primary transcript
annotated property: IAO_0000118
annotated source: nc_primary_transcript

Axiom
IAO scope: EXACT
annotated target: nc primary transcript
annotated property: IAO_0000118
annotated source: nc_primary_transcript

Axiom
annotated target: A primary transcript that is never translated into a protein.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: nc_primary_transcript

three_prime_coding_exon_noncoding_region
type: Class
subclass of: noncoding_region_of_exon
subclass of: Restriction
  on property: part_of
  some values from: three_prime_coding_exon
IAO id: SO:0000484
IAO subset: SOFA
IAO_0000115: The sequence of the 3' exon that is not coding.
IAO_0000118: three prime coding exon noncoding region
IAO_0000118: three_prime_exon_noncoding_region

Axiom
IAO scope: EXACT
annotated target: three_prime_exon_noncoding_region
annotated property: IAO_0000118
annotated source: three_prime_coding_exon_noncoding_region

Axiom
IAO xref: SO:ke
annotated target: The sequence of the 3' exon that is not coding.
annotated property: IAO_0000115
annotated source: three_prime_coding_exon_noncoding_region

Axiom
IAO scope: EXACT
annotated target: three prime coding exon noncoding region
annotated property: IAO_0000118
annotated source: three_prime_coding_exon_noncoding_region

DJ_J_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: DJ_gene
subclass of: Restriction
  on property: has_part
  some values from: J_gene
IAO_0000118: (DJ)-J-CLUSTER
IAO_0000118: DJ J cluster
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene.
IAO id: SO:0000485

Axiom
annotated target: DJ J cluster
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DJ_J_cluster

Axiom
annotated target: (DJ)-J-CLUSTER
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DJ_J_cluster

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: DJ_J_cluster

five_prime_coding_exon_noncoding_region
type: Class
subclass of: noncoding_region_of_exon
subclass of: Restriction
  on property: part_of
  some values from: five_prime_coding_exon
IAO id: SO:0000486
IAO subset: SOFA
IAO_0000115: The sequence of the 5' exon preceding the start codon.
IAO_0000118: five prime coding exon noncoding region
IAO_0000118: five_prime_exon_noncoding_region

Axiom
IAO scope: EXACT
annotated target: five prime coding exon noncoding region
annotated property: IAO_0000118
annotated source: five_prime_coding_exon_noncoding_region

Axiom
IAO xref: SO:ke
annotated target: The sequence of the 5' exon preceding the start codon.
annotated property: IAO_0000115
annotated source: five_prime_coding_exon_noncoding_region

Axiom
IAO scope: EXACT
annotated target: five_prime_exon_noncoding_region
annotated property: IAO_0000118
annotated source: five_prime_coding_exon_noncoding_region

VDJ_J_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: J_gene
subclass of: Restriction
  on property: has_part
  some values from: VDJ_gene
subclass of: Restriction
  on property: has_part
  some values from: C_gene
IAO_0000118: (VDJ)-J-C-CLUSTER
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene.
IAO id: SO:0000487
IAO_0000118: VDJ J C cluster

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: VDJ_J_C_cluster

Axiom
annotated target: (VDJ)-J-C-CLUSTER
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: VDJ_J_C_cluster

Axiom
IAO scope: EXACT
annotated target: VDJ J C cluster
annotated property: IAO_0000118
annotated source: VDJ_J_C_cluster

VDJ_J_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: VDJ_gene
subclass of: Restriction
  on property: has_part
  some values from: J_gene
IAO_0000118: (VDJ)-J-CLUSTER
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene.
IAO id: SO:0000488
IAO_0000118: VDJ J cluster

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: VDJ_J_cluster

Axiom
annotated target: (VDJ)-J-CLUSTER
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: VDJ_J_cluster

Axiom
IAO scope: EXACT
annotated target: VDJ J cluster
annotated property: IAO_0000118
annotated source: VDJ_J_cluster

VJ_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: VJ_gene
subclass of: Restriction
  on property: has_part
  some values from: C_gene
IAO_0000118: (VJ)-C-CLUSTER
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene.
IAO id: SO:0000489
IAO_0000118: VJ C cluster

Axiom
annotated target: (VJ)-C-CLUSTER
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: VJ_C_cluster

Axiom
IAO scope: EXACT
annotated target: VJ C cluster
annotated property: IAO_0000118
annotated source: VJ_C_cluster

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: VJ_C_cluster

VJ_J_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: VJ_gene
subclass of: Restriction
  on property: has_part
  some values from: C_gene
subclass of: Restriction
  on property: has_part
  some values from: J_gene
IAO_0000118: (VJ)-J-C-CLUSTER
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene.
IAO id: SO:0000490
IAO_0000118: VJ J C cluster

Axiom
IAO scope: EXACT
annotated target: VJ J C cluster
annotated property: IAO_0000118
annotated source: VJ_J_C_cluster

Axiom
annotated target: (VJ)-J-C-CLUSTER
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: VJ_J_C_cluster

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: VJ_J_C_cluster

VJ_J_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: VJ_gene
subclass of: Restriction
  on property: has_part
  some values from: J_gene
IAO_0000118: (VJ)-J-CLUSTER
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene.
IAO id: SO:0000491
IAO_0000118: VJ J cluster

Axiom
IAO scope: EXACT
annotated target: VJ J cluster
annotated property: IAO_0000118
annotated source: VJ_J_cluster

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: VJ_J_cluster

Axiom
annotated target: (VJ)-J-CLUSTER
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: VJ_J_cluster

D_gene_recombination_feature
type: Class
subclass of: vertebrate_immune_system_gene_recombination_signal_feature
IAO_0000118: D gene recombination feature
IAO id: SO:0000492

Axiom
annotated target: D gene recombination feature
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: D_gene_recombination_feature

three_prime_D_heptamer
type: Class
subclass of: heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
subclass of: Restriction
  on property: part_of
  some values from: three_prime_D_recombination_signal_sequence
IAO_0000118: 3'D-HEPTAMER
IAO_0000115: 7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene.
IAO id: SO:0000493
IAO_0000118: three prime D heptamer

Axiom
IAO scope: EXACT
annotated target: three prime D heptamer
annotated property: IAO_0000118
annotated source: three_prime_D_heptamer

Axiom
annotated target: 3'D-HEPTAMER
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: three_prime_D_heptamer

Axiom
annotated target: 7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: three_prime_D_heptamer

three_prime_D_nonamer
type: Class
subclass of: nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
subclass of: Restriction
  on property: part_of
  some values from: three_prime_D_recombination_signal_sequence
IAO_0000118: 3'D-NOMAMER
IAO_0000115: A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene.
IAO id: SO:0000494
IAO_0000118: three prime D nonamer

Axiom
annotated target: 3'D-NOMAMER
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: three_prime_D_nonamer

Axiom
IAO scope: EXACT
annotated target: three prime D nonamer
annotated property: IAO_0000118
annotated source: three_prime_D_nonamer

Axiom
annotated target: A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: three_prime_D_nonamer

three_prime_D_spacer
type: Class
subclass of: vertebrate_immune_system_gene_recombination_spacer
subclass of: Restriction
  on property: part_of
  some values from: three_prime_D_recombination_signal_sequence
IAO_0000118: 3'D-SPACER
IAO_0000115: A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS.
IAO id: SO:0000495
IAO_0000118: three prime D spacer

Axiom
annotated target: 3'D-SPACER
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: three_prime_D_spacer

Axiom
IAO scope: EXACT
annotated target: three prime D spacer
annotated property: IAO_0000118
annotated source: three_prime_D_spacer

Axiom
annotated target: A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: three_prime_D_spacer

five_prime_D_heptamer
type: Class
subclass of: heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
subclass of: Restriction
  on property: part_of
  some values from: five_prime_D_recombination_signal_sequence
IAO_0000118: 5'D-HEPTAMER
IAO_0000115: 7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.
IAO id: SO:0000496
IAO_0000118: five prime D heptamer

Axiom
IAO scope: EXACT
annotated target: five prime D heptamer
annotated property: IAO_0000118
annotated source: five_prime_D_heptamer

Axiom
annotated target: 7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: five_prime_D_heptamer

Axiom
annotated target: 5'D-HEPTAMER
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: five_prime_D_heptamer

five_prime_D_nonamer
type: Class
subclass of: nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
subclass of: Restriction
  on property: part_of
  some values from: five_prime_D_recombination_signal_sequence
IAO_0000118: 5'D-NONAMER
IAO_0000115: 9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.
IAO id: SO:0000497
IAO_0000118: five prime D nonamer

Axiom
annotated target: 5'D-NONAMER
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: five_prime_D_nonamer

Axiom
annotated target: 9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: five_prime_D_nonamer

Axiom
IAO scope: EXACT
annotated target: five prime D nonamer
annotated property: IAO_0000118
annotated source: five_prime_D_nonamer

five_prime_D_spacer
type: Class
subclass of: vertebrate_immune_system_gene_recombination_spacer
subclass of: Restriction
  on property: part_of
  some values from: five_prime_D_recombination_signal_sequence
IAO_0000115: 12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.
IAO_0000118: 5'-SPACER
IAO id: SO:0000498
IAO_0000118: five prime D spacer
IAO_0000118: five prime D-spacer

Axiom
IAO scope: EXACT
annotated target: five prime D-spacer
annotated property: IAO_0000118
annotated source: five_prime_D_spacer

Axiom
annotated target: 5'-SPACER
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: five_prime_D_spacer

Axiom
annotated target: 12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: five_prime_D_spacer

Axiom
IAO scope: EXACT
annotated target: five prime D spacer
annotated property: IAO_0000118
annotated source: five_prime_D_spacer

virtual_sequence
type: Class
subclass of: sequence_assembly
IAO_0000115: A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database.
IAO id: SO:0000499
IAO subset: SOFA
IAO_0000118: virtual sequence

Axiom
IAO scope: EXACT
annotated target: virtual sequence
annotated property: IAO_0000118
annotated source: virtual_sequence

Axiom
annotated target: A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: virtual_sequence

Hoogsteen_base_pair
type: Class
subclass of: base_pair
IAO_0000115: A type of non-canonical base-pairing. This is less energetically favourable than watson crick base pairing. Hoogsteen GC base pairs only have two hydrogen bonds.
IAO_0000118: Hoogsteen base pair
IAO id: SO:0000500
IAO xref: http://en.wikipedia.org/wiki/Hoogsteen_base_pair

Axiom
annotated target: A type of non-canonical base-pairing. This is less energetically favourable than watson crick base pairing. Hoogsteen GC base pairs only have two hydrogen bonds.
IAO xref: PMID:12177293
annotated property: IAO_0000115
annotated source: Hoogsteen_base_pair

Axiom
IAO scope: EXACT
annotated target: Hoogsteen base pair
annotated property: IAO_0000118
annotated source: Hoogsteen_base_pair

reverse_Hoogsteen_base_pair
type: Class
subclass of: base_pair
IAO_0000115: A type of non-canonical base-pairing.
IAO id: SO:0000501
IAO_0000118: reverse Hoogsteen base pair

Axiom
annotated target: A type of non-canonical base-pairing.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: reverse_Hoogsteen_base_pair

Axiom
IAO scope: EXACT
annotated target: reverse Hoogsteen base pair
annotated property: IAO_0000118
annotated source: reverse_Hoogsteen_base_pair

transcribed_region
type: Class
IAO_0000115: A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes.
IAO id: SO:0000502
IAO subset: SOFA
comment: This concept cam about as a direct result of the SO meeting August 2004.nThe exact nature of the relationship between transcribed_region and gene is still up for discussion. We are going with 'associated_with' for the time being.
deprecated: true

Axiom
annotated target: A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: transcribed_region

alternately_spliced_gene_encodeing_one_transcript
type: Class
IAO id: SO:0000503
deprecated: true

D_DJ_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: D_gene
subclass of: Restriction
  on property: has_part
  some values from: DJ_gene
subclass of: Restriction
  on property: has_part
  some values from: C_gene
IAO_0000118: D DJ C cluster
IAO_0000118: D-(DJ)-C-CLUSTER
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene.
IAO id: SO:0000504

Axiom
annotated target: D DJ C cluster
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: D_DJ_C_cluster

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: D_DJ_C_cluster

Axiom
annotated target: D-(DJ)-C-CLUSTER
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: D_DJ_C_cluster

D_DJ_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: D_gene
subclass of: Restriction
  on property: has_part
  some values from: DJ_gene
IAO_0000118: D DJ cluster
IAO_0000118: D-(DJ)-CLUSTER
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene.
IAO id: SO:0000505

Axiom
annotated target: D DJ cluster
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: D_DJ_cluster

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: D_DJ_cluster

Axiom
annotated target: D-(DJ)-CLUSTER
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: D_DJ_cluster

D_DJ_J_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: DJ_gene
subclass of: Restriction
  on property: has_part
  some values from: D_gene
subclass of: Restriction
  on property: has_part
  some values from: J_gene
subclass of: Restriction
  on property: has_part
  some values from: C_gene
IAO_0000118: D DJ J C cluster
IAO_0000118: D-(DJ)-J-C-CLUSTER
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene.
IAO id: SO:0000506

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: D_DJ_J_C_cluster

Axiom
annotated target: D-(DJ)-J-C-CLUSTER
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: D_DJ_J_C_cluster

Axiom
annotated target: D DJ J C cluster
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: D_DJ_J_C_cluster

pseudogenic_exon
type: Class
subclass of: pseudogenic_region
subclass of: Restriction
  on property: non_functional_homolog_of
  some values from: exon
subclass of: Restriction
  on property: part_of
  some values from: pseudogenic_transcript
IAO_0000115: A non functional descendant of an exon, part of a pseudogene.
IAO id: SO:0000507
comment: This is the analog of the exon of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations.
IAO_0000118: pseudogenic exon

Axiom
annotated target: A non functional descendant of an exon, part of a pseudogene.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: pseudogenic_exon

Axiom
IAO scope: EXACT
annotated target: pseudogenic exon
annotated property: IAO_0000118
annotated source: pseudogenic_exon

D_DJ_J_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: DJ_gene
subclass of: Restriction
  on property: has_part
  some values from: D_gene
subclass of: Restriction
  on property: has_part
  some values from: J_gene
IAO_0000118: D DJ J cluster
IAO_0000118: D-(DJ)-J-CLUSTER
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene.
IAO id: SO:0000508

Axiom
annotated target: D-(DJ)-J-CLUSTER
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: D_DJ_J_cluster

Axiom
annotated target: D DJ J cluster
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: D_DJ_J_cluster

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: D_DJ_J_cluster

D_J_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: D_gene
subclass of: Restriction
  on property: has_part
  some values from: C_gene
subclass of: Restriction
  on property: has_part
  some values from: J_gene
IAO_0000118: D J C cluster
IAO_0000118: D-J-C-CLUSTER
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene.
IAO id: SO:0000509

Axiom
annotated target: D-J-C-CLUSTER
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: D_J_C_cluster

Axiom
annotated target: D J C cluster
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: D_J_C_cluster

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: D_J_C_cluster

VD_gene
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205).
IAO id: SO:0000510
IAO_0000118: VD gene
IAO_0000118: V_D_GENE

Axiom
IAO scope: EXACT
annotated target: VD gene
annotated property: IAO_0000118
annotated source: VD_gene

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205).
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: VD_gene

Axiom
IAO scope: EXACT
annotated target: V_D_GENE
annotated property: IAO_0000118
annotated source: VD_gene

J_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: J_gene
subclass of: Restriction
  on property: has_part
  some values from: C_gene
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene.
IAO_0000118: J C cluster
IAO_0000118: J-C-CLUSTER
IAO id: SO:0000511

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: J_C_cluster

Axiom
IAO scope: EXACT
annotated target: J C cluster
annotated property: IAO_0000118
annotated source: J_C_cluster

Axiom
IAO scope: EXACT
annotated target: J-C-CLUSTER
annotated property: IAO_0000118
annotated source: J_C_cluster

inversion_derived_deficiency_plus_aneuploid
type: Class
subclass of: SO_1000029
IAO_0000115: A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion.
IAO id: SO:0000512
IAO_0000118: inversion derived deficiency plus aneuploid

Axiom
IAO scope: EXACT
annotated target: inversion derived deficiency plus aneuploid
annotated property: IAO_0000118
annotated source: inversion_derived_deficiency_plus_aneuploid

Axiom
annotated target: A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion.
IAO xref: FB:km
annotated property: IAO_0000115
annotated source: inversion_derived_deficiency_plus_aneuploid

J_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: J_gene
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene.
IAO_0000118: J cluster
IAO_0000118: J-CLUSTER
IAO id: SO:0000513

Axiom
IAO scope: EXACT
annotated target: J-CLUSTER
annotated property: IAO_0000118
annotated source: J_cluster

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: J_cluster

Axiom
IAO scope: EXACT
annotated target: J cluster
annotated property: IAO_0000118
annotated source: J_cluster

J_nonamer
type: Class
subclass of: nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
subclass of: Restriction
  on property: part_of
  some values from: J_gene_recombination_feature
IAO_0000115: 9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.
IAO_0000118: J nonamer
IAO_0000118: J-NONAMER
IAO id: SO:0000514

Axiom
IAO scope: EXACT
annotated target: J-NONAMER
annotated property: IAO_0000118
annotated source: J_nonamer

Axiom
annotated target: 9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: J_nonamer

Axiom
IAO scope: EXACT
annotated target: J nonamer
annotated property: IAO_0000118
annotated source: J_nonamer

J_heptamer
type: Class
subclass of: heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
subclass of: Restriction
  on property: part_of
  some values from: J_gene_recombination_feature
IAO_0000115: 7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.
IAO_0000118: J heptamer
IAO_0000118: J-HEPTAMER
IAO id: SO:0000515

Axiom
IAO scope: EXACT
annotated target: J-HEPTAMER
annotated property: IAO_0000118
annotated source: J_heptamer

Axiom
IAO scope: EXACT
annotated target: J heptamer
annotated property: IAO_0000118
annotated source: J_heptamer

Axiom
annotated target: 7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: J_heptamer

pseudogenic_transcript
type: Class
subclass of: pseudogenic_region
subclass of: Restriction
  on property: non_functional_homolog_of
  some values from: transcript
subclass of: Restriction
  on property: part_of
  some values from: pseudogene
IAO_0000115: A non functional descendant of a transcript, part of a pseudogene.
IAO id: SO:0000516
comment: This is the analog of the transcript of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations.
IAO_0000118: pseudogenic transcript

Axiom
annotated target: A non functional descendant of a transcript, part of a pseudogene.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: pseudogenic_transcript

Axiom
IAO scope: EXACT
annotated target: pseudogenic transcript
annotated property: IAO_0000118
annotated source: pseudogenic_transcript

J_spacer
type: Class
subclass of: vertebrate_immune_system_gene_recombination_spacer
subclass of: Restriction
  on property: part_of
  some values from: J_gene_recombination_feature
IAO_0000115: 12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.
IAO_0000118: J spacer
IAO_0000118: J-SPACER
IAO id: SO:0000517

Axiom
annotated target: 12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: J_spacer

Axiom
IAO scope: EXACT
annotated target: J spacer
annotated property: IAO_0000118
annotated source: J_spacer

Axiom
IAO scope: EXACT
annotated target: J-SPACER
annotated property: IAO_0000118
annotated source: J_spacer

V_DJ_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: DJ_gene
subclass of: Restriction
  on property: has_part
  some values from: V_gene
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene.
IAO id: SO:0000518
IAO_0000118: V DJ cluster
IAO_0000118: V-(DJ)-CLUSTER

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: V_DJ_cluster

Axiom
IAO scope: EXACT
annotated target: V DJ cluster
annotated property: IAO_0000118
annotated source: V_DJ_cluster

Axiom
IAO scope: EXACT
annotated target: V-(DJ)-CLUSTER
annotated property: IAO_0000118
annotated source: V_DJ_cluster

V_DJ_J_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: J_gene
subclass of: Restriction
  on property: has_part
  some values from: V_gene
subclass of: Restriction
  on property: has_part
  some values from: DJ_gene
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene.
IAO id: SO:0000519
IAO_0000118: V DJ J cluster
IAO_0000118: V-(DJ)-J-CLUSTER

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: V_DJ_J_cluster

Axiom
IAO scope: RELATED
annotated target: V-(DJ)-J-CLUSTER
annotated property: IAO_0000118
annotated source: V_DJ_J_cluster

Axiom
IAO scope: EXACT
annotated target: V DJ J cluster
annotated property: IAO_0000118
annotated source: V_DJ_J_cluster

V_VDJ_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: VDJ_gene
subclass of: Restriction
  on property: has_part
  some values from: C_gene
subclass of: Restriction
  on property: has_part
  some values from: V_gene
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene.
IAO id: SO:0000520
IAO_0000118: V VDJ C cluster
IAO_0000118: V-(VDJ)-C-CLUSTER

Axiom
IAO scope: EXACT
annotated target: V-(VDJ)-C-CLUSTER
annotated property: IAO_0000118
annotated source: V_VDJ_C_cluster

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: V_VDJ_C_cluster

Axiom
IAO scope: EXACT
annotated target: V VDJ C cluster
annotated property: IAO_0000118
annotated source: V_VDJ_C_cluster

V_VDJ_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: VDJ_gene
subclass of: Restriction
  on property: has_part
  some values from: V_gene
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene.
IAO id: SO:0000521
IAO_0000118: V VDJ cluster
IAO_0000118: V-(VDJ)-CLUSTER

Axiom
IAO scope: EXACT
annotated target: V VDJ cluster
annotated property: IAO_0000118
annotated source: V_VDJ_cluster

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: V_VDJ_cluster

Axiom
IAO scope: EXACT
annotated target: V-(VDJ)-CLUSTER
annotated property: IAO_0000118
annotated source: V_VDJ_cluster

V_VDJ_J_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: J_gene
subclass of: Restriction
  on property: has_part
  some values from: V_gene
subclass of: Restriction
  on property: has_part
  some values from: VDJ_gene
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene.
IAO id: SO:0000522
IAO_0000118: V VDJ J cluster
IAO_0000118: V-(VDJ)-J-CLUSTER

Axiom
IAO scope: RELATED
annotated target: V-(VDJ)-J-CLUSTER
annotated property: IAO_0000118
annotated source: V_VDJ_J_cluster

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: V_VDJ_J_cluster

Axiom
IAO scope: EXACT
annotated target: V VDJ J cluster
annotated property: IAO_0000118
annotated source: V_VDJ_J_cluster

V_VJ_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: C_gene
subclass of: Restriction
  on property: has_part
  some values from: VJ_gene
subclass of: Restriction
  on property: has_part
  some values from: V_gene
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene.
IAO id: SO:0000523
IAO_0000118: V VJ C cluster
IAO_0000118: V-(VJ)-C-CLUSTER

Axiom
IAO scope: EXACT
annotated target: V VJ C cluster
annotated property: IAO_0000118
annotated source: V_VJ_C_cluster

Axiom
IAO scope: EXACT
annotated target: V-(VJ)-C-CLUSTER
annotated property: IAO_0000118
annotated source: V_VJ_C_cluster

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: V_VJ_C_cluster

V_VJ_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: VJ_gene
subclass of: Restriction
  on property: has_part
  some values from: V_gene
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene.
IAO id: SO:0000524
IAO_0000118: V VJ cluster
IAO_0000118: V-(VJ)-CLUSTER

Axiom
IAO scope: EXACT
annotated target: V VJ cluster
annotated property: IAO_0000118
annotated source: V_VJ_cluster

Axiom
IAO scope: EXACT
annotated target: V-(VJ)-CLUSTER
annotated property: IAO_0000118
annotated source: V_VJ_cluster

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: V_VJ_cluster

V_VJ_J_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: J_gene
subclass of: Restriction
  on property: has_part
  some values from: V_gene
subclass of: Restriction
  on property: has_part
  some values from: VJ_gene
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene.
IAO id: SO:0000525
IAO_0000118: V VJ J cluster
IAO_0000118: V-(VJ)-J-CLUSTER

Axiom
IAO scope: EXACT
annotated target: V-(VJ)-J-CLUSTER
annotated property: IAO_0000118
annotated source: V_VJ_J_cluster

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: V_VJ_J_cluster

Axiom
IAO scope: EXACT
annotated target: V VJ J cluster
annotated property: IAO_0000118
annotated source: V_VJ_J_cluster

V_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: V_gene
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene.
IAO id: SO:0000526
IAO_0000118: V cluster
IAO_0000118: V-CLUSTER

Axiom
IAO scope: EXACT
annotated target: V cluster
annotated property: IAO_0000118
annotated source: V_cluster

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: V_cluster

Axiom
IAO scope: EXACT
annotated target: V-CLUSTER
annotated property: IAO_0000118
annotated source: V_cluster

V_D_DJ_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: C_gene
subclass of: Restriction
  on property: has_part
  some values from: V_gene
subclass of: Restriction
  on property: has_part
  some values from: DJ_gene
subclass of: Restriction
  on property: has_part
  some values from: D_gene
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene.
IAO id: SO:0000527
IAO_0000118: V D DJ C cluster
IAO_0000118: V-D-(DJ)-C-CLUSTER

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: V_D_DJ_C_cluster

Axiom
IAO scope: EXACT
annotated target: V-D-(DJ)-C-CLUSTER
annotated property: IAO_0000118
annotated source: V_D_DJ_C_cluster

Axiom
IAO scope: EXACT
annotated target: V D DJ C cluster
annotated property: IAO_0000118
annotated source: V_D_DJ_C_cluster

V_D_DJ_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: DJ_gene
subclass of: Restriction
  on property: has_part
  some values from: V_gene
subclass of: Restriction
  on property: has_part
  some values from: D_gene
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene.
IAO id: SO:0000528
IAO_0000118: V D DJ cluster
IAO_0000118: V-D-(DJ)-CLUSTER

Axiom
IAO scope: EXACT
annotated target: V-D-(DJ)-CLUSTER
annotated property: IAO_0000118
annotated source: V_D_DJ_cluster

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: V_D_DJ_cluster

Axiom
IAO scope: EXACT
annotated target: V D DJ cluster
annotated property: IAO_0000118
annotated source: V_D_DJ_cluster

V_D_DJ_J_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: J_gene
subclass of: Restriction
  on property: has_part
  some values from: C_gene
subclass of: Restriction
  on property: has_part
  some values from: D_gene
subclass of: Restriction
  on property: has_part
  some values from: V_gene
subclass of: Restriction
  on property: has_part
  some values from: DJ_gene
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene.
IAO id: SO:0000529
IAO_0000118: V D DJ J C cluster
IAO_0000118: V-D-(DJ)-J-C-CLUSTER

Axiom
IAO scope: EXACT
annotated target: V D DJ J C cluster
annotated property: IAO_0000118
annotated source: V_D_DJ_J_C_cluster

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: V_D_DJ_J_C_cluster

Axiom
IAO scope: EXACT
annotated target: V-D-(DJ)-J-C-CLUSTER
annotated property: IAO_0000118
annotated source: V_D_DJ_J_C_cluster

V_D_DJ_J_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: V_gene
subclass of: Restriction
  on property: has_part
  some values from: DJ_gene
subclass of: Restriction
  on property: has_part
  some values from: D_gene
subclass of: Restriction
  on property: has_part
  some values from: J_gene
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene.
IAO id: SO:0000530
IAO_0000118: V D DJ J cluster
IAO_0000118: V-D-(DJ)-J-CLUSTER

Axiom
IAO scope: EXACT
annotated target: V D DJ J cluster
annotated property: IAO_0000118
annotated source: V_D_DJ_J_cluster

Axiom
IAO scope: EXACT
annotated target: V-D-(DJ)-J-CLUSTER
annotated property: IAO_0000118
annotated source: V_D_DJ_J_cluster

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: V_D_DJ_J_cluster

V_D_J_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: V_gene
subclass of: Restriction
  on property: has_part
  some values from: C_gene
subclass of: Restriction
  on property: has_part
  some values from: J_gene
subclass of: Restriction
  on property: has_part
  some values from: D_gene
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene.
IAO id: SO:0000531
IAO_0000118: V D J C cluster
IAO_0000118: V-D-J-C-CLUSTER

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: V_D_J_C_cluster

Axiom
IAO scope: EXACT
annotated target: V-D-J-C-CLUSTER
annotated property: IAO_0000118
annotated source: V_D_J_C_cluster

Axiom
IAO scope: EXACT
annotated target: V D J C cluster
annotated property: IAO_0000118
annotated source: V_D_J_C_cluster

V_D_J_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: D_gene
subclass of: Restriction
  on property: has_part
  some values from: J_gene
subclass of: Restriction
  on property: has_part
  some values from: V_gene
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene.
IAO id: SO:0000532
IAO_0000118: V D J cluster
IAO_0000118: V-D-J-CLUSTER

Axiom
IAO scope: EXACT
annotated target: V D J cluster
annotated property: IAO_0000118
annotated source: V_D_J_cluster

Axiom
IAO scope: EXACT
annotated target: V-D-J-CLUSTER
annotated property: IAO_0000118
annotated source: V_D_J_cluster

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: V_D_J_cluster

V_heptamer
type: Class
subclass of: heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
subclass of: Restriction
  on property: part_of
  some values from: V_gene_recombination_feature
IAO_0000115: 7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene.
IAO id: SO:0000533
IAO_0000118: V heptamer
IAO_0000118: V-HEPTAMER

Axiom
annotated target: 7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: V_heptamer

Axiom
IAO scope: EXACT
annotated target: V-HEPTAMER
annotated property: IAO_0000118
annotated source: V_heptamer

Axiom
IAO scope: EXACT
annotated target: V heptamer
annotated property: IAO_0000118
annotated source: V_heptamer

V_J_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: V_gene
subclass of: Restriction
  on property: has_part
  some values from: J_gene
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene.
IAO id: SO:0000534
IAO_0000118: V J cluster
IAO_0000118: V-J-CLUSTER

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: V_J_cluster

Axiom
IAO scope: EXACT
annotated target: V-J-CLUSTER
annotated property: IAO_0000118
annotated source: V_J_cluster

Axiom
IAO scope: EXACT
annotated target: V J cluster
annotated property: IAO_0000118
annotated source: V_J_cluster

V_J_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: V_gene
subclass of: Restriction
  on property: has_part
  some values from: J_gene
subclass of: Restriction
  on property: has_part
  some values from: C_gene
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene.
IAO id: SO:0000535
IAO_0000118: V J C cluster
IAO_0000118: V-J-C-CLUSTER

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: V_J_C_cluster

Axiom
IAO scope: EXACT
annotated target: V J C cluster
annotated property: IAO_0000118
annotated source: V_J_C_cluster

Axiom
IAO scope: EXACT
annotated target: V-J-C-CLUSTER
annotated property: IAO_0000118
annotated source: V_J_C_cluster

V_nonamer
type: Class
subclass of: nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
subclass of: Restriction
  on property: part_of
  some values from: V_gene_recombination_feature
IAO_0000115: 9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene.
IAO id: SO:0000536
IAO_0000118: V nonamer
IAO_0000118: V-NONAMER

Axiom
annotated target: 9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: V_nonamer

Axiom
IAO scope: EXACT
annotated target: V-NONAMER
annotated property: IAO_0000118
annotated source: V_nonamer

Axiom
IAO scope: EXACT
annotated target: V nonamer
annotated property: IAO_0000118
annotated source: V_nonamer

V_spacer
type: Class
subclass of: vertebrate_immune_system_gene_recombination_spacer
subclass of: Restriction
  on property: part_of
  some values from: V_gene_recombination_feature
IAO_0000115: 12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene.
IAO id: SO:0000537
IAO_0000118: V spacer
IAO_0000118: V-SPACER

Axiom
IAO scope: EXACT
annotated target: V-SPACER
annotated property: IAO_0000118
annotated source: V_spacer

Axiom
annotated target: 12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: V_spacer

Axiom
IAO scope: EXACT
annotated target: V spacer
annotated property: IAO_0000118
annotated source: V_spacer

V_gene_recombination_feature
type: Class
subclass of: vertebrate_immune_system_gene_recombination_signal_feature
IAO_0000115: Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene.
IAO id: SO:0000538
IAO_0000118: V gene recombination feature
IAO_0000118: V-RS

Axiom
IAO scope: EXACT
annotated target: V gene recombination feature
annotated property: IAO_0000118
annotated source: V_gene_recombination_feature

Axiom
annotated target: Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: V_gene_recombination_feature

Axiom
IAO scope: EXACT
annotated target: V-RS
annotated property: IAO_0000118
annotated source: V_gene_recombination_feature

DJ_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: DJ_gene
subclass of: Restriction
  on property: has_part
  some values from: C_gene
IAO_0000118: (DJ)-C-CLUSTER
IAO_0000118: DJ C cluster
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene.
IAO id: SO:0000539

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: DJ_C_cluster

Axiom
annotated target: DJ C cluster
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DJ_C_cluster

Axiom
annotated target: (DJ)-C-CLUSTER
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DJ_C_cluster

DJ_J_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: C_gene
subclass of: Restriction
  on property: has_part
  some values from: DJ_gene
subclass of: Restriction
  on property: has_part
  some values from: J_gene
IAO_0000118: (DJ)-J-C-CLUSTER
IAO_0000118: DJ J C cluster
IAO_0000115: Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE.
IAO id: SO:0000540

Axiom
annotated target: Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: DJ_J_C_cluster

Axiom
annotated target: DJ J C cluster
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DJ_J_C_cluster

Axiom
annotated target: (DJ)-J-C-CLUSTER
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DJ_J_C_cluster

VDJ_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: VDJ_gene
subclass of: Restriction
  on property: has_part
  some values from: C_gene
IAO_0000118: (VDJ)-C-CLUSTER
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene.
IAO id: SO:0000541
IAO_0000118: VDJ C cluster

Axiom
annotated target: (VDJ)-C-CLUSTER
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: VDJ_C_cluster

Axiom
IAO scope: EXACT
annotated target: VDJ C cluster
annotated property: IAO_0000118
annotated source: VDJ_C_cluster

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: VDJ_C_cluster

V_DJ_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: V_gene
subclass of: Restriction
  on property: has_part
  some values from: C_gene
subclass of: Restriction
  on property: has_part
  some values from: DJ_gene
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene.
IAO id: SO:0000542
IAO_0000118: V DJ C cluster
IAO_0000118: V-(DJ)-C-CLUSTER

Axiom
IAO scope: EXACT
annotated target: V DJ C cluster
annotated property: IAO_0000118
annotated source: V_DJ_C_cluster

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: V_DJ_C_cluster

Axiom
IAO scope: EXACT
annotated target: V-(DJ)-C-CLUSTER
annotated property: IAO_0000118
annotated source: V_DJ_C_cluster

alternately_spliced_gene_encoding_greater_than_one_transcript
type: Class
IAO id: SO:0000543
deprecated: true

helitron
type: Class
subclass of: DNA_transposon
IAO_0000115: A rolling circle transposon. Autonomous helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons.
IAO_0000118: ISCR
IAO id: SO:0000544
IAO xref: http://en.wikipedia.org/wiki/Helitron

Axiom
annotated target: ISCR
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: helitron

Axiom
annotated target: A rolling circle transposon. Autonomous helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons.
IAO xref: http://www.pnas.org/cgi/content/full/100/11/6569
annotated property: IAO_0000115
annotated source: helitron

recoding_pseudoknot
type: Class
subclass of: pseudoknot
subclass of: Restriction
  on property: part_of
  some values from: SO_1001268
IAO id: SO:0000545
IAO_0000115: The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding.
IAO_0000118: recoding pseudoknot

Axiom
annotated target: The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding.
IAO xref: http://www.pubmedcentral.nih.gov/articlerender.fcgi
annotated property: IAO_0000115
annotated source: recoding_pseudoknot

Axiom
IAO scope: EXACT
annotated target: recoding pseudoknot
annotated property: IAO_0000118
annotated source: recoding_pseudoknot

designed_sequence
type: Class
subclass of: synthetic_sequence
IAO id: SO:0000546
IAO_0000118: designed sequence

Axiom
IAO scope: EXACT
annotated target: designed sequence
annotated property: IAO_0000118
annotated source: designed_sequence

inversion_derived_bipartite_duplication
type: Class
subclass of: SO_1000038
IAO_0000115: A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion.
IAO id: SO:0000547
IAO_0000118: inversion derived bipartite duplication

Axiom
IAO scope: EXACT
annotated target: inversion derived bipartite duplication
annotated property: IAO_0000118
annotated source: inversion_derived_bipartite_duplication

Axiom
annotated target: A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion.
IAO xref: FB:km
annotated property: IAO_0000115
annotated source: inversion_derived_bipartite_duplication

gene_with_edited_transcript
type: Class
equivalent class: Class
  intersection of: protein_coding_gene
  intersection of: Restriction
    on property: transcribed_to
    some values from: edited_transcript
subclass of: protein_coding_gene
IAO_0000115: A gene that encodes a transcript that is edited.
IAO id: SO:0000548
IAO_0000118: gene with edited transcript

Axiom
IAO scope: EXACT
annotated target: gene with edited transcript
annotated property: IAO_0000118
annotated source: gene_with_edited_transcript

Axiom
annotated target: A gene that encodes a transcript that is edited.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: gene_with_edited_transcript

inversion_derived_duplication_plus_aneuploid
type: Class
subclass of: SO_1000038
IAO_0000115: A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion.
IAO id: SO:0000549
IAO_0000118: inversion derived duplication plus aneuploid

Axiom
annotated target: A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion.
IAO xref: FB:km
annotated property: IAO_0000115
annotated source: inversion_derived_duplication_plus_aneuploid

Axiom
IAO scope: EXACT
annotated target: inversion derived duplication plus aneuploid
annotated property: IAO_0000118
annotated source: inversion_derived_duplication_plus_aneuploid

aneuploid_chromosome
type: Class
subclass of: SO_1000183
IAO_0000115: A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking.
comment: Examples are Nullo-4, Haplo-4 and triplo-4 in Drosophila.
IAO id: SO:0000550
IAO_0000118: aneuploid chromosome

Axiom
IAO scope: EXACT
annotated target: aneuploid chromosome
annotated property: IAO_0000118
annotated source: aneuploid_chromosome

Axiom
annotated target: A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: aneuploid_chromosome

polyA_signal_sequence
type: Class
subclass of: SO_0001679
IAO id: SO:0000551
IAO subset: SOFA
IAO_0000115: The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA.
IAO_0000118: poly(A) signal
IAO_0000118: polyA signal sequence
IAO_0000118: polyadenylation termination signal

Axiom
IAO scope: EXACT
annotated target: polyA signal sequence
annotated property: IAO_0000118
annotated source: polyA_signal_sequence

Axiom
annotated target: The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA.
IAO xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
annotated property: IAO_0000115
annotated source: polyA_signal_sequence

Axiom
IAO scope: EXACT
annotated target: polyadenylation termination signal
annotated property: IAO_0000118
annotated source: polyA_signal_sequence

Axiom
IAO scope: EXACT
annotated target: poly(A) signal
annotated property: IAO_0000118
annotated source: polyA_signal_sequence

Shine_Dalgarno_sequence
type: Class
subclass of: ribosome_entry_site
IAO_0000115: A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex.
comment: Not found in Eukaryotic sequence.
IAO_0000118: RBS
IAO id: SO:0000552
IAO_0000118: Shine Dalgarno sequence
IAO_0000118: Shine-Dalgarno sequence
IAO_0000118: five prime ribosome binding site
IAO xref: http://en.wikipedia.org/wiki/Shine-Dalgarno_sequence

Axiom
IAO scope: EXACT
annotated target: Shine Dalgarno sequence
annotated property: IAO_0000118
annotated source: Shine_Dalgarno_sequence

Axiom
annotated target: A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex.
IAO xref: SO:jh
annotated property: IAO_0000115
annotated source: Shine_Dalgarno_sequence

Axiom
IAO scope: EXACT
annotated target: five prime ribosome binding site
annotated property: IAO_0000118
annotated source: Shine_Dalgarno_sequence

Axiom
IAO scope: EXACT
annotated target: Shine-Dalgarno sequence
annotated property: IAO_0000118
annotated source: Shine_Dalgarno_sequence

Axiom
annotated target: RBS
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: Shine_Dalgarno_sequence

polyA_site
type: Class
subclass of: junction
subclass of: Restriction
  on property: part_of
  some values from: three_prime_UTR
subclass of: Restriction
  on property: part_of
  some values from: mature_transcript
IAO id: SO:0000553
IAO alt id: SO:0001430
IAO subset: SOFA
IAO_0000115: The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence.
IAO_0000118: polyA cleavage site
IAO_0000118: polyA junction
IAO_0000118: polyA site
IAO_0000118: polyA_junction
IAO_0000118: polyadenylation site

Axiom
IAO scope: EXACT
annotated target: polyA site
annotated property: IAO_0000118
annotated source: polyA_site

Axiom
IAO scope: EXACT
annotated target: polyA cleavage site
annotated property: IAO_0000118
annotated source: polyA_site

Axiom
IAO scope: EXACT
annotated target: polyA_junction
annotated property: IAO_0000118
annotated source: polyA_site

Axiom
IAO scope: RELATED
annotated target: polyadenylation site
annotated property: IAO_0000118
annotated source: polyA_site

Axiom
IAO scope: EXACT
annotated target: polyA junction
annotated property: IAO_0000118
annotated source: polyA_site

Axiom
annotated target: The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence.
IAO xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
annotated property: IAO_0000115
annotated source: polyA_site

assortment_derived_deficiency_plus_duplication
type: Class
IAO id: SO:0000554
deprecated: true

five_prime_clip
type: Class
subclass of: clip
IAO_0000118: 5' clip
IAO_0000115: 5' most region of a precursor transcript that is clipped off during processing.
IAO id: SO:0000555
IAO_0000118: five prime clip

Axiom
annotated target: 5' clip
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: five_prime_clip

Axiom
IAO scope: EXACT
annotated target: five prime clip
annotated property: IAO_0000118
annotated source: five_prime_clip

Axiom
annotated target: 5' most region of a precursor transcript that is clipped off during processing.
IAO xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
annotated property: IAO_0000115
annotated source: five_prime_clip

five_prime_D_recombination_signal_sequence
type: Class
subclass of: D_gene_recombination_feature
IAO_0000118: 5'RS
IAO_0000115: Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene.
IAO id: SO:0000556
IAO_0000118: five prime D recombination signal sequence
IAO_0000118: five prime D-recombination signal sequence

Axiom
IAO scope: EXACT
annotated target: five prime D-recombination signal sequence
annotated property: IAO_0000118
annotated source: five_prime_D_recombination_signal_sequence

Axiom
annotated target: Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: five_prime_D_recombination_signal_sequence

Axiom
annotated target: 5'RS
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: five_prime_D_recombination_signal_sequence

Axiom
IAO scope: EXACT
annotated target: five prime D recombination signal sequence
annotated property: IAO_0000118
annotated source: five_prime_D_recombination_signal_sequence

three_prime_clip
type: Class
subclass of: clip
IAO_0000118: 3'-clip
IAO_0000115: 3'-most region of a precursor transcript that is clipped off during processing.
IAO id: SO:0000557
IAO_0000118: three prime clip

Axiom
annotated target: 3'-most region of a precursor transcript that is clipped off during processing.
IAO xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
annotated property: IAO_0000115
annotated source: three_prime_clip

Axiom
annotated target: 3'-clip
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: three_prime_clip

Axiom
IAO scope: EXACT
annotated target: three prime clip
annotated property: IAO_0000118
annotated source: three_prime_clip

C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: C_gene
IAO_0000118: C cluster
IAO_0000118: C-CLUSTER
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene.
IAO id: SO:0000558

Axiom
annotated target: C cluster
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: C_cluster

Axiom
annotated target: C-CLUSTER
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: C_cluster

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: C_cluster

D_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: D_gene
IAO_0000118: D cluster
IAO_0000118: D-CLUSTER
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene.
IAO id: SO:0000559

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: D_cluster

Axiom
annotated target: D-CLUSTER
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: D_cluster

Axiom
annotated target: D cluster
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: D_cluster

D_J_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: J_gene
subclass of: Restriction
  on property: has_part
  some values from: D_gene
IAO_0000118: D J cluster
IAO_0000118: D-J-CLUSTER
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene.
IAO id: SO:0000560

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: D_J_cluster

Axiom
annotated target: D-J-CLUSTER
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: D_J_cluster

Axiom
annotated target: D J cluster
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: D_J_cluster

heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
type: Class
subclass of: vertebrate_immune_system_gene_recombination_signal_feature
IAO_0000118: HEPTAMER
IAO id: SO:0000561
IAO_0000115: Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene.
IAO_0000118: heptamer of recombination feature of vertebrate immune system gene

Axiom
annotated target: HEPTAMER
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: heptamer_of_recombination_feature_of_vertebrate_immune_system_gene

Axiom
IAO scope: EXACT
annotated target: heptamer of recombination feature of vertebrate immune system gene
annotated property: IAO_0000118
annotated source: heptamer_of_recombination_feature_of_vertebrate_immune_system_gene

Axiom
annotated target: Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: heptamer_of_recombination_feature_of_vertebrate_immune_system_gene

nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
type: Class
subclass of: vertebrate_immune_system_gene_recombination_signal_feature
IAO id: SO:0000562
IAO_0000118: nonamer of recombination feature of vertebrate immune system gene

Axiom
IAO scope: EXACT
annotated target: nonamer of recombination feature of vertebrate immune system gene
annotated property: IAO_0000118
annotated source: nonamer_of_recombination_feature_of_vertebrate_immune_system_gene

vertebrate_immune_system_gene_recombination_spacer
type: Class
subclass of: vertebrate_immune_system_gene_recombination_feature
IAO id: SO:0000563
IAO_0000118: vertebrate immune system gene recombination spacer

Axiom
IAO scope: EXACT
annotated target: vertebrate immune system gene recombination spacer
annotated property: IAO_0000118
annotated source: vertebrate_immune_system_gene_recombination_spacer

V_DJ_J_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: J_gene
subclass of: Restriction
  on property: has_part
  some values from: C_gene
subclass of: Restriction
  on property: has_part
  some values from: DJ_gene
subclass of: Restriction
  on property: has_part
  some values from: V_gene
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene.
IAO id: SO:0000564
IAO_0000118: V DJ J C cluster
IAO_0000118: V-(DJ)-J-C-CLUSTER

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: V_DJ_J_C_cluster

Axiom
IAO scope: EXACT
annotated target: V DJ J C cluster
annotated property: IAO_0000118
annotated source: V_DJ_J_C_cluster

Axiom
IAO scope: EXACT
annotated target: V-(DJ)-J-C-CLUSTER
annotated property: IAO_0000118
annotated source: V_DJ_J_C_cluster

V_VDJ_J_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: VDJ_gene
subclass of: Restriction
  on property: has_part
  some values from: V_gene
subclass of: Restriction
  on property: has_part
  some values from: C_gene
subclass of: Restriction
  on property: has_part
  some values from: J_gene
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene.
IAO id: SO:0000565
IAO_0000118: V VDJ J C cluster
IAO_0000118: V-(VDJ)-J-C-CLUSTER

Axiom
IAO scope: EXACT
annotated target: V-(VDJ)-J-C-CLUSTER
annotated property: IAO_0000118
annotated source: V_VDJ_J_C_cluster

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: V_VDJ_J_C_cluster

Axiom
IAO scope: EXACT
annotated target: V VDJ J C cluster
annotated property: IAO_0000118
annotated source: V_VDJ_J_C_cluster

V_VJ_J_C_cluster
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
subclass of: Restriction
  on property: has_part
  some values from: J_gene
subclass of: Restriction
  on property: has_part
  some values from: VJ_gene
subclass of: Restriction
  on property: has_part
  some values from: C_gene
subclass of: Restriction
  on property: has_part
  some values from: V_gene
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene.
IAO id: SO:0000566
IAO_0000118: V VJ J C cluster
IAO_0000118: V-(VJ)-J-C-CLUSTER

Axiom
IAO scope: EXACT
annotated target: V VJ J C cluster
annotated property: IAO_0000118
annotated source: V_VJ_J_C_cluster

Axiom
IAO scope: EXACT
annotated target: V-(VJ)-J-C-CLUSTER
annotated property: IAO_0000118
annotated source: V_VJ_J_C_cluster

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: V_VJ_J_C_cluster

inversion_derived_aneuploid_chromosome
type: Class
subclass of: aneuploid_chromosome
IAO_0000115: A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion.
IAO id: SO:0000567
IAO_0000118: inversion derived aneuploid chromosome

Axiom
IAO scope: EXACT
annotated target: inversion derived aneuploid chromosome
annotated property: IAO_0000118
annotated source: inversion_derived_aneuploid_chromosome

Axiom
annotated target: A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion.
IAO xref: FB:km
annotated property: IAO_0000115
annotated source: inversion_derived_aneuploid_chromosome

bidirectional_promoter
type: Class
subclass of: promoter
IAO id: SO:0000568
IAO_0000118: bidirectional promoter

Axiom
IAO scope: EXACT
annotated target: bidirectional promoter
annotated property: IAO_0000118
annotated source: bidirectional_promoter

retrotransposed
type: Class
subclass of: feature_attribute
IAO_0000115: An attribute of a feature that occurred as the product of a reverse transcriptase mediated event.
comment: GO:0003964 RNA-directed DNA polymerase activity.
IAO id: SO:0000569
IAO alt id: SO:0100042
IAO xref: http://en.wikipedia.org/wiki/Retrotransposed

Axiom
annotated target: An attribute of a feature that occurred as the product of a reverse transcriptase mediated event.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: retrotransposed

three_prime_D_recombination_signal_sequence
type: Class
subclass of: D_gene_recombination_feature
IAO_0000118: 3'D-RS
IAO_0000115: Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene.
IAO id: SO:0000570
IAO_0000118: three prime D recombination signal sequence
IAO_0000118: three_prime_D-recombination_signal_sequence

Axiom
IAO scope: EXACT
annotated target: three prime D recombination signal sequence
annotated property: IAO_0000118
annotated source: three_prime_D_recombination_signal_sequence

Axiom
annotated target: Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: three_prime_D_recombination_signal_sequence

Axiom
annotated target: 3'D-RS
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: three_prime_D_recombination_signal_sequence

Axiom
IAO scope: EXACT
annotated target: three_prime_D-recombination_signal_sequence
annotated property: IAO_0000118
annotated source: three_prime_D_recombination_signal_sequence

miRNA_encoding
type: Class
subclass of: non_protein_coding
IAO id: SO:0000571
IAO_0000118: miRNA encoding

Axiom
IAO scope: EXACT
annotated target: miRNA encoding
annotated property: IAO_0000118
annotated source: miRNA_encoding

DJ_gene
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
IAO_0000118: D-J-GENE
IAO_0000118: DJ gene
IAO_0000115: Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment.
IAO id: SO:0000572

Axiom
annotated target: D-J-GENE
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DJ_gene

Axiom
annotated target: Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment.
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: DJ_gene

Axiom
annotated target: DJ gene
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DJ_gene

rRNA_encoding
type: Class
subclass of: non_protein_coding
IAO id: SO:0000573
IAO_0000118: rRNA encoding

Axiom
IAO scope: EXACT
annotated target: rRNA encoding
annotated property: IAO_0000118
annotated source: rRNA_encoding

VDJ_gene
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
IAO_0000115: Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205).
IAO id: SO:0000574
IAO_0000118: V-D-J-GENE
IAO_0000118: VDJ gene

Axiom
IAO scope: EXACT
annotated target: V-D-J-GENE
annotated property: IAO_0000118
annotated source: VDJ_gene

Axiom
annotated target: Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205).
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: VDJ_gene

Axiom
IAO scope: EXACT
annotated target: VDJ gene
annotated property: IAO_0000118
annotated source: VDJ_gene

scRNA_encoding
type: Class
subclass of: non_protein_coding
IAO id: SO:0000575
IAO_0000118: scRNA encoding

Axiom
IAO scope: EXACT
annotated target: scRNA encoding
annotated property: IAO_0000118
annotated source: scRNA_encoding

VJ_gene
type: Class
subclass of: vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
IAO_0000115: Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205).
IAO id: SO:0000576
IAO_0000118: V-J-GENE
IAO_0000118: VJ gene

Axiom
IAO scope: EXACT
annotated target: VJ gene
annotated property: IAO_0000118
annotated source: VJ_gene

Axiom
annotated target: Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205).
IAO xref: http://www.imgt.org/cgi-bin/IMGTlect.jv#
annotated property: IAO_0000115
annotated source: VJ_gene

Axiom
IAO scope: EXACT
annotated target: V-J-GENE
annotated property: IAO_0000118
annotated source: VJ_gene

centromere
type: Class
subclass of: chromosomal_structural_element
IAO_0000115: A region of chromosome where the spindle fibers attach during mitosis and meiosis.
IAO id: SO:0000577
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/Centromere

Axiom
annotated target: A region of chromosome where the spindle fibers attach during mitosis and meiosis.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: centromere

snoRNA_encoding
type: Class
subclass of: non_protein_coding
IAO id: SO:0000578
IAO_0000118: snoRNA encoding

Axiom
IAO scope: EXACT
annotated target: snoRNA encoding
annotated property: IAO_0000118
annotated source: snoRNA_encoding

edited_transcript_feature
type: Class
subclass of: transcript_region
IAO_0000115: A locatable feature on a transcript that is edited.
IAO id: SO:0000579
IAO_0000118: edited transcript feature

Axiom
IAO scope: EXACT
annotated target: edited transcript feature
annotated property: IAO_0000118
annotated source: edited_transcript_feature

Axiom
annotated target: A locatable feature on a transcript that is edited.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: edited_transcript_feature

methylation_guide_snoRNA_primary_transcript
type: Class
subclass of: snoRNA_primary_transcript
IAO_0000115: A primary transcript encoding a methylation guide small nucleolar RNA.
IAO id: SO:0000580
IAO_0000118: methylation guide snoRNA primary transcript

Axiom
annotated target: A primary transcript encoding a methylation guide small nucleolar RNA.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: methylation_guide_snoRNA_primary_transcript

Axiom
IAO scope: EXACT
annotated target: methylation guide snoRNA primary transcript
annotated property: IAO_0000118
annotated source: methylation_guide_snoRNA_primary_transcript

cap
type: Class
subclass of: SO_0001411
IAO_0000115: A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA.
IAO id: SO:0000581
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/5%27_cap

Axiom
annotated target: A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA.
IAO xref: http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html
annotated property: IAO_0000115
annotated source: cap

rRNA_cleavage_snoRNA_primary_transcript
type: Class
subclass of: snoRNA_primary_transcript
IAO_0000115: A primary transcript encoding an rRNA cleavage snoRNA.
IAO id: SO:0000582
IAO_0000118: rRNA cleavage snoRNA primary transcript

Axiom
IAO scope: EXACT
annotated target: rRNA cleavage snoRNA primary transcript
annotated property: IAO_0000118
annotated source: rRNA_cleavage_snoRNA_primary_transcript

Axiom
annotated target: A primary transcript encoding an rRNA cleavage snoRNA.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: rRNA_cleavage_snoRNA_primary_transcript

pre_edited_region
type: Class
subclass of: edited_transcript_feature
IAO id: SO:0000583
IAO_0000115: The region of a transcript that will be edited.
IAO_0000118: pre edited region
IAO_0000118: pre-edited region

Axiom
annotated target: The region of a transcript that will be edited.
IAO xref: http://dna.kdna.ucla.edu/rna/index.aspx
annotated property: IAO_0000115
annotated source: pre_edited_region

Axiom
IAO scope: EXACT
annotated target: pre edited region
annotated property: IAO_0000118
annotated source: pre_edited_region

Axiom
IAO scope: EXACT
annotated target: pre-edited region
annotated property: IAO_0000118
annotated source: pre_edited_region

tmRNA
type: Class
subclass of: small_regulatory_ncRNA
IAO_0000118: 10Sa RNA
IAO_0000115: A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes.
IAO id: SO:0000584
IAO xref: http://en.wikipedia.org/wiki/TmRNA
IAO_0000118: ssrA

Axiom
annotated target: 10Sa RNA
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: tmRNA

Axiom
IAO scope: RELATED
annotated target: ssrA
annotated property: IAO_0000118
annotated source: tmRNA

Axiom
annotated target: A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes.
IAO xref: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc
annotated property: IAO_0000115
annotated source: tmRNA

C_D_box_snoRNA_encoding
type: Class
subclass of: snoRNA_encoding
IAO_0000118: C/D box snoRNA encoding
IAO id: SO:0000585

Axiom
annotated target: C/D box snoRNA encoding
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: C_D_box_snoRNA_encoding

tmRNA_primary_transcript
type: Class
subclass of: nc_primary_transcript
IAO_0000118: 10Sa RNA primary transcript
IAO_0000115: A primary transcript encoding a tmRNA (SO:0000584).
IAO id: SO:0000586
IAO_0000118: ssrA RNA primary transcript
IAO_0000118: tmRNA primary transcript

Axiom
IAO scope: RELATED
annotated target: ssrA RNA primary transcript
annotated property: IAO_0000118
annotated source: tmRNA_primary_transcript

Axiom
annotated target: 10Sa RNA primary transcript
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: tmRNA_primary_transcript

Axiom
annotated target: A primary transcript encoding a tmRNA (SO:0000584).
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: tmRNA_primary_transcript

Axiom
IAO scope: EXACT
annotated target: tmRNA primary transcript
annotated property: IAO_0000118
annotated source: tmRNA_primary_transcript

group_I_intron
type: Class
subclass of: autocatalytically_spliced_intron
comment: GO:0000372.
IAO_0000115: Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions.
IAO id: SO:0000587
IAO subset: SOFA
IAO_0000118: group I intron
IAO xref: http://en.wikipedia.org/wiki/Group_I_intron

Axiom
IAO scope: EXACT
annotated target: group I intron
annotated property: IAO_0000118
annotated source: group_I_intron

Axiom
annotated target: Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions.
IAO xref: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc
annotated property: IAO_0000115
annotated source: group_I_intron

autocatalytically_spliced_intron
type: Class
equivalent class: Class
  intersection of: intron
  intersection of: Restriction
    on property: has_quality
    some values from: ribozymic
subclass of: intron
IAO_0000115: A self spliced intron.
IAO id: SO:0000588
IAO subset: SOFA
IAO_0000118: autocatalytically spliced intron

Axiom
IAO scope: EXACT
annotated target: autocatalytically spliced intron
annotated property: IAO_0000118
annotated source: autocatalytically_spliced_intron

Axiom
annotated target: A self spliced intron.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: autocatalytically_spliced_intron

SRP_RNA_primary_transcript
type: Class
subclass of: nc_primary_transcript
IAO_0000115: A primary transcript encoding a signal recognition particle RNA.
IAO id: SO:0000589
IAO_0000118: SRP RNA primary transcript

Axiom
IAO scope: EXACT
annotated target: SRP RNA primary transcript
annotated property: IAO_0000118
annotated source: SRP_RNA_primary_transcript

Axiom
annotated target: A primary transcript encoding a signal recognition particle RNA.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: SRP_RNA_primary_transcript

SRP_RNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: SRP_RNA_primary_transcript
IAO_0000118: 7S RNA
IAO id: SO:0000590
IAO subset: SOFA
IAO_0000118: SRP RNA
IAO_0000115: The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding.
IAO_0000118: signal recognition particle RNA

Axiom
IAO scope: RELATED
annotated target: signal recognition particle RNA
annotated property: IAO_0000118
annotated source: SRP_RNA

Axiom
IAO scope: EXACT
annotated target: SRP RNA
annotated property: IAO_0000118
annotated source: SRP_RNA

Axiom
annotated target: The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding.
IAO xref: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc
annotated property: IAO_0000115
annotated source: SRP_RNA

Axiom
annotated target: 7S RNA
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: SRP_RNA

pseudoknot
type: Class
subclass of: sequence_secondary_structure
IAO_0000115: A tertiary structure in RNA where nucleotides in a loop form base pairs with a region of RNA downstream of the loop.
IAO id: SO:0000591
IAO xref: http://en.wikipedia.org/wiki/Pseudoknot

Axiom
annotated target: A tertiary structure in RNA where nucleotides in a loop form base pairs with a region of RNA downstream of the loop.
IAO xref: RSC:cb
annotated property: IAO_0000115
annotated source: pseudoknot

H_pseudoknot
type: Class
subclass of: pseudoknot
IAO_0000115: A pseudoknot which contains two stems and at least two loops.
IAO_0000118: H pseudoknot
IAO_0000118: H-pseudoknot
IAO_0000118: H-type pseudoknot
IAO id: SO:0000592
IAO_0000118: classical pseudoknot
IAO_0000118: hairpin-type pseudoknot

Axiom
IAO scope: EXACT
annotated target: H pseudoknot
annotated property: IAO_0000118
annotated source: H_pseudoknot

Axiom
IAO scope: EXACT
annotated target: H-type pseudoknot
annotated property: IAO_0000118
annotated source: H_pseudoknot

Axiom
IAO scope: EXACT
annotated target: classical pseudoknot
annotated property: IAO_0000118
annotated source: H_pseudoknot

Axiom
IAO scope: EXACT
annotated target: hairpin-type pseudoknot
annotated property: IAO_0000118
annotated source: H_pseudoknot

Axiom
IAO scope: EXACT
annotated target: H-pseudoknot
annotated property: IAO_0000118
annotated source: H_pseudoknot

Axiom
annotated target: A pseudoknot which contains two stems and at least two loops.
IAO xref: http://www.ncbi.nlm.nih.gov\:80/entrez/query.fcgi
annotated property: IAO_0000115
annotated source: H_pseudoknot

C_D_box_snoRNA
type: Class
subclass of: snoRNA
subclass of: Restriction
  on property: derives_from
  some values from: C_D_box_snoRNA_primary_transcript
IAO_0000118: C D box snoRNA
IAO_0000118: C/D box snoRNA
IAO_0000115: Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'.
IAO id: SO:0000593
IAO subset: SOFA
IAO_0000118: box C/D snoRNA

Axiom
IAO scope: EXACT
annotated target: box C/D snoRNA
annotated property: IAO_0000118
annotated source: C_D_box_snoRNA

Axiom
annotated target: C D box snoRNA
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: C_D_box_snoRNA

Axiom
annotated target: C/D box snoRNA
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: C_D_box_snoRNA

Axiom
annotated target: Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'.
IAO xref: http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html
annotated property: IAO_0000115
annotated source: C_D_box_snoRNA

H_ACA_box_snoRNA
type: Class
subclass of: snoRNA
subclass of: Restriction
  on property: derives_from
  some values from: H_ACA_box_snoRNA_primary_transcript
IAO_0000118: H ACA box snoRNA
IAO_0000118: H/ACA box snoRNA
IAO_0000115: Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains.
IAO id: SO:0000594
IAO_0000118: box H/ACA snoRNA

Axiom
annotated target: Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains.
IAO xref: http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html
annotated property: IAO_0000115
annotated source: H_ACA_box_snoRNA

Axiom
IAO scope: EXACT
annotated target: H/ACA box snoRNA
annotated property: IAO_0000118
annotated source: H_ACA_box_snoRNA

Axiom
IAO scope: EXACT
annotated target: box H/ACA snoRNA
annotated property: IAO_0000118
annotated source: H_ACA_box_snoRNA

Axiom
IAO scope: EXACT
annotated target: H ACA box snoRNA
annotated property: IAO_0000118
annotated source: H_ACA_box_snoRNA

C_D_box_snoRNA_primary_transcript
type: Class
subclass of: snoRNA_primary_transcript
IAO_0000115: A primary transcript encoding a small nucleolar RNA of the box C/D family.
IAO_0000118: C/D box snoRNA primary transcript
IAO id: SO:0000595

Axiom
annotated target: C/D box snoRNA primary transcript
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: C_D_box_snoRNA_primary_transcript

Axiom
annotated target: A primary transcript encoding a small nucleolar RNA of the box C/D family.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: C_D_box_snoRNA_primary_transcript

H_ACA_box_snoRNA_primary_transcript
type: Class
subclass of: snoRNA_primary_transcript
IAO_0000115: A primary transcript encoding a small nucleolar RNA of the box H/ACA family.
IAO_0000118: H ACA box snoRNA primary transcript
IAO id: SO:0000596

Axiom
IAO scope: EXACT
annotated target: H ACA box snoRNA primary transcript
annotated property: IAO_0000118
annotated source: H_ACA_box_snoRNA_primary_transcript

Axiom
annotated target: A primary transcript encoding a small nucleolar RNA of the box H/ACA family.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: H_ACA_box_snoRNA_primary_transcript

transcript_edited_by_U_insertion/deletion
type: Class
IAO id: SO:0000597
IAO_0000115: The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.
deprecated: true

Axiom
annotated target: The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.
IAO xref: http://www.rna.ucla.edu/index.html
annotated property: IAO_0000115
annotated source: transcript_edited_by_U_insertion/deletion

edited_by_C_insertion_and_dinucleotide_insertion
type: Class
IAO id: SO:0000598
IAO_0000118: transcript_edited_by_C-insertion_and_dinucleotide_insertion
deprecated: true

Axiom
IAO scope: RELATED
annotated target: transcript_edited_by_C-insertion_and_dinucleotide_insertion
annotated property: IAO_0000118
annotated source: edited_by_C_insertion_and_dinucleotide_insertion

edited_by_C_to_U_substitution
type: Class
IAO id: SO:0000599
deprecated: true

edited_by_A_to_I_substitution
type: Class
IAO id: SO:0000600
deprecated: true

edited_by_G_addition
type: Class
IAO id: SO:0000601
deprecated: true

guide_RNA
type: Class
subclass of: ncRNA
IAO_0000115: A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA.
IAO id: SO:0000602
IAO subset: SOFA
IAO_0000118: gRNA
IAO_0000118: guide RNA
IAO xref: http://en.wikipedia.org/wiki/Guide_RNA

Axiom
IAO scope: EXACT
annotated target: gRNA
annotated property: IAO_0000118
annotated source: guide_RNA

Axiom
IAO scope: EXACT
annotated target: guide RNA
annotated property: IAO_0000118
annotated source: guide_RNA

Axiom
annotated target: A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA.
IAO xref: http://www.rna.ucla.edu/index.html
annotated property: IAO_0000115
annotated source: guide_RNA

group_II_intron
type: Class
subclass of: autocatalytically_spliced_intron
comment: GO:0000373.
IAO_0000115: Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny.
IAO id: SO:0000603
IAO subset: SOFA
IAO_0000118: group II intron
IAO xref: http://en.wikipedia.org/wiki/Group_II_intron

Axiom
IAO scope: EXACT
annotated target: group II intron
annotated property: IAO_0000118
annotated source: group_II_intron

Axiom
annotated target: Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny.
IAO xref: http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml
annotated property: IAO_0000115
annotated source: group_II_intron

editing_block
type: Class
subclass of: edited_transcript_feature
IAO_0000115: Edited mRNA sequence mediated by a single guide RNA (SO:0000602).
IAO id: SO:0000604
IAO_0000118: editing block

Axiom
IAO scope: EXACT
annotated target: editing block
annotated property: IAO_0000118
annotated source: editing_block

Axiom
annotated target: Edited mRNA sequence mediated by a single guide RNA (SO:0000602).
IAO xref: http://dna.kdna.ucla.edu/rna/index.aspx
annotated property: IAO_0000115
annotated source: editing_block

intergenic_region
type: Class
subclass of: SO_0001411
IAO_0000115: A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome.
IAO id: SO:0000605
IAO subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
IAO xref: http://en.wikipedia.org/wiki/Intergenic_region
IAO_0000118: intergenic region

Axiom
IAO scope: EXACT
annotated target: intergenic region
annotated property: IAO_0000118
annotated source: intergenic_region

Axiom
annotated target: A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome.
IAO xref: SO:cjm
annotated property: IAO_0000115
annotated source: intergenic_region

editing_domain
type: Class
subclass of: edited_transcript_feature
IAO_0000115: Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602).
IAO id: SO:0000606
IAO_0000118: editing domain

Axiom
IAO scope: EXACT
annotated target: editing domain
annotated property: IAO_0000118
annotated source: editing_domain

Axiom
annotated target: Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602).
IAO xref: http://dna.kdna.ucla.edu/rna/index.aspx
annotated property: IAO_0000115
annotated source: editing_domain

unedited_region
type: Class
subclass of: edited_transcript_feature
IAO id: SO:0000607
IAO_0000115: The region of an edited transcript that will not be edited.
IAO_0000118: unedited region

Axiom
annotated target: The region of an edited transcript that will not be edited.
IAO xref: http://dna.kdna.ucla.edu/rna/index.aspx
annotated property: IAO_0000115
annotated source: unedited_region

Axiom
IAO scope: EXACT
annotated target: unedited region
annotated property: IAO_0000118
annotated source: unedited_region

H_ACA_box_snoRNA_encoding
type: Class
subclass of: snoRNA_encoding
IAO_0000118: H ACA box snoRNA encoding
IAO id: SO:0000608

Axiom
IAO scope: EXACT
annotated target: H ACA box snoRNA encoding
annotated property: IAO_0000118
annotated source: H_ACA_box_snoRNA_encoding

oligo_U_tail
type: Class
subclass of: SO_0001411
subclass of: Restriction
  on property: adjacent_to
  some values from: guide_RNA
IAO id: SO:0000609
IAO_0000115: The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602).
IAO_0000118: oligo U tail

Axiom
annotated target: The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602).
IAO xref: http://www.rna.ucla.edu/
annotated property: IAO_0000115
annotated source: oligo_U_tail

Axiom
IAO scope: EXACT
annotated target: oligo U tail
annotated property: IAO_0000118
annotated source: oligo_U_tail

polyA_sequence
type: Class
subclass of: SO_0001411
subclass of: Restriction
  on property: adjacent_to
  some values from: mRNA
IAO id: SO:0000610
IAO subset: SOFA
IAO_0000115: Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs.
IAO_0000118: polyA sequence

Axiom
IAO xref: SO:ke
annotated target: Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs.
annotated property: IAO_0000115
annotated source: polyA_sequence

Axiom
IAO scope: EXACT
annotated target: polyA sequence
annotated property: IAO_0000118
annotated source: polyA_sequence

branch_site
type: Class
subclass of: spliceosomal_intron_region
IAO_0000115: A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat.
IAO id: SO:0000611
IAO subset: SOFA
IAO_0000118: branch point
IAO_0000118: branch site
IAO_0000118: branch_point

Axiom
IAO scope: EXACT
annotated target: branch site
annotated property: IAO_0000118
annotated source: branch_site

Axiom
IAO scope: EXACT
annotated target: branch_point
annotated property: IAO_0000118
annotated source: branch_site

Axiom
IAO scope: EXACT
annotated target: branch point
annotated property: IAO_0000118
annotated source: branch_site

Axiom
annotated target: A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: branch_site

polypyrimidine_tract
type: Class
subclass of: spliceosomal_intron_region
IAO id: SO:0000612
IAO subset: SOFA
IAO_0000115: The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing.
IAO xref: http://en.wikipedia.org/wiki/Polypyrimidine_tract
IAO_0000118: polypyrimidine tract

Axiom
IAO scope: EXACT
annotated target: polypyrimidine tract
annotated property: IAO_0000118
annotated source: polypyrimidine_tract

Axiom
annotated target: The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing.
IAO xref: http://nar.oupjournals.org/cgi/content/full/25/4/888
annotated property: IAO_0000115
annotated source: polypyrimidine_tract

bacterial_RNApol_promoter
type: Class
subclass of: gene_group_regulatory_region
subclass of: RNA_polymerase_promoter
IAO_0000115: A DNA sequence to which bacterial RNA polymerase binds, to begin transcription.
IAO id: SO:0000613
IAO_0000118: bacterial RNApol promoter

Axiom
IAO scope: EXACT
annotated target: bacterial RNApol promoter
annotated property: IAO_0000118
annotated source: bacterial_RNApol_promoter

Axiom
annotated target: A DNA sequence to which bacterial RNA polymerase binds, to begin transcription.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: bacterial_RNApol_promoter

bacterial_terminator
type: Class
subclass of: terminator
subclass of: gene_group_regulatory_region
IAO_0000115: A terminator signal for bacterial transcription.
IAO id: SO:0000614
IAO_0000118: bacterial terminator

Axiom
IAO scope: EXACT
annotated target: bacterial terminator
annotated property: IAO_0000118
annotated source: bacterial_terminator

Axiom
annotated target: A terminator signal for bacterial transcription.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: bacterial_terminator

terminator_of_type_2_RNApol_III_promoter
type: Class
subclass of: eukaryotic_terminator
IAO_0000115: A terminator signal for RNA polymerase III transcription.
IAO id: SO:0000615
IAO_0000118: terminator of type 2 RNApol III promoter

Axiom
IAO scope: EXACT
annotated target: terminator of type 2 RNApol III promoter
annotated property: IAO_0000118
annotated source: terminator_of_type_2_RNApol_III_promoter

Axiom
annotated target: A terminator signal for RNA polymerase III transcription.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: terminator_of_type_2_RNApol_III_promoter

transcription_end_site
type: Class
subclass of: primary_transcript_region
IAO id: SO:0000616
IAO subset: SOFA
IAO_0000115: The base where transcription ends.
IAO_0000118: transcription end site

Axiom
IAO scope: EXACT
annotated target: transcription end site
annotated property: IAO_0000118
annotated source: transcription_end_site

Axiom
IAO xref: SO:ke
annotated target: The base where transcription ends.
annotated property: IAO_0000115
annotated source: transcription_end_site

RNApol_III_promoter_type_1
type: Class
subclass of: RNApol_III_promoter
IAO_0000118: RNApol III promoter type 1
IAO id: SO:0000617

Axiom
IAO scope: EXACT
annotated target: RNApol III promoter type 1
annotated property: IAO_0000118
annotated source: RNApol_III_promoter_type_1

RNApol_III_promoter_type_2
type: Class
subclass of: RNApol_III_promoter
IAO_0000118: RNApol III promoter type 2
IAO id: SO:0000618
IAO_0000118: tRNA promoter

Axiom
IAO scope: EXACT
annotated target: RNApol III promoter type 2
annotated property: IAO_0000118
annotated source: RNApol_III_promoter_type_2

Axiom
IAO scope: RELATED
annotated target: tRNA promoter
annotated property: IAO_0000118
annotated source: RNApol_III_promoter_type_2

A_box
type: Class
subclass of: SO_0001660
IAO_0000115: A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG.
IAO_0000118: A-box
comment: Binds TFIIIC.
IAO id: SO:0000619
IAO xref: http://en.wikipedia.org/wiki/A-box

Axiom
annotated target: A-box
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: A_box

Axiom
annotated target: A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: A_box

B_box
type: Class
subclass of: SO_0001660
subclass of: Restriction
  on property: part_of
  some values from: RNApol_III_promoter_type_2
IAO_0000115: A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC.
IAO_0000118: B-box
comment: Binds TFIIIC.
IAO id: SO:0000620

Axiom
annotated target: A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: B_box

Axiom
annotated target: B-box
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: B_box

RNApol_III_promoter_type_3
type: Class
subclass of: RNApol_III_promoter
IAO_0000118: RNApol III promoter type 3
IAO id: SO:0000621

Axiom
IAO scope: EXACT
annotated target: RNApol III promoter type 3
annotated property: IAO_0000118
annotated source: RNApol_III_promoter_type_3

C_box
type: Class
subclass of: SO_0001660
subclass of: Restriction
  on property: part_of
  some values from: RNApol_III_promoter_type_1
IAO_0000115: An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn.
IAO_0000118: C-box
IAO id: SO:0000622

Axiom
annotated target: An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: C_box

Axiom
annotated target: C-box
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: C_box

snRNA_encoding
type: Class
subclass of: non_protein_coding
IAO id: SO:0000623
IAO_0000118: snRNA encoding

Axiom
IAO scope: EXACT
annotated target: snRNA encoding
annotated property: IAO_0000118
annotated source: snRNA_encoding

telomere
type: Class
subclass of: chromosomal_structural_element
IAO_0000115: A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end.
IAO id: SO:0000624
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/Telomere
IAO_0000118: telomeric DNA
IAO_0000118: telomeric sequence

Axiom
annotated target: A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: telomere

Axiom
IAO scope: EXACT
annotated target: telomeric sequence
annotated property: IAO_0000118
annotated source: telomere

Axiom
IAO scope: EXACT
annotated target: telomeric DNA
annotated property: IAO_0000118
annotated source: telomere

silencer
type: Class
subclass of: CRM
IAO_0000115: A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control.
IAO id: SO:0000625
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/Silencer_(DNA)

Axiom
annotated target: A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: silencer

chromosomal_regulatory_element
type: Class
subclass of: chromosome_part
IAO id: SO:0000626
IAO_0000118: chromosomal regulatory element

Axiom
IAO scope: EXACT
annotated target: chromosomal regulatory element
annotated property: IAO_0000118
annotated source: chromosomal_regulatory_element

insulator
type: Class
subclass of: transcriptional_cis_regulatory_region
IAO_0000115: A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression.
IAO id: SO:0000627
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/Insulator_(genetics)
IAO_0000118: insulator element

Axiom
IAO scope: EXACT
annotated target: insulator element
annotated property: IAO_0000118
annotated source: insulator

Axiom
annotated target: A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression.
IAO xref: SO:regcreative
annotated property: IAO_0000115
annotated source: insulator

chromosomal_structural_element
type: Class
subclass of: chromosome_part
IAO id: SO:0000628
IAO subset: SOFA
IAO_0000118: chromosomal structural element

Axiom
IAO scope: EXACT
annotated target: chromosomal structural element
annotated property: IAO_0000118
annotated source: chromosomal_structural_element

five_prime_open_reading_frame
type: Class
subclass of: mRNA_region
subclass of: Restriction
  on property: part_of
  some values from: five_prime_UTR
IAO id: SO:0000629
IAO_0000118: five prime open reading frame

Axiom
IAO scope: EXACT
annotated target: five prime open reading frame
annotated property: IAO_0000118
annotated source: five_prime_open_reading_frame

upstream_AUG_codon
type: Class
subclass of: UTR_region
subclass of: Restriction
  on property: part_of
  some values from: UTR
IAO_0000115: A start codon upstream of the ORF.
IAO id: SO:0000630
IAO_0000118: upstream AUG codon

Axiom
annotated target: A start codon upstream of the ORF.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: upstream_AUG_codon

Axiom
IAO scope: EXACT
annotated target: upstream AUG codon
annotated property: IAO_0000118
annotated source: upstream_AUG_codon

polycistronic_primary_transcript
type: Class
equivalent class: Class
  intersection of: primary_transcript
  intersection of: Restriction
    on property: has_quality
    some values from: polycistronic
subclass of: polycistronic_transcript
subclass of: primary_transcript
IAO_0000115: A primary transcript encoding for more than one gene product.
IAO id: SO:0000631
IAO_0000118: polycistronic primary transcript

Axiom
annotated target: A primary transcript encoding for more than one gene product.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: polycistronic_primary_transcript

Axiom
IAO scope: EXACT
annotated target: polycistronic primary transcript
annotated property: IAO_0000118
annotated source: polycistronic_primary_transcript

monocistronic_primary_transcript
type: Class
equivalent class: Class
  intersection of: primary_transcript
  intersection of: Restriction
    on property: has_quality
    some values from: monocistronic
subclass of: primary_transcript
subclass of: monocistronic_transcript
IAO_0000115: A primary transcript encoding for one gene product.
IAO id: SO:0000632
IAO_0000118: monocistronic primary transcript

Axiom
IAO scope: EXACT
annotated target: monocistronic primary transcript
annotated property: IAO_0000118
annotated source: monocistronic_primary_transcript

Axiom
annotated target: A primary transcript encoding for one gene product.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: monocistronic_primary_transcript

monocistronic_mRNA
type: Class
equivalent class: Class
  intersection of: mRNA
  intersection of: Restriction
    on property: has_quality
    some values from: monocistronic
subclass of: mRNA
subclass of: monocistronic_transcript
IAO_0000115: An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap.
IAO id: SO:0000633
IAO xref: http://en.wikipedia.org/wiki/Monocistronic_mRNA
IAO_0000118: monocistronic mRNA
IAO_0000118: monocistronic processed transcript

Axiom
IAO scope: EXACT
annotated target: monocistronic mRNA
annotated property: IAO_0000118
annotated source: monocistronic_mRNA

Axiom
annotated target: An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap.
IAO xref: SO:rd
annotated property: IAO_0000115
annotated source: monocistronic_mRNA

Axiom
IAO scope: EXACT
annotated target: monocistronic processed transcript
annotated property: IAO_0000118
annotated source: monocistronic_mRNA

polycistronic_mRNA
type: Class
equivalent class: Class
  intersection of: mRNA
  intersection of: Restriction
    on property: has_quality
    some values from: polycistronic
subclass of: polycistronic_transcript
subclass of: mRNA
IAO_0000115: An mRNA that encodes multiple proteins from at least two non-overlapping regions.
IAO id: SO:0000634
IAO xref: http://en.wikipedia.org/wiki/Polycistronic_mRNA
IAO_0000118: polycistronic mRNA
IAO_0000118: polycistronic processed transcript

Axiom
IAO scope: RELATED
annotated target: polycistronic processed transcript
annotated property: IAO_0000118
annotated source: polycistronic_mRNA

Axiom
annotated target: An mRNA that encodes multiple proteins from at least two non-overlapping regions.
IAO xref: SO:rd
annotated property: IAO_0000115
annotated source: polycistronic_mRNA

Axiom
IAO scope: EXACT
annotated target: polycistronic mRNA
annotated property: IAO_0000118
annotated source: polycistronic_mRNA

mini_exon_donor_RNA
type: Class
subclass of: primary_transcript
IAO_0000115: A primary transcript that donates the spliced leader to other mRNA.
IAO id: SO:0000635
IAO_0000118: mini exon donor RNA
IAO_0000118: mini-exon donor RNA

Axiom
IAO scope: EXACT
annotated target: mini exon donor RNA
annotated property: IAO_0000118
annotated source: mini_exon_donor_RNA

Axiom
IAO scope: EXACT
annotated target: mini-exon donor RNA
annotated property: IAO_0000118
annotated source: mini_exon_donor_RNA

Axiom
annotated target: A primary transcript that donates the spliced leader to other mRNA.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: mini_exon_donor_RNA

spliced_leader_RNA
type: Class
subclass of: primary_transcript_region
subclass of: Restriction
  on property: part_of
  some values from: mini_exon_donor_RNA
IAO id: SO:0000636
IAO_0000118: mini-exon
IAO_0000118: spliced leader RNA

Axiom
IAO scope: EXACT
annotated target: spliced leader RNA
annotated property: IAO_0000118
annotated source: spliced_leader_RNA

Axiom
IAO scope: RELATED
annotated target: mini-exon
annotated property: IAO_0000118
annotated source: spliced_leader_RNA

engineered_plasmid
type: Class
equivalent class: Class
  intersection of: plasmid
  intersection of: Restriction
    on property: has_quality
    some values from: engineered
subclass of: plasmid
subclass of: engineered_region
IAO_0000115: A plasmid that is engineered.
IAO id: SO:0000637
IAO_0000118: engineered plasmid
IAO_0000118: engineered plasmid gene

Axiom
annotated target: A plasmid that is engineered.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: engineered_plasmid

Axiom
IAO scope: EXACT
annotated target: engineered plasmid
annotated property: IAO_0000118
annotated source: engineered_plasmid

Axiom
IAO scope: RELATED
annotated target: engineered plasmid gene
annotated property: IAO_0000118
annotated source: engineered_plasmid

transcribed_spacer_region
type: Class
subclass of: rRNA_primary_transcript_region
IAO_0000115: Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA.
IAO id: SO:0000638
IAO_0000118: transcribed spacer region

Axiom
IAO scope: EXACT
annotated target: transcribed spacer region
annotated property: IAO_0000118
annotated source: transcribed_spacer_region

Axiom
annotated target: Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA.
IAO xref: http://oregonstate.edu/instruction/bb492/general/glossary.html
annotated property: IAO_0000115
annotated source: transcribed_spacer_region

internal_transcribed_spacer_region
type: Class
subclass of: transcribed_spacer_region
IAO_0000115: Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs.
IAO id: SO:0000639
IAO_0000118: internal transcribed spacer region

Axiom
annotated target: Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: internal_transcribed_spacer_region

Axiom
IAO scope: EXACT
annotated target: internal transcribed spacer region
annotated property: IAO_0000118
annotated source: internal_transcribed_spacer_region

external_transcribed_spacer_region
type: Class
subclass of: transcribed_spacer_region
IAO_0000115: Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA.
IAO id: SO:0000640
IAO_0000118: external transcribed spacer region

Axiom
IAO scope: EXACT
annotated target: external transcribed spacer region
annotated property: IAO_0000118
annotated source: external_transcribed_spacer_region

Axiom
annotated target: Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: external_transcribed_spacer_region

tetranucleotide_repeat_microsatellite_feature
type: Class
subclass of: microsatellite
IAO id: SO:0000641
IAO_0000118: tetranucleotide repeat microsatellite feature

Axiom
IAO scope: EXACT
annotated target: tetranucleotide repeat microsatellite feature
annotated property: IAO_0000118
annotated source: tetranucleotide_repeat_microsatellite_feature

SRP_RNA_encoding
type: Class
subclass of: non_protein_coding
IAO id: SO:0000642
IAO_0000118: SRP RNA encoding

Axiom
IAO scope: EXACT
annotated target: SRP RNA encoding
annotated property: IAO_0000118
annotated source: SRP_RNA_encoding

minisatellite
type: Class
subclass of: satellite_DNA
IAO_0000115: A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp.
IAO id: SO:0000643
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/Minisatellite

Axiom
annotated target: A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp.
IAO xref: http://www.informatics.jax.org/silver/glossary.shtml
annotated property: IAO_0000115
annotated source: minisatellite

antisense_RNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: antisense_primary_transcript
IAO_0000115: Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA.
IAO id: SO:0000644
IAO subset: SOFA
IAO_0000118: antisense RNA
IAO xref: http://en.wikipedia.org/wiki/Antisense_RNA

Axiom
annotated target: Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: antisense_RNA

Axiom
IAO scope: EXACT
annotated target: antisense RNA
annotated property: IAO_0000118
annotated source: antisense_RNA

antisense_primary_transcript
type: Class
subclass of: primary_transcript
IAO id: SO:0000645
IAO subset: SOFA
IAO_0000115: The reverse complement of the primary transcript.
IAO_0000118: antisense primary transcript

Axiom
IAO xref: SO:ke
annotated target: The reverse complement of the primary transcript.
annotated property: IAO_0000115
annotated source: antisense_primary_transcript

Axiom
IAO scope: EXACT
annotated target: antisense primary transcript
annotated property: IAO_0000118
annotated source: antisense_primary_transcript

siRNA
type: Class
subclass of: ncRNA
IAO_0000115: A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules.
IAO id: SO:0000646
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/SiRNA
IAO_0000118: small interfering RNA

Axiom
annotated target: A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules.
IAO xref: PMID:12592000
annotated property: IAO_0000115
annotated source: siRNA

Axiom
IAO scope: EXACT
annotated target: small interfering RNA
annotated property: IAO_0000118
annotated source: siRNA

miRNA_primary_transcript
type: Class
subclass of: nc_primary_transcript
IAO_0000115: A primary transcript encoding a micro RNA.
IAO id: SO:0000647
IAO_0000118: miRNA primary transcript
IAO_0000118: micro RNA primary transcript

Axiom
IAO scope: EXACT
annotated target: miRNA primary transcript
annotated property: IAO_0000118
annotated source: miRNA_primary_transcript

Axiom
IAO scope: EXACT
annotated target: micro RNA primary transcript
annotated property: IAO_0000118
annotated source: miRNA_primary_transcript

Axiom
annotated target: A primary transcript encoding a micro RNA.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: miRNA_primary_transcript

stRNA_primary_transcript
type: Class
subclass of: miRNA_primary_transcript
IAO_0000115: A primary transcript encoding a small temporal mRNA (SO:0000649).
IAO id: SO:0000648
IAO_0000118: small temporal RNA primary transcript
IAO_0000118: stRNA primary transcript

Axiom
annotated target: A primary transcript encoding a small temporal mRNA (SO:0000649).
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: stRNA_primary_transcript

Axiom
IAO scope: EXACT
annotated target: small temporal RNA primary transcript
annotated property: IAO_0000118
annotated source: stRNA_primary_transcript

Axiom
IAO scope: EXACT
annotated target: stRNA primary transcript
annotated property: IAO_0000118
annotated source: stRNA_primary_transcript

stRNA
type: Class
subclass of: ncRNA
IAO_0000115: Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans.
IAO id: SO:0000649
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/StRNA
IAO_0000118: small temporal RNA

Axiom
annotated target: Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans.
IAO xref: PMID:11081512
annotated property: IAO_0000115
annotated source: stRNA

Axiom
IAO scope: EXACT
annotated target: small temporal RNA
annotated property: IAO_0000118
annotated source: stRNA

small_subunit_rRNA
type: Class
subclass of: rRNA
subclass of: Restriction
  on property: derives_from
  some values from: rRNA_small_subunit_primary_transcript
IAO_0000115: Ribosomal RNA transcript that structures the small subunit of the ribosome.
IAO id: SO:0000650
IAO subset: SOFA
IAO_0000118: SSU RNA
IAO_0000118: SSU rRNA
IAO_0000118: small subunit rRNA

Axiom
IAO scope: EXACT
IAO xref: RSC:cb
annotated target: SSU RNA
annotated property: IAO_0000118
annotated source: small_subunit_rRNA

Axiom
IAO scope: EXACT
annotated target: small subunit rRNA
annotated property: IAO_0000118
annotated source: small_subunit_rRNA

Axiom
IAO scope: EXACT
IAO xref: RSC:cb
annotated target: SSU rRNA
annotated property: IAO_0000118
annotated source: small_subunit_rRNA

Axiom
annotated target: Ribosomal RNA transcript that structures the small subunit of the ribosome.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: small_subunit_rRNA

large_subunit_rRNA
type: Class
subclass of: rRNA
subclass of: Restriction
  on property: derives_from
  some values from: rRNA_large_subunit_primary_transcript
IAO_0000118: LSU RNA
IAO_0000118: LSU rRNA
IAO_0000115: Ribosomal RNA transcript that structures the large subunit of the ribosome.
IAO id: SO:0000651
IAO subset: SOFA
IAO_0000118: large subunit rRNA

Axiom
IAO scope: EXACT
annotated target: large subunit rRNA
annotated property: IAO_0000118
annotated source: large_subunit_rRNA

Axiom
IAO scope: EXACT
annotated target: LSU rRNA
IAO xref: RSC:cb
annotated property: IAO_0000118
annotated source: large_subunit_rRNA

Axiom
annotated target: Ribosomal RNA transcript that structures the large subunit of the ribosome.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: large_subunit_rRNA

Axiom
IAO scope: EXACT
annotated target: LSU RNA
IAO xref: RSC:cb
annotated property: IAO_0000118
annotated source: large_subunit_rRNA

rRNA_5S
type: Class
subclass of: large_subunit_rRNA
IAO_0000118: 5S LSU rRNA
IAO_0000118: 5S rRNA
IAO_0000118: 5S ribosomal RNA
IAO_0000115: 5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription.
IAO id: SO:0000652
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/5S_ribosomal_RNA
IAO_0000118: rRNA 5S

Axiom
annotated target: 5S ribosomal RNA
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: rRNA_5S

Axiom
annotated target: 5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription.
IAO xref: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc
annotated property: IAO_0000115
annotated source: rRNA_5S

Axiom
IAO scope: EXACT
annotated target: rRNA 5S
annotated property: IAO_0000118
annotated source: rRNA_5S

Axiom
annotated target: 5S rRNA
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: rRNA_5S

Axiom
annotated target: 5S LSU rRNA
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: rRNA_5S

rRNA_28S
type: Class
subclass of: large_subunit_rRNA
IAO_0000118: 28S LSU rRNA
IAO_0000118: 28S rRNA
IAO_0000118: 28S ribosomal RNA
IAO_0000115: A component of the large ribosomal subunit.
IAO id: SO:0000653
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/28S_ribosomal_RNA
IAO_0000118: rRNA 28S

Axiom
annotated target: A component of the large ribosomal subunit.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: rRNA_28S

Axiom
IAO scope: EXACT
annotated target: rRNA 28S
annotated property: IAO_0000118
annotated source: rRNA_28S

Axiom
annotated target: 28S rRNA
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: rRNA_28S

Axiom
annotated target: 28S ribosomal RNA
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: rRNA_28S

Axiom
annotated target: 28S LSU rRNA
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: rRNA_28S

maxicircle_gene
type: Class
equivalent class: Class
  intersection of: kinetoplast_gene
  intersection of: Restriction
    on property: part_of
    some values from: maxicircle
subclass of: kinetoplast_gene
IAO_0000115: A mitochondrial gene located in a maxicircle.
IAO id: SO:0000654
IAO_0000118: maxi-circle gene
IAO_0000118: maxicircle gene

Axiom
IAO scope: EXACT
annotated target: maxi-circle gene
annotated property: IAO_0000118
annotated source: maxicircle_gene

Axiom
IAO scope: EXACT
annotated target: maxicircle gene
annotated property: IAO_0000118
annotated source: maxicircle_gene

Axiom
annotated target: A mitochondrial gene located in a maxicircle.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: maxicircle_gene

ncRNA
type: Class
subclass of: mature_transcript
comment: A ncRNA is a processed_transcript, so it may not contain parts such as transcribed_spacer_regions that are removed in the act of processing. For the corresponding primary_transcripts, please see term SO:0000483 nc_primary_transcript.
IAO_0000115: An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.
IAO id: SO:0000655
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/NcRNA
IAO_0000118: noncoding RNA

Axiom
IAO scope: EXACT
annotated target: noncoding RNA
annotated property: IAO_0000118
annotated source: ncRNA

Axiom
annotated target: An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: ncRNA

stRNA_encoding
type: Class
subclass of: non_protein_coding
IAO id: SO:0000656
IAO_0000118: stRNA encoding

Axiom
IAO scope: EXACT
annotated target: stRNA encoding
annotated property: IAO_0000118
annotated source: stRNA_encoding

repeat_region
type: Class
subclass of: SO_0001411
subclass of: Restriction
  on property: has_part
  some values from: repeat_unit
IAO_0000115: A region of sequence containing one or more repeat units.
IAO id: SO:0000657
IAO subset: SOFA
IAO_0000118: repeat region

Axiom
annotated target: A region of sequence containing one or more repeat units.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: repeat_region

Axiom
IAO scope: EXACT
annotated target: repeat region
annotated property: IAO_0000118
annotated source: repeat_region

dispersed_repeat
type: Class
subclass of: repeat_region
IAO_0000115: A repeat that is located at dispersed sites in the genome.
IAO id: SO:0000658
IAO subset: SOFA
IAO_0000118: dispersed repeat
IAO xref: http://en.wikipedia.org/wiki/Interspersed_repeat
IAO_0000118: interspersed repeat

Axiom
IAO scope: EXACT
annotated target: dispersed repeat
annotated property: IAO_0000118
annotated source: dispersed_repeat

Axiom
annotated target: A repeat that is located at dispersed sites in the genome.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: dispersed_repeat

Axiom
IAO scope: EXACT
annotated target: interspersed repeat
annotated property: IAO_0000118
annotated source: dispersed_repeat

tmRNA_encoding
type: Class
subclass of: non_protein_coding
IAO id: SO:0000659
IAO_0000118: tmRNA encoding

Axiom
IAO scope: EXACT
annotated target: tmRNA encoding
annotated property: IAO_0000118
annotated source: tmRNA_encoding

DNA_invertase_target_sequence
type: Class
IAO id: SO:0000660
deprecated: true

intron_attribute
type: Class
IAO id: SO:0000661
deprecated: true

spliceosomal_intron
type: Class
subclass of: intron
IAO_0000115: An intron which is spliced by the spliceosome.
comment: GO:0000398.
IAO id: SO:0000662
IAO subset: SOFA
IAO_0000118: spliceosomal intron

Axiom
IAO scope: EXACT
annotated target: spliceosomal intron
annotated property: IAO_0000118
annotated source: spliceosomal_intron

Axiom
annotated target: An intron which is spliced by the spliceosome.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: spliceosomal_intron

tRNA_encoding
type: Class
subclass of: non_protein_coding
IAO id: SO:0000663
IAO_0000118: tRNA encoding

Axiom
IAO scope: EXACT
annotated target: tRNA encoding
annotated property: IAO_0000118
annotated source: tRNA_encoding

introgressed_chromosome_region
type: Class
subclass of: chromosome_part
IAO id: SO:0000664
IAO_0000118: introgressed chromosome region

Axiom
IAO scope: EXACT
annotated target: introgressed chromosome region
annotated property: IAO_0000118
annotated source: introgressed_chromosome_region

monocistronic_transcript
type: Class
equivalent class: Class
  intersection of: transcript
  intersection of: Restriction
    on property: has_quality
    some values from: monocistronic
subclass of: transcript
IAO_0000115: A transcript that is monocistronic.
IAO id: SO:0000665
IAO_0000118: monocistronic transcript

Axiom
IAO scope: EXACT
annotated target: monocistronic transcript
annotated property: IAO_0000118
annotated source: monocistronic_transcript

Axiom
annotated target: A transcript that is monocistronic.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: monocistronic_transcript

mobile_intron
type: Class
equivalent class: Class
  intersection of: intron
  intersection of: Restriction
    on property: has_quality
    some values from: mobile
subclass of: intron
subclass of: mobile_genetic_element
IAO_0000115: An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility.
IAO id: SO:0000666
IAO_0000118: mobile intron

Axiom
annotated target: An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: mobile_intron

Axiom
IAO scope: EXACT
annotated target: mobile intron
annotated property: IAO_0000118
annotated source: mobile_intron

insertion
type: Class
subclass of: sequence_alteration
subclass of: SO_0001411
IAO subset: DBVAR
IAO id: SO:0000667
IAO alt id: SO:1000034
IAO subset: SOFA
IAO_0000115: The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence.
IAO_0000118: insertion
IAO_0000118: nucleotide insertion
IAO_0000118: nucleotide_insertion

Axiom
IAO scope: EXACT
annotated target: nucleotide insertion
annotated property: IAO_0000118
annotated source: insertion

Axiom
IAO scope: EXACT
IAO type: dbvar
IAO xref: http://www.ncbi.nlm.nih.gov/dbvar/
annotated target: insertion
annotated property: IAO_0000118
annotated source: insertion

Axiom
IAO xref: SO:ke
annotated target: The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence.
annotated property: IAO_0000115
annotated source: insertion

Axiom
IAO scope: EXACT
annotated target: nucleotide_insertion
annotated property: IAO_0000118
annotated source: insertion

EST_match
type: Class
subclass of: expressed_sequence_match
IAO_0000115: A match against an EST sequence.
IAO_0000118: EST match
IAO id: SO:0000668
IAO subset: SOFA

Axiom
annotated target: EST match
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: EST_match

Axiom
annotated target: A match against an EST sequence.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: EST_match

sequence_rearrangement_feature
type: Class
subclass of: recombination_feature
IAO id: SO:0000669
IAO_0000118: sequence rearrangement feature

Axiom
IAO scope: EXACT
annotated target: sequence rearrangement feature
annotated property: IAO_0000118
annotated source: sequence_rearrangement_feature

chromosome_breakage_sequence
type: Class
subclass of: sequence_rearrangement_feature
IAO_0000115: A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation.
IAO id: SO:0000670
IAO_0000118: chromosome breakage sequence

Axiom
IAO scope: EXACT
annotated target: chromosome breakage sequence
annotated property: IAO_0000118
annotated source: chromosome_breakage_sequence

Axiom
annotated target: A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: chromosome_breakage_sequence

internal_eliminated_sequence
type: Class
subclass of: sequence_rearrangement_feature
IAO_0000115: A sequence eliminated from the genome of ciliates during nuclear differentiation.
IAO id: SO:0000671
IAO_0000118: internal eliminated sequence

Axiom
IAO scope: EXACT
annotated target: internal eliminated sequence
annotated property: IAO_0000118
annotated source: internal_eliminated_sequence

Axiom
annotated target: A sequence eliminated from the genome of ciliates during nuclear differentiation.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: internal_eliminated_sequence

macronucleus_destined_segment
type: Class
subclass of: sequence_rearrangement_feature
IAO_0000115: A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome.
IAO id: SO:0000672
IAO_0000118: macronucleus destined segment

Axiom
IAO scope: EXACT
annotated target: macronucleus destined segment
annotated property: IAO_0000118
annotated source: macronucleus_destined_segment

Axiom
annotated target: A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: macronucleus_destined_segment

transcript
type: Class
subclass of: gene_member_region
IAO_0000115: An RNA synthesized on a DNA or RNA template by an RNA polymerase.
IAO id: SO:0000673
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/RNA

Axiom
annotated target: An RNA synthesized on a DNA or RNA template by an RNA polymerase.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: transcript

non_canonical_splice_site
type: Class
IAO_0000115: A splice site where the donor and acceptor sites differ from the canonical form.
IAO id: SO:0000674
IAO consider: SO:0000678
IAO consider: SO:0000679
IAO_0000118: non canonical splice site
IAO_0000118: non-canonical splice site
deprecated: true

Axiom
IAO scope: EXACT
annotated target: non-canonical splice site
annotated property: IAO_0000118
annotated source: non_canonical_splice_site

Axiom
annotated target: A splice site where the donor and acceptor sites differ from the canonical form.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: non_canonical_splice_site

Axiom
IAO scope: EXACT
annotated target: non canonical splice site
annotated property: IAO_0000118
annotated source: non_canonical_splice_site

canonical_splice_site
type: Class
IAO id: SO:0000675
IAO consider: SO:0000676
IAO consider: SO:0000677
IAO_0000115: The major class of splice site with dinucleotides GT and AG for donor and acceptor sites, respectively.
IAO_0000118: canonical splice site
deprecated: true

Axiom
IAO xref: SO:ke
annotated target: The major class of splice site with dinucleotides GT and AG for donor and acceptor sites, respectively.
annotated property: IAO_0000115
annotated source: canonical_splice_site

Axiom
IAO scope: EXACT
annotated target: canonical splice site
annotated property: IAO_0000118
annotated source: canonical_splice_site

canonical_three_prime_splice_site
type: Class
subclass of: three_prime_cis_splice_site
IAO id: SO:0000676
IAO_0000115: The canonical 3' splice site has the sequence \"AG\".
IAO_0000118: canonical 3' splice site
IAO_0000118: canonical three prime splice site

Axiom
IAO scope: EXACT
annotated target: canonical 3' splice site
annotated property: IAO_0000118
annotated source: canonical_three_prime_splice_site

Axiom
IAO scope: EXACT
annotated target: canonical three prime splice site
annotated property: IAO_0000118
annotated source: canonical_three_prime_splice_site

Axiom
IAO xref: SO:ke
annotated target: The canonical 3' splice site has the sequence \"AG\".
annotated property: IAO_0000115
annotated source: canonical_three_prime_splice_site

canonical_five_prime_splice_site
type: Class
subclass of: five_prime_cis_splice_site
IAO id: SO:0000677
IAO_0000115: The canonical 5' splice site has the sequence \"GT\".
IAO_0000118: canonical 5' splice site
IAO_0000118: canonical five prime splice site

Axiom
IAO scope: EXACT
annotated target: canonical five prime splice site
annotated property: IAO_0000118
annotated source: canonical_five_prime_splice_site

Axiom
IAO xref: SO:ke
annotated target: The canonical 5' splice site has the sequence \"GT\".
annotated property: IAO_0000115
annotated source: canonical_five_prime_splice_site

Axiom
IAO scope: EXACT
annotated target: canonical 5' splice site
annotated property: IAO_0000118
annotated source: canonical_five_prime_splice_site

non_canonical_three_prime_splice_site
type: Class
subclass of: three_prime_cis_splice_site
IAO_0000115: A 3' splice site that does not have the sequence \"AG\".
IAO id: SO:0000678
IAO_0000118: non canonical 3' splice site
IAO_0000118: non canonical three prime splice site
IAO_0000118: non-canonical three prime splice site

Axiom
IAO scope: EXACT
annotated target: non-canonical three prime splice site
annotated property: IAO_0000118
annotated source: non_canonical_three_prime_splice_site

Axiom
IAO scope: RELATED
annotated target: non canonical 3' splice site
annotated property: IAO_0000118
annotated source: non_canonical_three_prime_splice_site

Axiom
IAO scope: EXACT
annotated target: non canonical three prime splice site
annotated property: IAO_0000118
annotated source: non_canonical_three_prime_splice_site

Axiom
annotated target: A 3' splice site that does not have the sequence \"AG\".
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: non_canonical_three_prime_splice_site

non_canonical_five_prime_splice_site
type: Class
subclass of: five_prime_cis_splice_site
IAO_0000115: A 5' splice site which does not have the sequence \"GT\".
IAO id: SO:0000679
IAO_0000118: non canonical 5' splice site
IAO_0000118: non canonical five prime splice site
IAO_0000118: non-canonical five prime splice site

Axiom
annotated target: A 5' splice site which does not have the sequence \"GT\".
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: non_canonical_five_prime_splice_site

Axiom
IAO scope: EXACT
annotated target: non-canonical five prime splice site
annotated property: IAO_0000118
annotated source: non_canonical_five_prime_splice_site

Axiom
IAO scope: EXACT
annotated target: non canonical 5' splice site
annotated property: IAO_0000118
annotated source: non_canonical_five_prime_splice_site

Axiom
IAO scope: EXACT
annotated target: non canonical five prime splice site
annotated property: IAO_0000118
annotated source: non_canonical_five_prime_splice_site

non_canonical_start_codon
type: Class
subclass of: start_codon
IAO_0000115: A start codon that is not the usual AUG sequence.
IAO id: SO:0000680
IAO_0000118: non ATG start codon
IAO_0000118: non canonical start codon
IAO_0000118: non-canonical start codon

Axiom
IAO scope: EXACT
annotated target: non canonical start codon
annotated property: IAO_0000118
annotated source: non_canonical_start_codon

Axiom
IAO scope: EXACT
annotated target: non ATG start codon
annotated property: IAO_0000118
annotated source: non_canonical_start_codon

Axiom
annotated target: A start codon that is not the usual AUG sequence.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: non_canonical_start_codon

Axiom
IAO scope: EXACT
annotated target: non-canonical start codon
annotated property: IAO_0000118
annotated source: non_canonical_start_codon

aberrant_processed_transcript
type: Class
subclass of: transcript
IAO_0000115: A transcript that has been processed \"incorrectly\", for example by the failure of splicing of one or more exons.
IAO id: SO:0000681
IAO_0000118: aberrant processed transcript

Axiom
IAO scope: EXACT
annotated target: aberrant processed transcript
annotated property: IAO_0000118
annotated source: aberrant_processed_transcript

Axiom
annotated target: A transcript that has been processed \"incorrectly\", for example by the failure of splicing of one or more exons.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: aberrant_processed_transcript

splicing_feature
type: Class
IAO id: SO:0000682
deprecated: true

exonic_splice_enhancer
type: Class
subclass of: splice_enhancer
IAO_0000115: Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron.
IAO id: SO:0000683
IAO_0000118: exonic splice enhancer

Axiom
IAO scope: EXACT
annotated target: exonic splice enhancer
annotated property: IAO_0000118
annotated source: exonic_splice_enhancer

Axiom
annotated target: Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron.
IAO xref: http://www.ncbi.nlm.nih.gov\:80/entrez/query.fcgi
annotated property: IAO_0000115
annotated source: exonic_splice_enhancer

nuclease_sensitive_site
type: Class
subclass of: nuclease_binding_site
IAO_0000115: A region of nucleotide sequence targeted by a nuclease enzyme.
IAO id: SO:0000684
IAO subset: SOFA
IAO_0000118: nuclease sensitive site

Axiom
annotated target: A region of nucleotide sequence targeted by a nuclease enzyme.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: nuclease_sensitive_site

Axiom
IAO scope: EXACT
annotated target: nuclease sensitive site
annotated property: IAO_0000118
annotated source: nuclease_sensitive_site

DNAseI_hypersensitive_site
type: Class
subclass of: nuclease_hypersensitive_site
IAO_0000118: DHS
IAO_0000118: DNAseI hypersensitive site
IAO id: SO:0000685

Axiom
annotated target: DNAseI hypersensitive site
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DNAseI_hypersensitive_site

Axiom
annotated target: DHS
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DNAseI_hypersensitive_site

translocation_element
type: Class
subclass of: SO_1000044
IAO_0000115: A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations.
IAO id: SO:0000686
IAO_0000118: translocation element

Axiom
annotated target: A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: translocation_element

Axiom
IAO scope: EXACT
annotated target: translocation element
annotated property: IAO_0000118
annotated source: translocation_element

deletion_junction
type: Class
subclass of: junction
IAO id: SO:0000687
IAO subset: SOFA
IAO_0000115: The space between two bases in a sequence which marks the position where a deletion has occurred.
IAO_0000118: deletion junction

Axiom
IAO scope: EXACT
annotated target: deletion junction
annotated property: IAO_0000118
annotated source: deletion_junction

Axiom
IAO xref: SO:ke
annotated target: The space between two bases in a sequence which marks the position where a deletion has occurred.
annotated property: IAO_0000115
annotated source: deletion_junction

golden_path
type: Class
subclass of: sequence_assembly
IAO_0000115: A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence.
IAO id: SO:0000688
IAO subset: SOFA
IAO_0000118: golden path

Axiom
annotated target: A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence.
IAO xref: SO:ls
annotated property: IAO_0000115
annotated source: golden_path

Axiom
IAO scope: EXACT
annotated target: golden path
annotated property: IAO_0000118
annotated source: golden_path

cDNA_match
type: Class
subclass of: expressed_sequence_match
IAO_0000115: A match against cDNA sequence.
IAO id: SO:0000689
IAO subset: SOFA
IAO_0000118: cDNA match

Axiom
annotated target: A match against cDNA sequence.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: cDNA_match

Axiom
IAO scope: EXACT
annotated target: cDNA match
annotated property: IAO_0000118
annotated source: cDNA_match

gene_with_polycistronic_transcript
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: transcribed_to
    some values from: polycistronic_transcript
subclass of: gene
IAO_0000115: A gene that encodes a polycistronic transcript.
IAO id: SO:0000690
IAO_0000118: gene with polycistronic transcript

Axiom
annotated target: A gene that encodes a polycistronic transcript.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: gene_with_polycistronic_transcript

Axiom
IAO scope: EXACT
annotated target: gene with polycistronic transcript
annotated property: IAO_0000118
annotated source: gene_with_polycistronic_transcript

cleaved_initiator_methionine
type: Class
subclass of: SO_0100011
IAO alt id: BS:00067
IAO id: SO:0000691
IAO_0000115: The initiator methionine that has been cleaved from a mature polypeptide sequence.
IAO subset: biosapiens
IAO_0000118: cleaved initiator methionine
IAO_0000118: init_met
IAO_0000118: initiator methionine

Axiom
IAO xref: EBIBS:GAR
annotated target: The initiator methionine that has been cleaved from a mature polypeptide sequence.
annotated property: IAO_0000115
annotated source: cleaved_initiator_methionine

Axiom
IAO scope: EXACT
annotated target: cleaved initiator methionine
annotated property: IAO_0000118
annotated source: cleaved_initiator_methionine

Axiom
IAO scope: RELATED
annotated target: initiator methionine
annotated property: IAO_0000118
annotated source: cleaved_initiator_methionine

Axiom
IAO scope: RELATED
annotated target: init_met
IAO xref: uniprot:feature_type
annotated property: IAO_0000118
annotated source: cleaved_initiator_methionine

gene_with_dicistronic_transcript
type: Class
equivalent class: Class
  intersection of: gene_with_polycistronic_transcript
  intersection of: Restriction
    on property: transcribed_to
    some values from: dicistronic_transcript
subclass of: gene_with_polycistronic_transcript
IAO_0000115: A gene that encodes a dicistronic transcript.
IAO id: SO:0000692
IAO_0000118: gene with dicistronic transcript

Axiom
IAO scope: EXACT
annotated target: gene with dicistronic transcript
annotated property: IAO_0000118
annotated source: gene_with_dicistronic_transcript

Axiom
annotated target: A gene that encodes a dicistronic transcript.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: gene_with_dicistronic_transcript

gene_with_recoded_mRNA
type: Class
equivalent class: Class
  intersection of: protein_coding_gene
  intersection of: Restriction
    on property: has_quality
    some values from: recoded
subclass of: protein_coding_gene
IAO_0000115: A gene that encodes an mRNA that is recoded.
IAO id: SO:0000693
IAO_0000118: gene with recoded mRNA

Axiom
IAO scope: EXACT
annotated target: gene with recoded mRNA
annotated property: IAO_0000118
annotated source: gene_with_recoded_mRNA

Axiom
annotated target: A gene that encodes an mRNA that is recoded.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: gene_with_recoded_mRNA

SNP
type: Class
subclass of: SO_0001483
IAO_0000115: SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater.
IAO id: SO:0000694
IAO subset: SOFA
IAO_0000118: single nucleotide polymorphism

Axiom
IAO scope: EXACT
annotated target: single nucleotide polymorphism
annotated property: IAO_0000118
annotated source: SNP

Axiom
annotated target: SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater.
IAO xref: SO:cb
annotated property: IAO_0000115
annotated source: SNP

reagent
type: Class
subclass of: SO_0001409
IAO_0000115: A sequence used in experiment.
comment: Requested by Lynn Crosby, jan 2006.
IAO id: SO:0000695
IAO subset: SOFA

Axiom
annotated target: A sequence used in experiment.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: reagent

oligo
type: Class
subclass of: reagent
IAO_0000115: A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded.
IAO id: SO:0000696
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/Oligonucleotide
IAO_0000118: oligonucleotide

Axiom
IAO scope: EXACT
annotated target: oligonucleotide
annotated property: IAO_0000118
annotated source: oligo

Axiom
annotated target: A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: oligo

gene_with_stop_codon_read_through
type: Class
equivalent class: Class
  intersection of: gene_with_recoded_mRNA
  intersection of: Restriction
    on property: has_part
    some values from: stop_codon_read_through
subclass of: gene_with_recoded_mRNA
IAO_0000115: A gene that encodes a transcript with stop codon readthrough.
IAO id: SO:0000697
IAO_0000118: gene with stop codon read through

Axiom
IAO scope: EXACT
annotated target: gene with stop codon read through
annotated property: IAO_0000118
annotated source: gene_with_stop_codon_read_through

Axiom
annotated target: A gene that encodes a transcript with stop codon readthrough.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: gene_with_stop_codon_read_through

gene_with_stop_codon_redefined_as_pyrrolysine
type: Class
equivalent class: Class
  intersection of: gene_with_recoded_mRNA
  intersection of: Restriction
    on property: has_part
    some values from: stop_codon_redefined_as_pyrrolysine
subclass of: gene_with_stop_codon_read_through
IAO_0000115: A gene encoding an mRNA that has the stop codon redefined as pyrrolysine.
IAO id: SO:0000698
IAO_0000118: gene with stop codon redefined as pyrrolysine

Axiom
annotated target: A gene encoding an mRNA that has the stop codon redefined as pyrrolysine.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: gene_with_stop_codon_redefined_as_pyrrolysine

Axiom
IAO scope: EXACT
annotated target: gene with stop codon redefined as pyrrolysine
annotated property: IAO_0000118
annotated source: gene_with_stop_codon_redefined_as_pyrrolysine

junction
type: Class
subclass of: sequence_feature
comment: A junction is a boundary between regions. A boundary has an extent of zero.
IAO_0000115: A sequence_feature with an extent of zero.
IAO id: SO:0000699
IAO subset: SOFA
IAO_0000118: boundary
IAO_0000118: breakpoint

Axiom
IAO scope: EXACT
annotated target: breakpoint
annotated property: IAO_0000118
annotated source: junction

Axiom
annotated target: A sequence_feature with an extent of zero.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: junction

Axiom
IAO scope: EXACT
annotated target: boundary
annotated property: IAO_0000118
annotated source: junction

remark
type: Class
subclass of: SO_0001410
IAO_0000115: A comment about the sequence.
IAO id: SO:0000700
IAO subset: SOFA

Axiom
annotated target: A comment about the sequence.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: remark

possible_base_call_error
type: Class
subclass of: sequence_difference
IAO_0000115: A region of sequence where the validity of the base calling is questionable.
IAO id: SO:0000701
IAO subset: SOFA
IAO_0000118: possible base call error

Axiom
annotated target: A region of sequence where the validity of the base calling is questionable.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: possible_base_call_error

Axiom
IAO scope: EXACT
annotated target: possible base call error
annotated property: IAO_0000118
annotated source: possible_base_call_error

possible_assembly_error
type: Class
subclass of: sequence_difference
IAO_0000115: A region of sequence where there may have been an error in the assembly.
IAO id: SO:0000702
IAO subset: SOFA
IAO_0000118: possible assembly error

Axiom
annotated target: A region of sequence where there may have been an error in the assembly.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: possible_assembly_error

Axiom
IAO scope: EXACT
annotated target: possible assembly error
annotated property: IAO_0000118
annotated source: possible_assembly_error

experimental_result_region
type: Class
subclass of: remark
IAO_0000115: A region of sequence implicated in an experimental result.
IAO id: SO:0000703
IAO subset: SOFA
IAO_0000118: experimental result region

Axiom
annotated target: A region of sequence implicated in an experimental result.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: experimental_result_region

Axiom
IAO scope: EXACT
annotated target: experimental result region
annotated property: IAO_0000118
annotated source: experimental_result_region

gene
type: Class
subclass of: SO_0001411
subclass of: Restriction
  on property: member_of
  some values from: SO_0005855
IAO_0000115: A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.
IAO id: SO:0000704
IAO subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance.
IAO xref: http://en.wikipedia.org/wiki/Gene

Axiom
annotated target: A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.
IAO xref: SO:immuno_workshop
annotated property: IAO_0000115
annotated source: gene

tandem_repeat
type: Class
subclass of: repeat_region
IAO id: SO:0000705
IAO subset: SOFA
IAO_0000115: Two or more adjcent copies of a region (of length greater than 1).
IAO xref: http://en.wikipedia.org/wiki/Tandem_repeat
IAO xref: http://www.sci.sdsu.edu/~smaloy/Glossary/T.html
IAO_0000118: tandem repeat

Axiom
IAO xref: SO:ke
annotated target: Two or more adjcent copies of a region (of length greater than 1).
annotated property: IAO_0000115
annotated source: tandem_repeat

Axiom
IAO scope: EXACT
annotated target: tandem repeat
annotated property: IAO_0000118
annotated source: tandem_repeat

trans_splice_acceptor_site
type: Class
subclass of: SO_0001420
IAO_0000118: 3' trans splice site
IAO id: SO:0000706
IAO subset: SOFA
IAO_0000115: The 3' splice site of the acceptor primary transcript.
comment: This region contains a polypyridine tract and AG dinucleotide in some organisms and is UUUCAG in C. elegans.
IAO_0000118: trans splice acceptor site

Axiom
annotated target: 3' trans splice site
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: trans_splice_acceptor_site

Axiom
IAO scope: EXACT
annotated target: trans splice acceptor site
annotated property: IAO_0000118
annotated source: trans_splice_acceptor_site

Axiom
IAO xref: SO:ke
annotated target: The 3' splice site of the acceptor primary transcript.
annotated property: IAO_0000115
annotated source: trans_splice_acceptor_site

trans_splice_donor_site
type: Class
subclass of: SO_0001420
IAO_0000118: 5 prime trans splice site
comment: SL RNA contains a donor site.
IAO id: SO:0000707
IAO_0000115: The 5' five prime splice site region of the donor RNA.
IAO_0000118: trans splice donor site
IAO_0000118: trans-splice donor site

Axiom
IAO xref: SO:ke
annotated target: The 5' five prime splice site region of the donor RNA.
annotated property: IAO_0000115
annotated source: trans_splice_donor_site

Axiom
IAO scope: EXACT
annotated target: trans splice donor site
annotated property: IAO_0000118
annotated source: trans_splice_donor_site

Axiom
annotated target: 5 prime trans splice site
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: trans_splice_donor_site

Axiom
IAO scope: EXACT
annotated target: trans-splice donor site
annotated property: IAO_0000118
annotated source: trans_splice_donor_site

SL1_acceptor_site
type: Class
subclass of: trans_splice_acceptor_site
IAO_0000115: A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs.
IAO_0000118: SL1 acceptor site
IAO id: SO:0000708

Axiom
IAO scope: EXACT
annotated target: SL1 acceptor site
annotated property: IAO_0000118
annotated source: SL1_acceptor_site

Axiom
annotated target: A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs.
IAO xref: SO:nlw
annotated property: IAO_0000115
annotated source: SL1_acceptor_site

SL2_acceptor_site
type: Class
subclass of: trans_splice_acceptor_site
IAO_0000115: A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts.
IAO_0000118: SL2 acceptor site
IAO id: SO:0000709

Axiom
IAO scope: EXACT
annotated target: SL2 acceptor site
annotated property: IAO_0000118
annotated source: SL2_acceptor_site

Axiom
annotated target: A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts.
IAO xref: SO:nlw
annotated property: IAO_0000115
annotated source: SL2_acceptor_site

gene_with_stop_codon_redefined_as_selenocysteine
type: Class
equivalent class: Class
  intersection of: gene_with_stop_codon_read_through
  intersection of: Restriction
    on property: has_part
    some values from: stop_codon_redefined_as_selenocysteine
subclass of: gene_with_stop_codon_read_through
IAO_0000115: A gene encoding an mRNA that has the stop codon redefined as selenocysteine.
IAO id: SO:0000710
IAO_0000118: gene with stop codon redefined as selenocysteine

Axiom
IAO scope: EXACT
annotated target: gene with stop codon redefined as selenocysteine
annotated property: IAO_0000118
annotated source: gene_with_stop_codon_redefined_as_selenocysteine

Axiom
annotated target: A gene encoding an mRNA that has the stop codon redefined as selenocysteine.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: gene_with_stop_codon_redefined_as_selenocysteine

gene_with_mRNA_recoded_by_translational_bypass
type: Class
equivalent class: Class
  intersection of: protein_coding_gene
  intersection of: Restriction
    on property: has_quality
    some values from: recoded_by_translational_bypass
subclass of: gene_with_recoded_mRNA
IAO_0000115: A gene with mRNA recoded by translational bypass.
IAO id: SO:0000711
IAO_0000118: gene with mRNA recoded by translational bypass

Axiom
annotated target: A gene with mRNA recoded by translational bypass.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: gene_with_mRNA_recoded_by_translational_bypass

Axiom
IAO scope: EXACT
annotated target: gene with mRNA recoded by translational bypass
annotated property: IAO_0000118
annotated source: gene_with_mRNA_recoded_by_translational_bypass

gene_with_transcript_with_translational_frameshift
type: Class
equivalent class: Class
  intersection of: gene_with_recoded_mRNA
  intersection of: Restriction
    on property: has_quality
    some values from: translationally_frameshifted
subclass of: gene_with_recoded_mRNA
IAO_0000115: A gene encoding a transcript that has a translational frameshift.
IAO id: SO:0000712
IAO_0000118: gene with transcript with translational frameshift

Axiom
annotated target: A gene encoding a transcript that has a translational frameshift.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: gene_with_transcript_with_translational_frameshift

Axiom
IAO scope: EXACT
annotated target: gene with transcript with translational frameshift
annotated property: IAO_0000118
annotated source: gene_with_transcript_with_translational_frameshift

DNA_motif
type: Class
subclass of: nucleotide_motif
IAO_0000115: A motif that is active in the DNA form of the sequence.
IAO_0000118: DNA motif
IAO id: SO:0000713
IAO xref: http://en.wikipedia.org/wiki/DNA_motif

Axiom
annotated target: DNA motif
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DNA_motif

Axiom
annotated target: A motif that is active in the DNA form of the sequence.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: DNA_motif

nucleotide_motif
type: Class
subclass of: SO_0001683
IAO_0000115: A region of nucleotide sequence corresponding to a known motif.
IAO id: SO:0000714
IAO subset: SOFA
IAO_0000118: nucleotide motif

Axiom
IAO scope: EXACT
annotated target: nucleotide motif
annotated property: IAO_0000118
annotated source: nucleotide_motif

Axiom
annotated target: A region of nucleotide sequence corresponding to a known motif.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: nucleotide_motif

RNA_motif
type: Class
subclass of: nucleotide_motif
IAO_0000115: A motif that is active in RNA sequence.
IAO_0000118: RNA motif
IAO id: SO:0000715
IAO subset: SOFA

Axiom
annotated target: A motif that is active in RNA sequence.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: RNA_motif

Axiom
IAO scope: EXACT
annotated target: RNA motif
annotated property: IAO_0000118
annotated source: RNA_motif

dicistronic_mRNA
type: Class
equivalent class: Class
  intersection of: mRNA
  intersection of: Restriction
    on property: has_quality
    some values from: dicistronic
subclass of: dicistronic_transcript
subclass of: polycistronic_mRNA
IAO_0000115: An mRNA that has the quality dicistronic.
IAO id: SO:0000716
IAO_0000118: dicistronic mRNA
IAO_0000118: dicistronic processed transcript

Axiom
IAO scope: EXACT
annotated target: dicistronic mRNA
annotated property: IAO_0000118
annotated source: dicistronic_mRNA

Axiom
annotated target: An mRNA that has the quality dicistronic.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: dicistronic_mRNA

Axiom
IAO scope: RELATED
annotated target: dicistronic processed transcript
annotated property: IAO_0000118
annotated source: dicistronic_mRNA

reading_frame
type: Class
subclass of: SO_0001410
IAO_0000115: A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon.
IAO id: SO:0000717
IAO subset: SOFA
comment: This term was added after a request by SGD. August 2004. Modified after SO meeting in Cambridge to not include start or stop.
IAO xref: http://en.wikipedia.org/wiki/Reading_frame
IAO_0000118: reading frame

Axiom
annotated target: A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon.
IAO xref: SGD:rb
annotated property: IAO_0000115
annotated source: reading_frame

Axiom
IAO scope: EXACT
annotated target: reading frame
annotated property: IAO_0000118
annotated source: reading_frame

blocked_reading_frame
type: Class
subclass of: reading_frame
IAO_0000115: A reading_frame that is interrupted by one or more stop codons; usually identified through intergenomic sequence comparisons.
IAO id: SO:0000718
comment: Term requested by Rama from SGD.
IAO_0000118: blocked reading frame

Axiom
IAO scope: EXACT
annotated target: blocked reading frame
annotated property: IAO_0000118
annotated source: blocked_reading_frame

Axiom
annotated target: A reading_frame that is interrupted by one or more stop codons; usually identified through intergenomic sequence comparisons.
IAO xref: SGD:rb
annotated property: IAO_0000115
annotated source: blocked_reading_frame

ultracontig
type: Class
subclass of: sequence_assembly
IAO_0000115: An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers.
IAO id: SO:0000719
IAO subset: SOFA
IAO_0000118: superscaffold

Axiom
IAO scope: RELATED
annotated target: superscaffold
annotated property: IAO_0000118
annotated source: ultracontig

Axiom
annotated target: An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers.
IAO xref: FB:WG
annotated property: IAO_0000115
annotated source: ultracontig

foreign_transposable_element
type: Class
equivalent class: Class
  intersection of: transposable_element
  intersection of: Restriction
    on property: has_quality
    some values from: foreign
subclass of: transposable_element
IAO_0000115: A transposable element that is foreign.
IAO id: SO:0000720
IAO_0000118: foreign transposable element
comment: requested by Michael on 19 Nov 2004.

Axiom
annotated target: A transposable element that is foreign.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: foreign_transposable_element

Axiom
IAO scope: EXACT
annotated target: foreign transposable element
annotated property: IAO_0000118
annotated source: foreign_transposable_element

gene_with_dicistronic_primary_transcript
type: Class
equivalent class: Class
  intersection of: gene_with_dicistronic_transcript
  intersection of: Restriction
    on property: transcribed_to
    some values from: SO_1001197
subclass of: gene_with_dicistronic_transcript
IAO_0000115: A gene that encodes a dicistronic primary transcript.
comment: Requested by Michael, 19 nov 2004.
IAO id: SO:0000721
IAO_0000118: gene with dicistronic primary transcript

Axiom
IAO scope: EXACT
annotated target: gene with dicistronic primary transcript
annotated property: IAO_0000118
annotated source: gene_with_dicistronic_primary_transcript

Axiom
annotated target: A gene that encodes a dicistronic primary transcript.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: gene_with_dicistronic_primary_transcript

gene_with_dicistronic_mRNA
type: Class
equivalent class: Class
  intersection of: gene_with_dicistronic_transcript
  intersection of: Restriction
    on property: transcribed_to
    some values from: dicistronic_mRNA
subclass of: gene_with_dicistronic_transcript
IAO_0000115: A gene that encodes a polycistronic mRNA.
comment: Requested by MA nov 19 2004.
IAO id: SO:0000722
IAO_0000118: gene with dicistronic mRNA
IAO_0000118: gene with dicistronic processed transcript

Axiom
annotated target: A gene that encodes a polycistronic mRNA.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: gene_with_dicistronic_mRNA

Axiom
IAO scope: EXACT
annotated target: gene with dicistronic processed transcript
annotated property: IAO_0000118
annotated source: gene_with_dicistronic_mRNA

Axiom
IAO scope: EXACT
annotated target: gene with dicistronic mRNA
annotated property: IAO_0000118
annotated source: gene_with_dicistronic_mRNA

iDNA
type: Class
subclass of: recombination_feature
IAO_0000115: Genomic sequence removed from the genome, as a normal event, by a process of recombination.
IAO id: SO:0000723
IAO xref: http://en.wikipedia.org/wiki/IDNA
IAO_0000118: intervening DNA

Axiom
annotated target: Genomic sequence removed from the genome, as a normal event, by a process of recombination.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: iDNA

Axiom
IAO scope: EXACT
annotated target: intervening DNA
annotated property: IAO_0000118
annotated source: iDNA

oriT
type: Class
subclass of: origin_of_replication
IAO_0000115: A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization.
IAO id: SO:0000724
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/Origin_of_transfer
IAO_0000118: origin of transfer

Axiom
annotated target: A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization.
IAO xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
annotated property: IAO_0000115
annotated source: oriT

Axiom
IAO scope: EXACT
annotated target: origin of transfer
annotated property: IAO_0000118
annotated source: oriT

transit_peptide
type: Class
subclass of: SO_0001527
comment: Added to bring SO inline with the embl ddbj genbank feature table. Old definition before biosapiens: The coding sequence for an N-terminal domain of a nuclear-encoded organellar protein. This domain is involved in post translational import of the protein into the organelle.
IAO alt id: BS:00055
IAO id: SO:0000725
IAO subset: SOFA
IAO_0000115: The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle).
IAO subset: biosapiens
IAO_0000118: signal
IAO_0000118: transit
IAO_0000118: transit peptide

Axiom
IAO scope: EXACT
annotated target: transit peptide
annotated property: IAO_0000118
annotated source: transit_peptide

Axiom
IAO scope: RELATED
annotated target: transit
IAO xref: uniprot:feature_type
annotated property: IAO_0000118
annotated source: transit_peptide

Axiom
annotated target: The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle).
IAO xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
annotated property: IAO_0000115
annotated source: transit_peptide

Axiom
IAO scope: RELATED
annotated target: signal
annotated property: IAO_0000118
annotated source: transit_peptide

repeat_unit
type: Class
subclass of: SO_0001411
comment: Added to comply with the feature table. A single repeat.
IAO id: SO:0000726
IAO_0000115: The simplest repeated component of a repeat region. A single repeat.
IAO xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
IAO_0000118: repeat unit

Axiom
IAO scope: EXACT
annotated target: repeat unit
annotated property: IAO_0000118
annotated source: repeat_unit

Axiom
IAO xref: SO:ke
annotated target: The simplest repeated component of a repeat region. A single repeat.
annotated property: IAO_0000115
annotated source: repeat_unit

CRM
type: Class
equivalent class: Class
  intersection of: transcriptional_cis_regulatory_region
  intersection of: Restriction
    on property: has_part
    some values from: TF_binding_site
subclass of: transcriptional_cis_regulatory_region
IAO_0000115: A regulatory_region where more than 1 TF_binding_site together are regulatorily active.
comment: Requested by Stepen Grossmann Dec 2004.
IAO id: SO:0000727
IAO subset: SOFA
IAO_0000118: TF module
IAO_0000118: cis regulatory module

Axiom
IAO scope: EXACT
annotated target: TF module
annotated property: IAO_0000118
annotated source: CRM

Axiom
annotated target: A regulatory_region where more than 1 TF_binding_site together are regulatorily active.
IAO xref: SO:SG
annotated property: IAO_0000115
annotated source: CRM

Axiom
IAO scope: EXACT
annotated target: cis regulatory module
annotated property: IAO_0000118
annotated source: CRM

intein
type: Class
subclass of: SO_0100011
IAO_0000115: A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond.
comment: Intein-mediated protein splicing occurs after mRNA has been translated into a protein.
IAO id: SO:0000728
IAO xref: http://en.wikipedia.org/wiki/Intein
IAO_0000118: protein intron

Axiom
annotated target: A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: intein

Axiom
IAO scope: RELATED
annotated target: protein intron
annotated property: IAO_0000118
annotated source: intein

intein_containing
type: Class
subclass of: protein_coding
IAO_0000115: An attribute of protein-coding genes where the initial protein product contains an intein.
IAO id: SO:0000729
IAO_0000118: intein containing

Axiom
IAO scope: EXACT
annotated target: intein containing
annotated property: IAO_0000118
annotated source: intein_containing

Axiom
annotated target: An attribute of protein-coding genes where the initial protein product contains an intein.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: intein_containing

gap
type: Class
subclass of: assembly_component
subclass of: Restriction
  on property: part_of
  some values from: sequence_assembly
IAO_0000115: A gap in the sequence of known length. The unknown bases are filled in with N's.
IAO id: SO:0000730
IAO subset: SOFA

Axiom
annotated target: A gap in the sequence of known length. The unknown bases are filled in with N's.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: gap

fragmentary
type: Class
subclass of: status
IAO_0000115: An attribute to describe a feature that is incomplete.
IAO id: SO:0000731
comment: Term added because of request by MO people.
IAO_0000118: fragment

Axiom
annotated target: An attribute to describe a feature that is incomplete.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: fragmentary

Axiom
IAO scope: EXACT
annotated target: fragment
annotated property: IAO_0000118
annotated source: fragmentary

predicted
type: Class
subclass of: status
IAO_0000115: An attribute describing an unverified region.
IAO id: SO:0000732
IAO xref: http://en.wikipedia.org/wiki/Predicted

Axiom
annotated target: An attribute describing an unverified region.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: predicted

feature_attribute
type: Class
subclass of: sequence_attribute
IAO_0000115: An attribute describing a located_sequence_feature.
IAO id: SO:0000733
IAO_0000118: feature attribute

Axiom
annotated target: An attribute describing a located_sequence_feature.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: feature_attribute

Axiom
IAO scope: EXACT
annotated target: feature attribute
annotated property: IAO_0000118
annotated source: feature_attribute

exemplar_mRNA
type: Class
equivalent class: Class
  intersection of: mRNA
  intersection of: Restriction
    on property: has_quality
    some values from: exemplar
subclass of: mRNA
comment: Added for the MO people.
IAO_0000115: An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group.
IAO id: SO:0000734
IAO_0000118: exemplar mRNA

Axiom
annotated target: An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group.
IAO xref: http://mged.sourceforge.net/ontologies/MGEDontology.php
annotated property: IAO_0000115
annotated source: exemplar_mRNA

Axiom
IAO scope: EXACT
annotated target: exemplar mRNA
annotated property: IAO_0000118
annotated source: exemplar_mRNA

sequence_location
type: Class
subclass of: sequence_attribute
IAO id: SO:0000735
IAO_0000118: sequence location

Axiom
IAO scope: EXACT
annotated target: sequence location
annotated property: IAO_0000118
annotated source: sequence_location

organelle_sequence
type: Class
subclass of: sequence_location
IAO id: SO:0000736
IAO_0000118: organelle sequence

Axiom
IAO scope: EXACT
annotated target: organelle sequence
annotated property: IAO_0000118
annotated source: organelle_sequence

mitochondrial_sequence
type: Class
subclass of: organelle_sequence
IAO id: SO:0000737
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
IAO_0000118: mitochondrial sequence

Axiom
IAO scope: EXACT
annotated target: mitochondrial sequence
annotated property: IAO_0000118
annotated source: mitochondrial_sequence

nuclear_sequence
type: Class
subclass of: organelle_sequence
IAO id: SO:0000738
IAO_0000118: nuclear sequence

Axiom
IAO scope: EXACT
annotated target: nuclear sequence
annotated property: IAO_0000118
annotated source: nuclear_sequence

nucleomorphic_sequence
type: Class
subclass of: organelle_sequence
IAO id: SO:0000739
IAO_0000118: nucleomorphic sequence

Axiom
IAO scope: EXACT
annotated target: nucleomorphic sequence
annotated property: IAO_0000118
annotated source: nucleomorphic_sequence

plastid_sequence
type: Class
subclass of: organelle_sequence
IAO id: SO:0000740
IAO_0000118: plastid sequence

Axiom
IAO scope: EXACT
annotated target: plastid sequence
annotated property: IAO_0000118
annotated source: plastid_sequence

kinetoplast
type: Class
equivalent class: Class
  intersection of: sequence_collection
  intersection of: Restriction
    on property: has_part
    some values from: maxicircle
  intersection of: Restriction
    on property: has_part
    some values from: minicircle
subclass of: genome
subclass of: sequence_collection
IAO_0000115: A kinetoplast is an interlocked network of thousands of minicircles and tens of maxi circles, located near the base of the flagellum of some protozoan species.
IAO id: SO:0000741
IAO alt id: SO:0000826
IAO xref: http://en.wikipedia.org/wiki/Kinetoplast
IAO_0000118: kinetoplast_chromosome

Axiom
annotated target: A kinetoplast is an interlocked network of thousands of minicircles and tens of maxi circles, located near the base of the flagellum of some protozoan species.
IAO xref: PMID:8395055
annotated property: IAO_0000115
annotated source: kinetoplast

Axiom
IAO scope: EXACT
annotated target: kinetoplast_chromosome
annotated property: IAO_0000118
annotated source: kinetoplast

maxicircle
type: Class
subclass of: replicon
subclass of: Restriction
  on property: part_of
  some values from: kinetoplast
IAO_0000115: A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method.
IAO id: SO:0000742
IAO alt id: SO:0000827
IAO_0000118: maxicircle_chromosome

Axiom
IAO scope: EXACT
annotated target: maxicircle_chromosome
annotated property: IAO_0000118
annotated source: maxicircle

Axiom
annotated target: A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method.
IAO xref: PMID:8395055
annotated property: IAO_0000115
annotated source: maxicircle

apicoplast_sequence
type: Class
subclass of: plastid_sequence
IAO id: SO:0000743
IAO_0000118: apicoplast sequence

Axiom
IAO scope: EXACT
annotated target: apicoplast sequence
annotated property: IAO_0000118
annotated source: apicoplast_sequence

chromoplast_sequence
type: Class
subclass of: plastid_sequence
IAO id: SO:0000744
IAO_0000118: chromoplast sequence

Axiom
IAO scope: EXACT
annotated target: chromoplast sequence
annotated property: IAO_0000118
annotated source: chromoplast_sequence

chloroplast_sequence
type: Class
subclass of: plastid_sequence
IAO id: SO:0000745
IAO_0000118: chloroplast sequence

Axiom
IAO scope: EXACT
annotated target: chloroplast sequence
annotated property: IAO_0000118
annotated source: chloroplast_sequence

cyanelle_sequence
type: Class
subclass of: plastid_sequence
IAO id: SO:0000746
IAO_0000118: cyanelle sequence

Axiom
IAO scope: EXACT
annotated target: cyanelle sequence
annotated property: IAO_0000118
annotated source: cyanelle_sequence

leucoplast_sequence
type: Class
subclass of: plastid_sequence
IAO id: SO:0000747
IAO_0000118: leucoplast sequence

Axiom
IAO scope: EXACT
annotated target: leucoplast sequence
annotated property: IAO_0000118
annotated source: leucoplast_sequence

proplastid_sequence
type: Class
subclass of: plastid_sequence
IAO id: SO:0000748
IAO_0000118: proplastid sequence

Axiom
IAO scope: EXACT
annotated target: proplastid sequence
annotated property: IAO_0000118
annotated source: proplastid_sequence

plasmid_location
type: Class
subclass of: sequence_location
IAO id: SO:0000749
IAO_0000118: plasmid location

Axiom
IAO scope: EXACT
annotated target: plasmid location
annotated property: IAO_0000118
annotated source: plasmid_location

amplification_origin
type: Class
subclass of: origin_of_replication
IAO_0000115: An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence.
IAO id: SO:0000750
IAO_0000118: amplification origin

Axiom
IAO scope: EXACT
annotated target: amplification origin
annotated property: IAO_0000118
annotated source: amplification_origin

Axiom
annotated target: An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: amplification_origin

proviral_location
type: Class
subclass of: sequence_location
IAO id: SO:0000751
IAO_0000118: proviral location

Axiom
IAO scope: EXACT
annotated target: proviral location
annotated property: IAO_0000118
annotated source: proviral_location

gene_group_regulatory_region
type: Class
subclass of: SO_0001679
subclass of: Restriction
  on property: member_of
  some values from: SO_0005855
IAO id: SO:0000752
IAO subset: SOFA
IAO_0000118: gene group regulatory region

Axiom
IAO scope: EXACT
annotated target: gene group regulatory region
annotated property: IAO_0000118
annotated source: gene_group_regulatory_region

clone_insert
type: Class
subclass of: reagent
subclass of: Restriction
  on property: part_of
  some values from: clone
IAO id: SO:0000753
IAO subset: SOFA
IAO_0000115: The region of sequence that has been inserted and is being propagated by the clone.
IAO_0000118: clone insert

Axiom
IAO scope: EXACT
annotated target: clone insert
annotated property: IAO_0000118
annotated source: clone_insert

Axiom
IAO xref: SO:ke
annotated target: The region of sequence that has been inserted and is being propagated by the clone.
annotated property: IAO_0000115
annotated source: clone_insert

lambda_vector
type: Class
subclass of: vector_replicon
IAO id: SO:0000754
IAO_0000115: The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome.
IAO_0000118: lambda vector

Axiom
IAO xref: ISBN:0-1767-2380-8
annotated target: The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome.
annotated property: IAO_0000115
annotated source: lambda_vector

Axiom
IAO scope: EXACT
annotated target: lambda vector
annotated property: IAO_0000118
annotated source: lambda_vector

plasmid_vector
type: Class
equivalent class: Class
  intersection of: replicon
  intersection of: Restriction
    on property: derives_from
    some values from: plasmid
subclass of: vector_replicon
IAO id: SO:0000755
IAO xref: http://en.wikipedia.org/wiki/Plasmid_vector#Vectors
IAO_0000118: plasmid vector

Axiom
IAO scope: EXACT
annotated target: plasmid vector
annotated property: IAO_0000118
annotated source: plasmid_vector

cDNA
type: Class
subclass of: DNA
IAO_0000115: DNA synthesized by reverse transcriptase using RNA as a template.
IAO id: SO:0000756
IAO xref: http://en.wikipedia.org/wiki/CDNA

Axiom
annotated target: DNA synthesized by reverse transcriptase using RNA as a template.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: cDNA

single_stranded_cDNA
type: Class
subclass of: cDNA
IAO id: SO:0000757
IAO_0000118: single strand cDNA
IAO_0000118: single stranded cDNA
IAO_0000118: single-strand cDNA

Axiom
IAO scope: RELATED
annotated target: single-strand cDNA
annotated property: IAO_0000118
annotated source: single_stranded_cDNA

Axiom
IAO scope: EXACT
annotated target: single strand cDNA
annotated property: IAO_0000118
annotated source: single_stranded_cDNA

Axiom
IAO scope: EXACT
annotated target: single stranded cDNA
annotated property: IAO_0000118
annotated source: single_stranded_cDNA

double_stranded_cDNA
type: Class
subclass of: cDNA
IAO id: SO:0000758
IAO_0000118: double strand cDNA
IAO_0000118: double stranded cDNA
IAO_0000118: double-strand cDNA

Axiom
IAO scope: EXACT
annotated target: double stranded cDNA
annotated property: IAO_0000118
annotated source: double_stranded_cDNA

Axiom
IAO scope: RELATED
annotated target: double-strand cDNA
annotated property: IAO_0000118
annotated source: double_stranded_cDNA

Axiom
IAO scope: RELATED
annotated target: double strand cDNA
annotated property: IAO_0000118
annotated source: double_stranded_cDNA

plasmid_clone
type: Class
IAO id: SO:0000759
deprecated: true

YAC_clone
type: Class
IAO id: SO:0000760
deprecated: true

phagemid_clone
type: Class
IAO id: SO:0000761
deprecated: true

PAC_clone
type: Class
IAO_0000118: P1_clone
IAO id: SO:0000762
deprecated: true

Axiom
annotated target: P1_clone
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: PAC_clone

fosmid_clone
type: Class
IAO id: SO:0000763
deprecated: true

BAC_clone
type: Class
IAO id: SO:0000764
deprecated: true

cosmid_clone
type: Class
IAO id: SO:0000765
deprecated: true

pyrrolysyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: pyrrolysine_tRNA_primary_transcript
IAO_0000115: A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region.
IAO id: SO:0000766
IAO_0000118: pyrrolysyl tRNA
IAO_0000118: pyrrolysyl-transfer RNA
IAO_0000118: pyrrolysyl-transfer ribonucleic acid

Axiom
IAO scope: EXACT
annotated target: pyrrolysyl tRNA
annotated property: IAO_0000118
annotated source: pyrrolysyl_tRNA

Axiom
IAO scope: EXACT
annotated target: pyrrolysyl-transfer ribonucleic acid
annotated property: IAO_0000118
annotated source: pyrrolysyl_tRNA

Axiom
annotated target: A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: pyrrolysyl_tRNA

Axiom
IAO scope: EXACT
annotated target: pyrrolysyl-transfer RNA
annotated property: IAO_0000118
annotated source: pyrrolysyl_tRNA

clone_insert_start
type: Class
IAO id: SO:0000767
deprecated: true

episome
type: Class
subclass of: plasmid
IAO_0000115: A plasmid that may integrate with a chromosome.
IAO id: SO:0000768

Axiom
annotated target: A plasmid that may integrate with a chromosome.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: episome

tmRNA_coding_piece
type: Class
subclass of: tmRNA_region
comment: Added in response to comment from Kelly Williams from Indiana. Nov 2005.
IAO id: SO:0000769
IAO_0000115: The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together.
IAO_0000118: tmRNA coding piece

Axiom
IAO xref: Indiana:kw
annotated target: The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together.
IAO xref: doi:10.1093/nar/gkh795
IAO xref: issn:1362-4962
annotated property: IAO_0000115
annotated source: tmRNA_coding_piece

Axiom
IAO scope: EXACT
annotated target: tmRNA coding piece
annotated property: IAO_0000118
annotated source: tmRNA_coding_piece

tmRNA_acceptor_piece
type: Class
subclass of: tmRNA_region
comment: Added in response to Kelly Williams from Indiana. Date: Nov 2005.
IAO id: SO:0000770
IAO_0000115: The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together.
IAO_0000118: tmRNA acceptor piece

Axiom
IAO xref: Indiana:kw
annotated target: The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together.
IAO xref: doi:10.1093/nar/gkh795
annotated property: IAO_0000115
annotated source: tmRNA_acceptor_piece

Axiom
IAO scope: EXACT
annotated target: tmRNA acceptor piece
annotated property: IAO_0000118
annotated source: tmRNA_acceptor_piece

QTL
type: Class
subclass of: SO_0001411
IAO_0000115: A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci.
comment: Added in respose to request by Simon Twigger November 14th 2005.
IAO id: SO:0000771
IAO_0000118: quantitative trait locus

Axiom
IAO scope: EXACT
annotated target: quantitative trait locus
annotated property: IAO_0000118
annotated source: QTL

Axiom
annotated target: A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci.
IAO xref: http://rgd.mcw.edu/tu/qtls/
annotated property: IAO_0000115
annotated source: QTL

genomic_island
type: Class
subclass of: integrated_mobile_genetic_element
IAO_0000115: A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility.
comment: Genomic islands are transmissible elements characterized by large size (>10kb).
IAO id: SO:0000772
IAO_0000118: genomic island
IAO xref: http://en.wikipedia.org/wiki/Genomic_island

Axiom
IAO scope: EXACT
annotated target: genomic island
annotated property: IAO_0000118
annotated source: genomic_island

Axiom
annotated target: A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility.
IAO xref: Phigo:at
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: genomic_island

pathogenic_island
type: Class
subclass of: genomic_island
IAO_0000115: Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species.
comment: Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker.
IAO id: SO:0000773
IAO_0000118: pathogenic island

Axiom
annotated target: Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: pathogenic_island

Axiom
IAO scope: EXACT
annotated target: pathogenic island
annotated property: IAO_0000118
annotated source: pathogenic_island

metabolic_island
type: Class
subclass of: genomic_island
IAO_0000115: A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria.
comment: Genes for phenolic compound degradation in Pseudomonas putida are found on metabolic islands.
IAO id: SO:0000774
IAO_0000118: metabolic island

Axiom
annotated target: A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: metabolic_island

Axiom
IAO scope: EXACT
annotated target: metabolic island
annotated property: IAO_0000118
annotated source: metabolic_island

adaptive_island
type: Class
subclass of: genomic_island
IAO_0000115: An adaptive island is a genomic island that provides an adaptive advantage to the host.
IAO id: SO:0000775
comment: The iron-uptake ability of many pathogens are conveyed by adaptive islands. Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker.
IAO_0000118: adaptive island

Axiom
annotated target: An adaptive island is a genomic island that provides an adaptive advantage to the host.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: adaptive_island

Axiom
IAO scope: EXACT
annotated target: adaptive island
annotated property: IAO_0000118
annotated source: adaptive_island

symbiosis_island
type: Class
subclass of: genomic_island
IAO_0000115: A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria.
comment: Nitrogen fixation in Rhizobiaceae species is encoded by symbiosis islands. Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene. John T. Sullivan and Clive W. Ronso PNAS 1998 Apr 28 95 (9) 5145-5149.
IAO id: SO:0000776
IAO_0000118: symbiosis island

Axiom
IAO scope: EXACT
annotated target: symbiosis island
annotated property: IAO_0000118
annotated source: symbiosis_island

Axiom
annotated target: A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: symbiosis_island

pseudogenic_rRNA
type: Class
subclass of: pseudogenic_region
IAO_0000115: A non functional descendent of an rRNA.
comment: Added Jan 2006 to allow the annotation of the pseudogenic rRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations.
IAO id: SO:0000777
IAO subset: SOFA
IAO_0000118: pseudogenic rRNA

Axiom
IAO scope: EXACT
annotated target: pseudogenic rRNA
annotated property: IAO_0000118
annotated source: pseudogenic_rRNA

Axiom
annotated target: A non functional descendent of an rRNA.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: pseudogenic_rRNA

pseudogenic_tRNA
type: Class
subclass of: pseudogenic_region
IAO_0000115: A non functional descendent of a tRNA.
comment: Added Jan 2006 to allow the annotation of the pseudogenic tRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations.
IAO id: SO:0000778
IAO subset: SOFA
IAO_0000118: pseudogenic tRNA

Axiom
IAO scope: EXACT
annotated target: pseudogenic tRNA
annotated property: IAO_0000118
annotated source: pseudogenic_tRNA

Axiom
annotated target: A non functional descendent of a tRNA.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: pseudogenic_tRNA

engineered_episome
type: Class
equivalent class: Class
  intersection of: episome
  intersection of: Restriction
    on property: has_quality
    some values from: engineered
subclass of: engineered_plasmid
subclass of: episome
IAO_0000115: An episome that is engineered.
comment: Requested by Lynn Crosby Jan 2006.
IAO id: SO:0000779
IAO_0000118: engineered episome

Axiom
IAO scope: EXACT
annotated target: engineered episome
annotated property: IAO_0000118
annotated source: engineered_episome

Axiom
annotated target: An episome that is engineered.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: engineered_episome

transposable_element_attribute
type: Class
comment: Added by KE Jan 2006 to capture the kinds of attributes of TEs
IAO id: SO:0000780
deprecated: true

transgenic
type: Class
subclass of: feature_attribute
IAO_0000115: Attribute describing sequence that has been integrated with foreign sequence.
IAO id: SO:0000781

Axiom
annotated target: Attribute describing sequence that has been integrated with foreign sequence.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: transgenic

natural
type: Class
subclass of: feature_attribute
IAO_0000115: An attribute describing a feature that occurs in nature.
IAO id: SO:0000782

Axiom
annotated target: An attribute describing a feature that occurs in nature.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: natural

engineered
type: Class
subclass of: feature_attribute
IAO_0000115: An attribute to describe a region that was modified in vitro.
IAO id: SO:0000783

Axiom
annotated target: An attribute to describe a region that was modified in vitro.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: engineered

foreign
type: Class
subclass of: feature_attribute
IAO_0000115: An attribute to describe a region from another species.
IAO id: SO:0000784

Axiom
annotated target: An attribute to describe a region from another species.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: foreign

cloned_region
type: Class
subclass of: reagent
subclass of: Restriction
  on property: part_of
  some values from: clone_insert
comment: Added in response to Lynn Crosby. A clone insert may be composed of many cloned regions.
IAO id: SO:0000785
IAO_0000118: cloned region
IAO_0000118: cloned segment

Axiom
IAO scope: EXACT
annotated target: cloned segment
annotated property: IAO_0000118
annotated source: cloned_region

Axiom
IAO scope: EXACT
annotated target: cloned region
annotated property: IAO_0000118
annotated source: cloned_region

reagent_attribute
type: Class
comment: Added jan 2006 by KE.
IAO id: SO:0000786
IAO_0000118: reagent attribute
deprecated: true

Axiom
IAO scope: EXACT
annotated target: reagent attribute
annotated property: IAO_0000118
annotated source: reagent_attribute

clone_attribute
type: Class
IAO id: SO:0000787
deprecated: true

cloned
type: Class
IAO id: SO:0000788
deprecated: true

validated
type: Class
subclass of: status
IAO_0000115: An attribute to describe a feature that has been proven.
IAO id: SO:0000789

Axiom
annotated target: An attribute to describe a feature that has been proven.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: validated

invalidated
type: Class
subclass of: status
IAO_0000115: An attribute describing a feature that is invalidated.
IAO id: SO:0000790

Axiom
annotated target: An attribute describing a feature that is invalidated.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: invalidated

cloned_genomic
type: Class
IAO id: SO:0000791
deprecated: true

cloned_cDNA
type: Class
IAO id: SO:0000792
deprecated: true

engineered_DNA
type: Class
IAO id: SO:0000793
deprecated: true

engineered_rescue_region
type: Class
equivalent class: Class
  intersection of: rescue_region
  intersection of: Restriction
    on property: has_quality
    some values from: engineered
subclass of: rescue_region
subclass of: engineered_region
IAO_0000115: A rescue region that is engineered.
IAO id: SO:0000794
IAO_0000118: engineered rescue fragment
IAO_0000118: engineered rescue region
IAO_0000118: engineered rescue segment

Axiom
IAO scope: EXACT
annotated target: engineered rescue segment
annotated property: IAO_0000118
annotated source: engineered_rescue_region

Axiom
IAO scope: EXACT
annotated target: engineered rescue fragment
annotated property: IAO_0000118
annotated source: engineered_rescue_region

Axiom
IAO scope: EXACT
annotated target: engineered rescue region
annotated property: IAO_0000118
annotated source: engineered_rescue_region

Axiom
annotated target: A rescue region that is engineered.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: engineered_rescue_region

rescue_mini_gene
type: Class
equivalent class: Class
  intersection of: mini_gene
  intersection of: Restriction
    on property: has_quality
    some values from: rescue
subclass of: mini_gene
IAO_0000115: A mini_gene that rescues.
IAO id: SO:0000795
IAO_0000118: rescue mini gene
IAO_0000118: rescue mini-gene

Axiom
annotated target: A mini_gene that rescues.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: rescue_mini_gene

Axiom
IAO scope: EXACT
annotated target: rescue mini gene
annotated property: IAO_0000118
annotated source: rescue_mini_gene

Axiom
IAO scope: EXACT
annotated target: rescue mini-gene
annotated property: IAO_0000118
annotated source: rescue_mini_gene

transgenic_transposable_element
type: Class
equivalent class: Class
  intersection of: transposable_element
  intersection of: Restriction
    on property: derives_from
    some values from: clone
  intersection of: Restriction
    on property: has_quality
    some values from: transgenic
subclass of: transposable_element
comment: Modified as requested by Lynn - FB. May 2007.
IAO id: SO:0000796
IAO_0000115: TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE.
IAO_0000118: transgenic transposable element

Axiom
IAO scope: EXACT
annotated target: transgenic transposable element
annotated property: IAO_0000118
annotated source: transgenic_transposable_element

Axiom
IAO xref: FB:mc
annotated target: TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE.
annotated property: IAO_0000115
annotated source: transgenic_transposable_element

natural_transposable_element
type: Class
equivalent class: Class
  intersection of: transposable_element
  intersection of: Restriction
    on property: has_quality
    some values from: natural
subclass of: transposable_element
subclass of: extrachromosomal_mobile_genetic_element
IAO id: SO:0000797
IAO_0000115: TE that exists (or existed) in nature.
IAO_0000118: natural transposable element

Axiom
IAO xref: FB:mc
annotated target: TE that exists (or existed) in nature.
annotated property: IAO_0000115
annotated source: natural_transposable_element

Axiom
IAO scope: EXACT
annotated target: natural transposable element
annotated property: IAO_0000118
annotated source: natural_transposable_element

engineered_transposable_element
type: Class
equivalent class: Class
  intersection of: transposable_element
  intersection of: Restriction
    on property: has_quality
    some values from: engineered
subclass of: transposable_element
subclass of: engineered_region
IAO id: SO:0000798
IAO_0000115: TE that has been modified by manipulations in vitro.
IAO_0000118: engineered transposable element

Axiom
IAO xref: FB:mc
annotated target: TE that has been modified by manipulations in vitro.
annotated property: IAO_0000115
annotated source: engineered_transposable_element

Axiom
IAO scope: EXACT
annotated target: engineered transposable element
annotated property: IAO_0000118
annotated source: engineered_transposable_element

engineered_foreign_transposable_element
type: Class
equivalent class: Class
  intersection of: transposable_element
  intersection of: Restriction
    on property: has_quality
    some values from: engineered
  intersection of: Restriction
    on property: has_quality
    some values from: foreign
subclass of: foreign_transposable_element
subclass of: engineered_transposable_element
subclass of: engineered_foreign_region
IAO_0000115: A transposable_element that is engineered and foreign.
IAO id: SO:0000799
IAO_0000118: engineered foreign transposable element

Axiom
IAO scope: EXACT
annotated target: engineered foreign transposable element
annotated property: IAO_0000118
annotated source: engineered_foreign_transposable_element

Axiom
annotated target: A transposable_element that is engineered and foreign.
IAO xref: FB:mc
annotated property: IAO_0000115
annotated source: engineered_foreign_transposable_element

assortment_derived_duplication
type: Class
subclass of: SO_0001504
IAO_0000115: A multi-chromosome duplication aberration generated by reassortment of other aberration components.
IAO id: SO:0000800
IAO_0000118: assortment derived duplication

Axiom
IAO scope: EXACT
annotated target: assortment derived duplication
annotated property: IAO_0000118
annotated source: assortment_derived_duplication

Axiom
annotated target: A multi-chromosome duplication aberration generated by reassortment of other aberration components.
IAO xref: FB:gm
annotated property: IAO_0000115
annotated source: assortment_derived_duplication

assortment_derived_deficiency_plus_duplication
type: Class
subclass of: SO_0001504
IAO_0000115: A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication.
IAO id: SO:0000801
IAO_0000118: assortment derived deficiency plus duplication

Axiom
annotated target: A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication.
IAO xref: FB:gm
annotated property: IAO_0000115
annotated source: assortment_derived_deficiency_plus_duplication

Axiom
IAO scope: EXACT
annotated target: assortment derived deficiency plus duplication
annotated property: IAO_0000118
annotated source: assortment_derived_deficiency_plus_duplication

assortment_derived_deficiency
type: Class
subclass of: SO_0001504
IAO_0000115: A multi-chromosome deficiency aberration generated by reassortment of other aberration components.
IAO id: SO:0000802
IAO_0000118: assortment-derived deficiency

Axiom
annotated target: A multi-chromosome deficiency aberration generated by reassortment of other aberration components.
IAO xref: FB:gm
annotated property: IAO_0000115
annotated source: assortment_derived_deficiency

Axiom
IAO scope: EXACT
annotated target: assortment-derived deficiency
annotated property: IAO_0000118
annotated source: assortment_derived_deficiency

assortment_derived_aneuploid
type: Class
subclass of: SO_0001504
IAO_0000115: A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication.
IAO id: SO:0000803
IAO_0000118: assortment derived aneuploid

Axiom
IAO scope: EXACT
annotated target: assortment derived aneuploid
annotated property: IAO_0000118
annotated source: assortment_derived_aneuploid

Axiom
annotated target: A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication.
IAO xref: FB:gm
annotated property: IAO_0000115
annotated source: assortment_derived_aneuploid

engineered_region
type: Class
equivalent class: Class
  intersection of: region
  intersection of: Restriction
    on property: has_quality
    some values from: engineered
subclass of: SO_0001409
IAO_0000115: A region that is engineered.
IAO id: SO:0000804
IAO_0000118: construct
IAO_0000118: engineered region
IAO_0000118: engineered sequence

Axiom
IAO scope: EXACT
annotated target: construct
annotated property: IAO_0000118
annotated source: engineered_region

Axiom
IAO scope: EXACT
annotated target: engineered sequence
annotated property: IAO_0000118
annotated source: engineered_region

Axiom
IAO scope: EXACT
annotated target: engineered region
annotated property: IAO_0000118
annotated source: engineered_region

Axiom
annotated target: A region that is engineered.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: engineered_region

engineered_foreign_region
type: Class
equivalent class: Class
  intersection of: region
  intersection of: Restriction
    on property: has_quality
    some values from: engineered
  intersection of: Restriction
    on property: has_quality
    some values from: foreign
subclass of: engineered_region
IAO_0000115: A region that is engineered and foreign.
IAO id: SO:0000805
IAO_0000118: engineered foreign region

Axiom
IAO scope: EXACT
annotated target: engineered foreign region
annotated property: IAO_0000118
annotated source: engineered_foreign_region

Axiom
annotated target: A region that is engineered and foreign.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: engineered_foreign_region

fusion
type: Class
subclass of: feature_attribute
IAO id: SO:0000806

engineered_tag
type: Class
equivalent class: Class
  intersection of: tag
  intersection of: Restriction
    on property: has_quality
    some values from: engineered
subclass of: tag
subclass of: engineered_region
IAO_0000115: A tag that is engineered.
IAO id: SO:0000807
IAO_0000118: engineered tag

Axiom
IAO scope: EXACT
annotated target: engineered tag
annotated property: IAO_0000118
annotated source: engineered_tag

Axiom
annotated target: A tag that is engineered.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: engineered_tag

validated_cDNA_clone
type: Class
equivalent class: Class
  intersection of: cDNA_clone
  intersection of: Restriction
    on property: has_quality
    some values from: validated
subclass of: cDNA_clone
IAO_0000115: A cDNA clone that has been validated.
IAO id: SO:0000808
IAO_0000118: validated cDNA clone

Axiom
IAO scope: EXACT
annotated target: validated cDNA clone
annotated property: IAO_0000118
annotated source: validated_cDNA_clone

Axiom
annotated target: A cDNA clone that has been validated.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: validated_cDNA_clone

invalidated_cDNA_clone
type: Class
equivalent class: Class
  intersection of: cDNA_clone
  intersection of: Restriction
    on property: has_quality
    some values from: invalidated
subclass of: cDNA_clone
IAO_0000115: A cDNA clone that is invalid.
IAO id: SO:0000809
IAO_0000118: invalidated cDNA clone

Axiom
IAO scope: EXACT
annotated target: invalidated cDNA clone
annotated property: IAO_0000118
annotated source: invalidated_cDNA_clone

Axiom
annotated target: A cDNA clone that is invalid.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: invalidated_cDNA_clone

chimeric_cDNA_clone
type: Class
equivalent class: Class
  intersection of: invalidated_cDNA_clone
  intersection of: Restriction
    on property: has_quality
    some values from: invalidated_by_chimeric_cDNA
subclass of: invalidated_cDNA_clone
IAO_0000115: A cDNA clone invalidated because it is chimeric.
IAO id: SO:0000810
IAO_0000118: chimeric cDNA clone

Axiom
IAO scope: EXACT
annotated target: chimeric cDNA clone
annotated property: IAO_0000118
annotated source: chimeric_cDNA_clone

Axiom
annotated target: A cDNA clone invalidated because it is chimeric.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: chimeric_cDNA_clone

genomically_contaminated_cDNA_clone
type: Class
equivalent class: Class
  intersection of: invalidated_cDNA_clone
  intersection of: Restriction
    on property: has_quality
    some values from: invalidated_by_genomic_contamination
subclass of: invalidated_cDNA_clone
IAO_0000115: A cDNA clone invalidated by genomic contamination.
IAO id: SO:0000811
IAO_0000118: genomically contaminated cDNA clone

Axiom
annotated target: A cDNA clone invalidated by genomic contamination.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: genomically_contaminated_cDNA_clone

Axiom
IAO scope: EXACT
annotated target: genomically contaminated cDNA clone
annotated property: IAO_0000118
annotated source: genomically_contaminated_cDNA_clone

polyA_primed_cDNA_clone
type: Class
equivalent class: Class
  intersection of: invalidated_cDNA_clone
  intersection of: Restriction
    on property: has_quality
    some values from: invalidated_by_genomic_polyA_primed_cDNA
subclass of: invalidated_cDNA_clone
IAO_0000115: A cDNA clone invalidated by polyA priming.
IAO id: SO:0000812
IAO_0000118: polyA primed cDNA clone

Axiom
IAO scope: EXACT
annotated target: polyA primed cDNA clone
annotated property: IAO_0000118
annotated source: polyA_primed_cDNA_clone

Axiom
annotated target: A cDNA clone invalidated by polyA priming.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: polyA_primed_cDNA_clone

partially_processed_cDNA_clone
type: Class
equivalent class: Class
  intersection of: invalidated_cDNA_clone
  intersection of: Restriction
    on property: has_quality
    some values from: invalidated_by_partial_processing
subclass of: invalidated_cDNA_clone
IAO_0000115: A cDNA invalidated clone by partial processing.
IAO id: SO:0000813
IAO_0000118: partially processed cDNA clone

Axiom
annotated target: A cDNA invalidated clone by partial processing.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: partially_processed_cDNA_clone

Axiom
IAO scope: EXACT
annotated target: partially processed cDNA clone
annotated property: IAO_0000118
annotated source: partially_processed_cDNA_clone

rescue
type: Class
subclass of: feature_attribute
IAO_0000115: An attribute describing a region's ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype.
IAO id: SO:0000814

Axiom
annotated target: An attribute describing a region's ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: rescue

mini_gene
type: Class
subclass of: ORF
IAO_0000115: By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL)) and MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA.
IAO id: SO:0000815
IAO_0000118: mini gene

Axiom
IAO scope: EXACT
annotated target: mini gene
annotated property: IAO_0000118
annotated source: mini_gene

Axiom
annotated target: By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL)) and MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA.
IAO xref: PMID:15992143
annotated property: IAO_0000115
annotated source: mini_gene

rescue_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: rescue
subclass of: gene
IAO_0000115: A gene that rescues.
IAO id: SO:0000816
IAO_0000118: rescue gene

Axiom
annotated target: A gene that rescues.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: rescue_gene

Axiom
IAO scope: EXACT
annotated target: rescue gene
annotated property: IAO_0000118
annotated source: rescue_gene

wild_type
type: Class
subclass of: feature_attribute
IAO_0000115: An attribute describing sequence with the genotype found in nature and/or standard laboratory stock.
IAO id: SO:0000817
IAO xref: http://en.wikipedia.org/wiki/Wild_type
IAO_0000118: wild type

Axiom
IAO scope: EXACT
annotated target: wild type
annotated property: IAO_0000118
annotated source: wild_type

Axiom
annotated target: An attribute describing sequence with the genotype found in nature and/or standard laboratory stock.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: wild_type

wild_type_rescue_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: wild_type
subclass of: rescue_gene
IAO_0000115: A gene that rescues.
IAO id: SO:0000818
IAO_0000118: wild type rescue gene

Axiom
annotated target: A gene that rescues.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: wild_type_rescue_gene

Axiom
IAO scope: EXACT
annotated target: wild type rescue gene
annotated property: IAO_0000118
annotated source: wild_type_rescue_gene

mitochondrial_chromosome
type: Class
equivalent class: Class
  intersection of: chromosome
  intersection of: Restriction
    on property: has_origin
    some values from: mitochondrial_sequence
subclass of: chromosome
IAO_0000115: A chromosome originating in a mitochondria.
IAO id: SO:0000819
IAO_0000118: mitochondrial chromosome

Axiom
annotated target: A chromosome originating in a mitochondria.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: mitochondrial_chromosome

Axiom
IAO scope: EXACT
annotated target: mitochondrial chromosome
annotated property: IAO_0000118
annotated source: mitochondrial_chromosome

chloroplast_chromosome
type: Class
equivalent class: Class
  intersection of: chromosome
  intersection of: Restriction
    on property: has_origin
    some values from: chloroplast_sequence
subclass of: chromosome
IAO_0000115: A chromosome originating in a chloroplast.
IAO id: SO:0000820
IAO_0000118: chloroplast chromosome

Axiom
annotated target: A chromosome originating in a chloroplast.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: chloroplast_chromosome

Axiom
IAO scope: EXACT
annotated target: chloroplast chromosome
annotated property: IAO_0000118
annotated source: chloroplast_chromosome

chromoplast_chromosome
type: Class
equivalent class: Class
  intersection of: chromosome
  intersection of: Restriction
    on property: has_origin
    some values from: chromoplast_sequence
subclass of: chromosome
IAO_0000115: A chromosome originating in a chromoplast.
IAO id: SO:0000821
IAO_0000118: chromoplast chromosome

Axiom
IAO scope: EXACT
annotated target: chromoplast chromosome
annotated property: IAO_0000118
annotated source: chromoplast_chromosome

Axiom
annotated target: A chromosome originating in a chromoplast.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: chromoplast_chromosome

cyanelle_chromosome
type: Class
equivalent class: Class
  intersection of: chromosome
  intersection of: Restriction
    on property: has_origin
    some values from: cyanelle_sequence
subclass of: chromosome
IAO_0000115: A chromosome originating in a cyanelle.
IAO id: SO:0000822
IAO_0000118: cyanelle chromosome

Axiom
IAO scope: EXACT
annotated target: cyanelle chromosome
annotated property: IAO_0000118
annotated source: cyanelle_chromosome

Axiom
annotated target: A chromosome originating in a cyanelle.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: cyanelle_chromosome

leucoplast_chromosome
type: Class
equivalent class: Class
  intersection of: chromosome
  intersection of: Restriction
    on property: has_origin
    some values from: leucoplast_sequence
subclass of: chromosome
IAO_0000115: A chromosome with origin in a leucoplast.
IAO id: SO:0000823
IAO_0000118: leucoplast chromosome

Axiom
annotated target: A chromosome with origin in a leucoplast.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: leucoplast_chromosome

Axiom
IAO scope: EXACT
annotated target: leucoplast chromosome
annotated property: IAO_0000118
annotated source: leucoplast_chromosome

macronuclear_chromosome
type: Class
equivalent class: Class
  intersection of: chromosome
  intersection of: Restriction
    on property: has_origin
    some values from: macronuclear_sequence
subclass of: chromosome
IAO_0000115: A chromosome originating in a macronucleus.
IAO id: SO:0000824
IAO_0000118: macronuclear chromosome

Axiom
annotated target: A chromosome originating in a macronucleus.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: macronuclear_chromosome

Axiom
IAO scope: EXACT
annotated target: macronuclear chromosome
annotated property: IAO_0000118
annotated source: macronuclear_chromosome

micronuclear_chromosome
type: Class
equivalent class: Class
  intersection of: chromosome
  intersection of: Restriction
    on property: has_origin
    some values from: micronuclear_sequence
subclass of: chromosome
IAO_0000115: A chromosome originating in a micronucleus.
IAO id: SO:0000825
IAO_0000118: micronuclear chromosome

Axiom
annotated target: A chromosome originating in a micronucleus.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: micronuclear_chromosome

Axiom
IAO scope: EXACT
annotated target: micronuclear chromosome
annotated property: IAO_0000118
annotated source: micronuclear_chromosome

nuclear_chromosome
type: Class
equivalent class: Class
  intersection of: chromosome
  intersection of: Restriction
    on property: has_origin
    some values from: nuclear_sequence
subclass of: chromosome
IAO_0000115: A chromosome originating in a nucleus.
IAO id: SO:0000828
IAO_0000118: nuclear chromosome

Axiom
annotated target: A chromosome originating in a nucleus.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: nuclear_chromosome

Axiom
IAO scope: EXACT
annotated target: nuclear chromosome
annotated property: IAO_0000118
annotated source: nuclear_chromosome

nucleomorphic_chromosome
type: Class
equivalent class: Class
  intersection of: chromosome
  intersection of: Restriction
    on property: has_origin
    some values from: nucleomorphic_sequence
subclass of: chromosome
IAO_0000115: A chromosome originating in a nucleomorph.
IAO id: SO:0000829
IAO_0000118: nucleomorphic chromosome

Axiom
IAO scope: EXACT
annotated target: nucleomorphic chromosome
annotated property: IAO_0000118
annotated source: nucleomorphic_chromosome

Axiom
annotated target: A chromosome originating in a nucleomorph.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: nucleomorphic_chromosome

chromosome_part
type: Class
subclass of: SO_0001411
subclass of: Restriction
  on property: part_of
  some values from: chromosome
IAO_0000115: A region of a chromosome.
IAO id: SO:0000830
IAO subset: SOFA
comment: This is a manufactured term, that serves the purpose of allow the parts of a chromosome to have an is_a path to the root.
IAO_0000118: chromosome part

Axiom
annotated target: A region of a chromosome.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: chromosome_part

Axiom
IAO scope: EXACT
annotated target: chromosome part
annotated property: IAO_0000118
annotated source: chromosome_part

gene_member_region
type: Class
subclass of: SO_0001411
subclass of: Restriction
  on property: member_of
  some values from: gene
comment: A manufactured term used to allow the parts of a gene to have an is_a path to the root.
IAO_0000115: A region of a gene.
IAO id: SO:0000831
IAO subset: SOFA
IAO_0000118: gene member region

Axiom
annotated target: A region of a gene.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: gene_member_region

Axiom
IAO scope: EXACT
annotated target: gene member region
annotated property: IAO_0000118
annotated source: gene_member_region

promoter_region
type: Class
IAO_0000115: A region of sequence which is part of a promoter.
IAO id: SO:0000832
comment: This is a manufactured term to allow the parts of promoter to have an is_a path back to the root.
deprecated: true

Axiom
annotated target: A region of sequence which is part of a promoter.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: promoter_region

transcript_region
type: Class
subclass of: SO_0001411
subclass of: Restriction
  on property: part_of
  some values from: transcript
IAO_0000115: A region of a transcript.
IAO id: SO:0000833
IAO subset: SOFA
comment: This term was added to provide a grouping term for the region parts of transcript, thus giving them an is_a path back to the root.
IAO_0000118: transcript region

Axiom
IAO scope: EXACT
annotated target: transcript region
annotated property: IAO_0000118
annotated source: transcript_region

Axiom
annotated target: A region of a transcript.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: transcript_region

mature_transcript_region
type: Class
subclass of: transcript_region
comment: A manufactured term to collect together the parts of a mature transcript and give them an is_a path to the root.
IAO_0000115: A region of a mature transcript.
IAO id: SO:0000834
IAO subset: SOFA
IAO_0000118: mature transcript region

Axiom
annotated target: A region of a mature transcript.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: mature_transcript_region

Axiom
IAO scope: EXACT
annotated target: mature transcript region
annotated property: IAO_0000118
annotated source: mature_transcript_region

primary_transcript_region
type: Class
subclass of: transcript_region
subclass of: Restriction
  on property: part_of
  some values from: primary_transcript
IAO_0000115: A part of a primary transcript.
IAO id: SO:0000835
IAO subset: SOFA
comment: This term was added to provide a grouping term for the region parts of primary_transcript, thus giving them an is_a path back to the root.
IAO_0000118: primary transcript region

Axiom
annotated target: A part of a primary transcript.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: primary_transcript_region

Axiom
IAO scope: EXACT
annotated target: primary transcript region
annotated property: IAO_0000118
annotated source: primary_transcript_region

mRNA_region
type: Class
subclass of: mature_transcript_region
subclass of: Restriction
  on property: part_of
  some values from: mRNA
IAO_0000115: A region of an mRNA.
IAO id: SO:0000836
IAO subset: SOFA
comment: This term was added to provide a grouping term for the region parts of mRNA, thus giving them an is_a path back to the root.
IAO_0000118: mRNA region

Axiom
IAO scope: EXACT
annotated target: mRNA region
annotated property: IAO_0000118
annotated source: mRNA_region

Axiom
annotated target: A region of an mRNA.
IAO xref: SO:cb
annotated property: IAO_0000115
annotated source: mRNA_region

UTR_region
type: Class
subclass of: mRNA_region
IAO_0000115: A region of UTR.
comment: A region of UTR. This term is a grouping term to allow the parts of UTR to have an is_a path to the root.
IAO id: SO:0000837
IAO subset: SOFA
IAO_0000118: UTR region

Axiom
IAO scope: EXACT
annotated target: UTR region
annotated property: IAO_0000118
annotated source: UTR_region

Axiom
annotated target: A region of UTR.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: UTR_region

rRNA_primary_transcript_region
type: Class
subclass of: primary_transcript_region
subclass of: Restriction
  on property: part_of
  some values from: rRNA_primary_transcript
IAO_0000115: A region of an rRNA primary transcript.
IAO id: SO:0000838
comment: To allow transcribed_spacer_region to have a path to the root.
IAO_0000118: rRNA primary transcript region

Axiom
annotated target: A region of an rRNA primary transcript.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: rRNA_primary_transcript_region

Axiom
IAO scope: EXACT
annotated target: rRNA primary transcript region
annotated property: IAO_0000118
annotated source: rRNA_primary_transcript_region

polypeptide_region
type: Class
subclass of: SO_0001411
subclass of: Restriction
  on property: part_of
  some values from: polypeptide
comment: Added to allow the polypeptide regions to have is_a paths back to the root.
IAO alt id: BS:00124
IAO alt id: BS:00331
IAO_0000115: Biological sequence region that can be assigned to a specific subsequence of a polypeptide.
IAO id: SO:0000839
IAO subset: SOFA
IAO subset: biosapiens
IAO_0000118: positional
IAO_0000118: positional polypeptide feature
IAO_0000118: region
IAO_0000118: region or site annotation
IAO_0000118: site

Axiom
IAO scope: RELATED
annotated target: region or site annotation
annotated property: IAO_0000118
annotated source: polypeptide_region

Axiom
IAO scope: NARROW
annotated target: region
IAO xref: uniprot:feature_type
annotated property: IAO_0000118
annotated source: polypeptide_region

Axiom
annotated target: Biological sequence region that can be assigned to a specific subsequence of a polypeptide.
IAO xref: SO:GAR
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: polypeptide_region

Axiom
IAO scope: NARROW
annotated target: site
IAO xref: uniprot:feature_type
annotated property: IAO_0000118
annotated source: polypeptide_region

Axiom
IAO scope: RELATED
annotated target: positional
annotated property: IAO_0000118
annotated source: polypeptide_region

Axiom
IAO scope: RELATED
annotated target: positional polypeptide feature
annotated property: IAO_0000118
annotated source: polypeptide_region

repeat_component
type: Class
subclass of: SO_0001412
comment: A manufactured to group the parts of repeats, to give them an is_a path back to the root.
IAO_0000115: A region of a repeated sequence.
IAO id: SO:0000840
IAO_0000118: repeat component

Axiom
IAO scope: EXACT
annotated target: repeat component
annotated property: IAO_0000118
annotated source: repeat_component

Axiom
annotated target: A region of a repeated sequence.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: repeat_component

spliceosomal_intron_region
type: Class
subclass of: primary_transcript_region
subclass of: Restriction
  on property: part_of
  some values from: spliceosomal_intron
IAO_0000115: A region within an intron.
comment: A terms added to allow the parts of introns to have is_a paths to the root.
IAO id: SO:0000841
IAO subset: SOFA
IAO_0000118: spliceosomal intron region

Axiom
annotated target: A region within an intron.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: spliceosomal_intron_region

Axiom
IAO scope: EXACT
annotated target: spliceosomal intron region
annotated property: IAO_0000118
annotated source: spliceosomal_intron_region

gene_component_region
type: Class
subclass of: SO_0001411
subclass of: Restriction
  on property: part_of
  some values from: gene
IAO id: SO:0000842
IAO subset: SOFA
IAO_0000118: gene component region

Axiom
IAO scope: EXACT
annotated target: gene component region
annotated property: IAO_0000118
annotated source: gene_component_region

bacterial_RNApol_promoter_region
type: Class
IAO_0000115: A region which is part of a bacterial RNA polymerase promoter.
IAO id: SO:0000843
comment: This is a manufactured term to allow the parts of bacterial_RNApol_promoter to have an is_a path back to the root.
deprecated: true

Axiom
annotated target: A region which is part of a bacterial RNA polymerase promoter.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: bacterial_RNApol_promoter_region

RNApol_II_promoter_region
type: Class
IAO_0000115: A region of sequence which is a promoter for RNA polymerase II.
IAO id: SO:0000844
comment: This is a manufactured term to allow the parts of RNApol_II_promoter to have an is_a path back to the root.
deprecated: true

Axiom
annotated target: A region of sequence which is a promoter for RNA polymerase II.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: RNApol_II_promoter_region

RNApol_III_promoter_type_1_region
type: Class
IAO_0000115: A region of sequence which is a promoter for RNA polymerase III type 1.
IAO id: SO:0000845
comment: This is a manufactured term to allow the parts of RNApol_III_promoter_type_1 to have an is_a path back to the root.
deprecated: true

Axiom
annotated target: A region of sequence which is a promoter for RNA polymerase III type 1.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: RNApol_III_promoter_type_1_region

RNApol_III_promoter_type_2_region
type: Class
IAO_0000115: A region of sequence which is a promoter for RNA polymerase III type 2.
IAO id: SO:0000846
comment: This is a manufactured term to allow the parts of RNApol_III_promoter_type_2 to have an is_a path back to the root.
deprecated: true

Axiom
annotated target: A region of sequence which is a promoter for RNA polymerase III type 2.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: RNApol_III_promoter_type_2_region

tmRNA_region
type: Class
subclass of: mature_transcript_region
subclass of: Restriction
  on property: part_of
  some values from: tmRNA
IAO_0000115: A region of a tmRNA.
IAO id: SO:0000847
comment: This term was added to provide a grouping term for the region parts of tmRNA, thus giving them an is_a path back to the root.
IAO_0000118: tmRNA region

Axiom
annotated target: A region of a tmRNA.
IAO xref: SO:cb
annotated property: IAO_0000115
annotated source: tmRNA_region

Axiom
IAO scope: EXACT
annotated target: tmRNA region
annotated property: IAO_0000118
annotated source: tmRNA_region

LTR_component
type: Class
subclass of: repeat_component
subclass of: Restriction
  on property: part_of
  some values from: long_terminal_repeat
IAO_0000118: LTR component
IAO id: SO:0000848
IAO_0000118: long term repeat component

Axiom
IAO scope: EXACT
annotated target: long term repeat component
annotated property: IAO_0000118
annotated source: LTR_component

Axiom
IAO scope: EXACT
annotated target: LTR component
annotated property: IAO_0000118
annotated source: LTR_component

three_prime_LTR_component
type: Class
subclass of: LTR_component
subclass of: Restriction
  on property: part_of
  some values from: three_prime_LTR
IAO_0000118: 3' long terminal repeat component
IAO id: SO:0000849
IAO_0000118: three prime LTR component

Axiom
annotated target: 3' long terminal repeat component
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: three_prime_LTR_component

Axiom
IAO scope: EXACT
annotated target: three prime LTR component
annotated property: IAO_0000118
annotated source: three_prime_LTR_component

five_prime_LTR_component
type: Class
subclass of: LTR_component
subclass of: Restriction
  on property: part_of
  some values from: five_prime_LTR
IAO_0000118: 5' long term repeat component
IAO id: SO:0000850
IAO_0000118: five prime LTR component

Axiom
annotated target: 5' long term repeat component
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: five_prime_LTR_component

Axiom
IAO scope: EXACT
annotated target: five prime LTR component
annotated property: IAO_0000118
annotated source: five_prime_LTR_component

CDS_region
type: Class
subclass of: mRNA_region
subclass of: Restriction
  on property: part_of
  some values from: CDS
IAO_0000115: A region of a CDS.
IAO_0000118: CDS region
IAO id: SO:0000851
IAO subset: SOFA

Axiom
annotated target: CDS region
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: CDS_region

Axiom
annotated target: A region of a CDS.
IAO xref: SO:cb
annotated property: IAO_0000115
annotated source: CDS_region

exon_region
type: Class
subclass of: transcript_region
subclass of: Restriction
  on property: part_of
  some values from: exon
IAO_0000115: A region of an exon.
IAO id: SO:0000852
IAO subset: SOFA
IAO_0000118: exon region

Axiom
IAO scope: EXACT
annotated target: exon region
annotated property: IAO_0000118
annotated source: exon_region

Axiom
annotated target: A region of an exon.
IAO xref: RSC:cb
annotated property: IAO_0000115
annotated source: exon_region

homologous_region
type: Class
equivalent class: Class
  intersection of: conserved_region
  intersection of: Restriction
    on property: has_quality
    some values from: homologous
subclass of: conserved_region
IAO_0000115: A region that is homologous to another region.
IAO id: SO:0000853
IAO_0000118: homolog
IAO_0000118: homologous region
IAO_0000118: homologue
IAO xref: http://en.wikipedia.org/wiki/Homology_(biology)

Axiom
IAO scope: EXACT
annotated target: homolog
annotated property: IAO_0000118
annotated source: homologous_region

Axiom
IAO scope: EXACT
annotated target: homologous region
annotated property: IAO_0000118
annotated source: homologous_region

Axiom
annotated target: A region that is homologous to another region.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: homologous_region

Axiom
IAO scope: EXACT
annotated target: homologue
annotated property: IAO_0000118
annotated source: homologous_region

paralogous_region
type: Class
equivalent class: Class
  intersection of: homologous_region
  intersection of: Restriction
    on property: has_quality
    some values from: paralogous
subclass of: homologous_region
IAO_0000115: A homologous_region that is paralogous to another region.
comment: A term to be used in conjunction with the paralogous_to relationship.
IAO id: SO:0000854
IAO xref: http://en.wikipedia.org/wiki/Paralog#Paralogy
IAO_0000118: paralog
IAO_0000118: paralogous region
IAO_0000118: paralogue

Axiom
IAO scope: EXACT
annotated target: paralog
annotated property: IAO_0000118
annotated source: paralogous_region

Axiom
IAO scope: EXACT
annotated target: paralogue
annotated property: IAO_0000118
annotated source: paralogous_region

Axiom
annotated target: A homologous_region that is paralogous to another region.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: paralogous_region

Axiom
IAO scope: EXACT
annotated target: paralogous region
annotated property: IAO_0000118
annotated source: paralogous_region

orthologous_region
type: Class
equivalent class: Class
  intersection of: homologous_region
  intersection of: Restriction
    on property: has_quality
    some values from: orthologous
subclass of: homologous_region
IAO_0000115: A homologous_region that is orthologous to another region.
IAO id: SO:0000855
comment: This term should be used in conjunction with the similarity relationships defined in SO.
IAO xref: http://en.wikipedia.org/wiki/Ortholog#Orthology
IAO_0000118: ortholog
IAO_0000118: orthologous region
IAO_0000118: orthologue

Axiom
annotated target: A homologous_region that is orthologous to another region.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: orthologous_region

Axiom
IAO scope: EXACT
annotated target: ortholog
annotated property: IAO_0000118
annotated source: orthologous_region

Axiom
IAO scope: EXACT
annotated target: orthologous region
annotated property: IAO_0000118
annotated source: orthologous_region

Axiom
IAO scope: EXACT
annotated target: orthologue
annotated property: IAO_0000118
annotated source: orthologous_region

conserved
type: Class
subclass of: feature_attribute
IAO id: SO:0000856

homologous
type: Class
subclass of: conserved
IAO id: SO:0000857
IAO_0000115: Similarity due to common ancestry.

Axiom
IAO xref: SO:ke
annotated target: Similarity due to common ancestry.
annotated property: IAO_0000115
annotated source: homologous

orthologous
type: Class
subclass of: homologous
IAO_0000115: An attribute describing a kind of homology where divergence occured after a speciation event.
IAO id: SO:0000858

Axiom
annotated target: An attribute describing a kind of homology where divergence occured after a speciation event.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: orthologous

paralogous
type: Class
subclass of: homologous
IAO_0000115: An attribute describing a kind of homology where divergence occurred after a duplication event.
IAO id: SO:0000859

Axiom
annotated target: An attribute describing a kind of homology where divergence occurred after a duplication event.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: paralogous

syntenic
type: Class
subclass of: conserved
IAO_0000115: Attribute describing sequence regions occurring in same order on chromosome of different species.
IAO id: SO:0000860
IAO xref: http://en.wikipedia.org/wiki/Syntenic

Axiom
annotated target: Attribute describing sequence regions occurring in same order on chromosome of different species.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: syntenic

capped_primary_transcript
type: Class
equivalent class: Class
  intersection of: primary_transcript
  intersection of: Restriction
    on property: adjacent_to
    some values from: cap
  intersection of: Restriction
    on property: has_quality
    some values from: capped
subclass of: primary_transcript
IAO_0000115: A primary transcript that is capped.
IAO id: SO:0000861
IAO_0000118: capped primary transcript

Axiom
annotated target: A primary transcript that is capped.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: capped_primary_transcript

Axiom
IAO scope: EXACT
annotated target: capped primary transcript
annotated property: IAO_0000118
annotated source: capped_primary_transcript

capped_mRNA
type: Class
equivalent class: Class
  intersection of: mRNA
  intersection of: Restriction
    on property: adjacent_to
    some values from: cap
  intersection of: Restriction
    on property: has_quality
    some values from: capped
subclass of: mRNA
IAO_0000115: An mRNA that is capped.
IAO id: SO:0000862
IAO_0000118: capped mRNA

Axiom
annotated target: An mRNA that is capped.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: capped_mRNA

Axiom
IAO scope: EXACT
annotated target: capped mRNA
annotated property: IAO_0000118
annotated source: capped_mRNA

mRNA_attribute
type: Class
subclass of: transcript_attribute
IAO_0000115: An attribute describing an mRNA feature.
IAO id: SO:0000863
IAO_0000118: mRNA attribute

Axiom
annotated target: An attribute describing an mRNA feature.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: mRNA_attribute

Axiom
IAO scope: EXACT
annotated target: mRNA attribute
annotated property: IAO_0000118
annotated source: mRNA_attribute

exemplar
type: Class
subclass of: mRNA_attribute
IAO_0000115: An attribute describing a sequence is representative of a class of similar sequences.
IAO id: SO:0000864

Axiom
annotated target: An attribute describing a sequence is representative of a class of similar sequences.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: exemplar

frameshift
type: Class
subclass of: mRNA_attribute
IAO_0000115: An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3.
IAO id: SO:0000865
IAO xref: http://en.wikipedia.org/wiki/Frameshift

Axiom
annotated target: An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: frameshift

minus_1_frameshift
type: Class
subclass of: frameshift
IAO_0000115: A frameshift caused by deleting one base.
IAO id: SO:0000866
IAO_0000118: minus 1 frameshift

Axiom
IAO scope: EXACT
annotated target: minus 1 frameshift
annotated property: IAO_0000118
annotated source: minus_1_frameshift

Axiom
annotated target: A frameshift caused by deleting one base.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: minus_1_frameshift

minus_2_frameshift
type: Class
subclass of: frameshift
IAO_0000115: A frameshift caused by deleting two bases.
IAO id: SO:0000867
IAO_0000118: minus 2 frameshift

Axiom
IAO scope: EXACT
annotated target: minus 2 frameshift
annotated property: IAO_0000118
annotated source: minus_2_frameshift

Axiom
annotated target: A frameshift caused by deleting two bases.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: minus_2_frameshift

plus_1_frameshift
type: Class
subclass of: frameshift
IAO_0000115: A frameshift caused by inserting one base.
IAO id: SO:0000868
IAO_0000118: plus 1 frameshift

Axiom
IAO scope: EXACT
annotated target: plus 1 frameshift
annotated property: IAO_0000118
annotated source: plus_1_frameshift

Axiom
annotated target: A frameshift caused by inserting one base.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: plus_1_frameshift

plus_2_framshift
type: Class
subclass of: frameshift
IAO_0000115: A frameshift caused by inserting two bases.
IAO id: SO:0000869
IAO_0000118: plus 2 framshift

Axiom
IAO scope: EXACT
annotated target: plus 2 framshift
annotated property: IAO_0000118
annotated source: plus_2_framshift

Axiom
annotated target: A frameshift caused by inserting two bases.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: plus_2_framshift

trans_spliced
type: Class
subclass of: transcript_attribute
IAO_0000115: An attribute describing transcript sequence that is created by splicing exons from diferent genes.
IAO id: SO:0000870
IAO_0000118: trans-spliced

Axiom
IAO scope: EXACT
annotated target: trans-spliced
annotated property: IAO_0000118
annotated source: trans_spliced

Axiom
annotated target: An attribute describing transcript sequence that is created by splicing exons from diferent genes.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: trans_spliced

polyadenylated_mRNA
type: Class
equivalent class: Class
  intersection of: mRNA
  intersection of: Restriction
    on property: adjacent_to
    some values from: polyA_sequence
  intersection of: Restriction
    on property: has_quality
    some values from: polyadenylated
subclass of: mRNA
IAO_0000115: An mRNA that is polyadenylated.
IAO id: SO:0000871
IAO_0000118: polyadenylated mRNA

Axiom
IAO scope: EXACT
annotated target: polyadenylated mRNA
annotated property: IAO_0000118
annotated source: polyadenylated_mRNA

Axiom
annotated target: An mRNA that is polyadenylated.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: polyadenylated_mRNA

trans_spliced_mRNA
type: Class
equivalent class: Class
  intersection of: mRNA
  intersection of: Restriction
    on property: adjacent_to
    some values from: spliced_leader_RNA
  intersection of: Restriction
    on property: has_quality
    some values from: trans_spliced
subclass of: mRNA
subclass of: trans_spliced_transcript
IAO_0000115: An mRNA that is trans-spliced.
IAO id: SO:0000872
IAO_0000118: trans-spliced mRNA

Axiom
annotated target: An mRNA that is trans-spliced.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: trans_spliced_mRNA

Axiom
IAO scope: EXACT
annotated target: trans-spliced mRNA
annotated property: IAO_0000118
annotated source: trans_spliced_mRNA

edited_transcript
type: Class
equivalent class: Class
  intersection of: transcript
  intersection of: Restriction
    on property: has_quality
    some values from: edited
subclass of: transcript
subclass of: Restriction
  on property: guided_by
  some values from: guide_RNA
subclass of: Restriction
  on property: has_part
  some values from: anchor_binding_site
IAO_0000115: A transcript that is edited.
IAO id: SO:0000873
IAO_0000118: edited transcript

Axiom
IAO scope: EXACT
annotated target: edited transcript
annotated property: IAO_0000118
annotated source: edited_transcript

Axiom
annotated target: A transcript that is edited.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: edited_transcript

edited_transcript_by_A_to_I_substitution
type: Class
subclass of: edited_transcript
IAO_0000115: A transcript that has been edited by A to I substitution.
IAO id: SO:0000874
IAO_0000118: edited transcript by A to I substitution

Axiom
annotated target: A transcript that has been edited by A to I substitution.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: edited_transcript_by_A_to_I_substitution

Axiom
IAO scope: EXACT
annotated target: edited transcript by A to I substitution
annotated property: IAO_0000118
annotated source: edited_transcript_by_A_to_I_substitution

bound_by_protein
type: Class
subclass of: bound_by_factor
IAO_0000115: An attribute describing a sequence that is bound by a protein.
IAO id: SO:0000875
IAO_0000118: bound by protein

Axiom
annotated target: An attribute describing a sequence that is bound by a protein.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: bound_by_protein

Axiom
IAO scope: EXACT
annotated target: bound by protein
annotated property: IAO_0000118
annotated source: bound_by_protein

bound_by_nucleic_acid
type: Class
subclass of: bound_by_factor
IAO_0000115: An attribute describing a sequence that is bound by a nucleic acid.
IAO id: SO:0000876
IAO_0000118: bound by nucleic acid

Axiom
annotated target: An attribute describing a sequence that is bound by a nucleic acid.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: bound_by_nucleic_acid

Axiom
IAO scope: EXACT
annotated target: bound by nucleic acid
annotated property: IAO_0000118
annotated source: bound_by_nucleic_acid

alternatively_spliced
type: Class
subclass of: transcript_attribute
IAO_0000115: An attribute describing a situation where a gene may encode for more than 1 transcript.
IAO id: SO:0000877
IAO_0000118: alternatively spliced

Axiom
IAO scope: EXACT
annotated target: alternatively spliced
annotated property: IAO_0000118
annotated source: alternatively_spliced

Axiom
annotated target: An attribute describing a situation where a gene may encode for more than 1 transcript.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: alternatively_spliced

monocistronic
type: Class
subclass of: transcript_attribute
IAO_0000115: An attribute describing a sequence that contains the code for one gene product.
IAO id: SO:0000878

Axiom
annotated target: An attribute describing a sequence that contains the code for one gene product.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: monocistronic

dicistronic
type: Class
subclass of: polycistronic
IAO_0000115: An attribute describing a sequence that contains the code for two gene products.
IAO id: SO:0000879

Axiom
annotated target: An attribute describing a sequence that contains the code for two gene products.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: dicistronic

polycistronic
type: Class
subclass of: transcript_attribute
IAO_0000115: An attribute describing a sequence that contains the code for more than one gene product.
IAO id: SO:0000880

Axiom
annotated target: An attribute describing a sequence that contains the code for more than one gene product.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: polycistronic

recoded
type: Class
subclass of: mRNA_attribute
IAO_0000115: An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations.
IAO id: SO:0000881

Axiom
annotated target: An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: recoded

codon_redefined
type: Class
subclass of: recoded
IAO_0000115: An attribute describing the alteration of codon meaning.
IAO id: SO:0000882
IAO_0000118: codon redefined

Axiom
annotated target: An attribute describing the alteration of codon meaning.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: codon_redefined

Axiom
IAO scope: EXACT
annotated target: codon redefined
annotated property: IAO_0000118
annotated source: codon_redefined

stop_codon_read_through
type: Class
subclass of: recoded_codon
IAO_0000115: A stop codon redefined to be a new amino acid.
IAO id: SO:0000883
IAO_0000118: stop codon read through
IAO_0000118: stop codon readthrough

Axiom
annotated target: A stop codon redefined to be a new amino acid.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: stop_codon_read_through

Axiom
IAO scope: EXACT
annotated target: stop codon read through
annotated property: IAO_0000118
annotated source: stop_codon_read_through

Axiom
IAO scope: RELATED
annotated target: stop codon readthrough
annotated property: IAO_0000118
annotated source: stop_codon_read_through

stop_codon_redefined_as_pyrrolysine
type: Class
subclass of: stop_codon_read_through
IAO_0000115: A stop codon redefined to be the new amino acid, pyrrolysine.
IAO id: SO:0000884
IAO_0000118: stop codon redefined as pyrrolysine

Axiom
IAO scope: EXACT
annotated target: stop codon redefined as pyrrolysine
annotated property: IAO_0000118
annotated source: stop_codon_redefined_as_pyrrolysine

Axiom
annotated target: A stop codon redefined to be the new amino acid, pyrrolysine.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: stop_codon_redefined_as_pyrrolysine

stop_codon_redefined_as_selenocysteine
type: Class
subclass of: stop_codon_read_through
IAO_0000115: A stop codon redefined to be the new amino acid, selenocysteine.
IAO id: SO:0000885
IAO_0000118: stop codon redefined as selenocysteine

Axiom
annotated target: A stop codon redefined to be the new amino acid, selenocysteine.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: stop_codon_redefined_as_selenocysteine

Axiom
IAO scope: EXACT
annotated target: stop codon redefined as selenocysteine
annotated property: IAO_0000118
annotated source: stop_codon_redefined_as_selenocysteine

recoded_by_translational_bypass
type: Class
subclass of: recoded
IAO_0000115: Recoded mRNA where a block of nucleotides is not translated.
IAO id: SO:0000886
IAO_0000118: recoded by translational bypass

Axiom
IAO scope: EXACT
annotated target: recoded by translational bypass
annotated property: IAO_0000118
annotated source: recoded_by_translational_bypass

Axiom
annotated target: Recoded mRNA where a block of nucleotides is not translated.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: recoded_by_translational_bypass

translationally_frameshifted
type: Class
subclass of: recoded
IAO_0000115: Recoding by frameshifting a particular site.
IAO id: SO:0000887
IAO_0000118: translationally frameshifted

Axiom
annotated target: Recoding by frameshifting a particular site.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: translationally_frameshifted

Axiom
IAO scope: EXACT
annotated target: translationally frameshifted
annotated property: IAO_0000118
annotated source: translationally_frameshifted

maternally_imprinted_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: maternally_imprinted
subclass of: epigenetically_modified_gene
IAO_0000115: A gene that is maternally_imprinted.
IAO id: SO:0000888
IAO_0000118: maternally imprinted gene

Axiom
annotated target: A gene that is maternally_imprinted.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: maternally_imprinted_gene

Axiom
IAO scope: EXACT
annotated target: maternally imprinted gene
annotated property: IAO_0000118
annotated source: maternally_imprinted_gene

paternally_imprinted_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: paternally_imprinted
subclass of: epigenetically_modified_gene
IAO_0000115: A gene that is paternally imprinted.
IAO id: SO:0000889
IAO_0000118: paternally imprinted gene

Axiom
annotated target: A gene that is paternally imprinted.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: paternally_imprinted_gene

Axiom
IAO scope: EXACT
annotated target: paternally imprinted gene
annotated property: IAO_0000118
annotated source: paternally_imprinted_gene

post_translationally_regulated_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: post_translationally_regulated
subclass of: gene
IAO_0000115: A gene that is post translationally regulated.
IAO id: SO:0000890
IAO_0000118: post translationally regulated gene

Axiom
IAO scope: EXACT
annotated target: post translationally regulated gene
annotated property: IAO_0000118
annotated source: post_translationally_regulated_gene

Axiom
annotated target: A gene that is post translationally regulated.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: post_translationally_regulated_gene

negatively_autoregulated_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: negatively_autoregulated
subclass of: gene
IAO_0000115: A gene that is negatively autoreguated.
IAO id: SO:0000891
IAO_0000118: negatively autoregulated gene

Axiom
IAO scope: EXACT
annotated target: negatively autoregulated gene
annotated property: IAO_0000118
annotated source: negatively_autoregulated_gene

Axiom
annotated target: A gene that is negatively autoreguated.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: negatively_autoregulated_gene

positively_autoregulated_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: positively_autoregulated
subclass of: gene
IAO_0000115: A gene that is positively autoregulated.
IAO id: SO:0000892
IAO_0000118: positively autoregulated gene

Axiom
IAO scope: EXACT
annotated target: positively autoregulated gene
annotated property: IAO_0000118
annotated source: positively_autoregulated_gene

Axiom
annotated target: A gene that is positively autoregulated.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: positively_autoregulated_gene

silenced
type: Class
subclass of: transcriptionally_repressed
IAO_0000115: An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level.
IAO id: SO:0000893
IAO xref: http://en.wikipedia.org/wiki/Silenced

Axiom
annotated target: An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: silenced

silenced_by_DNA_modification
type: Class
subclass of: silenced
IAO_0000115: An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription.
IAO id: SO:0000894
IAO_0000118: silenced by DNA modification

Axiom
annotated target: An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: silenced_by_DNA_modification

Axiom
IAO scope: EXACT
annotated target: silenced by DNA modification
annotated property: IAO_0000118
annotated source: silenced_by_DNA_modification

silenced_by_DNA_methylation
type: Class
subclass of: silenced_by_DNA_modification
IAO_0000115: An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription.
IAO id: SO:0000895
IAO_0000118: silenced by DNA methylation

Axiom
annotated target: An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: silenced_by_DNA_methylation

Axiom
IAO scope: EXACT
annotated target: silenced by DNA methylation
annotated property: IAO_0000118
annotated source: silenced_by_DNA_methylation

translationally_regulated_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: translationally_regulated
subclass of: gene
IAO_0000115: A gene that is translationally regulated.
IAO id: SO:0000896
IAO_0000118: translationally regulated gene

Axiom
IAO scope: EXACT
annotated target: translationally regulated gene
annotated property: IAO_0000118
annotated source: translationally_regulated_gene

Axiom
annotated target: A gene that is translationally regulated.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: translationally_regulated_gene

allelically_excluded_gene
type: Class
equivalent class: Class
  intersection of: epigenetically_modified_gene
  intersection of: Restriction
    on property: has_quality
    some values from: allelically_excluded
subclass of: epigenetically_modified_gene
IAO_0000115: A gene that is allelically_excluded.
IAO id: SO:0000897
IAO_0000118: allelically excluded gene

Axiom
IAO scope: EXACT
annotated target: allelically excluded gene
annotated property: IAO_0000118
annotated source: allelically_excluded_gene

Axiom
annotated target: A gene that is allelically_excluded.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: allelically_excluded_gene

epigenetically_modified_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: epigenetically_modified
subclass of: gene
subclass of: SO_0001720
IAO_0000115: A gene that is epigenetically modified.
IAO id: SO:0000898
IAO_0000118: epigenetically modified gene

Axiom
IAO scope: EXACT
annotated target: epigenetically modified gene
annotated property: IAO_0000118
annotated source: epigenetically_modified_gene

Axiom
annotated target: A gene that is epigenetically modified.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: epigenetically_modified_gene

nuclear_mitochondrial
type: Class
IAO_0000115: An attribute describing a nuclear pseudogene of a mitochndrial gene.
IAO id: SO:0000899
IAO_0000118: nuclear mitochondrial
deprecated: true

Axiom
IAO scope: EXACT
annotated target: nuclear mitochondrial
annotated property: IAO_0000118
annotated source: nuclear_mitochondrial

Axiom
annotated target: An attribute describing a nuclear pseudogene of a mitochndrial gene.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: nuclear_mitochondrial

processed
type: Class
IAO_0000115: An attribute describing a pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promotors, but often including a polyA tail.
IAO id: SO:0000900
deprecated: true

Axiom
annotated target: An attribute describing a pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promotors, but often including a polyA tail.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: processed

unequally_crossed_over
type: Class
IAO_0000115: An attribute describing a pseudogene that was created by tandem duplication and unequal crossing over during recombination.
IAO id: SO:0000901
deprecated: true
IAO_0000118: unequally crossed over

Axiom
annotated target: An attribute describing a pseudogene that was created by tandem duplication and unequal crossing over during recombination.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: unequally_crossed_over

Axiom
IAO scope: EXACT
annotated target: unequally crossed over
annotated property: IAO_0000118
annotated source: unequally_crossed_over

transgene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: transgenic
subclass of: gene
IAO_0000115: A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another.
IAO id: SO:0000902
IAO xref: http://en.wikipedia.org/wiki/Transgene

Axiom
annotated target: A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: transgene

endogenous_retroviral_sequence
type: Class
subclass of: proviral_location
IAO id: SO:0000903
IAO_0000118: endogenous retroviral sequence

Axiom
IAO scope: EXACT
annotated target: endogenous retroviral sequence
annotated property: IAO_0000118
annotated source: endogenous_retroviral_sequence

rearranged_at_DNA_level
type: Class
subclass of: epigenetically_modified
IAO_0000115: An attribute to describe the sequence of a feature, where the DNA is rearranged.
IAO id: SO:0000904
IAO_0000118: rearranged at DNA level

Axiom
IAO scope: EXACT
annotated target: rearranged at DNA level
annotated property: IAO_0000118
annotated source: rearranged_at_DNA_level

Axiom
annotated target: An attribute to describe the sequence of a feature, where the DNA is rearranged.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: rearranged_at_DNA_level

status
type: Class
subclass of: feature_attribute
IAO_0000115: An attribute describing the status of a feature, based on the available evidence.
IAO id: SO:0000905
comment: This term is the hypernym of attributes and should not be annotated to.

Axiom
annotated target: An attribute describing the status of a feature, based on the available evidence.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: status

independently_known
type: Class
subclass of: status
IAO_0000115: Attribute to describe a feature that is independently known - not predicted.
IAO id: SO:0000906
IAO_0000118: independently known

Axiom
IAO scope: EXACT
annotated target: independently known
annotated property: IAO_0000118
annotated source: independently_known

Axiom
annotated target: Attribute to describe a feature that is independently known - not predicted.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: independently_known

supported_by_sequence_similarity
type: Class
subclass of: predicted
IAO_0000115: An attribute to describe a feature that has been predicted using sequence similarity techniques.
IAO id: SO:0000907
IAO_0000118: supported by sequence similarity

Axiom
annotated target: An attribute to describe a feature that has been predicted using sequence similarity techniques.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: supported_by_sequence_similarity

Axiom
IAO scope: EXACT
annotated target: supported by sequence similarity
annotated property: IAO_0000118
annotated source: supported_by_sequence_similarity

supported_by_domain_match
type: Class
subclass of: supported_by_sequence_similarity
IAO_0000115: An attribute to describe a feature that has been predicted using sequence similarity of a known domain.
IAO id: SO:0000908
IAO_0000118: supported by domain match

Axiom
IAO scope: EXACT
annotated target: supported by domain match
annotated property: IAO_0000118
annotated source: supported_by_domain_match

Axiom
annotated target: An attribute to describe a feature that has been predicted using sequence similarity of a known domain.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: supported_by_domain_match

supported_by_EST_or_cDNA
type: Class
subclass of: supported_by_sequence_similarity
IAO_0000115: An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data.
IAO id: SO:0000909
IAO_0000118: supported by EST or cDNA

Axiom
annotated target: An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: supported_by_EST_or_cDNA

Axiom
IAO scope: EXACT
annotated target: supported by EST or cDNA
annotated property: IAO_0000118
annotated source: supported_by_EST_or_cDNA

orphan
type: Class
subclass of: predicted
IAO id: SO:0000910

predicted_by_ab_initio_computation
type: Class
subclass of: predicted
IAO_0000115: An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity.
IAO id: SO:0000911
IAO_0000118: predicted by ab initio computation

Axiom
IAO scope: EXACT
annotated target: predicted by ab initio computation
annotated property: IAO_0000118
annotated source: predicted_by_ab_initio_computation

Axiom
annotated target: An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: predicted_by_ab_initio_computation

asx_turn
type: Class
subclass of: polypeptide_turn_motif
IAO_0000115: A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2).
IAO alt id: BS:00203
IAO id: SO:0000912
IAO_0000118: asx turn
IAO subset: biosapiens

Axiom
annotated target: A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2).
IAO xref: http://www.ebi.ac.uk/msd-srv/msdmotif/
annotated property: IAO_0000115
annotated source: asx_turn

Axiom
IAO scope: EXACT
annotated target: asx turn
annotated property: IAO_0000118
annotated source: asx_turn

cloned_cDNA_insert
type: Class
equivalent class: Class
  intersection of: clone_insert
  intersection of: Restriction
    on property: has_quality
    some values from: cDNA
subclass of: clone_insert
IAO_0000115: A clone insert made from cDNA.
IAO id: SO:0000913
IAO_0000118: cloned cDNA insert

Axiom
IAO scope: EXACT
annotated target: cloned cDNA insert
annotated property: IAO_0000118
annotated source: cloned_cDNA_insert

Axiom
annotated target: A clone insert made from cDNA.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: cloned_cDNA_insert

cloned_genomic_insert
type: Class
equivalent class: Class
  intersection of: clone_insert
  intersection of: Restriction
    on property: has_quality
    some values from: genomic_DNA
subclass of: clone_insert
IAO_0000115: A clone insert made from genomic DNA.
IAO id: SO:0000914
IAO_0000118: cloned genomic insert

Axiom
annotated target: A clone insert made from genomic DNA.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: cloned_genomic_insert

Axiom
IAO scope: EXACT
annotated target: cloned genomic insert
annotated property: IAO_0000118
annotated source: cloned_genomic_insert

engineered_insert
type: Class
equivalent class: Class
  intersection of: clone_insert
  intersection of: Restriction
    on property: has_quality
    some values from: engineered
subclass of: clone_insert
subclass of: engineered_region
IAO_0000115: A clone insert that is engineered.
IAO id: SO:0000915
IAO_0000118: engineered insert

Axiom
IAO scope: EXACT
annotated target: engineered insert
annotated property: IAO_0000118
annotated source: engineered_insert

Axiom
annotated target: A clone insert that is engineered.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: engineered_insert

edit_operation
type: Class
IAO id: SO:0000916
IAO_0000118: edit operation
deprecated: true

Axiom
IAO scope: EXACT
annotated target: edit operation
annotated property: IAO_0000118
annotated source: edit_operation

insert_U
type: Class
IAO_0000115: An edit to insert a U.
IAO id: SO:0000917
comment: The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.
IAO_0000118: insert U
deprecated: true

Axiom
IAO scope: EXACT
annotated target: insert U
annotated property: IAO_0000118
annotated source: insert_U

Axiom
annotated target: An edit to insert a U.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: insert_U

delete_U
type: Class
IAO_0000115: An edit to delete a uridine.
IAO id: SO:0000918
comment: The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.
IAO_0000118: delete U
deprecated: true

Axiom
IAO scope: EXACT
annotated target: delete U
annotated property: IAO_0000118
annotated source: delete_U

Axiom
annotated target: An edit to delete a uridine.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: delete_U

substitute_A_to_I
type: Class
IAO_0000115: An edit to substitute an I for an A.
IAO id: SO:0000919
IAO_0000118: substitute A to I
deprecated: true

Axiom
annotated target: An edit to substitute an I for an A.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: substitute_A_to_I

Axiom
IAO scope: EXACT
annotated target: substitute A to I
annotated property: IAO_0000118
annotated source: substitute_A_to_I

insert_C
type: Class
IAO_0000115: An edit to insert a cytidine.
IAO id: SO:0000920
IAO_0000118: insert C
deprecated: true

Axiom
IAO scope: EXACT
annotated target: insert C
annotated property: IAO_0000118
annotated source: insert_C

Axiom
annotated target: An edit to insert a cytidine.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: insert_C

insert_dinucleotide
type: Class
IAO_0000115: An edit to insert a dinucleotide.
IAO id: SO:0000921
IAO_0000118: insert dinucleotide
deprecated: true

Axiom
IAO scope: EXACT
annotated target: insert dinucleotide
annotated property: IAO_0000118
annotated source: insert_dinucleotide

Axiom
annotated target: An edit to insert a dinucleotide.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: insert_dinucleotide

substitute_C_to_U
type: Class
IAO_0000115: An edit to substitute an U for a C.
IAO id: SO:0000922
IAO_0000118: substitute C to U
deprecated: true

Axiom
IAO scope: EXACT
annotated target: substitute C to U
annotated property: IAO_0000118
annotated source: substitute_C_to_U

Axiom
annotated target: An edit to substitute an U for a C.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: substitute_C_to_U

insert_G
type: Class
IAO_0000115: An edit to insert a G.
IAO id: SO:0000923
IAO_0000118: insert G
deprecated: true

Axiom
IAO scope: EXACT
annotated target: insert G
annotated property: IAO_0000118
annotated source: insert_G

Axiom
annotated target: An edit to insert a G.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: insert_G

insert_GC
type: Class
IAO_0000115: An edit to insert a GC dinucleotide.
IAO id: SO:0000924
comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
IAO_0000118: insert GC
deprecated: true

Axiom
IAO scope: EXACT
annotated target: insert GC
annotated property: IAO_0000118
annotated source: insert_GC

Axiom
annotated target: An edit to insert a GC dinucleotide.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: insert_GC

insert_GU
type: Class
IAO_0000115: An edit to insert a GU dinucleotide.
IAO id: SO:0000925
comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
IAO_0000118: insert GU
deprecated: true

Axiom
annotated target: An edit to insert a GU dinucleotide.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: insert_GU

Axiom
IAO scope: EXACT
annotated target: insert GU
annotated property: IAO_0000118
annotated source: insert_GU

insert_CU
type: Class
IAO_0000115: An edit to insert a CU dinucleotide.
IAO id: SO:0000926
comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
IAO_0000118: insert CU
deprecated: true

Axiom
annotated target: An edit to insert a CU dinucleotide.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: insert_CU

Axiom
IAO scope: EXACT
annotated target: insert CU
annotated property: IAO_0000118
annotated source: insert_CU

insert_AU
type: Class
IAO_0000115: An edit to insert a AU dinucleotide.
IAO id: SO:0000927
comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
IAO_0000118: insert AU
deprecated: true

Axiom
annotated target: An edit to insert a AU dinucleotide.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: insert_AU

Axiom
IAO scope: EXACT
annotated target: insert AU
annotated property: IAO_0000118
annotated source: insert_AU

insert_AA
type: Class
IAO_0000115: An edit to insert a AA dinucleotide.
IAO id: SO:0000928
comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
IAO_0000118: insert AA
deprecated: true

Axiom
IAO scope: EXACT
annotated target: insert AA
annotated property: IAO_0000118
annotated source: insert_AA

Axiom
annotated target: An edit to insert a AA dinucleotide.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: insert_AA

edited_mRNA
type: Class
equivalent class: Class
  intersection of: mRNA
  intersection of: Restriction
    on property: has_quality
    some values from: edited
subclass of: mRNA
subclass of: edited_transcript
IAO_0000115: An mRNA that is edited.
IAO id: SO:0000929
IAO_0000118: edited mRNA

Axiom
annotated target: An mRNA that is edited.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: edited_mRNA

Axiom
IAO scope: EXACT
annotated target: edited mRNA
annotated property: IAO_0000118
annotated source: edited_mRNA

guide_RNA_region
type: Class
subclass of: mature_transcript_region
subclass of: Restriction
  on property: part_of
  some values from: guide_RNA
IAO_0000115: A region of guide RNA.
IAO id: SO:0000930
IAO_0000118: guide RNA region

Axiom
IAO scope: EXACT
annotated target: guide RNA region
annotated property: IAO_0000118
annotated source: guide_RNA_region

Axiom
annotated target: A region of guide RNA.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: guide_RNA_region

anchor_region
type: Class
subclass of: guide_RNA_region
IAO_0000115: A region of a guide_RNA that base-pairs to a target mRNA.
IAO id: SO:0000931
IAO_0000118: anchor region

Axiom
annotated target: A region of a guide_RNA that base-pairs to a target mRNA.
IAO xref: SO:jk
annotated property: IAO_0000115
annotated source: anchor_region

Axiom
IAO scope: EXACT
annotated target: anchor region
annotated property: IAO_0000118
annotated source: anchor_region

pre_edited_mRNA
type: Class
subclass of: protein_coding_primary_transcript
IAO id: SO:0000932
IAO_0000118: pre-edited mRNA

Axiom
IAO scope: EXACT
annotated target: pre-edited mRNA
annotated property: IAO_0000118
annotated source: pre_edited_mRNA

intermediate
type: Class
subclass of: feature_attribute
IAO_0000115: An attribute to describe a feature between stages of processing.
IAO id: SO:0000933

Axiom
annotated target: An attribute to describe a feature between stages of processing.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: intermediate

miRNA_target_site
type: Class
subclass of: SO_0001655
IAO_0000115: A miRNA target site is a binding site where the molecule is a micro RNA.
IAO id: SO:0000934
IAO_0000118: miRNA target site

Axiom
annotated target: A miRNA target site is a binding site where the molecule is a micro RNA.
IAO xref: FB:cds
annotated property: IAO_0000115
annotated source: miRNA_target_site

Axiom
IAO scope: EXACT
annotated target: miRNA target site
annotated property: IAO_0000118
annotated source: miRNA_target_site

edited_CDS
type: Class
equivalent class: Class
  intersection of: CDS
  intersection of: Restriction
    on property: has_quality
    some values from: edited
subclass of: CDS
IAO_0000115: A CDS that is edited.
IAO id: SO:0000935
IAO_0000118: edited CDS

Axiom
annotated target: A CDS that is edited.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: edited_CDS

Axiom
IAO scope: EXACT
annotated target: edited CDS
annotated property: IAO_0000118
annotated source: edited_CDS

vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
type: Class
subclass of: vertebrate_immune_system_gene_recombination_feature
IAO id: SO:0000936
IAO_0000118: vertebrate immunoglobulin T cell receptor rearranged segment

Axiom
IAO scope: EXACT
annotated target: vertebrate immunoglobulin T cell receptor rearranged segment
annotated property: IAO_0000118
annotated source: vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment

vertebrate_immune_system_feature
type: Class
IAO id: SO:0000937
deprecated: true

vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
type: Class
subclass of: vertebrate_immune_system_gene_recombination_feature
IAO id: SO:0000938
IAO_0000118: vertebrate immunoglobulin T cell receptor rearranged gene cluster

Axiom
IAO scope: EXACT
annotated target: vertebrate immunoglobulin T cell receptor rearranged gene cluster
annotated property: IAO_0000118
annotated source: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster

vertebrate_immune_system_gene_recombination_signal_feature
type: Class
subclass of: vertebrate_immune_system_gene_recombination_feature
IAO id: SO:0000939
IAO_0000118: vertebrate immune system gene recombination signal feature

Axiom
IAO scope: EXACT
annotated target: vertebrate immune system gene recombination signal feature
annotated property: IAO_0000118
annotated source: vertebrate_immune_system_gene_recombination_signal_feature

recombinationally_rearranged
type: Class
subclass of: feature_attribute
IAO id: SO:0000940
IAO_0000118: recombinationally rearranged

Axiom
IAO scope: EXACT
annotated target: recombinationally rearranged
annotated property: IAO_0000118
annotated source: recombinationally_rearranged

recombinationally_rearranged_vertebrate_immune_system_gene
type: Class
subclass of: recombinationally_rearranged_gene
IAO_0000115: A recombinationally rearranged gene of the vertebrate immune system.
IAO id: SO:0000941
IAO_0000118: recombinationally rearranged vertebrate immune system gene

Axiom
IAO scope: EXACT
annotated target: recombinationally rearranged vertebrate immune system gene
annotated property: IAO_0000118
annotated source: recombinationally_rearranged_vertebrate_immune_system_gene

Axiom
annotated target: A recombinationally rearranged gene of the vertebrate immune system.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: recombinationally_rearranged_vertebrate_immune_system_gene

attP_site
type: Class
subclass of: integration_excision_site
subclass of: Restriction
  on property: part_of
  some values from: phage_sequence
IAO_0000115: An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome.
IAO id: SO:0000942
IAO_0000118: attP site

Axiom
IAO scope: EXACT
annotated target: attP site
annotated property: IAO_0000118
annotated source: attP_site

Axiom
annotated target: An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome.
IAO xref: SO:as
annotated property: IAO_0000115
annotated source: attP_site

attB_site
type: Class
subclass of: integration_excision_site
IAO_0000115: An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site.
IAO id: SO:0000943
IAO_0000118: attB site

Axiom
annotated target: An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site.
IAO xref: SO:as
annotated property: IAO_0000115
annotated source: attB_site

Axiom
IAO scope: EXACT
annotated target: attB site
annotated property: IAO_0000118
annotated source: attB_site

attL_site
type: Class
subclass of: integration_excision_site
IAO_0000115: A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site.
IAO id: SO:0000944
IAO_0000118: attBP'
IAO_0000118: attL site

Axiom
IAO scope: RELATED
annotated target: attL site
annotated property: IAO_0000118
annotated source: attL_site

Axiom
IAO scope: RELATED
annotated target: attBP'
annotated property: IAO_0000118
annotated source: attL_site

Axiom
annotated target: A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site.
IAO xref: SO:as
annotated property: IAO_0000115
annotated source: attL_site

attR_site
type: Class
subclass of: integration_excision_site
IAO_0000115: A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site.
IAO id: SO:0000945
IAO_0000118: attPB'
IAO_0000118: attR site

Axiom
IAO scope: RELATED
annotated target: attPB'
annotated property: IAO_0000118
annotated source: attR_site

Axiom
IAO scope: EXACT
annotated target: attR site
annotated property: IAO_0000118
annotated source: attR_site

Axiom
annotated target: A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site.
IAO xref: SO:as
annotated property: IAO_0000115
annotated source: attR_site

integration_excision_site
type: Class
subclass of: site_specific_recombination_target_region
IAO_0000115: A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site.
IAO id: SO:0000946
IAO_0000118: attachment site
IAO_0000118: integration excision site

Axiom
annotated target: A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site.
IAO xref: SO:as
annotated property: IAO_0000115
annotated source: integration_excision_site

Axiom
IAO scope: EXACT
annotated target: integration excision site
annotated property: IAO_0000118
annotated source: integration_excision_site

Axiom
IAO scope: RELATED
annotated target: attachment site
annotated property: IAO_0000118
annotated source: integration_excision_site

resolution_site
type: Class
subclass of: site_specific_recombination_target_region
IAO_0000115: A region specifically recognised by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles.
IAO id: SO:0000947
IAO_0000118: res site
IAO_0000118: resolution site

Axiom
IAO scope: EXACT
annotated target: resolution site
annotated property: IAO_0000118
annotated source: resolution_site

Axiom
IAO scope: EXACT
annotated target: res site
annotated property: IAO_0000118
annotated source: resolution_site

Axiom
annotated target: A region specifically recognised by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles.
IAO xref: SO:as
annotated property: IAO_0000115
annotated source: resolution_site

inversion_site
type: Class
subclass of: site_specific_recombination_target_region
IAO_0000115: A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites.
comment: A target region for site-specific inversion of a DNA region and which carries binding sites for a site-specific recombinase and accessory proteins as well as the site for specific cleavage by the recombinase.
IAO id: SO:0000948
IAO_0000118: inversion site

Axiom
annotated target: A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: inversion_site

Axiom
IAO scope: EXACT
annotated target: inversion site
annotated property: IAO_0000118
annotated source: inversion_site

dif_site
type: Class
subclass of: resolution_site
IAO_0000115: A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase.
IAO id: SO:0000949
IAO_0000118: dif site

Axiom
IAO scope: EXACT
annotated target: dif site
annotated property: IAO_0000118
annotated source: dif_site

Axiom
annotated target: A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase.
IAO xref: SO:as
annotated property: IAO_0000115
annotated source: dif_site

attC_site
type: Class
subclass of: integration_excision_site
subclass of: Restriction
  on property: part_of
  some values from: integron
IAO_0000115: An attC site is a sequence required for the integration of a DNA of an integron.
IAO id: SO:0000950
IAO_0000118: attC site

Axiom
annotated target: An attC site is a sequence required for the integration of a DNA of an integron.
IAO xref: SO:as
annotated property: IAO_0000115
annotated source: attC_site

Axiom
IAO scope: EXACT
annotated target: attC site
annotated property: IAO_0000118
annotated source: attC_site

eukaryotic_terminator
type: Class
subclass of: terminator
IAO id: SO:0000951
IAO_0000118: eukaryotic terminator

Axiom
IAO scope: EXACT
annotated target: eukaryotic terminator
annotated property: IAO_0000118
annotated source: eukaryotic_terminator

oriV
type: Class
subclass of: origin_of_replication
IAO_0000115: An origin of vegetative replication in plasmids and phages.
IAO id: SO:0000952
IAO_0000118: origin of vegetative replication

Axiom
IAO scope: EXACT
annotated target: origin of vegetative replication
annotated property: IAO_0000118
annotated source: oriV

Axiom
annotated target: An origin of vegetative replication in plasmids and phages.
IAO xref: SO:as
annotated property: IAO_0000115
annotated source: oriV

oriC
type: Class
subclass of: origin_of_replication
IAO_0000115: An origin of bacterial chromosome replication.
IAO id: SO:0000953
IAO_0000118: origin of bacterial chromosome replication

Axiom
IAO scope: EXACT
annotated target: origin of bacterial chromosome replication
annotated property: IAO_0000118
annotated source: oriC

Axiom
annotated target: An origin of bacterial chromosome replication.
IAO xref: SO:as
annotated property: IAO_0000115
annotated source: oriC

DNA_chromosome
type: Class
equivalent class: Class
  intersection of: chromosome
  intersection of: Restriction
    on property: has_quality
    some values from: DNA
subclass of: chromosome
IAO_0000118: DNA chromosome
IAO id: SO:0000954
IAO_0000115: Structural unit composed of a self-replicating, DNA molecule.

Axiom
annotated target: DNA chromosome
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DNA_chromosome

Axiom
IAO xref: SO:ma
annotated target: Structural unit composed of a self-replicating, DNA molecule.
annotated property: IAO_0000115
annotated source: DNA_chromosome

double_stranded_DNA_chromosome
type: Class
equivalent class: Class
  intersection of: DNA_chromosome
  intersection of: Restriction
    on property: has_quality
    some values from: double
subclass of: DNA_chromosome
IAO id: SO:0000955
IAO_0000115: Structural unit composed of a self-replicating, double-stranded DNA molecule.
IAO_0000118: double stranded DNA chromosome

Axiom
IAO xref: SO:ma
annotated target: Structural unit composed of a self-replicating, double-stranded DNA molecule.
annotated property: IAO_0000115
annotated source: double_stranded_DNA_chromosome

Axiom
IAO scope: EXACT
annotated target: double stranded DNA chromosome
annotated property: IAO_0000118
annotated source: double_stranded_DNA_chromosome

single_stranded_DNA_chromosome
type: Class
equivalent class: Class
  intersection of: DNA_chromosome
  intersection of: Restriction
    on property: has_quality
    some values from: single
subclass of: DNA_chromosome
IAO id: SO:0000956
IAO_0000115: Structural unit composed of a self-replicating, single-stranded DNA molecule.
IAO_0000118: single stranded DNA chromosome

Axiom
IAO scope: EXACT
annotated target: single stranded DNA chromosome
annotated property: IAO_0000118
annotated source: single_stranded_DNA_chromosome

Axiom
IAO xref: SO:ma
annotated target: Structural unit composed of a self-replicating, single-stranded DNA molecule.
annotated property: IAO_0000115
annotated source: single_stranded_DNA_chromosome

linear_double_stranded_DNA_chromosome
type: Class
equivalent class: Class
  intersection of: double_stranded_DNA_chromosome
  intersection of: Restriction
    on property: has_quality
    some values from: linear
subclass of: double_stranded_DNA_chromosome
IAO id: SO:0000957
IAO_0000115: Structural unit composed of a self-replicating, double-stranded, linear DNA molecule.
IAO_0000118: linear double stranded DNA chromosome

Axiom
IAO scope: EXACT
annotated target: linear double stranded DNA chromosome
annotated property: IAO_0000118
annotated source: linear_double_stranded_DNA_chromosome

Axiom
IAO xref: SO:ma
annotated target: Structural unit composed of a self-replicating, double-stranded, linear DNA molecule.
annotated property: IAO_0000115
annotated source: linear_double_stranded_DNA_chromosome

circular_double_stranded_DNA_chromosome
type: Class
equivalent class: Class
  intersection of: double_stranded_DNA_chromosome
  intersection of: Restriction
    on property: has_quality
    some values from: circular
subclass of: double_stranded_DNA_chromosome
IAO id: SO:0000958
IAO_0000115: Structural unit composed of a self-replicating, double-stranded, circular DNA molecule.
IAO_0000118: circular double stranded DNA chromosome

Axiom
IAO xref: SO:ma
annotated target: Structural unit composed of a self-replicating, double-stranded, circular DNA molecule.
annotated property: IAO_0000115
annotated source: circular_double_stranded_DNA_chromosome

Axiom
IAO scope: EXACT
annotated target: circular double stranded DNA chromosome
annotated property: IAO_0000118
annotated source: circular_double_stranded_DNA_chromosome

linear_single_stranded_DNA_chromosome
type: Class
equivalent class: Class
  intersection of: single_stranded_DNA_chromosome
  intersection of: Restriction
    on property: has_quality
    some values from: linear
subclass of: single_stranded_DNA_chromosome
IAO id: SO:0000959
IAO_0000115: Structural unit composed of a self-replicating, single-stranded, linear DNA molecule.
IAO_0000118: linear single stranded DNA chromosome

Axiom
IAO xref: SO:ma
annotated target: Structural unit composed of a self-replicating, single-stranded, linear DNA molecule.
annotated property: IAO_0000115
annotated source: linear_single_stranded_DNA_chromosome

Axiom
IAO scope: EXACT
annotated target: linear single stranded DNA chromosome
annotated property: IAO_0000118
annotated source: linear_single_stranded_DNA_chromosome

circular_single_stranded_DNA_chromosome
type: Class
equivalent class: Class
  intersection of: single_stranded_DNA_chromosome
  intersection of: Restriction
    on property: has_quality
    some values from: circular
subclass of: single_stranded_DNA_chromosome
IAO id: SO:0000960
IAO_0000115: Structural unit composed of a self-replicating, single-stranded, circular DNA molecule.
IAO_0000118: circular single stranded DNA chromosome

Axiom
IAO scope: EXACT
annotated target: circular single stranded DNA chromosome
annotated property: IAO_0000118
annotated source: circular_single_stranded_DNA_chromosome

Axiom
IAO xref: SO:ma
annotated target: Structural unit composed of a self-replicating, single-stranded, circular DNA molecule.
annotated property: IAO_0000115
annotated source: circular_single_stranded_DNA_chromosome

RNA_chromosome
type: Class
equivalent class: Class
  intersection of: chromosome
  intersection of: Restriction
    on property: has_quality
    some values from: RNA
subclass of: chromosome
IAO_0000118: RNA chromosome
IAO id: SO:0000961
IAO_0000115: Structural unit composed of a self-replicating, RNA molecule.

Axiom
IAO xref: SO:ma
annotated target: Structural unit composed of a self-replicating, RNA molecule.
annotated property: IAO_0000115
annotated source: RNA_chromosome

Axiom
IAO scope: EXACT
annotated target: RNA chromosome
annotated property: IAO_0000118
annotated source: RNA_chromosome

single_stranded_RNA_chromosome
type: Class
equivalent class: Class
  intersection of: RNA_chromosome
  intersection of: Restriction
    on property: has_quality
    some values from: single
subclass of: RNA_chromosome
IAO id: SO:0000962
IAO_0000115: Structural unit composed of a self-replicating, single-stranded RNA molecule.
IAO_0000118: single stranded RNA chromosome

Axiom
IAO xref: SO:ma
annotated target: Structural unit composed of a self-replicating, single-stranded RNA molecule.
annotated property: IAO_0000115
annotated source: single_stranded_RNA_chromosome

Axiom
IAO scope: EXACT
annotated target: single stranded RNA chromosome
annotated property: IAO_0000118
annotated source: single_stranded_RNA_chromosome

linear_single_stranded_RNA_chromosome
type: Class
equivalent class: Class
  intersection of: single_stranded_RNA_chromosome
  intersection of: Restriction
    on property: has_quality
    some values from: linear
subclass of: single_stranded_RNA_chromosome
IAO id: SO:0000963
IAO_0000115: Structural unit composed of a self-replicating, single-stranded, linear RNA molecule.
IAO_0000118: linear single stranded RNA chromosome

Axiom
IAO scope: EXACT
annotated target: linear single stranded RNA chromosome
annotated property: IAO_0000118
annotated source: linear_single_stranded_RNA_chromosome

Axiom
IAO xref: SO:ma
annotated target: Structural unit composed of a self-replicating, single-stranded, linear RNA molecule.
annotated property: IAO_0000115
annotated source: linear_single_stranded_RNA_chromosome

linear_double_stranded_RNA_chromosome
type: Class
equivalent class: Class
  intersection of: double_stranded_RNA_chromosome
  intersection of: Restriction
    on property: has_quality
    some values from: linear
subclass of: double_stranded_RNA_chromosome
IAO id: SO:0000964
IAO_0000115: Structural unit composed of a self-replicating, double-stranded, linear RNA molecule.
IAO_0000118: linear double stranded RNA chromosome

Axiom
IAO xref: SO:ma
annotated target: Structural unit composed of a self-replicating, double-stranded, linear RNA molecule.
annotated property: IAO_0000115
annotated source: linear_double_stranded_RNA_chromosome

Axiom
IAO scope: EXACT
annotated target: linear double stranded RNA chromosome
annotated property: IAO_0000118
annotated source: linear_double_stranded_RNA_chromosome

double_stranded_RNA_chromosome
type: Class
equivalent class: Class
  intersection of: RNA_chromosome
  intersection of: Restriction
    on property: has_quality
    some values from: double
subclass of: RNA_chromosome
IAO id: SO:0000965
IAO_0000115: Structural unit composed of a self-replicating, double-stranded RNA molecule.
IAO_0000118: double stranded RNA chromosome

Axiom
IAO xref: SO:ma
annotated target: Structural unit composed of a self-replicating, double-stranded RNA molecule.
annotated property: IAO_0000115
annotated source: double_stranded_RNA_chromosome

Axiom
IAO scope: EXACT
annotated target: double stranded RNA chromosome
annotated property: IAO_0000118
annotated source: double_stranded_RNA_chromosome

circular_single_stranded_RNA_chromosome
type: Class
equivalent class: Class
  intersection of: single_stranded_RNA_chromosome
  intersection of: Restriction
    on property: has_quality
    some values from: circular
subclass of: single_stranded_RNA_chromosome
IAO id: SO:0000966
IAO_0000115: Structural unit composed of a self-replicating, single-stranded, circular DNA molecule.
IAO_0000118: circular single stranded RNA chromosome

Axiom
IAO scope: EXACT
annotated target: circular single stranded RNA chromosome
annotated property: IAO_0000118
annotated source: circular_single_stranded_RNA_chromosome

Axiom
IAO xref: SO:ma
annotated target: Structural unit composed of a self-replicating, single-stranded, circular DNA molecule.
annotated property: IAO_0000115
annotated source: circular_single_stranded_RNA_chromosome

circular_double_stranded_RNA_chromosome
type: Class
equivalent class: Class
  intersection of: double_stranded_RNA_chromosome
  intersection of: Restriction
    on property: has_quality
    some values from: circular
subclass of: double_stranded_RNA_chromosome
IAO id: SO:0000967
IAO_0000115: Structural unit composed of a self-replicating, double-stranded, circular RNA molecule.
IAO_0000118: circular double stranded RNA chromosome

Axiom
IAO xref: SO:ma
annotated target: Structural unit composed of a self-replicating, double-stranded, circular RNA molecule.
annotated property: IAO_0000115
annotated source: circular_double_stranded_RNA_chromosome

Axiom
IAO scope: EXACT
annotated target: circular double stranded RNA chromosome
annotated property: IAO_0000118
annotated source: circular_double_stranded_RNA_chromosome

sequence_replication_mode
type: Class
IAO id: SO:0000968
comment: This has been obsoleted as it represents a process. replaced_by: GO:0034961.
IAO_0000118: sequence replication mode
deprecated: true

Axiom
IAO scope: EXACT
annotated target: sequence replication mode
annotated property: IAO_0000118
annotated source: sequence_replication_mode

rolling_circle
type: Class
IAO id: SO:0000969
comment: This has been obsoleted as it represents a process. replaced_by: GO:0070581.
IAO xref: http://en.wikipedia.org/wiki/Rolling_circle
IAO_0000118: rolling circle
deprecated: true

Axiom
IAO scope: EXACT
annotated target: rolling circle
annotated property: IAO_0000118
annotated source: rolling_circle

theta_replication
type: Class
IAO id: SO:0000970
comment: This has been obsoleted as it represents a process. replaced_by: GO:0070582
IAO_0000118: theta replication
deprecated: true

Axiom
IAO scope: EXACT
annotated target: theta replication
annotated property: IAO_0000118
annotated source: theta_replication

DNA_replication_mode
type: Class
IAO_0000118: DNA replication mode
IAO id: SO:0000971
comment: This has been obsoleted as it represents a process. replaced_by: GO:0006260.
deprecated: true

Axiom
annotated target: DNA replication mode
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DNA_replication_mode

RNA_replication_mode
type: Class
IAO_0000118: RNA replication mode
IAO id: SO:0000972
comment: This has been obsoleted as it represents a process. replaced_by: GO:0034961.
deprecated: true

Axiom
IAO scope: EXACT
annotated target: RNA replication mode
annotated property: IAO_0000118
annotated source: RNA_replication_mode

insertion_sequence
type: Class
subclass of: terminal_inverted_repeat_element
IAO_0000115: A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats.
IAO_0000118: IS
IAO id: SO:0000973
IAO xref: http://en.wikipedia.org/wiki/Insertion_sequence
IAO_0000118: insertion sequence

Axiom
annotated target: IS
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: insertion_sequence

Axiom
IAO scope: EXACT
annotated target: insertion sequence
annotated property: IAO_0000118
annotated source: insertion_sequence

Axiom
annotated target: A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats.
IAO xref: SO:as
annotated property: IAO_0000115
annotated source: insertion_sequence

minicircle_gene
type: Class
equivalent class: Class
  intersection of: kinetoplast_gene
  intersection of: Restriction
    on property: part_of
    some values from: minicircle
subclass of: kinetoplast_gene
IAO id: SO:0000975
IAO_0000118: minicircle gene

Axiom
IAO scope: EXACT
annotated target: minicircle gene
annotated property: IAO_0000118
annotated source: minicircle_gene

cryptic
type: Class
subclass of: feature_attribute
IAO_0000115: A feature_attribute describing a feature that is not manifest under normal conditions.
IAO id: SO:0000976

Axiom
annotated target: A feature_attribute describing a feature that is not manifest under normal conditions.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: cryptic

anchor_binding_site
type: Class
subclass of: transcript_region
comment: Part of an edited transcript only.
IAO id: SO:0000977
IAO_0000118: anchor binding site

Axiom
IAO scope: EXACT
annotated target: anchor binding site
annotated property: IAO_0000118
annotated source: anchor_binding_site

template_region
type: Class
subclass of: guide_RNA_region
IAO_0000115: A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA.
IAO id: SO:0000978
IAO_0000118: information region
IAO_0000118: template region

Axiom
IAO scope: EXACT
annotated target: information region
annotated property: IAO_0000118
annotated source: template_region

Axiom
IAO scope: EXACT
annotated target: template region
annotated property: IAO_0000118
annotated source: template_region

Axiom
annotated target: A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA.
IAO xref: SO:jk
annotated property: IAO_0000115
annotated source: template_region

gRNA_encoding
type: Class
subclass of: non_protein_coding
IAO_0000115: A non-protein_coding gene that encodes a guide_RNA.
IAO id: SO:0000979
IAO_0000118: gRNA encoding

Axiom
IAO scope: EXACT
annotated target: gRNA encoding
annotated property: IAO_0000118
annotated source: gRNA_encoding

Axiom
annotated target: A non-protein_coding gene that encodes a guide_RNA.
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: gRNA_encoding

minicircle
type: Class
subclass of: replicon
subclass of: Restriction
  on property: part_of
  some values from: kinetoplast
IAO_0000115: A minicircle is a replicon, part of a kinetoplast, that encodes for guide RNAs.
IAO alt id: SO:0000974
IAO id: SO:0000980
IAO xref: http://en.wikipedia.org/wiki/Minicircle
IAO_0000118: minicircle_chromosome

Axiom
IAO scope: EXACT
annotated target: minicircle_chromosome
annotated property: IAO_0000118
annotated source: minicircle

Axiom
annotated target: A minicircle is a replicon, part of a kinetoplast, that encodes for guide RNAs.
IAO xref: PMID:8395055
annotated property: IAO_0000115
annotated source: minicircle

rho_dependent_bacterial_terminator
type: Class
subclass of: bacterial_terminator
IAO id: SO:0000981
IAO_0000118: rho dependent bacterial terminator

Axiom
IAO scope: EXACT
annotated target: rho dependent bacterial terminator
annotated property: IAO_0000118
annotated source: rho_dependent_bacterial_terminator

rho_independent_bacterial_terminator
type: Class
subclass of: bacterial_terminator
IAO id: SO:0000982
IAO_0000118: rho independent bacterial terminator

Axiom
IAO scope: EXACT
annotated target: rho independent bacterial terminator
annotated property: IAO_0000118
annotated source: rho_independent_bacterial_terminator

strand_attribute
type: Class
subclass of: feature_attribute
comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
IAO id: SO:0000983
IAO_0000118: strand attribute

Axiom
IAO scope: EXACT
annotated target: strand attribute
annotated property: IAO_0000118
annotated source: strand_attribute

single
type: Class
subclass of: strand_attribute
comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
IAO id: SO:0000984

double
type: Class
subclass of: strand_attribute
comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
IAO id: SO:0000985

topology_attribute
type: Class
subclass of: polymer_attribute
comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
IAO id: SO:0000986
IAO_0000118: topology attribute

Axiom
IAO scope: EXACT
annotated target: topology attribute
annotated property: IAO_0000118
annotated source: topology_attribute

linear
type: Class
subclass of: topology_attribute
disjoint with: circular
IAO_0000115: A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue.
comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
IAO id: SO:0000987
IAO_0000118: two-ended

Axiom
annotated target: A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue.
IAO xref: SO:cb
annotated property: IAO_0000115
annotated source: linear

Axiom
IAO scope: RELATED
annotated target: two-ended
annotated property: IAO_0000118
annotated source: linear

circular
type: Class
subclass of: topology_attribute
IAO_0000115: A quality of a nucleotide polymer that has no terminal nucleotide residues.
comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
IAO id: SO:0000988
IAO_0000118: zero-ended

Axiom
IAO scope: RELATED
annotated target: zero-ended
annotated property: IAO_0000118
annotated source: circular

Axiom
annotated target: A quality of a nucleotide polymer that has no terminal nucleotide residues.
IAO xref: SO:cb
annotated property: IAO_0000115
annotated source: circular

class_II_RNA
type: Class
subclass of: ncRNA
IAO id: SO:0000989
IAO_0000115: Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm.
IAO_0000118: class II RNA

Axiom
IAO xref: PMID:15333696
annotated target: Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm.
annotated property: IAO_0000115
annotated source: class_II_RNA

Axiom
IAO scope: EXACT
annotated target: class II RNA
annotated property: IAO_0000118
annotated source: class_II_RNA

class_I_RNA
type: Class
subclass of: ncRNA
comment: Requested by Karen Pilcher - Dictybase. song-Term Tracker-1574577.
IAO id: SO:0000990
IAO_0000115: Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm.
IAO_0000118: class I RNA

Axiom
IAO scope: EXACT
annotated target: class I RNA
annotated property: IAO_0000118
annotated source: class_I_RNA

Axiom
IAO xref: PMID:15333696
annotated target: Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm.
annotated property: IAO_0000115
annotated source: class_I_RNA

genomic_DNA
type: Class
subclass of: DNA
IAO id: SO:0000991
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
IAO_0000118: genomic DNA

Axiom
IAO scope: EXACT
annotated target: genomic DNA
annotated property: IAO_0000118
annotated source: genomic_DNA

BAC_cloned_genomic_insert
type: Class
equivalent class: Class
  intersection of: cloned_genomic_insert
  intersection of: Restriction
    on property: derives_from
    some values from: BAC
subclass of: cloned_genomic_insert
IAO_0000118: BAC cloned genomic insert
comment: Requested by Andy Schroder - Flybase Harvard, Nov 2006.
IAO id: SO:0000992

Axiom
annotated target: BAC cloned genomic insert
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: BAC_cloned_genomic_insert

consensus
type: Class
subclass of: status
IAO id: SO:0000993
comment: Term added Dec 06 to comply with mapping to MGED terms. It should be used to generate consensus regions. The specific cross product terms they require are consensus_region and consensus_mRNA.

consensus_region
type: Class
equivalent class: Class
  intersection of: region
  intersection of: Restriction
    on property: has_quality
    some values from: consensus
subclass of: SO_0001410
comment: DO not obsolete without considering MGED mapping.
IAO id: SO:0000994
IAO_0000118: consensus region

Axiom
IAO scope: EXACT
annotated target: consensus region
annotated property: IAO_0000118
annotated source: consensus_region

consensus_mRNA
type: Class
equivalent class: Class
  intersection of: mRNA
  intersection of: Restriction
    on property: has_quality
    some values from: consensus
subclass of: mRNA
subclass of: consensus_region
comment: DO not obsolete without considering MGED mapping.
IAO id: SO:0000995
IAO_0000118: consensus mRNA

Axiom
IAO scope: EXACT
annotated target: consensus mRNA
annotated property: IAO_0000118
annotated source: consensus_mRNA

predicted_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: predicted
subclass of: gene
IAO id: SO:0000996
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
IAO_0000118: predicted gene

Axiom
IAO scope: EXACT
annotated target: predicted gene
annotated property: IAO_0000118
annotated source: predicted_gene

gene_fragment
type: Class
equivalent class: Class
  intersection of: gene_component_region
  intersection of: Restriction
    on property: has_quality
    some values from: fragmentary
subclass of: gene_component_region
IAO id: SO:0000997
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
IAO_0000118: gene fragment

Axiom
IAO scope: EXACT
annotated target: gene fragment
annotated property: IAO_0000118
annotated source: gene_fragment

recursive_splice_site
type: Class
subclass of: SO_0001419
IAO_0000115: A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons.
IAO id: SO:0000998
IAO_0000118: recursive splice site

Axiom
IAO scope: EXACT
annotated target: recursive splice site
annotated property: IAO_0000118
annotated source: recursive_splice_site

Axiom
annotated target: A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons.
IAO xref: http://www.genetics.org/cgi/content/full/170/2/661
annotated property: IAO_0000115
annotated source: recursive_splice_site

BAC_end
type: Class
subclass of: read
subclass of: Restriction
  on property: part_of
  some values from: BAC
IAO_0000115: A region of sequence from the end of a BAC clone that may provide a highly specific marker.
IAO_0000118: BAC end
IAO_0000118: BAC end sequence
IAO_0000118: BES
comment: Requested by Keith Boroevich December, 2006.
IAO id: SO:0000999

Axiom
annotated target: BES
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: BAC_end

Axiom
annotated target: BAC end sequence
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: BAC_end

Axiom
annotated target: A region of sequence from the end of a BAC clone that may provide a highly specific marker.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: BAC_end

Axiom
annotated target: BAC end
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: BAC_end

rRNA_16S
type: Class
subclass of: small_subunit_rRNA
IAO_0000118: 16S SSU RNA
IAO_0000118: 16S rRNA
IAO_0000118: 16S ribosomal RNA
IAO_0000115: A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome.
IAO id: SO:0001000
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/16S_ribosomal_RNA
IAO_0000118: rRNA 16S

Axiom
annotated target: 16S rRNA
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: rRNA_16S

Axiom
annotated target: 16S ribosomal RNA
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: rRNA_16S

Axiom
annotated target: 16S SSU RNA
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: rRNA_16S

Axiom
annotated target: A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: rRNA_16S

Axiom
IAO scope: EXACT
annotated target: rRNA 16S
annotated property: IAO_0000118
annotated source: rRNA_16S

rRNA_23S
type: Class
subclass of: large_subunit_rRNA
IAO_0000118: 23S LSU rRNA
IAO_0000118: 23S rRNA
IAO_0000118: 23S ribosomal RNA
IAO_0000115: A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome.
IAO id: SO:0001001
IAO subset: SOFA
IAO_0000118: rRNA 23S

Axiom
annotated target: 23S rRNA
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: rRNA_23S

Axiom
annotated target: A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: rRNA_23S

Axiom
annotated target: 23S LSU rRNA
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: rRNA_23S

Axiom
annotated target: 23S ribosomal RNA
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: rRNA_23S

Axiom
IAO scope: EXACT
annotated target: rRNA 23S
annotated property: IAO_0000118
annotated source: rRNA_23S

rRNA_25S
type: Class
subclass of: large_subunit_rRNA
IAO_0000118: 25S LSU rRNA
IAO_0000118: 25S rRNA
IAO_0000118: 25S ribosomal RNA
IAO_0000115: A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes.
IAO id: SO:0001002
IAO subset: SOFA
IAO_0000118: rRNA 25S

Axiom
annotated target: A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes.
IAO xref: RSC:cb
annotated property: IAO_0000115
annotated source: rRNA_25S

Axiom
IAO scope: EXACT
annotated target: rRNA 25S
annotated property: IAO_0000118
annotated source: rRNA_25S

Axiom
annotated target: 25S LSU rRNA
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: rRNA_25S

Axiom
annotated target: 25S ribosomal RNA
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: rRNA_25S

Axiom
annotated target: 25S rRNA
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: rRNA_25S

solo_LTR
type: Class
subclass of: long_terminal_repeat
IAO_0000115: A recombination product between the 2 LTR of the same element.
comment: Requested by Hadi Quesneville January 2007.
IAO id: SO:0001003
IAO_0000118: solo LTR

Axiom
IAO scope: EXACT
annotated target: solo LTR
annotated property: IAO_0000118
annotated source: solo_LTR

Axiom
annotated target: A recombination product between the 2 LTR of the same element.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: solo_LTR

low_complexity
type: Class
subclass of: status
IAO id: SO:0001004
IAO_0000118: low complexity

Axiom
IAO scope: EXACT
annotated target: low complexity
annotated property: IAO_0000118
annotated source: low_complexity

low_complexity_region
type: Class
equivalent class: Class
  intersection of: region
  intersection of: Restriction
    on property: has_quality
    some values from: low_complexity
subclass of: SO_0001410
IAO id: SO:0001005
IAO_0000118: low complexity region

Axiom
IAO scope: EXACT
annotated target: low complexity region
annotated property: IAO_0000118
annotated source: low_complexity_region

prophage
type: Class
subclass of: proviral_region
IAO_0000115: A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated \"island\".
IAO id: SO:0001006
IAO xref: http://en.wikipedia.org/wiki/Prophage

Axiom
annotated target: A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated \"island\".
IAO xref: GOC:jl
annotated property: IAO_0000115
annotated source: prophage

cryptic_prophage
type: Class
subclass of: genomic_island
IAO_0000115: A remnant of an integrated prophage in the host genome or an \"island\" in the host genome that includes phage like-genes.
IAO id: SO:0001007
comment: This is not cryptic in the same sense as a cryptic gene or cryptic splice site.
IAO_0000118: cryptic prophage
IAO xref: http://ecoliwiki.net/colipedia/index.php/Category\:Cryptic_Prophage.w

Axiom
IAO scope: EXACT
annotated target: cryptic prophage
annotated property: IAO_0000118
annotated source: cryptic_prophage

Axiom
annotated target: A remnant of an integrated prophage in the host genome or an \"island\" in the host genome that includes phage like-genes.
IAO xref: GOC:jl
annotated property: IAO_0000115
annotated source: cryptic_prophage

tetraloop
type: Class
subclass of: stem_loop
IAO_0000115: A base-paired stem with loop of 4 non-hydrogen bonded nucleotides.
IAO id: SO:0001008
IAO xref: http://en.wikipedia.org/wiki/Tetraloop

Axiom
annotated target: A base-paired stem with loop of 4 non-hydrogen bonded nucleotides.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: tetraloop

DNA_constraint_sequence
type: Class
subclass of: ds_oligo
IAO_0000115: A double-stranded DNA used to control macromolecular structure and function.
IAO_0000118: DNA constraint
IAO_0000118: DNA constraint sequence
IAO id: SO:0001009

Axiom
annotated target: DNA constraint
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DNA_constraint_sequence

Axiom
annotated target: DNA constraint sequence
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DNA_constraint_sequence

Axiom
annotated target: A double-stranded DNA used to control macromolecular structure and function.
annotated property: IAO_0000115
annotated source: DNA_constraint_sequence

i_motif
type: Class
subclass of: DNA_sequence_secondary_structure
IAO_0000115: A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH.
IAO id: SO:0001010
IAO_0000118: i motif
IAO_0000118: short intercalated motif

Axiom
IAO scope: EXACT
annotated target: i motif
annotated property: IAO_0000118
annotated source: i_motif

Axiom
annotated target: A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH.
IAO xref: PMID:9753739
annotated property: IAO_0000115
annotated source: i_motif

Axiom
IAO scope: EXACT
annotated target: short intercalated motif
annotated property: IAO_0000118
annotated source: i_motif

PNA_oligo
type: Class
equivalent class: Class
  intersection of: synthetic_oligo
  intersection of: Restriction
    on property: has_quality
    some values from: PNA
subclass of: synthetic_oligo
IAO_0000118: PNA oligo
IAO_0000115: Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds.
IAO id: SO:0001011
IAO xref: http://en.wikipedia.org/wiki/Peptide_nucleic_acid
IAO_0000118: peptide nucleic acid

Axiom
annotated target: Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: PNA_oligo

Axiom
IAO scope: EXACT
annotated target: peptide nucleic acid
annotated property: IAO_0000118
annotated source: PNA_oligo

Axiom
IAO scope: EXACT
annotated target: PNA oligo
annotated property: IAO_0000118
annotated source: PNA_oligo

DNAzyme
type: Class
equivalent class: Class
  intersection of: oligo
  intersection of: Restriction
    on property: has_quality
    some values from: enzymatic
subclass of: oligo
IAO_0000115: A DNA sequence with catalytic activity.
comment: Added by request from Colin Batchelor.
IAO_0000118: DNA enzyme
IAO id: SO:0001012
IAO_0000118: catalytic DNA
IAO_0000118: deoxyribozyme

Axiom
annotated target: DNA enzyme
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DNAzyme

Axiom
IAO scope: RELATED
annotated target: deoxyribozyme
annotated property: IAO_0000118
annotated source: DNAzyme

Axiom
annotated target: A DNA sequence with catalytic activity.
IAO xref: SO:cb
annotated property: IAO_0000115
annotated source: DNAzyme

Axiom
IAO scope: EXACT
annotated target: catalytic DNA
annotated property: IAO_0000118
annotated source: DNAzyme

MNP
type: Class
subclass of: SO_1000002
IAO_0000115: A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT.
IAO id: SO:0001013
IAO_0000118: multiple nucleotide polymorphism

Axiom
IAO scope: RELATED
annotated target: multiple nucleotide polymorphism
annotated property: IAO_0000118
annotated source: MNP

Axiom
annotated target: A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT.
IAO xref: http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi
annotated property: IAO_0000115
annotated source: MNP

intron_domain
type: Class
subclass of: primary_transcript_region
subclass of: Restriction
  on property: part_of
  some values from: intron
comment: Requested by Colin Batchelor, Feb 2007.
IAO id: SO:0001014
IAO_0000118: intron domain

Axiom
IAO scope: EXACT
annotated target: intron domain
annotated property: IAO_0000118
annotated source: intron_domain

wobble_base_pair
type: Class
subclass of: base_pair
IAO_0000115: A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C.
IAO id: SO:0001015
IAO xref: http://en.wikipedia.org/wiki/Wobble_base_pair
IAO_0000118: wobble base pair
IAO_0000118: wobble pair

Axiom
IAO scope: EXACT
annotated target: wobble base pair
annotated property: IAO_0000118
annotated source: wobble_base_pair

Axiom
annotated target: A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C.
IAO xref: PMID:11256617
annotated property: IAO_0000115
annotated source: wobble_base_pair

Axiom
IAO scope: EXACT
annotated target: wobble pair
annotated property: IAO_0000118
annotated source: wobble_base_pair

internal_guide_sequence
type: Class
subclass of: intron_domain
subclass of: Restriction
  on property: part_of
  some values from: group_I_intron
IAO_0000115: A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity.
IAO_0000118: IGS
IAO id: SO:0001016
IAO_0000118: internal guide sequence

Axiom
annotated target: A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity.
IAO xref: SO:cb
annotated property: IAO_0000115
annotated source: internal_guide_sequence

Axiom
IAO scope: EXACT
annotated target: IGS
annotated property: IAO_0000118
annotated source: internal_guide_sequence

Axiom
IAO scope: EXACT
annotated target: internal guide sequence
annotated property: IAO_0000118
annotated source: internal_guide_sequence

silent_mutation
type: Class
subclass of: SO_0001537
IAO_0000115: A sequence variant that does not affect protein function. Silent mutations may occur in genic ( CDS, UTR, intron etc) and intergenic regions. Silent mutations may have affects on processes such as splicing and regulation.
comment: Added in March 2007 in after meeting with pharmgkb. Although this term is in common usage, it is better to annotate with the most specific term possible, such as synonymous codon, intron variant etc.
IAO id: SO:0001017
IAO xref: http://en.wikipedia.org/wiki/Silent_mutation
IAO_0000118: silent mutation

Axiom
annotated target: A sequence variant that does not affect protein function. Silent mutations may occur in genic ( CDS, UTR, intron etc) and intergenic regions. Silent mutations may have affects on processes such as splicing and regulation.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: silent_mutation

Axiom
IAO scope: EXACT
annotated target: silent mutation
annotated property: IAO_0000118
annotated source: silent_mutation

epitope
type: Class
subclass of: binding_site
IAO_0000115: A binding site that, in the molecule, interacts selectively and non-covalently with antibodies, B cells or T cells.
comment: Requested by Trish Whetzel.
IAO id: SO:0001018
IAO xref: http://en.wikipedia.org/wiki/Epitope

Axiom
annotated target: A binding site that, in the molecule, interacts selectively and non-covalently with antibodies, B cells or T cells.
IAO xref: SO:cb
IAO xref: http://en.wikipedia.org/wiki/Epitope
annotated property: IAO_0000115
annotated source: epitope

copy_number_variation
type: Class
subclass of: sequence_alteration
IAO_0000115: A variation that increases or decreases the copy number of a given region.
IAO_0000118: CNP
IAO_0000118: CNV
IAO id: SO:0001019
IAO subset: SOFA
IAO_0000118: copy number polymorphism
IAO_0000118: copy number variation
IAO xref: http://en.wikipedia.org/wiki/Copy_number_variation

Axiom
annotated target: CNV
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: copy_number_variation

Axiom
IAO scope: EXACT
annotated target: copy number polymorphism
annotated property: IAO_0000118
annotated source: copy_number_variation

Axiom
IAO scope: EXACT
annotated target: copy number variation
annotated property: IAO_0000118
annotated source: copy_number_variation

Axiom
annotated target: A variation that increases or decreases the copy number of a given region.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: copy_number_variation

Axiom
annotated target: CNP
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: copy_number_variation

sequence_variant_affecting_copy_number
type: Class
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
IAO id: SO:0001020
IAO_0100001: SO:0001563
IAO_0000118: mutation affecting copy number
IAO_0000118: sequence variant affecting copy number
deprecated: true

Axiom
IAO scope: EXACT
annotated target: mutation affecting copy number
annotated property: IAO_0000118
annotated source: sequence_variant_affecting_copy_number

Axiom
IAO scope: EXACT
annotated target: sequence variant affecting copy number
annotated property: IAO_0000118
annotated source: sequence_variant_affecting_copy_number

chromosome_breakpoint
type: Class
subclass of: junction
subclass of: Restriction
  on property: part_of
  some values from: chromosome
IAO id: SO:0001021
IAO alt id: SO:0001242
IAO_0000118: aberration breakpoint
IAO_0000118: aberration_junction
IAO_0000118: chromosome breakpoint

Axiom
IAO scope: EXACT
annotated target: aberration_junction
annotated property: IAO_0000118
annotated source: chromosome_breakpoint

Axiom
IAO scope: EXACT
annotated target: chromosome breakpoint
annotated property: IAO_0000118
annotated source: chromosome_breakpoint

Axiom
IAO scope: EXACT
annotated target: aberration breakpoint
annotated property: IAO_0000118
annotated source: chromosome_breakpoint

inversion_breakpoint
type: Class
subclass of: chromosome_breakpoint
IAO id: SO:0001022
IAO_0000115: The point within a chromosome where an inversion begins or ends.
IAO_0000118: inversion breakpoint

Axiom
IAO xref: SO:cb
annotated target: The point within a chromosome where an inversion begins or ends.
annotated property: IAO_0000115
annotated source: inversion_breakpoint

Axiom
IAO scope: EXACT
annotated target: inversion breakpoint
annotated property: IAO_0000118
annotated source: inversion_breakpoint

allele
type: Class
subclass of: SO_0001507
subclass of: Restriction
  on property: variant_of
  some values from: gene
IAO_0000115: An allele is one of a set of coexisting sequence variants of a gene.
IAO id: SO:0001023
IAO_0000118: allelomorph
IAO xref: http://en.wikipedia.org/wiki/Allele

Axiom
IAO scope: EXACT
annotated target: allelomorph
annotated property: IAO_0000118
annotated source: allele

Axiom
annotated target: An allele is one of a set of coexisting sequence variants of a gene.
IAO xref: SO:immuno_workshop
annotated property: IAO_0000115
annotated source: allele

haplotype
type: Class
subclass of: SO_0001507
subclass of: Restriction
  on property: variant_of
  some values from: haplotype_block
IAO_0000115: A haplotype is one of a set of coexisting sequence variants of a haplotype block.
IAO id: SO:0001024
IAO xref: http://en.wikipedia.org/wiki/Haplotype

Axiom
annotated target: A haplotype is one of a set of coexisting sequence variants of a haplotype block.
IAO xref: SO:immuno_workshop
annotated property: IAO_0000115
annotated source: haplotype

polymorphic_sequence_variant
type: Class
subclass of: allele
IAO_0000115: A sequence variant that is segregating in one or more natural populations of a species.
IAO id: SO:0001025
IAO_0000118: polymorphic sequence variant

Axiom
annotated target: A sequence variant that is segregating in one or more natural populations of a species.
IAO xref: SO:immuno_workshop
annotated property: IAO_0000115
annotated source: polymorphic_sequence_variant

Axiom
IAO scope: EXACT
annotated target: polymorphic sequence variant
annotated property: IAO_0000118
annotated source: polymorphic_sequence_variant

genome
type: Class
equivalent class: Class
  intersection of: sequence_collection
  intersection of: Restriction
    on property: has_part
    some values from: replicon
subclass of: sequence_collection
IAO_0000115: A genome is the sum of genetic material within a cell or virion.
IAO id: SO:0001026
IAO xref: http://en.wikipedia.org/wiki/Genome

Axiom
annotated target: A genome is the sum of genetic material within a cell or virion.
IAO xref: SO:immuno_workshop
annotated property: IAO_0000115
annotated source: genome

genotype
type: Class
subclass of: SO_0001507
subclass of: Restriction
  on property: variant_of
  some values from: genome
IAO_0000115: A genotype is a variant genome, complete or incomplete.
IAO id: SO:0001027
IAO xref: http://en.wikipedia.org/wiki/Genotype

Axiom
annotated target: A genotype is a variant genome, complete or incomplete.
IAO xref: SO:immuno_workshop
annotated property: IAO_0000115
annotated source: genotype

diplotype
type: Class
subclass of: SO_0001507
IAO_0000115: A diplotype is a pair of haplotypes from a given individual. It is a genotype where the phase is known.
IAO id: SO:0001028

Axiom
annotated target: A diplotype is a pair of haplotypes from a given individual. It is a genotype where the phase is known.
IAO xref: SO:immuno_workshop
annotated property: IAO_0000115
annotated source: diplotype

direction_attribute
type: Class
subclass of: feature_attribute
IAO id: SO:0001029
IAO_0000118: direction attribute

Axiom
IAO scope: EXACT
annotated target: direction attribute
annotated property: IAO_0000118
annotated source: direction_attribute

forward
type: Class
subclass of: direction_attribute
IAO_0000115: Forward is an attribute of the feature, where the feature is in the 5' to 3' direction.
IAO id: SO:0001030

Axiom
annotated target: Forward is an attribute of the feature, where the feature is in the 5' to 3' direction.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: forward

reverse
type: Class
subclass of: direction_attribute
IAO_0000115: Reverse is an attribute of the feature, where the feature is in the 3' to 5' direction. Again could be applied to primer.
IAO id: SO:0001031

Axiom
annotated target: Reverse is an attribute of the feature, where the feature is in the 3' to 5' direction. Again could be applied to primer.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: reverse

mitochondrial_DNA
type: Class
equivalent class: Class
  intersection of: mitochondrial_sequence
  intersection of: Restriction
    on property: has_quality
    some values from: DNA
subclass of: mitochondrial_sequence
IAO id: SO:0001032
comment: This terms is used by MO.
IAO xref: http://en.wikipedia.org/wiki/Mitochondrial_DNA
IAO_0000118: mitochondrial DNA

Axiom
IAO scope: EXACT
annotated target: mitochondrial DNA
annotated property: IAO_0000118
annotated source: mitochondrial_DNA

chloroplast_DNA
type: Class
equivalent class: Class
  intersection of: chloroplast_sequence
  intersection of: Restriction
    on property: has_quality
    some values from: DNA
subclass of: chloroplast_sequence
IAO id: SO:0001033
comment: This term is used by MO.
IAO_0000118: chloroplast DNA

Axiom
IAO scope: EXACT
annotated target: chloroplast DNA
annotated property: IAO_0000118
annotated source: chloroplast_DNA

mirtron
type: Class
subclass of: intron_domain
IAO_0000115: A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage.
comment: Ruby et al. Nature 448:83 describe a new class of miRNAs that are derived from de-branched introns.
IAO id: SO:0001034

Axiom
annotated target: A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage.
IAO xref: PMID:17589500
IAO xref: SO:ma
annotated property: IAO_0000115
annotated source: mirtron

piRNA
type: Class
subclass of: ncRNA
IAO_0000115: A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements.
IAO id: SO:0001035
IAO xref: http://en.wikipedia.org/wiki/PiRNA
IAO_0000118: piwi-associated RNA

Axiom
annotated target: A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: piRNA

Axiom
IAO scope: EXACT
annotated target: piwi-associated RNA
annotated property: IAO_0000118
annotated source: piRNA

arginyl_tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: arginine_tRNA_primary_transcript
IAO_0000115: A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region.
IAO id: SO:0001036
IAO_0000118: arginyl tRNA

Axiom
annotated target: A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: arginyl_tRNA

Axiom
IAO scope: EXACT
annotated target: arginyl tRNA
annotated property: IAO_0000118
annotated source: arginyl_tRNA

mobile_genetic_element
type: Class
equivalent class: Class
  intersection of: region
  intersection of: Restriction
    on property: has_quality
    some values from: mobile
subclass of: SO_0001411
IAO_0000115: A nucleotide region with either intra-genome or intracellular moblity, of varying length, which often carry the information necessary for transfer and recombination with the host genome.
IAO_0000118: MGE
IAO id: SO:0001037
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/Mobile_genetic_element
IAO_0000118: mobile genetic element

Axiom
IAO scope: EXACT
annotated target: MGE
annotated property: IAO_0000118
annotated source: mobile_genetic_element

Axiom
annotated target: A nucleotide region with either intra-genome or intracellular moblity, of varying length, which often carry the information necessary for transfer and recombination with the host genome.
IAO xref: PMID:14681355
annotated property: IAO_0000115
annotated source: mobile_genetic_element

Axiom
IAO scope: EXACT
annotated target: mobile genetic element
annotated property: IAO_0000118
annotated source: mobile_genetic_element

extrachromosomal_mobile_genetic_element
type: Class
subclass of: mobile_genetic_element
IAO_0000115: An MGE that is not integrated into the host chromosome.
IAO id: SO:0001038
IAO_0000118: extrachromosomal mobile genetic element

Axiom
IAO scope: EXACT
annotated target: extrachromosomal mobile genetic element
annotated property: IAO_0000118
annotated source: extrachromosomal_mobile_genetic_element

Axiom
annotated target: An MGE that is not integrated into the host chromosome.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: extrachromosomal_mobile_genetic_element

integrated_mobile_genetic_element
type: Class
subclass of: mobile_genetic_element
IAO_0000115: An MGE that is integrated into the host chromosome.
IAO id: SO:0001039
IAO subset: SOFA
IAO_0000118: integrated mobile genetic element

Axiom
IAO scope: EXACT
annotated target: integrated mobile genetic element
annotated property: IAO_0000118
annotated source: integrated_mobile_genetic_element

Axiom
annotated target: An MGE that is integrated into the host chromosome.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: integrated_mobile_genetic_element

integrated_plasmid
type: Class
equivalent class: Class
  intersection of: integrated_mobile_genetic_element
  intersection of: Restriction
    on property: derives_from
    some values from: plasmid
subclass of: integrated_mobile_genetic_element
IAO_0000115: A plasmid sequence that is integrated within the host chromosome.
IAO id: SO:0001040
IAO_0000118: integrated plasmid

Axiom
annotated target: A plasmid sequence that is integrated within the host chromosome.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: integrated_plasmid

Axiom
IAO scope: EXACT
annotated target: integrated plasmid
annotated property: IAO_0000118
annotated source: integrated_plasmid

viral_sequence
type: Class
subclass of: extrachromosomal_mobile_genetic_element
subclass of: replicon
IAO id: SO:0001041
comment: The definitions of the children of this term were revised Decemeber 2007 after discussion on song-devel. The resulting definitions are slightly unweildy but hopefully more logically correct.
IAO_0000115: The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell.
IAO_0000118: viral sequence
IAO_0000118: virus sequence

Axiom
IAO scope: EXACT
annotated target: virus sequence
annotated property: IAO_0000118
annotated source: viral_sequence

Axiom
IAO xref: SO:ke
annotated target: The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell.
annotated property: IAO_0000115
annotated source: viral_sequence

Axiom
IAO scope: EXACT
annotated target: viral sequence
annotated property: IAO_0000118
annotated source: viral_sequence

phage_sequence
type: Class
subclass of: viral_sequence
IAO id: SO:0001042
IAO_0000115: The nucleotide sequence of a virus that infects bacteria.
IAO_0000118: bacteriophage
IAO xref: http://en.wikipedia.org/wiki/Bacteriophage
IAO_0000118: phage
IAO_0000118: phage sequence

Axiom
IAO xref: SO:ke
annotated target: The nucleotide sequence of a virus that infects bacteria.
annotated property: IAO_0000115
annotated source: phage_sequence

Axiom
IAO scope: EXACT
annotated target: bacteriophage
annotated property: IAO_0000118
annotated source: phage_sequence

Axiom
IAO scope: EXACT
annotated target: phage
annotated property: IAO_0000118
annotated source: phage_sequence

Axiom
IAO scope: EXACT
annotated target: phage sequence
annotated property: IAO_0000118
annotated source: phage_sequence

attCtn_site
type: Class
subclass of: integration_excision_site
subclass of: Restriction
  on property: part_of
  some values from: conjugative_transposon
IAO_0000115: An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon.
IAO id: SO:0001043
IAO_0000118: attCtn site

Axiom
IAO scope: EXACT
annotated target: attCtn site
annotated property: IAO_0000118
annotated source: attCtn_site

Axiom
annotated target: An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon.
IAO xref: Phigo:at
annotated property: IAO_0000115
annotated source: attCtn_site

nuclear_mt_pseudogene
type: Class
subclass of: SO_0001760
IAO_0000115: A nuclear pseudogene of either coding or non-coding mitochondria derived sequence.
comment: Definition change requested by Val, 3172757.
IAO_0000118: NUMT
IAO id: SO:0001044
IAO xref: http://en.wikipedia.org/wiki/Numt
IAO_0000118: nuclear mitochondrial pseudogene
IAO_0000118: nuclear mt pseudogene

Axiom
IAO scope: EXACT
annotated target: NUMT
annotated property: IAO_0000118
annotated source: nuclear_mt_pseudogene

Axiom
annotated target: A nuclear pseudogene of either coding or non-coding mitochondria derived sequence.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: nuclear_mt_pseudogene

Axiom
IAO scope: EXACT
annotated target: nuclear mt pseudogene
annotated property: IAO_0000118
annotated source: nuclear_mt_pseudogene

Axiom
IAO scope: EXACT
annotated target: nuclear mitochondrial pseudogene
annotated property: IAO_0000118
annotated source: nuclear_mt_pseudogene

cointegrated_plasmid
type: Class
subclass of: integrated_mobile_genetic_element
IAO_0000115: A MGE region consisting of two fused plasmids resulting from a replicative transposition event.
IAO id: SO:0001045
IAO_0000118: cointegrated plasmid
IAO_0000118: cointegrated replicon

Axiom
IAO scope: EXACT
annotated target: cointegrated replicon
annotated property: IAO_0000118
annotated source: cointegrated_plasmid

Axiom
IAO scope: EXACT
annotated target: cointegrated plasmid
annotated property: IAO_0000118
annotated source: cointegrated_plasmid

Axiom
annotated target: A MGE region consisting of two fused plasmids resulting from a replicative transposition event.
IAO xref: phigo:at
annotated property: IAO_0000115
annotated source: cointegrated_plasmid

IRLinv_site
type: Class
subclass of: inversion_site_part
subclass of: Restriction
  on property: part_of
  some values from: inversion_site
IAO_0000115: Component of the inversion site located at the left of a region susceptible to site-specific inversion.
IAO_0000118: IRLinv site
IAO id: SO:0001046

Axiom
IAO scope: EXACT
annotated target: IRLinv site
annotated property: IAO_0000118
annotated source: IRLinv_site

Axiom
annotated target: Component of the inversion site located at the left of a region susceptible to site-specific inversion.
IAO xref: Phigo:at
annotated property: IAO_0000115
annotated source: IRLinv_site

IRRinv_site
type: Class
subclass of: inversion_site_part
subclass of: Restriction
  on property: part_of
  some values from: inversion_site
IAO_0000115: Component of the inversion site located at the right of a region susceptible to site-specific inversion.
IAO_0000118: IRRinv site
IAO id: SO:0001047

Axiom
annotated target: Component of the inversion site located at the right of a region susceptible to site-specific inversion.
IAO xref: Phigo:at
annotated property: IAO_0000115
annotated source: IRRinv_site

Axiom
IAO scope: EXACT
annotated target: IRRinv site
annotated property: IAO_0000118
annotated source: IRRinv_site

inversion_site_part
type: Class
subclass of: site_specific_recombination_target_region
IAO_0000115: A region located within an inversion site.
comment: A term created to allow the parts of an inversion site have an is_a path back to the root.
IAO id: SO:0001048
IAO_0000118: inversion site part

Axiom
IAO scope: EXACT
annotated target: inversion site part
annotated property: IAO_0000118
annotated source: inversion_site_part

Axiom
annotated target: A region located within an inversion site.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: inversion_site_part

defective_conjugative_transposon
type: Class
subclass of: genomic_island
IAO_0000115: An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon.
IAO id: SO:0001049
IAO_0000118: defective conjugative transposon

Axiom
IAO scope: EXACT
annotated target: defective conjugative transposon
annotated property: IAO_0000118
annotated source: defective_conjugative_transposon

Axiom
annotated target: An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon.
IAO xref: Phigo:ariane
annotated property: IAO_0000115
annotated source: defective_conjugative_transposon

repeat_fragment
type: Class
subclass of: repeat_component
subclass of: Restriction
  on property: part_of
  some values from: SO_0001649
IAO_0000115: A portion of a repeat, interrupted by the insertion of another element.
comment: Requested by Chris Smith, and others at Flybase to help annotate nested repeats.
IAO id: SO:0001050
IAO_0000118: repeat fragment

Axiom
IAO scope: EXACT
annotated target: repeat fragment
annotated property: IAO_0000118
annotated source: repeat_fragment

Axiom
annotated target: A portion of a repeat, interrupted by the insertion of another element.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: repeat_fragment

nested_region
type: Class
IAO id: SO:0001051
deprecated: true

nested_repeat
type: Class
IAO id: SO:0001052
deprecated: true

nested_transposon
type: Class
IAO id: SO:0001053
deprecated: true

transposon_fragment
type: Class
subclass of: repeat_component
subclass of: Restriction
  on property: part_of
  some values from: SO_0001648
IAO_0000115: A portion of a transposon, interrupted by the insertion of another element.
IAO id: SO:0001054
IAO_0000118: transposon fragment

Axiom
IAO scope: EXACT
annotated target: transposon fragment
annotated property: IAO_0000118
annotated source: transposon_fragment

Axiom
annotated target: A portion of a transposon, interrupted by the insertion of another element.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: transposon_fragment

transcriptional_cis_regulatory_region
type: Class
subclass of: SO_0001679
IAO_0000115: A regulatory_region that modulates the transcription of a gene or genes.
IAO id: SO:0001055
IAO subset: SOFA
IAO_0000118: transcriptional cis regulatory region

Axiom
annotated target: A regulatory_region that modulates the transcription of a gene or genes.
IAO xref: SO:regcreative
annotated property: IAO_0000115
annotated source: transcriptional_cis_regulatory_region

Axiom
IAO scope: EXACT
annotated target: transcriptional cis regulatory region
annotated property: IAO_0000118
annotated source: transcriptional_cis_regulatory_region

splicing_regulatory_region
type: Class
subclass of: SO_0001679
IAO_0000115: A regulatory_region that modulates splicing.
IAO id: SO:0001056
IAO subset: SOFA
IAO_0000118: splicing regulatory region

Axiom
IAO scope: EXACT
annotated target: splicing regulatory region
annotated property: IAO_0000118
annotated source: splicing_regulatory_region

Axiom
annotated target: A regulatory_region that modulates splicing.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: splicing_regulatory_region

enhanceosome
type: Class
IAO id: SO:0001057
deprecated: true

promoter_targeting_sequence
type: Class
subclass of: transcriptional_cis_regulatory_region
IAO_0000115: A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter.
IAO id: SO:0001058
IAO_0000118: promoter targeting sequence

Axiom
IAO scope: EXACT
annotated target: promoter targeting sequence
annotated property: IAO_0000118
annotated source: promoter_targeting_sequence

Axiom
annotated target: A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter.
IAO xref: SO:regcreative
annotated property: IAO_0000115
annotated source: promoter_targeting_sequence

sequence_alteration
type: Class
subclass of: sequence_feature
IAO_0000115: A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence.
comment: Merged with partially characterized change in nucleotide sequence.
IAO id: SO:0001059
IAO alt id: SO:1000004
IAO alt id: SO:1000007
IAO subset: SOFA
IAO_0000118: partially characterised change in DNA sequence
IAO_0000118: partially_characterised_change_in_DNA_sequence
IAO_0000118: sequence alteration

Axiom
IAO scope: EXACT
annotated target: partially_characterised_change_in_DNA_sequence
annotated property: IAO_0000118
annotated source: sequence_alteration

Axiom
IAO scope: EXACT
annotated target: partially characterised change in DNA sequence
annotated property: IAO_0000118
annotated source: sequence_alteration

Axiom
annotated target: A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: sequence_alteration

Axiom
IAO scope: EXACT
annotated target: sequence alteration
annotated property: IAO_0000118
annotated source: sequence_alteration

sequence_variant
type: Class
IAO_0000115: A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.
IAO id: SO:0001060
IAO_0000118: sequence variant

Axiom
annotated target: A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: sequence_variant

Axiom
IAO scope: EXACT
annotated target: sequence variant
annotated property: IAO_0000118
annotated source: sequence_variant

propeptide_cleavage_site
type: Class
subclass of: SO_0100011
subclass of: Restriction
  on property: part_of
  some values from: propeptide
IAO alt id: BS:00063
comment: Discrete.
IAO id: SO:0001061
IAO_0000115: The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs.
IAO subset: biosapiens
IAO_0000118: propeptide cleavage site

Axiom
IAO scope: EXACT
annotated target: propeptide cleavage site
annotated property: IAO_0000118
annotated source: propeptide_cleavage_site

Axiom
IAO xref: EBIBS:GAR
annotated target: The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs.
annotated property: IAO_0000115
annotated source: propeptide_cleavage_site

propeptide
type: Class
subclass of: SO_0100011
IAO alt id: BS:00077
IAO_0000115: Part of a peptide chain which is cleaved off during the formation of the mature protein.
comment: Range.
IAO id: SO:0001062
IAO subset: biosapiens
IAO xref: http://en.wikipedia.org/wiki/Propeptide
IAO_0000118: propep

Axiom
IAO scope: RELATED
annotated target: propep
IAO xref: uniprot:feature_type
annotated property: IAO_0000118
annotated source: propeptide

Axiom
IAO xref: EBIBS:GAR
annotated target: Part of a peptide chain which is cleaved off during the formation of the mature protein.
annotated property: IAO_0000115
annotated source: propeptide

immature_peptide_region
type: Class
subclass of: polypeptide_region
IAO_0000115: An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs.
IAO alt id: BS:00129
comment: Range.
IAO id: SO:0001063
IAO subset: SOFA
IAO subset: biosapiens
IAO_0000118: immature_peptide_region

Axiom
annotated target: An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs.
IAO xref: EBIBS:GAR
annotated property: IAO_0000115
annotated source: immature_peptide_region

Axiom
IAO scope: EXACT
annotated target: immature_peptide_region
annotated property: IAO_0000118
annotated source: immature_peptide_region

active_peptide
type: Class
subclass of: mature_protein_region
IAO_0000115: Active peptides are proteins which are biologically active, released from a precursor molecule.
IAO alt id: BS:00076
comment: Hormones, neuropeptides, antimicrobial peptides, are active peptides. They are typically short (<40 amino acids) in length.
IAO id: SO:0001064
IAO_0000118: active peptide
IAO subset: biosapiens
IAO xref: http://en.wikipedia.org/wiki/Peptide
IAO_0000118: peptide

Axiom
IAO scope: BROAD
annotated target: peptide
IAO xref: uniprot:feature_type
annotated property: IAO_0000118
annotated source: active_peptide

Axiom
annotated target: Active peptides are proteins which are biologically active, released from a precursor molecule.
IAO xref: EBIBS:GAR
IAO xref: UniProt:curation_manual
annotated property: IAO_0000115
annotated source: active_peptide

Axiom
IAO scope: EXACT
annotated target: active peptide
annotated property: IAO_0000118
annotated source: active_peptide

compositionally_biased_region_of_peptide
type: Class
subclass of: polypeptide_region
IAO alt id: BS:00068
IAO_0000115: Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length.
comment: Range.
IAO id: SO:0001066
IAO subset: biosapiens
IAO_0000118: compbias
IAO_0000118: compositional bias
IAO_0000118: compositionally biased
IAO_0000118: compositionally biased region of peptide
IAO_0000118: compositionally_biased_region

Axiom
IAO xref: EBIBS:GAR
annotated target: Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length.
IAO xref: UniProt:curation_manual
annotated property: IAO_0000115
annotated source: compositionally_biased_region_of_peptide

Axiom
IAO scope: RELATED
annotated target: compositionally biased
annotated property: IAO_0000118
annotated source: compositionally_biased_region_of_peptide

Axiom
IAO scope: RELATED
annotated target: compbias
IAO xref: uniprot:feature_type
annotated property: IAO_0000118
annotated source: compositionally_biased_region_of_peptide

Axiom
IAO scope: EXACT
annotated target: compositionally_biased_region
annotated property: IAO_0000118
annotated source: compositionally_biased_region_of_peptide

Axiom
IAO scope: RELATED
annotated target: compositional bias
annotated property: IAO_0000118
annotated source: compositionally_biased_region_of_peptide

Axiom
IAO scope: RELATED
annotated target: compositionally biased region of peptide
annotated property: IAO_0000118
annotated source: compositionally_biased_region_of_peptide

polypeptide_motif
type: Class
subclass of: SO_0100021
IAO_0000115: A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.).
IAO alt id: BS:00032
comment: Range.
IAO id: SO:0001067
IAO subset: biosapiens
IAO_0000118: motif
IAO_0000118: polypeptide motif

Axiom
IAO scope: EXACT
annotated target: polypeptide motif
annotated property: IAO_0000118
annotated source: polypeptide_motif

Axiom
annotated target: A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.).
IAO xref: EBIBS:GAR
IAO xref: UniProt:curation_manual
annotated property: IAO_0000115
annotated source: polypeptide_motif

Axiom
IAO scope: BROAD
annotated target: motif
IAO xref: uniprot:feature_type
annotated property: IAO_0000118
annotated source: polypeptide_motif

polypeptide_repeat
type: Class
subclass of: SO_0100021
IAO_0000115: A polypeptide_repeat is a single copy of an internal sequence repetition.
IAO alt id: BS:00070
comment: Range.
IAO id: SO:0001068
IAO subset: biosapiens
IAO_0000118: polypeptide repeat
IAO_0000118: repeat

Axiom
annotated target: A polypeptide_repeat is a single copy of an internal sequence repetition.
IAO xref: EBIBS:GAR
annotated property: IAO_0000115
annotated source: polypeptide_repeat

Axiom
IAO scope: RELATED
annotated target: repeat
IAO xref: uniprot:feature_type
annotated property: IAO_0000118
annotated source: polypeptide_repeat

Axiom
IAO scope: EXACT
annotated target: polypeptide repeat
annotated property: IAO_0000118
annotated source: polypeptide_repeat

polypeptide_structural_region
type: Class
subclass of: polypeptide_region
IAO alt id: BS:00337
comment: Range.
IAO_0000115: Region of polypeptide with a given structural property.
IAO id: SO:0001070
IAO subset: biosapiens
IAO_0000118: polypeptide structural region
IAO_0000118: structural_region

Axiom
IAO scope: RELATED
annotated target: structural_region
annotated property: IAO_0000118
annotated source: polypeptide_structural_region

Axiom
IAO xref: EBIBS:GAR
annotated target: Region of polypeptide with a given structural property.
IAO xref: SO:cb
annotated property: IAO_0000115
annotated source: polypeptide_structural_region

Axiom
IAO scope: EXACT
annotated target: polypeptide structural region
annotated property: IAO_0000118
annotated source: polypeptide_structural_region

membrane_structure
type: Class
subclass of: polypeptide_structural_region
IAO_0000115: Arrangement of the polypeptide with respect to the lipid bilayer.
IAO alt id: BS:00128
comment: Range.
IAO id: SO:0001071
IAO subset: biosapiens
IAO_0000118: membrane_structure

Axiom
IAO scope: EXACT
annotated target: membrane_structure
annotated property: IAO_0000118
annotated source: membrane_structure

Axiom
annotated target: Arrangement of the polypeptide with respect to the lipid bilayer.
IAO xref: EBIBS:GAR
annotated property: IAO_0000115
annotated source: membrane_structure

extramembrane_polypeptide_region
type: Class
subclass of: polypeptide_structural_region
subclass of: Restriction
  on property: part_of
  some values from: membrane_structure
IAO alt id: BS:00154
IAO_0000115: Polypeptide region that is localized outside of a lipid bilayer.
comment: Range.
IAO id: SO:0001072
IAO subset: biosapiens
IAO_0000118: extramembrane
IAO_0000118: extramembrane polypeptide region
IAO_0000118: extramembrane_region
IAO_0000118: topo_dom

Axiom
IAO type: BS
IAO scope: RELATED
annotated target: extramembrane
annotated property: IAO_0000118
annotated source: extramembrane_polypeptide_region

Axiom
IAO xref: EBIBS:GAR
annotated target: Polypeptide region that is localized outside of a lipid bilayer.
IAO xref: SO:cb
annotated property: IAO_0000115
annotated source: extramembrane_polypeptide_region

Axiom
IAO type: BS
IAO scope: RELATED
annotated target: extramembrane_region
annotated property: IAO_0000118
annotated source: extramembrane_polypeptide_region

Axiom
IAO type: BS
IAO scope: RELATED
annotated target: topo_dom
IAO xref: uniprot:feature_type
annotated property: IAO_0000118
annotated source: extramembrane_polypeptide_region

Axiom
IAO scope: EXACT
annotated target: extramembrane polypeptide region
annotated property: IAO_0000118
annotated source: extramembrane_polypeptide_region

cytoplasmic_polypeptide_region
type: Class
subclass of: extramembrane_polypeptide_region
IAO alt id: BS:00145
IAO_0000115: Polypeptide region that is localized inside the cytoplasm.
IAO id: SO:0001073
IAO subset: biosapiens
IAO_0000118: cytoplasm_location
IAO_0000118: cytoplasmic polypeptide region
IAO_0000118: inside

Axiom
IAO xref: EBIBS:GAR
annotated target: Polypeptide region that is localized inside the cytoplasm.
IAO xref: SO:cb
annotated property: IAO_0000115
annotated source: cytoplasmic_polypeptide_region

Axiom
IAO type: BS
IAO scope: EXACT
annotated target: cytoplasm_location
annotated property: IAO_0000118
annotated source: cytoplasmic_polypeptide_region

Axiom
IAO scope: EXACT
annotated target: cytoplasmic polypeptide region
annotated property: IAO_0000118
annotated source: cytoplasmic_polypeptide_region

Axiom
IAO type: BS
IAO scope: RELATED
annotated target: inside
annotated property: IAO_0000118
annotated source: cytoplasmic_polypeptide_region

non_cytoplasmic_polypeptide_region
type: Class
subclass of: extramembrane_polypeptide_region
IAO alt id: BS:00144
IAO_0000115: Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm.
IAO id: SO:0001074
comment: This could be inside an organelle within the cell.
IAO subset: biosapiens
IAO_0000118: non cytoplasmic polypeptide region
IAO_0000118: non_cytoplasm_location
IAO_0000118: outside

Axiom
IAO xref: EBIBS:GAR
annotated target: Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm.
IAO xref: SO:cb
annotated property: IAO_0000115
annotated source: non_cytoplasmic_polypeptide_region

Axiom
IAO type: BS
IAO scope: RELATED
annotated target: outside
annotated property: IAO_0000118
annotated source: non_cytoplasmic_polypeptide_region

Axiom
IAO type: BS
IAO scope: EXACT
annotated target: non_cytoplasm_location
annotated property: IAO_0000118
annotated source: non_cytoplasmic_polypeptide_region

Axiom
IAO scope: EXACT
annotated target: non cytoplasmic polypeptide region
annotated property: IAO_0000118
annotated source: non_cytoplasmic_polypeptide_region

intramembrane_polypeptide_region
type: Class
subclass of: polypeptide_structural_region
subclass of: Restriction
  on property: part_of
  some values from: membrane_structure
IAO alt id: BS:00156
IAO_0000115: Polypeptide region present in the lipid bilayer.
IAO id: SO:0001075
IAO subset: biosapiens
IAO_0000118: intramembrane
IAO_0000118: intramembrane polypeptide region

Axiom
IAO type: BS
IAO scope: RELATED
annotated target: intramembrane
annotated property: IAO_0000118
annotated source: intramembrane_polypeptide_region

Axiom
IAO scope: EXACT
annotated target: intramembrane polypeptide region
annotated property: IAO_0000118
annotated source: intramembrane_polypeptide_region

Axiom
IAO xref: EBIBS:GAR
annotated target: Polypeptide region present in the lipid bilayer.
annotated property: IAO_0000115
annotated source: intramembrane_polypeptide_region

membrane_peptide_loop
type: Class
subclass of: intramembrane_polypeptide_region
IAO alt id: BS:00155
IAO_0000115: Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane.
IAO id: SO:0001076
IAO subset: biosapiens
IAO_0000118: membrane peptide loop
IAO_0000118: membrane_loop

Axiom
IAO xref: EBIBS:GAR
annotated target: Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane.
IAO xref: SO:cb
annotated property: IAO_0000115
annotated source: membrane_peptide_loop

Axiom
IAO type: BS
IAO scope: RELATED
annotated target: membrane_loop
annotated property: IAO_0000118
annotated source: membrane_peptide_loop

Axiom
IAO scope: EXACT
annotated target: membrane peptide loop
annotated property: IAO_0000118
annotated source: membrane_peptide_loop

transmembrane_polypeptide_region
type: Class
subclass of: intramembrane_polypeptide_region
IAO alt id: BS:00158
IAO_0000115: Polypeptide region traversing the lipid bilayer.
IAO id: SO:0001077
IAO subset: biosapiens
IAO_0000118: transmem
IAO_0000118: transmembrane
IAO_0000118: transmembrane polypeptide region

Axiom
IAO type: BS
IAO scope: RELATED
annotated target: transmembrane
annotated property: IAO_0000118
annotated source: transmembrane_polypeptide_region

Axiom
IAO xref: EBIBS:GAR
annotated target: Polypeptide region traversing the lipid bilayer.
IAO xref: UniProt:curator_manual
annotated property: IAO_0000115
annotated source: transmembrane_polypeptide_region

Axiom
IAO type: BS
IAO scope: RELATED
annotated target: transmem
IAO xref: uniprot:feature_type
annotated property: IAO_0000118
annotated source: transmembrane_polypeptide_region

Axiom
IAO scope: EXACT
annotated target: transmembrane polypeptide region
annotated property: IAO_0000118
annotated source: transmembrane_polypeptide_region

polypeptide_secondary_structure
type: Class
subclass of: polypeptide_structural_region
IAO_0000118: 2nary structure
IAO_0000115: A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain.
IAO alt id: BS:00003
comment: Biosapien term was secondary_structure.
IAO id: SO:0001078
IAO subset: biosapiens
IAO xref: http://en.wikipedia.org/wiki/Secondary_structure
IAO_0000118: polypeptide secondary structure
IAO_0000118: secondary structure
IAO_0000118: secondary structure region
IAO_0000118: secondary_structure

Axiom
annotated target: A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain.
IAO xref: EBIBS:GAR
annotated property: IAO_0000115
annotated source: polypeptide_secondary_structure

Axiom
IAO scope: EXACT
annotated target: polypeptide secondary structure
annotated property: IAO_0000118
annotated source: polypeptide_secondary_structure

Axiom
IAO type: BS
IAO scope: RELATED
annotated target: secondary structure
annotated property: IAO_0000118
annotated source: polypeptide_secondary_structure

Axiom
IAO type: BS
IAO scope: RELATED
annotated target: secondary structure region
annotated property: IAO_0000118
annotated source: polypeptide_secondary_structure

Axiom
IAO type: BS
IAO scope: RELATED
annotated target: secondary_structure
annotated property: IAO_0000118
annotated source: polypeptide_secondary_structure

Axiom
annotated target: 2nary structure
IAO type: BS
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: polypeptide_secondary_structure

polypeptide_structural_motif
type: Class
subclass of: polypeptide_structural_region
IAO alt id: BS:0000338
IAO_0000115: Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit.
IAO id: SO:0001079
IAO subset: biosapiens
IAO xref: http://en.wikipedia.org/wiki/Structural_motif
IAO_0000118: polypeptide structural motif
IAO_0000118: structural_motif

Axiom
IAO type: BS
IAO scope: RELATED
annotated target: structural_motif
annotated property: IAO_0000118
annotated source: polypeptide_structural_motif

Axiom
IAO scope: RELATED
annotated target: polypeptide structural motif
annotated property: IAO_0000118
annotated source: polypeptide_structural_motif

Axiom
IAO xref: EBIBS:GAR
annotated target: Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit.
annotated property: IAO_0000115
annotated source: polypeptide_structural_motif

coiled_coil
type: Class
subclass of: polypeptide_structural_motif
IAO_0000115: A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope.
IAO alt id: BS:00041
comment: Range.
IAO id: SO:0001080
IAO subset: biosapiens
IAO_0000118: coiled
IAO_0000118: coiled coil
IAO xref: http://en.wikipedia.org/wiki/Coiled_coil

Axiom
IAO type: BS
IAO scope: RELATED
annotated target: coiled
IAO xref: uniprot:feature_type
annotated property: IAO_0000118
annotated source: coiled_coil

Axiom
IAO scope: EXACT
annotated target: coiled coil
annotated property: IAO_0000118
annotated source: coiled_coil

Axiom
annotated target: A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope.
IAO xref: EBIBS:GAR
IAO xref: UniProt:curation_manual
annotated property: IAO_0000115
annotated source: coiled_coil

helix_turn_helix
type: Class
subclass of: polypeptide_structural_motif
subclass of: Restriction
  on property: has_part
  some values from: peptide_helix
subclass of: Restriction
  on property: has_part
  some values from: polypeptide_turn_motif
IAO_0000115: A motif comprising two helices separated by a turn.
IAO alt id: BS:00147
IAO_0000118: HTH
IAO id: SO:0001081
IAO subset: biosapiens
IAO_0000118: helix turn helix
IAO_0000118: helix-turn-helix

Axiom
IAO scope: EXACT
annotated target: helix turn helix
annotated property: IAO_0000118
annotated source: helix_turn_helix

Axiom
IAO type: BS
annotated target: HTH
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: helix_turn_helix

Axiom
IAO scope: EXACT
annotated target: helix-turn-helix
annotated property: IAO_0000118
annotated source: helix_turn_helix

Axiom
annotated target: A motif comprising two helices separated by a turn.
IAO xref: EBIBS:GAR
annotated property: IAO_0000115
annotated source: helix_turn_helix

polypeptide_sequencing_information
type: Class
subclass of: remark
IAO alt id: BS:00125
IAO_0000115: Incompatibility in the sequence due to some experimental problem.
comment: Range.
IAO id: SO:0001082
IAO subset: biosapiens
IAO_0000118: sequencing_information

Axiom
IAO scope: EXACT
annotated target: sequencing_information
annotated property: IAO_0000118
annotated source: polypeptide_sequencing_information

Axiom
IAO xref: EBIBS:GAR
annotated target: Incompatibility in the sequence due to some experimental problem.
annotated property: IAO_0000115
annotated source: polypeptide_sequencing_information

non_adjacent_residues
type: Class
subclass of: polypeptide_sequencing_information
IAO alt id: BS:00182
IAO_0000115: Indicates that two consecutive residues in a fragment sequence are not consecutive in the full-length protein and that there are a number of unsequenced residues between them.
IAO id: SO:0001083
IAO subset: biosapiens
IAO_0000118: non consecutive
IAO_0000118: non_cons

Axiom
IAO scope: EXACT
annotated target: non_cons
IAO xref: uniprot:feature_type
annotated property: IAO_0000118
annotated source: non_adjacent_residues

Axiom
IAO xref: EBIBS:GAR
annotated target: Indicates that two consecutive residues in a fragment sequence are not consecutive in the full-length protein and that there are a number of unsequenced residues between them.
IAO xref: UniProt:curation_manual
annotated property: IAO_0000115
annotated source: non_adjacent_residues

Axiom
IAO scope: EXACT
annotated target: non consecutive
annotated property: IAO_0000118
annotated source: non_adjacent_residues

non_terminal_residue
type: Class
subclass of: polypeptide_sequencing_information
IAO alt id: BS:00072
comment: Discrete.
IAO id: SO:0001084
IAO_0000115: The residue at an extremity of the sequence is not the terminal residue.
IAO subset: biosapiens
IAO_0000118: non terminal
IAO_0000118: non_ter

Axiom
IAO xref: EBIBS:GAR
annotated target: The residue at an extremity of the sequence is not the terminal residue.
IAO xref: UniProt:curation_manual
annotated property: IAO_0000115
annotated source: non_terminal_residue

Axiom
IAO scope: EXACT
annotated target: non terminal
annotated property: IAO_0000118
annotated source: non_terminal_residue

Axiom
IAO scope: EXACT
annotated target: non_ter
IAO xref: uniprot:feature_type
annotated property: IAO_0000118
annotated source: non_terminal_residue

sequence_conflict
type: Class
subclass of: polypeptide_sequencing_information
IAO alt id: BS:00069
IAO_0000115: Different sources report differing sequences.
comment: Discrete.
IAO id: SO:0001085
IAO subset: biosapiens
IAO_0000118: conflict

Axiom
annotated target: Different sources report differing sequences.
IAO xref: EBIBS:GAR
IAO xref: UniProt:curation_manual
annotated property: IAO_0000115
annotated source: sequence_conflict

Axiom
IAO scope: EXACT
annotated target: conflict
IAO xref: uniprot:feature_type
annotated property: IAO_0000118
annotated source: sequence_conflict

sequence_uncertainty
type: Class
subclass of: polypeptide_sequencing_information
IAO alt id: BS:00181
IAO_0000115: Describes the positions in a sequence where the authors are unsure about the sequence assignment.
IAO id: SO:0001086
IAO subset: biosapiens
IAO_0000118: unsure

Axiom
annotated target: Describes the positions in a sequence where the authors are unsure about the sequence assignment.
IAO xref: EBIBS:GAR
IAO xref: UniProt:curation_manual
annotated property: IAO_0000115
annotated source: sequence_uncertainty

Axiom
IAO scope: EXACT
IAO xref: uniprot:feature_type
annotated target: unsure
annotated property: IAO_0000118
annotated source: sequence_uncertainty

cross_link
type: Class
IAO alt id: BS:00178
IAO_0000115: Posttranslationally formed amino acid bonds.
IAO id: SO:0001087
IAO subset: biosapiens
IAO_0000118: cross_link
IAO_0000118: crosslink
deprecated: true

Axiom
IAO xref: EBIBS:GAR
annotated target: Posttranslationally formed amino acid bonds.
IAO xref: UniProt:curation_manual
annotated property: IAO_0000115
annotated source: cross_link

Axiom
IAO scope: RELATED
annotated target: crosslink
annotated property: IAO_0000118
annotated source: cross_link

Axiom
IAO scope: EXACT
annotated target: cross_link
annotated property: IAO_0000118
annotated source: cross_link

disulfide_bond
type: Class
comment: 2 discreet & joined.
IAO alt id: BS:00028
IAO id: SO:0001088
IAO_0000115: The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain and is a structural determinant in many protein molecules.
IAO subset: biosapiens
IAO_0000118: disulfid
IAO_0000118: disulfide
IAO_0000118: disulfide bond
IAO_0000118: disulfide_bond
IAO_0000118: disulphide
IAO_0000118: disulphide bond
deprecated: true

Axiom
IAO scope: RELATED
annotated target: disulfide bond
annotated property: IAO_0000118
annotated source: disulfide_bond

Axiom
IAO scope: RELATED
annotated target: disulfide
annotated property: IAO_0000118
annotated source: disulfide_bond

Axiom
IAO scope: EXACT
annotated target: disulphide
annotated property: IAO_0000118
annotated source: disulfide_bond

Axiom
IAO scope: RELATED
annotated target: disulfid
annotated property: IAO_0000118
annotated source: disulfide_bond

Axiom
IAO scope: EXACT
annotated target: disulfide_bond
annotated property: IAO_0000118
annotated source: disulfide_bond

Axiom
IAO xref: EBIBS:GAR
annotated target: The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain and is a structural determinant in many protein molecules.
IAO xref: UniProt:curation_manual
annotated property: IAO_0000115
annotated source: disulfide_bond

Axiom
IAO scope: RELATED
annotated target: disulphide bond
annotated property: IAO_0000118
annotated source: disulfide_bond

post_translationally_modified_region
type: Class
subclass of: SO_0100001
IAO_0000115: A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein.
IAO alt id: BS:00052
comment: Discrete.
IAO id: SO:0001089
IAO subset: biosapiens
IAO xref: http://en.wikipedia.org/wiki/Post_translational_modification
IAO_0000118: mod_res
IAO_0000118: modified residue
IAO_0000118: post_translational_modification

Axiom
IAO scope: EXACT
annotated target: post_translational_modification
annotated property: IAO_0000118
annotated source: post_translationally_modified_region

Axiom
IAO scope: EXACT
annotated target: modified residue
annotated property: IAO_0000118
annotated source: post_translationally_modified_region

Axiom
annotated target: A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein.
IAO xref: EBIBS:GAR
IAO xref: UniProt:curation_manual
annotated property: IAO_0000115
annotated source: post_translationally_modified_region

Axiom
IAO scope: EXACT
annotated target: mod_res
IAO xref: uniprot:feature_type
annotated property: IAO_0000118
annotated source: post_translationally_modified_region

covalent_binding_site
type: Class
IAO alt id: BS:00246
IAO_0000115: Binding involving a covalent bond.
IAO id: SO:0001090
IAO subset: biosapiens
IAO_0000118: covalent_binding_site
deprecated: true

Axiom
annotated target: Binding involving a covalent bond.
IAO xref: EBIBS:GAR
annotated property: IAO_0000115
annotated source: covalent_binding_site

Axiom
IAO scope: EXACT
annotated target: covalent_binding_site
annotated property: IAO_0000118
annotated source: covalent_binding_site

non_covalent_binding_site
type: Class
IAO alt id: BS:00029
IAO_0000115: Binding site for any chemical group (co-enzyme, prosthetic group, etc.).
comment: Discrete.
IAO id: SO:0001091
IAO_0000118: binding
IAO_0000118: binding site
IAO subset: biosapiens
IAO_0000118: non_covalent_binding_site
deprecated: true

Axiom
IAO scope: RELATED
annotated target: binding site
annotated property: IAO_0000118
annotated source: non_covalent_binding_site

Axiom
annotated target: Binding site for any chemical group (co-enzyme, prosthetic group, etc.).
IAO xref: EBIBS:GAR
annotated property: IAO_0000115
annotated source: non_covalent_binding_site

Axiom
IAO scope: EXACT
annotated target: non_covalent_binding_site
annotated property: IAO_0000118
annotated source: non_covalent_binding_site

Axiom
IAO scope: RELATED
annotated target: binding
IAO xref: uniprot:curation
annotated property: IAO_0000118
annotated source: non_covalent_binding_site

polypeptide_metal_contact
type: Class
subclass of: SO_0001656
subclass of: SO_0100002
IAO_0000115: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions.
IAO alt id: BS:00027
comment: Residue is part of a binding site for a metal ion.
IAO id: SO:0001092
IAO subset: biosapiens
IAO_0000118: metal_binding

Axiom
IAO scope: RELATED
annotated target: metal_binding
annotated property: IAO_0000118
annotated source: polypeptide_metal_contact

Axiom
annotated target: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions.
IAO xref: EBIBS:GAR
IAO xref: SO:cb
IAO xref: UniProt:curation_manual
annotated property: IAO_0000115
annotated source: polypeptide_metal_contact

protein_protein_contact
type: Class
subclass of: protein_binding_site
subclass of: SO_0100002
IAO_0000115: A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues.
IAO alt id: BS:00131
IAO id: SO:0001093
IAO subset: biosapiens
IAO xref: http://en.wikipedia.org/wiki/Protein_protein_interaction
IAO_0000118: protein protein contact
IAO_0000118: protein protein contact site
IAO_0000118: protein_protein_interaction

Axiom
IAO scope: RELATED
annotated target: protein_protein_interaction
annotated property: IAO_0000118
annotated source: protein_protein_contact

Axiom
IAO scope: EXACT
annotated target: protein protein contact
annotated property: IAO_0000118
annotated source: protein_protein_contact

Axiom
IAO scope: EXACT
annotated target: protein protein contact site
annotated property: IAO_0000118
annotated source: protein_protein_contact

Axiom
annotated target: A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues.
IAO xref: EBIBS:GAR
IAO xref: UniProt:Curation_manual
annotated property: IAO_0000115
annotated source: protein_protein_contact

polypeptide_calcium_ion_contact_site
type: Class
subclass of: polypeptide_metal_contact
IAO_0000115: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions.
IAO alt id: BS:00186
IAO_0000118: Ca_contact_site
comment: Residue involved in contact with calcium.
IAO id: SO:0001094
IAO subset: biosapiens
IAO_0000118: ca bind
IAO_0000118: polypeptide calcium ion contact site

Axiom
annotated target: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions.
IAO xref: EBIBS:GAR
annotated property: IAO_0000115
annotated source: polypeptide_calcium_ion_contact_site

Axiom
IAO scope: EXACT
annotated target: polypeptide calcium ion contact site
annotated property: IAO_0000118
annotated source: polypeptide_calcium_ion_contact_site

Axiom
IAO scope: RELATED
annotated target: ca bind
annotated property: IAO_0000118
annotated source: polypeptide_calcium_ion_contact_site

Axiom
annotated target: Ca_contact_site
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: polypeptide_calcium_ion_contact_site

polypeptide_cobalt_ion_contact_site
type: Class
subclass of: polypeptide_metal_contact
IAO_0000115: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions.
IAO alt id: BS:00136
IAO_0000118: Co_contact_site
IAO id: SO:0001095
IAO subset: biosapiens
IAO_0000118: polypeptide cobalt ion contact site

Axiom
annotated target: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions.
IAO xref: EBIBS:GAR
IAO xref: SO:cb
annotated property: IAO_0000115
annotated source: polypeptide_cobalt_ion_contact_site

Axiom
IAO scope: EXACT
annotated target: polypeptide cobalt ion contact site
annotated property: IAO_0000118
annotated source: polypeptide_cobalt_ion_contact_site

Axiom
annotated target: Co_contact_site
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: polypeptide_cobalt_ion_contact_site

polypeptide_copper_ion_contact_site
type: Class
subclass of: polypeptide_metal_contact
IAO_0000115: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions.
IAO alt id: BS:00146
IAO_0000118: Cu_contact_site
IAO id: SO:0001096
IAO subset: biosapiens
IAO_0000118: polypeptide copper ion contact site

Axiom
annotated target: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions.
IAO xref: EBIBS:GAR
IAO xref: SO:cb
annotated property: IAO_0000115
annotated source: polypeptide_copper_ion_contact_site

Axiom
annotated target: Cu_contact_site
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: polypeptide_copper_ion_contact_site

Axiom
IAO scope: EXACT
annotated target: polypeptide copper ion contact site
annotated property: IAO_0000118
annotated source: polypeptide_copper_ion_contact_site

polypeptide_iron_ion_contact_site
type: Class
subclass of: polypeptide_metal_contact
IAO_0000115: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions.
IAO alt id: BS:00137
IAO_0000118: Fe_contact_site
IAO id: SO:0001097
IAO subset: biosapiens
IAO_0000118: polypeptide iron ion contact site

Axiom
IAO scope: EXACT
annotated target: Fe_contact_site
annotated property: IAO_0000118
annotated source: polypeptide_iron_ion_contact_site

Axiom
annotated target: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions.
IAO xref: EBIBS:GAR
IAO xref: SO:cb
annotated property: IAO_0000115
annotated source: polypeptide_iron_ion_contact_site

Axiom
IAO scope: EXACT
annotated target: polypeptide iron ion contact site
annotated property: IAO_0000118
annotated source: polypeptide_iron_ion_contact_site

polypeptide_magnesium_ion_contact_site
type: Class
subclass of: polypeptide_metal_contact
IAO_0000115: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions.
IAO alt id: BS:00187
IAO_0000118: Mg_contact_site
IAO id: SO:0001098
IAO subset: biosapiens
IAO_0000118: polypeptide magnesium ion contact site

Axiom
IAO scope: EXACT
annotated target: polypeptide magnesium ion contact site
annotated property: IAO_0000118
annotated source: polypeptide_magnesium_ion_contact_site

Axiom
annotated target: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions.
IAO xref: EBIBS:GAR
IAO xref: SO:cb
annotated property: IAO_0000115
annotated source: polypeptide_magnesium_ion_contact_site

Axiom
IAO scope: EXACT
annotated target: Mg_contact_site
annotated property: IAO_0000118
annotated source: polypeptide_magnesium_ion_contact_site

polypeptide_manganese_ion_contact_site
type: Class
subclass of: polypeptide_metal_contact
IAO_0000115: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions.
IAO alt id: BS:00140
IAO_0000118: Mn_contact_site
IAO id: SO:0001099
IAO subset: biosapiens
IAO_0000118: polypeptide manganese ion contact site

Axiom
IAO scope: EXACT
annotated target: polypeptide manganese ion contact site
annotated property: IAO_0000118
annotated source: polypeptide_manganese_ion_contact_site

Axiom
annotated target: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions.
IAO xref: EBIBS:GAR
IAO xref: SO:cb
annotated property: IAO_0000115
annotated source: polypeptide_manganese_ion_contact_site

Axiom
IAO scope: EXACT
annotated target: Mn_contact_site
annotated property: IAO_0000118
annotated source: polypeptide_manganese_ion_contact_site

polypeptide_molybdenum_ion_contact_site
type: Class
subclass of: polypeptide_metal_contact
IAO_0000115: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions.
IAO alt id: BS:00141
IAO_0000118: Mo_contact_site
IAO id: SO:0001100
IAO subset: biosapiens
IAO_0000118: polypeptide molybdenum ion contact site

Axiom
annotated target: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions.
IAO xref: EBIBS:GAR
IAO xref: SO:cb
annotated property: IAO_0000115
annotated source: polypeptide_molybdenum_ion_contact_site

Axiom
IAO scope: EXACT
annotated target: Mo_contact_site
annotated property: IAO_0000118
annotated source: polypeptide_molybdenum_ion_contact_site

Axiom
IAO scope: EXACT
annotated target: polypeptide molybdenum ion contact site
annotated property: IAO_0000118
annotated source: polypeptide_molybdenum_ion_contact_site

polypeptide_nickel_ion_contact_site
type: Class
subclass of: polypeptide_metal_contact
IAO_0000115: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions.
IAO alt id: BS:00142
IAO_0000118: Ni_contact_site
IAO id: SO:0001101
IAO subset: biosapiens
IAO_0000118: polypeptide nickel ion contact site

Axiom
IAO scope: EXACT
annotated target: polypeptide nickel ion contact site
annotated property: IAO_0000118
annotated source: polypeptide_nickel_ion_contact_site

Axiom
IAO scope: EXACT
annotated target: Ni_contact_site
annotated property: IAO_0000118
annotated source: polypeptide_nickel_ion_contact_site

Axiom
annotated target: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions.
IAO xref: EBIBS:GAR
annotated property: IAO_0000115
annotated source: polypeptide_nickel_ion_contact_site

polypeptide_tungsten_ion_contact_site
type: Class
subclass of: polypeptide_metal_contact
IAO_0000115: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions.
IAO alt id: BS:00143
IAO id: SO:0001102
IAO_0000118: W_contact_site
IAO subset: biosapiens
IAO_0000118: polypeptide tungsten ion contact site

Axiom
IAO scope: EXACT
annotated target: polypeptide tungsten ion contact site
annotated property: IAO_0000118
annotated source: polypeptide_tungsten_ion_contact_site

Axiom
annotated target: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions.
IAO xref: EBIBS:GAR
IAO xref: SO:cb
annotated property: IAO_0000115
annotated source: polypeptide_tungsten_ion_contact_site

Axiom
IAO scope: EXACT
annotated target: W_contact_site
annotated property: IAO_0000118
annotated source: polypeptide_tungsten_ion_contact_site

polypeptide_zinc_ion_contact_site
type: Class
subclass of: polypeptide_metal_contact
IAO_0000115: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions.
IAO alt id: BS:00185
IAO id: SO:0001103
IAO_0000118: Zn_contact_site
IAO subset: biosapiens
IAO_0000118: polypeptide zinc ion contact site

Axiom
IAO scope: EXACT
annotated target: Zn_contact_site
annotated property: IAO_0000118
annotated source: polypeptide_zinc_ion_contact_site

Axiom
IAO scope: EXACT
annotated target: polypeptide zinc ion contact site
annotated property: IAO_0000118
annotated source: polypeptide_zinc_ion_contact_site

Axiom
annotated target: A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions.
IAO xref: EBIBS:GAR
IAO xref: SO:cb
annotated property: IAO_0000115
annotated source: polypeptide_zinc_ion_contact_site

catalytic_residue
type: Class
subclass of: amino_acid
subclass of: Restriction
  on property: part_of
  some values from: SO_0100019
IAO_0000115: Amino acid involved in the activity of an enzyme.
IAO alt id: BS:00026
comment: Discrete.
IAO id: SO:0001104
IAO_0000118: act_site
IAO_0000118: active site residue
IAO subset: biosapiens
IAO_0000118: catalytic residue

Axiom
annotated target: Amino acid involved in the activity of an enzyme.
IAO xref: EBIBS:GAR
IAO xref: UniProt:curation_manual
annotated property: IAO_0000115
annotated source: catalytic_residue

Axiom
IAO scope: EXACT
annotated target: active site residue
annotated property: IAO_0000118
annotated source: catalytic_residue

Axiom
IAO scope: RELATED
annotated target: act_site
IAO xref: uniprot:feature_type
annotated property: IAO_0000118
annotated source: catalytic_residue

Axiom
IAO scope: EXACT
annotated target: catalytic residue
annotated property: IAO_0000118
annotated source: catalytic_residue

polypeptide_ligand_contact
type: Class
subclass of: SO_0001657
subclass of: SO_0100002
IAO alt id: BS:00157
IAO_0000115: Residues which interact with a ligand.
IAO id: SO:0001105
IAO subset: biosapiens
IAO_0000118: polypeptide ligand contact
IAO_0000118: protein-ligand interaction

Axiom
IAO scope: EXACT
annotated target: polypeptide ligand contact
annotated property: IAO_0000118
annotated source: polypeptide_ligand_contact

Axiom
IAO xref: EBIBS:GAR
annotated target: Residues which interact with a ligand.
annotated property: IAO_0000115
annotated source: polypeptide_ligand_contact

Axiom
IAO scope: RELATED
annotated target: protein-ligand interaction
annotated property: IAO_0000118
annotated source: polypeptide_ligand_contact

asx_motif
type: Class
subclass of: polypeptide_secondary_structure
IAO_0000115: A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4).
IAO alt id: BS:00202
IAO id: SO:0001106
IAO_0000118: asx motif
IAO subset: biosapiens

Axiom
IAO scope: EXACT
annotated target: asx motif
annotated property: IAO_0000118
annotated source: asx_motif

Axiom
annotated target: A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4).
IAO xref: EBIBS:GAR
IAO xref: http://www.ebi.ac.uk/msd-srv/msdmotif/
annotated property: IAO_0000115
annotated source: asx_motif

beta_bulge
type: Class
subclass of: polypeptide_secondary_structure
IAO_0000115: A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees.
IAO alt id: BS:00208
IAO id: SO:0001107
IAO_0000118: beta bulge
IAO subset: biosapiens
IAO xref: http://en.wikipedia.org/wiki/Beta_bulge

Axiom
annotated target: A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees.
IAO xref: EBIBS:GAR
IAO xref: http://www.ebi.ac.uk/msd-srv/msdmotif/
annotated property: IAO_0000115
annotated source: beta_bulge

Axiom
IAO scope: EXACT
annotated target: beta bulge
annotated property: IAO_0000118
annotated source: beta_bulge

beta_bulge_loop
type: Class
subclass of: polypeptide_secondary_structure
IAO_0000115: A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins.
IAO alt id: BS:00209
IAO id: SO:0001108
IAO_0000118: beta bulge loop
IAO subset: biosapiens

Axiom
IAO scope: EXACT
annotated target: beta bulge loop
annotated property: IAO_0000118
annotated source: beta_bulge_loop

Axiom
annotated target: A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins.
IAO xref: EBIBS:GAR
IAO xref: Http://www.ebi.ac.uk/msd-srv/msdmotif/
annotated property: IAO_0000115
annotated source: beta_bulge_loop

beta_bulge_loop_five
type: Class
subclass of: beta_bulge_loop
IAO_0000115: A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3.
IAO alt id: BS:00210
IAO id: SO:0001109
IAO_0000118: beta bulge loop five
IAO subset: biosapiens

Axiom
IAO scope: EXACT
annotated target: beta bulge loop five
annotated property: IAO_0000118
annotated source: beta_bulge_loop_five

Axiom
annotated target: A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3.
IAO xref: EBIBS:GAR
IAO xref: http://www.ebi.ac.uk/msd-srv/msdmotif/
annotated property: IAO_0000115
annotated source: beta_bulge_loop_five

beta_bulge_loop_six
type: Class
subclass of: beta_bulge_loop
IAO_0000115: A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4.
IAO alt id: BS:00211
IAO id: SO:0001110
IAO_0000118: beta bulge loop six
IAO subset: biosapiens

Axiom
IAO scope: EXACT
annotated target: beta bulge loop six
annotated property: IAO_0000118
annotated source: beta_bulge_loop_six

Axiom
annotated target: A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4.
IAO xref: EBIBS:GAR
IAO xref: http://www.ebi.ac.uk/msd-srv/msdmotif/
annotated property: IAO_0000115
annotated source: beta_bulge_loop_six

beta_strand
type: Class
subclass of: polypeptide_secondary_structure
IAO_0000115: A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array.
IAO alt id: BS:00042
comment: Range.
IAO id: SO:0001111
IAO subset: biosapiens
IAO xref: http://en.wikipedia.org/wiki/Beta_sheet
IAO_0000118: strand

Axiom
IAO type: BS
IAO scope: RELATED
annotated target: strand
IAO xref: uniprot:feature_type
annotated property: IAO_0000118
annotated source: beta_strand

Axiom
annotated target: A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array.
IAO xref: EBIBS:GAR
IAO xref: UniProt:curation_manual
annotated property: IAO_0000115
annotated source: beta_strand

antiparallel_beta_strand
type: Class
subclass of: beta_strand
IAO_0000115: A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets.
IAO alt id: BS:0000341
comment: Range.
IAO id: SO:0001112
IAO_0000118: antiparallel beta strand
IAO subset: biosapiens

Axiom
IAO scope: EXACT
annotated target: antiparallel beta strand
annotated property: IAO_0000118
annotated source: antiparallel_beta_strand

Axiom
annotated target: A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets.
IAO xref: EBIBS:GAR
IAO xref: UniProt:curation_manual
annotated property: IAO_0000115
annotated source: antiparallel_beta_strand

parallel_beta_strand
type: Class
subclass of: beta_strand
IAO_0000115: A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets.
IAO alt id: BS:00151
comment: Range.
IAO id: SO:0001113
IAO subset: biosapiens
IAO_0000118: parallel beta strand

Axiom
annotated target: A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets.
IAO xref: EBIBS:GAR
IAO xref: UniProt:curation_manual
annotated property: IAO_0000115
annotated source: parallel_beta_strand

Axiom
IAO scope: EXACT
annotated target: parallel beta strand
annotated property: IAO_0000118
annotated source: parallel_beta_strand

peptide_helix
type: Class
subclass of: polypeptide_secondary_structure
IAO_0000115: A helix is a secondary_structure conformation where the peptide backbone forms a coil.
IAO alt id: BS:00152
comment: Range.
IAO id: SO:0001114
IAO subset: biosapiens
IAO_0000118: helix

Axiom
IAO type: BS
IAO scope: RELATED
annotated target: helix
annotated property: IAO_0000118
annotated source: peptide_helix

Axiom
annotated target: A helix is a secondary_structure conformation where the peptide backbone forms a coil.
IAO xref: EBIBS:GAR
annotated property: IAO_0000115
annotated source: peptide_helix

left_handed_peptide_helix
type: Class
subclass of: peptide_helix
IAO_0000115: A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw.
IAO alt id: BS:00222
IAO id: SO:0001115
IAO subset: biosapiens
IAO_0000118: helix-l
IAO_0000118: left handed helix

Axiom
annotated target: A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw.
IAO xref: EBIBS:GAR
annotated property: IAO_0000115
annotated source: left_handed_peptide_helix

Axiom
IAO scope: RELATED
annotated target: helix-l
annotated property: IAO_0000118
annotated source: left_handed_peptide_helix

Axiom
IAO scope: EXACT
annotated target: left handed helix
annotated property: IAO_0000118
annotated source: left_handed_peptide_helix

right_handed_peptide_helix
type: Class
subclass of: peptide_helix
IAO_0000115: A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw.
IAO alt id: BS:0000339
IAO id: SO:0001116
IAO subset: biosapiens
IAO_0000118: helix
IAO_0000118: right handed helix

Axiom
annotated target: A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw.
IAO xref: EBIBS:GAR
annotated property: IAO_0000115
annotated source: right_handed_peptide_helix

Axiom
IAO scope: EXACT
annotated target: right handed helix
annotated property: IAO_0000118
annotated source: right_handed_peptide_helix

Axiom
IAO type: BS
IAO scope: RELATED
annotated target: helix
annotated property: IAO_0000118
annotated source: right_handed_peptide_helix

alpha_helix
type: Class
subclass of: right_handed_peptide_helix
IAO alt id: BS:00040
comment: Range.
IAO id: SO:0001117
IAO_0000115: The helix has 3.6 residues per turn which corersponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier.
IAO_0000118: a-helix
IAO subset: biosapiens
IAO_0000118: helix
IAO xref: http://en.wikipedia.org/wiki/Alpha_helix

Axiom
IAO xref: EBIBS:GAR
annotated target: The helix has 3.6 residues per turn which corersponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier.
annotated property: IAO_0000115
annotated source: alpha_helix

Axiom
IAO type: BS
IAO scope: RELATED
annotated target: helix
IAO xref: uniprot:feature_type
annotated property: IAO_0000118
annotated source: alpha_helix

Axiom
IAO type: BS
IAO scope: RELATED
annotated target: a-helix
annotated property: IAO_0000118
annotated source: alpha_helix

pi_helix
type: Class
subclass of: right_handed_peptide_helix
IAO alt id: BS:00153
comment: Range.
IAO id: SO:0001118
IAO_0000115: The pi helix has 4.1 residues per turn and a translation of 1.15 (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier.
IAO subset: biosapiens
IAO xref: http://en.wikipedia.org/wiki/Pi_helix
IAO_0000118: pi helix

Axiom
IAO xref: EBIBS:GAR
annotated target: The pi helix has 4.1 residues per turn and a translation of 1.15 (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier.
annotated property: IAO_0000115
annotated source: pi_helix

Axiom
IAO scope: EXACT
annotated target: pi helix
annotated property: IAO_0000118
annotated source: pi_helix

three_ten_helix
type: Class
subclass of: right_handed_peptide_helix
IAO_0000118: 3(10) helix
IAO_0000118: 3-10 helix
IAO_0000118: 310 helix
IAO alt id: BS:0000340
comment: Range.
IAO id: SO:0001119
IAO_0000115: The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier.
IAO subset: biosapiens
IAO xref: http://en.wikipedia.org/wiki/310_helix
IAO_0000118: three_ten_helix

Axiom
annotated target: 3-10 helix
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: three_ten_helix

Axiom
annotated target: 310 helix
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: three_ten_helix

Axiom
IAO scope: EXACT
annotated target: three_ten_helix
annotated property: IAO_0000118
annotated source: three_ten_helix

Axiom
IAO xref: EBIBS:GAR
annotated target: The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier.
annotated property: IAO_0000115
annotated source: three_ten_helix

Axiom
annotated target: 3(10) helix
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: three_ten_helix

polypeptide_nest_motif
type: Class
subclass of: polypeptide_secondary_structure
IAO_0000115: A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops.
IAO alt id: BS:00223
IAO id: SO:0001120
IAO subset: biosapiens
IAO_0000118: nest
IAO_0000118: nest_motif
IAO_0000118: polypeptide nest motif

Axiom
annotated target: A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops.
IAO xref: EBIBS:GAR
IAO xref: http://www.ebi.ac.uk/msd-srv/msdmotif/
annotated property: IAO_0000115
annotated source: polypeptide_nest_motif

Axiom
IAO scope: RELATED
annotated target: polypeptide nest motif
annotated property: IAO_0000118
annotated source: polypeptide_nest_motif

Axiom
IAO scope: EXACT
annotated target: nest_motif
annotated property: IAO_0000118
annotated source: polypeptide_nest_motif

Axiom
IAO type: BS
IAO scope: RELATED
annotated target: nest
annotated property: IAO_0000118
annotated source: polypeptide_nest_motif

polypeptide_nest_left_right_motif
type: Class
subclass of: polypeptide_nest_motif
IAO_0000115: A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.
IAO alt id: BS:00224
IAO id: SO:0001121
IAO subset: biosapiens
IAO_0000118: nest_left_right
IAO_0000118: nest_lr
IAO_0000118: polypeptide nest left right motif

Axiom
IAO scope: EXACT
annotated target: nest_lr
annotated property: IAO_0000118
annotated source: polypeptide_nest_left_right_motif

Axiom
IAO scope: EXACT
annotated target: polypeptide nest left right motif
annotated property: IAO_0000118
annotated source: polypeptide_nest_left_right_motif

Axiom
annotated target: A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.
IAO xref: EBIBS:GAR
IAO xref: http://www.ebi.ac.uk/msd-srv/msdmotif/
annotated property: IAO_0000115
annotated source: polypeptide_nest_left_right_motif

Axiom
IAO scope: EXACT
annotated target: nest_left_right
annotated property: IAO_0000118
annotated source: polypeptide_nest_left_right_motif

polypeptide_nest_right_left_motif
type: Class
subclass of: polypeptide_nest_motif
IAO_0000115: A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.
IAO alt id: BS:00225
IAO id: SO:0001122
IAO subset: biosapiens
IAO_0000118: nest_right_left
IAO_0000118: nest_rl
IAO_0000118: polypeptide nest right left motif

Axiom
IAO scope: EXACT
annotated target: nest_right_left
annotated property: IAO_0000118
annotated source: polypeptide_nest_right_left_motif

Axiom
annotated target: A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.
IAO xref: EBIBS:GAR
IAO xref: http://www.ebi.ac.uk/msd-srv/msdmotif/
annotated property: IAO_0000115
annotated source: polypeptide_nest_right_left_motif

Axiom
IAO scope: EXACT
annotated target: polypeptide nest right left motif
annotated property: IAO_0000118
annotated source: polypeptide_nest_right_left_motif

Axiom
IAO scope: EXACT
annotated target: nest_rl
annotated property: IAO_0000118
annotated source: polypeptide_nest_right_left_motif

schellmann_loop
type: Class
subclass of: polypeptide_secondary_structure
IAO_0000115: A motif of six or seven consecutive residues that contains two H-bonds.
IAO alt id: BS:00226
IAO id: SO:0001123
IAO subset: biosapiens
IAO_0000118: paperclip
IAO_0000118: paperclip loop
IAO_0000118: schellmann_loop

Axiom
IAO scope: RELATED
annotated target: paperclip loop
annotated property: IAO_0000118
annotated source: schellmann_loop

Axiom
IAO type: BS
IAO scope: RELATED
annotated target: paperclip
annotated property: IAO_0000118
annotated source: schellmann_loop

Axiom
annotated target: A motif of six or seven consecutive residues that contains two H-bonds.
IAO xref: EBIBS:GAR
IAO xref: http://www.ebi.ac.uk/msd-srv/msdmotif/
annotated property: IAO_0000115
annotated source: schellmann_loop

Axiom
IAO scope: EXACT
annotated target: schellmann_loop
annotated property: IAO_0000118
annotated source: schellmann_loop

schellmann_loop_seven
type: Class
subclass of: schellmann_loop
IAO alt id: BS:00228
IAO id: SO:0001124
IAO_0000115: Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5).
IAO subset: biosapiens
IAO_0000118: schellmann loop seven
IAO_0000118: seven-residue schellmann loop

Axiom
IAO scope: EXACT
annotated target: schellmann loop seven
annotated property: IAO_0000118
annotated source: schellmann_loop_seven

Axiom
IAO xref: EBIBS:GAR
annotated target: Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5).
IAO xref: http://www.ebi.ac.uk/msd-srv/msdmotif/
annotated property: IAO_0000115
annotated source: schellmann_loop_seven

Axiom
IAO scope: EXACT
annotated target: seven-residue schellmann loop
annotated property: IAO_0000118
annotated source: schellmann_loop_seven

schellmann_loop_six
type: Class
subclass of: schellmann_loop
IAO alt id: BS:00227
IAO_0000115: Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4).
IAO id: SO:0001125
IAO subset: biosapiens
IAO_0000118: schellmann loop six
IAO_0000118: six-residue schellmann loop

Axiom
IAO scope: EXACT
annotated target: schellmann loop six
annotated property: IAO_0000118
annotated source: schellmann_loop_six

Axiom
annotated target: Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4).
IAO xref: EBIBS:GAR
IAO xref: http://www.ebi.ac.uk/msd-srv/msdmotif/
annotated property: IAO_0000115
annotated source: schellmann_loop_six

Axiom
IAO scope: EXACT
annotated target: six-residue schellmann loop
annotated property: IAO_0000118
annotated source: schellmann_loop_six

serine_threonine_motif
type: Class
subclass of: polypeptide_secondary_structure
IAO_0000115: A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4).
IAO alt id: BS:00229
IAO id: SO:0001126
IAO subset: biosapiens
IAO_0000118: serine/threonine motif
IAO_0000118: st motif
IAO_0000118: st_motif

Axiom
IAO scope: EXACT
annotated target: st_motif
annotated property: IAO_0000118
annotated source: serine_threonine_motif

Axiom
annotated target: A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4).
IAO xref: EBIBS:GAR
IAO xref: http://www.ebi.ac.uk/msd-srv/msdmotif/
annotated property: IAO_0000115
annotated source: serine_threonine_motif

Axiom
IAO scope: EXACT
annotated target: st motif
annotated property: IAO_0000118
annotated source: serine_threonine_motif

Axiom
IAO scope: EXACT
annotated target: serine/threonine motif
annotated property: IAO_0000118
annotated source: serine_threonine_motif

serine_threonine_staple_motif
type: Class
subclass of: polypeptide_secondary_structure
IAO_0000115: A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative.
IAO alt id: BS:00230
IAO id: SO:0001127
IAO subset: biosapiens
IAO_0000118: serine threonine staple motif
IAO_0000118: st_staple

Axiom
IAO scope: EXACT
annotated target: serine threonine staple motif
annotated property: IAO_0000118
annotated source: serine_threonine_staple_motif

Axiom
IAO scope: EXACT
annotated target: st_staple
annotated property: IAO_0000118
annotated source: serine_threonine_staple_motif

Axiom
annotated target: A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative.
IAO xref: EBIBS:GAR
IAO xref: http://www.ebi.ac.uk/msd-srv/msdmotif/
annotated property: IAO_0000115
annotated source: serine_threonine_staple_motif

polypeptide_turn_motif
type: Class
subclass of: polypeptide_secondary_structure
IAO_0000115: A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues.
IAO alt id: BS:00148
comment: Range.
IAO id: SO:0001128
IAO subset: biosapiens
IAO_0000118: turn

Axiom
annotated target: A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues.
IAO xref: EBIBS:GAR
IAO xref: uniprot:feature_type
annotated property: IAO_0000115
annotated source: polypeptide_turn_motif

Axiom
IAO type: BS
IAO scope: RELATED
annotated target: turn
annotated property: IAO_0000118
annotated source: polypeptide_turn_motif

asx_turn_left_handed_type_one
type: Class
subclass of: asx_turn
IAO alt id: BS:00206
IAO_0000115: Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.
IAO id: SO:0001129
IAO_0000118: asx turn left handed type one
IAO_0000118: asx_turn_il
IAO subset: biosapiens

Axiom
IAO xref: EBIBS:GAR
annotated target: Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.
IAO xref: http://www.ebi.ac.uk/msd-srv/msdmotif/
annotated property: IAO_0000115
annotated source: asx_turn_left_handed_type_one

Axiom
IAO scope: RELATED
annotated target: asx_turn_il
annotated property: IAO_0000118
annotated source: asx_turn_left_handed_type_one

Axiom
IAO scope: EXACT
annotated target: asx turn left handed type one
annotated property: IAO_0000118
annotated source: asx_turn_left_handed_type_one

asx_turn_left_handed_type_two
type: Class
subclass of: asx_turn
IAO alt id: BS:00204
IAO_0000115: Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.
IAO id: SO:0001130
IAO_0000118: asx turn left handed type two
IAO_0000118: asx_turn_iil
IAO subset: biosapiens

Axiom
IAO scope: EXACT
annotated target: asx turn left handed type two
annotated property: IAO_0000118
annotated source: asx_turn_left_handed_type_two

Axiom
IAO xref: EBIBS:GAR
annotated target: Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.
IAO xref: http://www.ebi.ac.uk/msd-srv/msdmotif/
annotated property: IAO_0000115
annotated source: asx_turn_left_handed_type_two

Axiom
IAO scope: EXACT
annotated target: asx_turn_iil
annotated property: IAO_0000118
annotated source: asx_turn_left_handed_type_two

asx_turn_right_handed_type_two
type: Class
subclass of: asx_turn
IAO alt id: BS:00205
IAO_0000115: Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.
IAO id: SO:0001131
IAO_0000118: asx turn right handed type two
IAO_0000118: asx_turn_iir
IAO subset: biosapiens

Axiom
IAO scope: EXACT
annotated target: asx turn right handed type two
annotated property: IAO_0000118
annotated source: asx_turn_right_handed_type_two

Axiom
IAO xref: EBIBS:GAR
annotated target: Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.
IAO xref: http://www.ebi.ac.uk/msd-srv/msdmotif/
annotated property: IAO_0000115
annotated source: asx_turn_right_handed_type_two

Axiom
IAO scope: EXACT
annotated target: asx_turn_iir
annotated property: IAO_0000118
annotated source: asx_turn_right_handed_type_two

asx_turn_right_handed_type_one
type: Class
subclass of: asx_turn
IAO alt id: BS:00207
IAO_0000115: Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.
IAO id: SO:0001132
IAO_0000118: asx turn type right handed type one
IAO_0000118: asx_turn_ir
IAO subset: biosapiens

Axiom
IAO scope: EXACT
annotated target: asx_turn_ir
annotated property: IAO_0000118
annotated source: asx_turn_right_handed_type_one

Axiom
IAO xref: EBIBS:GAR
annotated target: Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.
IAO xref: http://www.ebi.ac.uk/msd-srv/msdmotif/
annotated property: IAO_0000115
annotated source: asx_turn_right_handed_type_one

Axiom
IAO scope: EXACT
annotated target: asx turn type right handed type one
annotated property: IAO_0000118
annotated source: asx_turn_right_handed_type_one

beta_turn
type: Class
subclass of: polypeptide_turn_motif
IAO_0000115: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization.
IAO alt id: BS:00212
IAO id: SO:0001133
IAO_0000118: beta turn
IAO subset: biosapiens

Axiom
annotated target: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization.
IAO xref: EBIBS:GAR
IAO xref: http://www.ebi.ac.uk/msd-srv/msdmotif/
annotated property: IAO_0000115
annotated source: beta_turn

Axiom
IAO scope: EXACT
annotated target: beta turn
annotated property: IAO_0000118
annotated source: beta_turn

beta_turn_left_handed_type_one
type: Class
subclass of: beta_turn
IAO alt id: BS:00215
IAO_0000115: Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees.
IAO id: SO:0001134
IAO_0000118: beta turn left handed type one
IAO_0000118: beta_turn_il
IAO subset: biosapiens
IAO_0000118: type I' beta turn
IAO_0000118: type I' turn

Axiom
IAO xref: EBIBS:GAR
annotated target: Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees.
IAO xref: http://www.ebi.ac.uk/msd-srv/msdmotif/
annotated property: IAO_0000115
annotated source: beta_turn_left_handed_type_one

Axiom
IAO scope: EXACT
annotated target: beta turn left handed type one
annotated property: IAO_0000118
annotated source: beta_turn_left_handed_type_one

Axiom
IAO scope: EXACT
annotated target: beta_turn_il
annotated property: IAO_0000118
annotated source: beta_turn_left_handed_type_one

Axiom
IAO scope: EXACT
annotated target: type I' beta turn
annotated property: IAO_0000118
annotated source: beta_turn_left_handed_type_one

Axiom
IAO scope: EXACT
annotated target: type I' turn
annotated property: IAO_0000118
annotated source: beta_turn_left_handed_type_one

beta_turn_left_handed_type_two
type: Class
subclass of: beta_turn
IAO alt id: BS:00213
IAO_0000115: Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees.
IAO id: SO:0001135
IAO_0000118: beta turn left handed type two
IAO_0000118: beta_turn_iil
IAO subset: biosapiens
IAO_0000118: type II' beta turn
IAO_0000118: type II' turn

Axiom
IAO scope: EXACT
annotated target: type II' turn
annotated property: IAO_0000118
annotated source: beta_turn_left_handed_type_two

Axiom
IAO scope: EXACT
annotated target: beta turn left handed type two
annotated property: IAO_0000118
annotated source: beta_turn_left_handed_type_two

Axiom
IAO scope: EXACT
annotated target: beta_turn_iil
annotated property: IAO_0000118
annotated source: beta_turn_left_handed_type_two

Axiom
IAO xref: EBIBS:GAR
annotated target: Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees.
IAO xref: http://www.ebi.ac.uk/msd-srv/msdmotif/
annotated property: IAO_0000115
annotated source: beta_turn_left_handed_type_two

Axiom
IAO scope: EXACT
annotated target: type II' beta turn
annotated property: IAO_0000118
annotated source: beta_turn_left_handed_type_two

beta_turn_right_handed_type_one
type: Class
subclass of: beta_turn
IAO alt id: BS:00216
IAO_0000115: Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.
IAO id: SO:0001136
IAO_0000118: beta turn right handed type one
IAO_0000118: beta_turn_ir
IAO subset: biosapiens
IAO_0000118: type I beta turn
IAO_0000118: type I turn

Axiom
IAO scope: EXACT
annotated target: type I turn
annotated property: IAO_0000118
annotated source: beta_turn_right_handed_type_one

Axiom
IAO scope: EXACT
annotated target: beta_turn_ir
annotated property: IAO_0000118
annotated source: beta_turn_right_handed_type_one

Axiom
IAO scope: EXACT
annotated target: type I beta turn
annotated property: IAO_0000118
annotated source: beta_turn_right_handed_type_one

Axiom
IAO scope: EXACT
annotated target: beta turn right handed type one
annotated property: IAO_0000118
annotated source: beta_turn_right_handed_type_one

Axiom
IAO xref: EBIBS:GAR
annotated target: Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.
IAO xref: http://www.ebi.ac.uk/msd-srv/msdmotif/
annotated property: IAO_0000115
annotated source: beta_turn_right_handed_type_one

beta_turn_right_handed_type_two
type: Class
subclass of: beta_turn
IAO alt id: BS:00214
IAO_0000115: Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.
IAO id: SO:0001137
IAO_0000118: beta turn right handed type two
IAO_0000118: beta_turn_iir
IAO subset: biosapiens
IAO_0000118: type II beta turn
IAO_0000118: type II turn

Axiom
IAO scope: EXACT
annotated target: beta_turn_iir
annotated property: IAO_0000118
annotated source: beta_turn_right_handed_type_two

Axiom
IAO xref: EBIBS:GAR
annotated target: Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.
IAO xref: http://www.ebi.ac.uk/msd-srv/msdmotif/
annotated property: IAO_0000115
annotated source: beta_turn_right_handed_type_two

Axiom
IAO scope: EXACT
annotated target: beta turn right handed type two
annotated property: IAO_0000118
annotated source: beta_turn_right_handed_type_two

Axiom
IAO scope: EXACT
annotated target: type II turn
annotated property: IAO_0000118
annotated source: beta_turn_right_handed_type_two

Axiom
IAO scope: EXACT
annotated target: type II beta turn
annotated property: IAO_0000118
annotated source: beta_turn_right_handed_type_two

gamma_turn
type: Class
subclass of: polypeptide_turn_motif
IAO alt id: BS:00219
IAO_0000115: Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees.
IAO id: SO:0001138
IAO subset: biosapiens
IAO_0000118: gamma turn

Axiom
IAO scope: EXACT
annotated target: gamma turn
annotated property: IAO_0000118
annotated source: gamma_turn

Axiom
IAO xref: EBIBS:GAR
annotated target: Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees.
IAO xref: http://www.ebi.ac.uk/msd-srv/msdmotif/
annotated property: IAO_0000115
annotated source: gamma_turn

gamma_turn_classic
type: Class
subclass of: gamma_turn
IAO alt id: BS:00220
IAO_0000115: Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0.
IAO id: SO:0001139
IAO subset: biosapiens
IAO_0000118: classic gamma turn
IAO_0000118: gamma turn classic

Axiom
IAO scope: EXACT
annotated target: classic gamma turn
annotated property: IAO_0000118
annotated source: gamma_turn_classic

Axiom
IAO scope: EXACT
annotated target: gamma turn classic
annotated property: IAO_0000118
annotated source: gamma_turn_classic

Axiom
IAO xref: EBIBS:GAR
annotated target: Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0.
IAO xref: http://www.ebi.ac.uk/msd-srv/msdmotif/
annotated property: IAO_0000115
annotated source: gamma_turn_classic

gamma_turn_inverse
type: Class
subclass of: gamma_turn
IAO alt id: BS:00221
IAO_0000115: Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0.
IAO id: SO:0001140
IAO subset: biosapiens
IAO_0000118: gamma turn inverse

Axiom
IAO scope: EXACT
annotated target: gamma turn inverse
annotated property: IAO_0000118
annotated source: gamma_turn_inverse

Axiom
IAO xref: EBIBS:GAR
annotated target: Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0.
IAO xref: http://www.ebi.ac.uk/msd-srv/msdmotif/
annotated property: IAO_0000115
annotated source: gamma_turn_inverse

serine_threonine_turn
type: Class
subclass of: polypeptide_turn_motif
IAO_0000115: A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2).
IAO alt id: BS:00231
IAO id: SO:0001141
IAO subset: biosapiens
IAO_0000118: serine/threonine turn
IAO_0000118: st_turn

Axiom
IAO scope: EXACT
annotated target: serine/threonine turn
annotated property: IAO_0000118
annotated source: serine_threonine_turn

Axiom
IAO scope: EXACT
annotated target: st_turn
annotated property: IAO_0000118
annotated source: serine_threonine_turn

Axiom
annotated target: A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2).
IAO xref: EBIBS:GAR
IAO xref: http://www.ebi.ac.uk/msd-srv/msdmotif/
annotated property: IAO_0000115
annotated source: serine_threonine_turn

st_turn_left_handed_type_one
type: Class
subclass of: serine_threonine_turn
IAO alt id: BS:00234
IAO id: SO:0001142
IAO_0000115: The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees.
IAO subset: biosapiens
IAO_0000118: st turn left handed type one
IAO_0000118: st_turn_il

Axiom
IAO scope: EXACT
annotated target: st turn left handed type one
annotated property: IAO_0000118
annotated source: st_turn_left_handed_type_one

Axiom
IAO scope: EXACT
annotated target: st_turn_il
annotated property: IAO_0000118
annotated source: st_turn_left_handed_type_one

Axiom
IAO xref: EBIBS:GAR
annotated target: The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees.
IAO xref: http://www.ebi.ac.uk/msd-srv/msdmotif/
annotated property: IAO_0000115
annotated source: st_turn_left_handed_type_one

st_turn_left_handed_type_two
type: Class
subclass of: serine_threonine_turn
IAO alt id: BS:00232
IAO id: SO:0001143
IAO_0000115: The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees.
IAO subset: biosapiens
IAO_0000118: st turn left handed type two
IAO_0000118: st_turn_iil

Axiom
IAO scope: EXACT
annotated target: st turn left handed type two
annotated property: IAO_0000118
annotated source: st_turn_left_handed_type_two

Axiom
IAO scope: EXACT
annotated target: st_turn_iil
annotated property: IAO_0000118
annotated source: st_turn_left_handed_type_two

Axiom
IAO xref: EBIBS:GAR
annotated target: The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees.
IAO xref: http://www.ebi.ac.uk/msd-srv/msdmotif/
annotated property: IAO_0000115
annotated source: st_turn_left_handed_type_two

st_turn_right_handed_type_one
type: Class
subclass of: serine_threonine_turn
IAO alt id: BS:00235
IAO id: SO:0001144
IAO_0000115: The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees.
IAO subset: biosapiens
IAO_0000118: st turn right handed type one
IAO_0000118: st_turn_ir

Axiom
IAO xref: EBIBS:GAR
annotated target: The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees.
IAO xref: http://www.ebi.ac.uk/msd-srv/msdmotif/
annotated property: IAO_0000115
annotated source: st_turn_right_handed_type_one

Axiom
IAO scope: EXACT
annotated target: st_turn_ir
annotated property: IAO_0000118
annotated source: st_turn_right_handed_type_one

Axiom
IAO scope: EXACT
annotated target: st turn right handed type one
annotated property: IAO_0000118
annotated source: st_turn_right_handed_type_one

st_turn_right_handed_type_two
type: Class
subclass of: serine_threonine_turn
IAO alt id: BS:00233
IAO id: SO:0001145
IAO_0000115: The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees.
IAO subset: biosapiens
IAO_0000118: st turn right handed type two
IAO_0000118: st_turn_iir

Axiom
IAO xref: EBIBS:GAR
annotated target: The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees.
IAO xref: http://www.ebi.ac.uk/msd-srv/msdmotif/
annotated property: IAO_0000115
annotated source: st_turn_right_handed_type_two

Axiom
IAO scope: EXACT
annotated target: st turn right handed type two
annotated property: IAO_0000118
annotated source: st_turn_right_handed_type_two

Axiom
IAO scope: EXACT
annotated target: st_turn_iir
annotated property: IAO_0000118
annotated source: st_turn_right_handed_type_two

polypeptide_variation_site
type: Class
subclass of: polypeptide_region
IAO_0000115: A site of sequence variation (alteration). Alternative sequence due to naturally occuring events such as polymorphisms and altermatve splicing or experimental methods such as site directed mutagenesis.
IAO alt id: BS:00336
comment: For example, was a substitution natural or mutated as part of an experiment? This term is added to merge the biosapiens term sequence_variations.
IAO id: SO:0001146
IAO subset: biosapiens
IAO_0000118: sequence_variations

Axiom
annotated target: A site of sequence variation (alteration). Alternative sequence due to naturally occuring events such as polymorphisms and altermatve splicing or experimental methods such as site directed mutagenesis.
IAO xref: EBIBS:GAR
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: polypeptide_variation_site

Axiom
IAO scope: EXACT
annotated target: sequence_variations
annotated property: IAO_0000118
annotated source: polypeptide_variation_site

natural_variant_site
type: Class
subclass of: polypeptide_variation_site
IAO alt id: BS:00071
IAO_0000115: Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars.
comment: Discrete.
IAO id: SO:0001147
IAO subset: biosapiens
IAO_0000118: natural_variant
IAO_0000118: sequence variation
IAO_0000118: variant

Axiom
IAO scope: BROAD
annotated target: sequence variation
annotated property: IAO_0000118
annotated source: natural_variant_site

Axiom
annotated target: Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars.
IAO xref: EBIBS:GAR
IAO xref: UniProt:curation_manual
annotated property: IAO_0000115
annotated source: natural_variant_site

Axiom
IAO scope: BROAD
IAO xref: uniprot:feature_type
annotated target: variant
annotated property: IAO_0000118
annotated source: natural_variant_site

Axiom
IAO scope: BROAD
annotated target: natural_variant
annotated property: IAO_0000118
annotated source: natural_variant_site

mutated_variant_site
type: Class
subclass of: polypeptide_variation_site
IAO alt id: BS:00036
comment: Discrete.
IAO id: SO:0001148
IAO_0000115: Site which has been experimentally altered.
IAO subset: biosapiens
IAO_0000118: mutagen
IAO_0000118: mutagenesis
IAO_0000118: mutated_site

Axiom
IAO type: BS
IAO scope: EXACT
annotated target: mutagen
IAO xref: uniprot:feature_type
annotated property: IAO_0000118
annotated source: mutated_variant_site

Axiom
IAO scope: EXACT
annotated target: mutated_site
annotated property: IAO_0000118
annotated source: mutated_variant_site

Axiom
IAO xref: EBIBS:GAR
annotated target: Site which has been experimentally altered.
IAO xref: UniProt:curation_manual
annotated property: IAO_0000115
annotated source: mutated_variant_site

Axiom
IAO scope: EXACT
annotated target: mutagenesis
annotated property: IAO_0000118
annotated source: mutated_variant_site

alternate_sequence_site
type: Class
subclass of: polypeptide_variation_site
IAO alt id: BS:00073
IAO_0000115: Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting.
comment: Discrete.
IAO alt id: SO:0001065
IAO id: SO:0001149
IAO_0000118: alternative_sequence
IAO subset: biosapiens
IAO_0000118: isoform
IAO_0000118: sequence variation
IAO_0000118: var_seq
IAO_0000118: varsplic

Axiom
IAO scope: EXACT
annotated target: alternative_sequence
annotated property: IAO_0000118
annotated source: alternate_sequence_site

Axiom
IAO scope: EXACT
IAO xref: uniprot:feature_type
annotated target: var_seq
annotated property: IAO_0000118
annotated source: alternate_sequence_site

Axiom
IAO scope: NARROW
annotated target: sequence variation
annotated property: IAO_0000118
annotated source: alternate_sequence_site

Axiom
annotated target: Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting.
IAO xref: EBIBS:GAR
IAO xref: UniProt:curation_manual
annotated property: IAO_0000115
annotated source: alternate_sequence_site

Axiom
IAO scope: NARROW
annotated target: varsplic
annotated property: IAO_0000118
annotated source: alternate_sequence_site

Axiom
IAO scope: NARROW
annotated target: isoform
annotated property: IAO_0000118
annotated source: alternate_sequence_site

beta_turn_type_six
type: Class
subclass of: beta_turn
IAO_0000115: A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline.
IAO id: SO:0001150
IAO_0000118: beta turn type six
IAO subset: biosapiens
IAO_0000118: cis-proline loop
IAO_0000118: type VI beta turn
IAO_0000118: type VI turn

Axiom
IAO scope: EXACT
annotated target: type VI turn
annotated property: IAO_0000118
annotated source: beta_turn_type_six

Axiom
IAO scope: EXACT
annotated target: type VI beta turn
annotated property: IAO_0000118
annotated source: beta_turn_type_six

Axiom
IAO scope: EXACT
annotated target: beta turn type six
annotated property: IAO_0000118
annotated source: beta_turn_type_six

Axiom
IAO scope: EXACT
annotated target: cis-proline loop
annotated property: IAO_0000118
annotated source: beta_turn_type_six

Axiom
annotated target: A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline.
IAO xref: SO:cb
annotated property: IAO_0000115
annotated source: beta_turn_type_six

beta_turn_type_six_a
type: Class
subclass of: beta_turn_type_six
IAO_0000115: A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees.
IAO id: SO:0001151
IAO_0000118: beta turn type six a
IAO subset: biosapiens
IAO_0000118: type VIa beta turn
IAO_0000118: type VIa turn

Axiom
IAO scope: EXACT
annotated target: type VIa beta turn
annotated property: IAO_0000118
annotated source: beta_turn_type_six_a

Axiom
IAO scope: EXACT
annotated target: beta turn type six a
annotated property: IAO_0000118
annotated source: beta_turn_type_six_a

Axiom
annotated target: A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees.
IAO xref: PMID:2371257
IAO xref: SO:cb
annotated property: IAO_0000115
annotated source: beta_turn_type_six_a

Axiom
IAO scope: EXACT
annotated target: type VIa turn
annotated property: IAO_0000118
annotated source: beta_turn_type_six_a

beta_turn_type_six_a_one
type: Class
subclass of: beta_turn_type_six_a
IAO id: SO:0001152
IAO_0000118: beta turn type six a one
IAO subset: biosapiens
IAO_0000118: type VIa1 beta turn
IAO_0000118: type VIa1 turn

Axiom
IAO scope: EXACT
annotated target: type VIa1 turn
annotated property: IAO_0000118
annotated source: beta_turn_type_six_a_one

Axiom
IAO scope: EXACT
annotated target: beta turn type six a one
annotated property: IAO_0000118
annotated source: beta_turn_type_six_a_one

Axiom
IAO scope: EXACT
annotated target: type VIa1 beta turn
annotated property: IAO_0000118
annotated source: beta_turn_type_six_a_one

beta_turn_type_six_a_two
type: Class
subclass of: beta_turn_type_six_a
IAO id: SO:0001153
IAO_0000118: beta turn type six a two
IAO subset: biosapiens
IAO_0000118: type VIa2 beta turn
IAO_0000118: type VIa2 turn

Axiom
IAO scope: EXACT
annotated target: type VIa2 beta turn
annotated property: IAO_0000118
annotated source: beta_turn_type_six_a_two

Axiom
IAO scope: EXACT
annotated target: beta turn type six a two
annotated property: IAO_0000118
annotated source: beta_turn_type_six_a_two

Axiom
IAO scope: EXACT
annotated target: type VIa2 turn
annotated property: IAO_0000118
annotated source: beta_turn_type_six_a_two

beta_turn_type_six_b
type: Class
subclass of: beta_turn_type_six
IAO_0000115: A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees.
IAO id: SO:0001154
IAO_0000118: beta turn type six b
IAO subset: biosapiens
IAO_0000118: type VIb beta turn
IAO_0000118: type VIb turn

Axiom
IAO scope: EXACT
annotated target: type VIb turn
annotated property: IAO_0000118
annotated source: beta_turn_type_six_b

Axiom
annotated target: A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees.
IAO xref: PMID:2371257
IAO xref: SO:cb
annotated property: IAO_0000115
annotated source: beta_turn_type_six_b

Axiom
IAO scope: EXACT
annotated target: type VIb beta turn
annotated property: IAO_0000118
annotated source: beta_turn_type_six_b

Axiom
IAO scope: EXACT
annotated target: beta turn type six b
annotated property: IAO_0000118
annotated source: beta_turn_type_six_b

beta_turn_type_eight
type: Class
subclass of: beta_turn
IAO_0000115: A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees.
IAO id: SO:0001155
IAO_0000118: beta turn type eight
IAO subset: biosapiens
IAO_0000118: type VIII beta turn
IAO_0000118: type VIII turn

Axiom
annotated target: A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees.
IAO xref: PMID:2371257
IAO xref: SO:cb
annotated property: IAO_0000115
annotated source: beta_turn_type_eight

Axiom
IAO scope: EXACT
annotated target: beta turn type eight
annotated property: IAO_0000118
annotated source: beta_turn_type_eight

Axiom
IAO scope: EXACT
annotated target: type VIII beta turn
annotated property: IAO_0000118
annotated source: beta_turn_type_eight

Axiom
IAO scope: EXACT
annotated target: type VIII turn
annotated property: IAO_0000118
annotated source: beta_turn_type_eight

DRE_motif
type: Class
subclass of: DNA_motif
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_promoter
IAO_0000115: A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW.
IAO_0000118: DRE motif
IAO_0000118: NDM4
IAO id: SO:0001156
comment: This consensus sequence was identified computationally using the MEME algorithm within core promoter sequences from -60 to +40, with an E value of 1.7e-183. Tends to co-occur with Motif 7. Tends to not occur with DPE motif (SO:0000015) or motif 10.
IAO_0000118: WATCGATW_motif

Axiom
IAO scope: EXACT
annotated target: NDM4
annotated property: IAO_0000118
annotated source: DRE_motif

Axiom
annotated target: A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW.
IAO xref: PMID:12537576
annotated property: IAO_0000115
annotated source: DRE_motif

Axiom
IAO scope: EXACT
annotated target: WATCGATW_motif
annotated property: IAO_0000118
annotated source: DRE_motif

Axiom
annotated target: DRE motif
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DRE_motif

DMv4_motif
type: Class
subclass of: SO_0001659
IAO_0000115: A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014).
IAO_0000118: DMv4
IAO_0000118: DMv4 motif
IAO id: SO:0001157
IAO_0000118: YGGTCACATR
IAO_0000118: directional motif v4
IAO_0000118: motif 1 element
IAO_0000118: promoter motif 1

Axiom
annotated target: DMv4
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DMv4_motif

Axiom
IAO scope: NARROW
annotated target: YGGTCACATR
annotated property: IAO_0000118
annotated source: DMv4_motif

Axiom
IAO scope: EXACT
annotated target: promoter motif 1
annotated property: IAO_0000118
annotated source: DMv4_motif

Axiom
IAO scope: EXACT
annotated target: directional motif v4
annotated property: IAO_0000118
annotated source: DMv4_motif

Axiom
annotated target: DMv4 motif
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DMv4_motif

Axiom
annotated target: A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014).
IAO xref: PMID:16827941\:12537576
annotated property: IAO_0000115
annotated source: DMv4_motif

Axiom
IAO scope: EXACT
annotated target: motif 1 element
annotated property: IAO_0000118
annotated source: DMv4_motif

E_box_motif
type: Class
subclass of: DNA_motif
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_promoter
IAO_0000115: A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015).
IAO_0000118: AWCAGCTGWT
IAO_0000118: E box motif
IAO_0000118: NDM5
IAO id: SO:0001158
IAO_0000118: generic E box motif

Axiom
annotated target: AWCAGCTGWT
IAO scope: NARROW
annotated property: IAO_0000118
annotated source: E_box_motif

Axiom
annotated target: NDM5
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: E_box_motif

Axiom
IAO scope: EXACT
annotated target: generic E box motif
annotated property: IAO_0000118
annotated source: E_box_motif

Axiom
annotated target: E box motif
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: E_box_motif

Axiom
annotated target: A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015).
IAO xref: PMID:12537576\:16827941
annotated property: IAO_0000115
annotated source: E_box_motif

DMv5_motif
type: Class
subclass of: SO_0001659
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_promoter
IAO_0000115: A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162).
IAO_0000118: DMv5
IAO_0000118: DMv5 motif
IAO_0000118: KTYRGTATWTTT
IAO id: SO:0001159
IAO_0000118: directional motif v5
IAO_0000118: promoter motif 6

Axiom
IAO scope: EXACT
annotated target: directional motif v5
annotated property: IAO_0000118
annotated source: DMv5_motif

Axiom
annotated target: KTYRGTATWTTT
IAO scope: NARROW
annotated property: IAO_0000118
annotated source: DMv5_motif

Axiom
annotated target: A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162).
IAO xref: PMID:12537576\:16827941
annotated property: IAO_0000115
annotated source: DMv5_motif

Axiom
annotated target: DMv5
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DMv5_motif

Axiom
annotated target: DMv5 motif
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DMv5_motif

Axiom
IAO scope: RELATED
annotated target: promoter motif 6
annotated property: IAO_0000118
annotated source: DMv5_motif

DMv3_motif
type: Class
subclass of: SO_0001659
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_promoter
IAO_0000115: A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162).
IAO_0000118: DMv3
IAO_0000118: DMv3 motif
IAO_0000118: KNNCAKCNCTRNY
IAO id: SO:0001160
IAO_0000118: directional motif v3
IAO_0000118: promoter motif 7

Axiom
IAO scope: EXACT
annotated target: directional motif v3
annotated property: IAO_0000118
annotated source: DMv3_motif

Axiom
annotated target: DMv3 motif
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DMv3_motif

Axiom
annotated target: A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162).
IAO xref: PMID:12537576\:16827941
annotated property: IAO_0000115
annotated source: DMv3_motif

Axiom
annotated target: DMv3
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DMv3_motif

Axiom
annotated target: KNNCAKCNCTRNY
IAO scope: NARROW
annotated property: IAO_0000118
annotated source: DMv3_motif

Axiom
IAO scope: EXACT
annotated target: promoter motif 7
annotated property: IAO_0000118
annotated source: DMv3_motif

DMv2_motif
type: Class
subclass of: SO_0001659
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_promoter
IAO_0000115: A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162).
IAO_0000118: DMv2
IAO_0000118: DMv2 motif
IAO_0000118: MKSYGGCARCGSYSS
IAO id: SO:0001161
IAO_0000118: directional motif v2
IAO_0000118: promoter motif 8

Axiom
IAO scope: EXACT
annotated target: directional motif v2
annotated property: IAO_0000118
annotated source: DMv2_motif

Axiom
annotated target: DMv2
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DMv2_motif

Axiom
annotated target: DMv2 motif
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DMv2_motif

Axiom
annotated target: A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162).
IAO xref: PMID:12537576\:16827941
annotated property: IAO_0000115
annotated source: DMv2_motif

Axiom
IAO scope: EXACT
annotated target: promoter motif 8
annotated property: IAO_0000118
annotated source: DMv2_motif

Axiom
annotated target: MKSYGGCARCGSYSS
IAO scope: NARROW
annotated property: IAO_0000118
annotated source: DMv2_motif

MTE
type: Class
subclass of: SO_0001660
subclass of: Restriction
  on property: part_of
  some values from: SO_0001669
IAO_0000115: A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159).
IAO_0000118: CSARCSSAACGS
IAO id: SO:0001162
IAO_0000118: motif ten element
IAO_0000118: motif_ten_element

Axiom
annotated target: CSARCSSAACGS
IAO scope: NARROW
annotated property: IAO_0000118
annotated source: MTE

Axiom
IAO scope: EXACT
annotated target: motif_ten_element
annotated property: IAO_0000118
annotated source: MTE

Axiom
IAO scope: EXACT
annotated target: motif ten element
annotated property: IAO_0000118
annotated source: MTE

Axiom
annotated target: A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159).
IAO xref: PMID:12537576\:15231738
IAO xref: PMID:16858867
annotated property: IAO_0000115
annotated source: MTE

INR1_motif
type: Class
subclass of: DNA_motif
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_promoter
IAO_0000115: A promoter motif with consensus sequence TCATTCG.
IAO_0000118: DMp3
IAO_0000118: INR1 motif
IAO id: SO:0001163
IAO_0000118: directional motif p3
IAO_0000118: directional promoter motif 3

Axiom
annotated target: DMp3
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: INR1_motif

Axiom
annotated target: A promoter motif with consensus sequence TCATTCG.
IAO xref: PMID:16827941
annotated property: IAO_0000115
annotated source: INR1_motif

Axiom
IAO scope: EXACT
annotated target: directional promoter motif 3
annotated property: IAO_0000118
annotated source: INR1_motif

Axiom
IAO scope: EXACT
annotated target: INR1 motif
annotated property: IAO_0000118
annotated source: INR1_motif

Axiom
IAO scope: EXACT
annotated target: directional motif p3
annotated property: IAO_0000118
annotated source: INR1_motif

DPE1_motif
type: Class
subclass of: SO_0001659
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_promoter
IAO_0000115: A promoter motif with consensus sequence CGGACGT.
IAO_0000118: DMp5
IAO_0000118: DPE1 motif
IAO id: SO:0001164
IAO_0000118: directional motif 5
IAO_0000118: directional promoter motif 5

Axiom
IAO scope: RELATED
annotated target: directional promoter motif 5
annotated property: IAO_0000118
annotated source: DPE1_motif

Axiom
IAO scope: EXACT
annotated target: directional motif 5
annotated property: IAO_0000118
annotated source: DPE1_motif

Axiom
annotated target: A promoter motif with consensus sequence CGGACGT.
IAO xref: PMID:16827941
annotated property: IAO_0000115
annotated source: DPE1_motif

Axiom
annotated target: DMp5
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DPE1_motif

Axiom
annotated target: DPE1 motif
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DPE1_motif

DMv1_motif
type: Class
subclass of: SO_0001659
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_promoter
IAO_0000115: A promoter motif with consensus sequence CARCCCT.
IAO_0000118: DMv1
IAO_0000118: DMv1 motif
IAO id: SO:0001165
IAO_0000118: directional promoter motif v1

Axiom
annotated target: DMv1 motif
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DMv1_motif

Axiom
annotated target: A promoter motif with consensus sequence CARCCCT.
IAO xref: PMID:16827941
annotated property: IAO_0000115
annotated source: DMv1_motif

Axiom
IAO scope: RELATED
annotated target: directional promoter motif v1
annotated property: IAO_0000118
annotated source: DMv1_motif

Axiom
annotated target: DMv1
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: DMv1_motif

GAGA_motif
type: Class
subclass of: DNA_motif
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_promoter
IAO_0000115: A non directional promoter motif with consensus sequence GAGAGCG.
IAO_0000118: GAGA
IAO_0000118: GAGA motif
IAO_0000118: NDM1
IAO id: SO:0001166

Axiom
IAO scope: EXACT
annotated target: GAGA
annotated property: IAO_0000118
annotated source: GAGA_motif

Axiom
IAO scope: EXACT
annotated target: NDM1
annotated property: IAO_0000118
annotated source: GAGA_motif

Axiom
IAO scope: EXACT
annotated target: GAGA motif
annotated property: IAO_0000118
annotated source: GAGA_motif

Axiom
annotated target: A non directional promoter motif with consensus sequence GAGAGCG.
IAO xref: PMID:16827941
annotated property: IAO_0000115
annotated source: GAGA_motif

NDM2_motif
type: Class
subclass of: SO_0001659
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_promoter
IAO_0000115: A non directional promoter motif with consensus CGMYGYCR.
IAO_0000118: NDM2
IAO_0000118: NDM2 motif
IAO id: SO:0001167
IAO_0000118: non directional promoter motif 2

Axiom
annotated target: A non directional promoter motif with consensus CGMYGYCR.
IAO xref: PMID:16827941
annotated property: IAO_0000115
annotated source: NDM2_motif

Axiom
IAO scope: EXACT
annotated target: non directional promoter motif 2
annotated property: IAO_0000118
annotated source: NDM2_motif

Axiom
IAO scope: EXACT
annotated target: NDM2 motif
annotated property: IAO_0000118
annotated source: NDM2_motif

Axiom
IAO scope: EXACT
annotated target: NDM2
annotated property: IAO_0000118
annotated source: NDM2_motif

NDM3_motif
type: Class
subclass of: SO_0001659
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_promoter
IAO_0000115: A non directional promoter motif with consensus sequence GAAAGCT.
IAO_0000118: NDM3
IAO_0000118: NDM3 motif
IAO id: SO:0001168
IAO_0000118: non directional motif 3

Axiom
annotated target: A non directional promoter motif with consensus sequence GAAAGCT.
IAO xref: PMID:16827941
annotated property: IAO_0000115
annotated source: NDM3_motif

Axiom
IAO scope: EXACT
annotated target: NDM3
annotated property: IAO_0000118
annotated source: NDM3_motif

Axiom
IAO scope: EXACT
annotated target: NDM3 motif
annotated property: IAO_0000118
annotated source: NDM3_motif

Axiom
IAO scope: EXACT
annotated target: non directional motif 3
annotated property: IAO_0000118
annotated source: NDM3_motif

ds_RNA_viral_sequence
type: Class
subclass of: viral_sequence
IAO_0000115: A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA.
IAO id: SO:0001169
IAO_0000118: double stranded RNA virus sequence
IAO_0000118: ds RNA viral sequence

Axiom
IAO scope: EXACT
annotated target: double stranded RNA virus sequence
annotated property: IAO_0000118
annotated source: ds_RNA_viral_sequence

Axiom
annotated target: A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: ds_RNA_viral_sequence

Axiom
IAO scope: EXACT
annotated target: ds RNA viral sequence
annotated property: IAO_0000118
annotated source: ds_RNA_viral_sequence

polinton
type: Class
subclass of: terminal_inverted_repeat_element
IAO_0000115: A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements.
IAO id: SO:0001170
IAO_0000118: maverick element

Axiom
IAO scope: RELATED
annotated target: maverick element
annotated property: IAO_0000118
annotated source: polinton

Axiom
annotated target: A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements.
IAO xref: PMID:16537396
annotated property: IAO_0000115
annotated source: polinton

rRNA_21S
type: Class
subclass of: large_subunit_rRNA
IAO_0000118: 21S LSU rRNA
IAO_0000118: 21S rRNA
IAO_0000118: 21S ribosomal RNA
IAO_0000115: A component of the large ribosomal subunit in mitochondrial rRNA.
IAO id: SO:0001171
IAO_0000118: rRNA 21S

Axiom
annotated target: 21S ribosomal RNA
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: rRNA_21S

Axiom
annotated target: 21S rRNA
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: rRNA_21S

Axiom
annotated target: 21S LSU rRNA
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: rRNA_21S

Axiom
IAO scope: EXACT
annotated target: rRNA 21S
annotated property: IAO_0000118
annotated source: rRNA_21S

Axiom
annotated target: A component of the large ribosomal subunit in mitochondrial rRNA.
IAO xref: RSC:cb
annotated property: IAO_0000115
annotated source: rRNA_21S

tRNA_region
type: Class
subclass of: mature_transcript_region
subclass of: Restriction
  on property: part_of
  some values from: tRNA
IAO_0000115: A region of a tRNA.
IAO id: SO:0001172
IAO_0000118: tRNA region

Axiom
annotated target: A region of a tRNA.
IAO xref: RSC:cb
annotated property: IAO_0000115
annotated source: tRNA_region

Axiom
IAO scope: EXACT
annotated target: tRNA region
annotated property: IAO_0000118
annotated source: tRNA_region

anticodon_loop
type: Class
subclass of: tRNA_region
IAO_0000115: A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3.
IAO id: SO:0001173
IAO_0000118: anti-codon loop
IAO_0000118: anticodon loop

Axiom
annotated target: A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3.
IAO xref: ISBN:0716719207
annotated property: IAO_0000115
annotated source: anticodon_loop

Axiom
IAO scope: EXACT
annotated target: anti-codon loop
annotated property: IAO_0000118
annotated source: anticodon_loop

Axiom
IAO scope: EXACT
annotated target: anticodon loop
annotated property: IAO_0000118
annotated source: anticodon_loop

anticodon
type: Class
subclass of: tRNA_region
subclass of: Restriction
  on property: part_of
  some values from: anticodon_loop
IAO_0000115: A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA.
IAO id: SO:0001174
IAO_0000118: anti-codon
IAO xref: http://en.wikipedia.org/wiki/Anticodon

Axiom
annotated target: A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA.
IAO xref: RSC:cb
annotated property: IAO_0000115
annotated source: anticodon

Axiom
IAO scope: EXACT
annotated target: anti-codon
annotated property: IAO_0000118
annotated source: anticodon

CCA_tail
type: Class
subclass of: tRNA_region
IAO_0000115: Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid.
IAO_0000118: CCA sequence
IAO_0000118: CCA tail
IAO id: SO:0001175

Axiom
annotated target: Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid.
IAO xref: ISBN:0716719207
annotated property: IAO_0000115
annotated source: CCA_tail

Axiom
annotated target: CCA sequence
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: CCA_tail

Axiom
annotated target: CCA tail
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: CCA_tail

DHU_loop
type: Class
subclass of: tRNA_region
IAO_0000118: D loop
IAO_0000118: DHU loop
IAO_0000115: Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues.
IAO id: SO:0001176

Axiom
annotated target: D loop
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: DHU_loop

Axiom
annotated target: DHU loop
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: DHU_loop

Axiom
IAO xref: ISBN:071671920
annotated target: Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues.
annotated property: IAO_0000115
annotated source: DHU_loop

T_loop
type: Class
subclass of: tRNA_region
IAO_0000115: Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C.
IAO id: SO:0001177
IAO_0000118: T loop
IAO_0000118: TpsiC loop

Axiom
IAO xref: ISBN:0716719207
annotated target: Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C.
annotated property: IAO_0000115
annotated source: T_loop

Axiom
IAO scope: EXACT
annotated target: T loop
annotated property: IAO_0000118
annotated source: T_loop

Axiom
IAO scope: EXACT
annotated target: TpsiC loop
annotated property: IAO_0000118
annotated source: T_loop

pyrrolysine_tRNA_primary_transcript
type: Class
subclass of: tRNA_primary_transcript
IAO_0000115: A primary transcript encoding pyrrolysyl tRNA (SO:0000766).
IAO id: SO:0001178
IAO_0000118: pyrrolysine tRNA primary transcript

Axiom
annotated target: A primary transcript encoding pyrrolysyl tRNA (SO:0000766).
IAO xref: RSC:cb
annotated property: IAO_0000115
annotated source: pyrrolysine_tRNA_primary_transcript

Axiom
IAO scope: EXACT
annotated target: pyrrolysine tRNA primary transcript
annotated property: IAO_0000118
annotated source: pyrrolysine_tRNA_primary_transcript

U3_snoRNA
type: Class
subclass of: C_D_box_snoRNA
IAO id: SO:0001179
comment: The definition is most of the old definition for snoRNA (SO:0000275).
IAO_0000118: U3 small nucleolar RNA
IAO_0000118: U3 snoRNA
IAO_0000115: U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA.
IAO xref: http://en.wikipedia.org/wiki/Small_nucleolar_RNA_U3
IAO_0000118: small nucleolar RNA U3
IAO_0000118: snoRNA U3

Axiom
IAO scope: EXACT
annotated target: small nucleolar RNA U3
annotated property: IAO_0000118
annotated source: U3_snoRNA

Axiom
IAO scope: EXACT
annotated target: snoRNA U3
annotated property: IAO_0000118
annotated source: U3_snoRNA

Axiom
annotated target: U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA.
IAO xref: http://www.sanger.ac.uk/cgi-bin/Rfam/getacc
annotated property: IAO_0000115
annotated source: U3_snoRNA

Axiom
IAO scope: EXACT
annotated target: U3 small nucleolar RNA
annotated property: IAO_0000118
annotated source: U3_snoRNA

Axiom
IAO scope: EXACT
annotated target: U3 snoRNA
annotated property: IAO_0000118
annotated source: U3_snoRNA

AU_rich_element
type: Class
subclass of: UTR_region
subclass of: Restriction
  on property: part_of
  some values from: three_prime_UTR
IAO_0000115: A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable.
IAO_0000118: ARE
IAO_0000118: AU rich element
IAO_0000118: AU-rich element
IAO id: SO:0001180
IAO xref: http://en.wikipedia.org/wiki/AU-rich_element

Axiom
annotated target: AU-rich element
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: AU_rich_element

Axiom
annotated target: A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable.
IAO xref: PMID:7892223
annotated property: IAO_0000115
annotated source: AU_rich_element

Axiom
annotated target: ARE
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: AU_rich_element

Axiom
annotated target: AU rich element
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: AU_rich_element

Bruno_response_element
type: Class
subclass of: UTR_region
subclass of: Restriction
  on property: part_of
  some values from: three_prime_UTR
IAO_0000115: A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs.
IAO_0000118: BRE
IAO_0000118: Bruno response element
comment: Not to be confused with BRE_motif (SO:0000016), which binds transcription factor II B.
IAO id: SO:0001181

Axiom
annotated target: A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs.
IAO xref: PMID:10893231
annotated property: IAO_0000115
annotated source: Bruno_response_element

Axiom
annotated target: Bruno response element
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: Bruno_response_element

Axiom
annotated target: BRE
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: Bruno_response_element

iron_responsive_element
type: Class
subclass of: UTR_region
subclass of: Restriction
  on property: part_of
  some values from: UTR
IAO_0000115: A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins.
IAO_0000118: IRE
IAO id: SO:0001182
IAO xref: http://en.wikipedia.org/wiki/Iron_responsive_element
IAO_0000118: iron responsive element

Axiom
IAO scope: EXACT
annotated target: IRE
annotated property: IAO_0000118
annotated source: iron_responsive_element

Axiom
IAO scope: EXACT
annotated target: iron responsive element
annotated property: IAO_0000118
annotated source: iron_responsive_element

Axiom
annotated target: A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins.
IAO xref: PMID:3198610
IAO xref: PMID:8710843
annotated property: IAO_0000115
annotated source: iron_responsive_element

morpholino_backbone
type: Class
subclass of: nucleic_acid
IAO_0000115: An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages.
comment: Do not use this for feature annotation. Use morpholino_oligo (SO:0000034) instead.
IAO id: SO:0001183
IAO xref: http://en.wikipedia.org/wiki/Morpholino

Axiom
annotated target: An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages.
IAO xref: RSC:cb
annotated property: IAO_0000115
annotated source: morpholino_backbone

PNA
type: Class
subclass of: nucleic_acid
IAO_0000115: An attribute describing a sequence composed of peptide nucleic acid (CHEBI:48021), a chemical consisting of nucleobases bound to a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds.
comment: Do not use this term for feature annotation. Use PNA_oligo (SO:0001011) instead.
IAO id: SO:0001184
IAO_0000118: peptide nucleic acid

Axiom
IAO scope: RELATED
annotated target: peptide nucleic acid
annotated property: IAO_0000118
annotated source: PNA

Axiom
annotated target: An attribute describing a sequence composed of peptide nucleic acid (CHEBI:48021), a chemical consisting of nucleobases bound to a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds.
IAO xref: RSC:cb
annotated property: IAO_0000115
annotated source: PNA

enzymatic
type: Class
subclass of: feature_attribute
IAO_0000115: An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein.
comment: Do not use this for feature annotation. Use enzymatic_RNA (SO:0000372) instead.
IAO id: SO:0001185

Axiom
annotated target: An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein.
IAO xref: RSC:cb
annotated property: IAO_0000115
annotated source: enzymatic

ribozymic
type: Class
subclass of: enzymatic
IAO_0000115: An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein.
comment: Do not use this for feature annotation. Use ribozyme (SO:0000374) instead.
IAO id: SO:0001186

Axiom
annotated target: An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein.
IAO xref: RSC:cb
annotated property: IAO_0000115
annotated source: ribozymic

pseudouridylation_guide_snoRNA
type: Class
subclass of: H_ACA_box_snoRNA
IAO_0000115: A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue.
comment: Has RNA pseudouridylation guide activity (GO:0030558).
IAO id: SO:0001187
IAO_0000118: pseudouridylation guide snoRNA

Axiom
annotated target: A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue.
IAO xref: GOC:mah
IAO xref: PMID:12457565
annotated property: IAO_0000115
annotated source: pseudouridylation_guide_snoRNA

Axiom
IAO scope: EXACT
annotated target: pseudouridylation guide snoRNA
annotated property: IAO_0000118
annotated source: pseudouridylation_guide_snoRNA

LNA
type: Class
subclass of: nucleic_acid
IAO_0000115: An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone. The deoxyribose unit's conformation is 'locked' by a 2'-C,4'-C-oxymethylene link.
comment: Do not use this term for feature annotation. Use LNA_oligo (SO:0001189) instead.
IAO id: SO:0001188

Axiom
annotated target: An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone. The deoxyribose unit's conformation is 'locked' by a 2'-C,4'-C-oxymethylene link.
IAO xref: CHEBI:48010
annotated property: IAO_0000115
annotated source: LNA

LNA_oligo
type: Class
equivalent class: Class
  intersection of: synthetic_oligo
  intersection of: Restriction
    on property: has_quality
    some values from: LNA
subclass of: synthetic_oligo
IAO_0000115: An oligo composed of LNA residues.
IAO_0000118: LNA oligo
IAO id: SO:0001189
IAO xref: http://en.wikipedia.org/wiki/Locked_nucleic_acid
IAO_0000118: locked nucleic acid

Axiom
IAO scope: EXACT
annotated target: locked nucleic acid
annotated property: IAO_0000118
annotated source: LNA_oligo

Axiom
IAO scope: EXACT
annotated target: LNA oligo
annotated property: IAO_0000118
annotated source: LNA_oligo

Axiom
annotated target: An oligo composed of LNA residues.
IAO xref: RSC:cb
annotated property: IAO_0000115
annotated source: LNA_oligo

TNA
type: Class
subclass of: nucleic_acid
IAO_0000115: An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone.
comment: Do not use this term for feature annotation. Use TNA_oligo (SO:0001191) instead.
IAO id: SO:0001190

Axiom
annotated target: An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone.
IAO xref: CHEBI:48019
annotated property: IAO_0000115
annotated source: TNA

TNA_oligo
type: Class
equivalent class: Class
  intersection of: synthetic_oligo
  intersection of: Restriction
    on property: has_quality
    some values from: TNA
subclass of: synthetic_oligo
IAO_0000115: An oligo composed of TNA residues.
IAO id: SO:0001191
IAO_0000118: TNA oligo
IAO xref: http://en.wikipedia.org/wiki/Threose_nucleic_acid
IAO_0000118: threose nucleic acid

Axiom
IAO scope: EXACT
annotated target: TNA oligo
annotated property: IAO_0000118
annotated source: TNA_oligo

Axiom
annotated target: An oligo composed of TNA residues.
IAO xref: RSC:cb
annotated property: IAO_0000115
annotated source: TNA_oligo

Axiom
IAO scope: EXACT
annotated target: threose nucleic acid
annotated property: IAO_0000118
annotated source: TNA_oligo

GNA
type: Class
subclass of: nucleic_acid
IAO_0000115: An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA.
comment: Do not use this term for feature annotation. Use GNA_oligo (SO:0001192) instead.
IAO id: SO:0001192

Axiom
annotated target: An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA.
IAO xref: CHEBI:48015
annotated property: IAO_0000115
annotated source: GNA

GNA_oligo
type: Class
equivalent class: Class
  intersection of: synthetic_oligo
  intersection of: Restriction
    on property: has_quality
    some values from: GNA
subclass of: synthetic_oligo
IAO_0000115: An oligo composed of GNA residues.
IAO_0000118: GNA oligo
IAO id: SO:0001193
IAO_0000118: glycerol nucleic acid
IAO_0000118: glycol nucleic acid
IAO xref: http://en.wikipedia.org/wiki/Glycerol_nucleic_acid

Axiom
annotated target: An oligo composed of GNA residues.
IAO xref: RSC:cb
annotated property: IAO_0000115
annotated source: GNA_oligo

Axiom
IAO scope: EXACT
annotated target: GNA oligo
annotated property: IAO_0000118
annotated source: GNA_oligo

Axiom
IAO scope: EXACT
annotated target: glycol nucleic acid
annotated property: IAO_0000118
annotated source: GNA_oligo

Axiom
IAO scope: EXACT
annotated target: glycerol nucleic acid
annotated property: IAO_0000118
annotated source: GNA_oligo

R_GNA
type: Class
subclass of: GNA
IAO_0000115: An attribute describing a GNA sequence in the (R)-GNA enantiomer.
comment: Do not use this term for feature annotation. Use R_GNA_oligo (SO:0001195) instead.
IAO_0000118: R GNA
IAO id: SO:0001194

Axiom
annotated target: An attribute describing a GNA sequence in the (R)-GNA enantiomer.
IAO xref: CHEBI:48016
annotated property: IAO_0000115
annotated source: R_GNA

Axiom
IAO scope: EXACT
annotated target: R GNA
annotated property: IAO_0000118
annotated source: R_GNA

R_GNA_oligo
type: Class
equivalent class: Class
  intersection of: GNA_oligo
  intersection of: Restriction
    on property: has_quality
    some values from: R_GNA
subclass of: GNA_oligo
IAO_0000118: (R)-glycerol nucleic acid
IAO_0000118: (R)-glycol nucleic acid
IAO_0000115: An oligo composed of (R)-GNA residues.
IAO_0000118: R GNA oligo
IAO id: SO:0001195

Axiom
IAO scope: EXACT
annotated target: R GNA oligo
annotated property: IAO_0000118
annotated source: R_GNA_oligo

Axiom
annotated target: An oligo composed of (R)-GNA residues.
IAO xref: RSC:cb
annotated property: IAO_0000115
annotated source: R_GNA_oligo

Axiom
annotated target: (R)-glycerol nucleic acid
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: R_GNA_oligo

Axiom
annotated target: (R)-glycol nucleic acid
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: R_GNA_oligo

S_GNA
type: Class
subclass of: GNA
IAO_0000115: An attribute describing a GNA sequence in the (S)-GNA enantiomer.
comment: Do not use this term for feature annotation. Use S_GNA_oligo (SO:0001197) instead.
IAO_0000118: S GNA
IAO id: SO:0001196

Axiom
annotated target: An attribute describing a GNA sequence in the (S)-GNA enantiomer.
IAO xref: CHEBI:48017
annotated property: IAO_0000115
annotated source: S_GNA

Axiom
IAO scope: EXACT
annotated target: S GNA
annotated property: IAO_0000118
annotated source: S_GNA

S_GNA_oligo
type: Class
equivalent class: Class
  intersection of: GNA_oligo
  intersection of: Restriction
    on property: has_quality
    some values from: S_GNA
subclass of: GNA_oligo
IAO_0000118: (S)-glycerol nucleic acid
IAO_0000118: (S)-glycol nucleic acid
IAO_0000115: An oligo composed of (S)-GNA residues.
IAO_0000118: S GNA oligo
IAO id: SO:0001197

Axiom
annotated target: An oligo composed of (S)-GNA residues.
IAO xref: RSC:cb
annotated property: IAO_0000115
annotated source: S_GNA_oligo

Axiom
annotated target: (S)-glycerol nucleic acid
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: S_GNA_oligo

Axiom
IAO scope: EXACT
annotated target: S GNA oligo
annotated property: IAO_0000118
annotated source: S_GNA_oligo

Axiom
annotated target: (S)-glycol nucleic acid
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: S_GNA_oligo

ds_DNA_viral_sequence
type: Class
subclass of: viral_sequence
IAO_0000115: A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA.
IAO id: SO:0001198
IAO_0000118: double stranded DNA virus
IAO_0000118: ds DNA viral sequence

Axiom
IAO scope: EXACT
annotated target: double stranded DNA virus
annotated property: IAO_0000118
annotated source: ds_DNA_viral_sequence

Axiom
IAO scope: EXACT
annotated target: ds DNA viral sequence
annotated property: IAO_0000118
annotated source: ds_DNA_viral_sequence

Axiom
annotated target: A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: ds_DNA_viral_sequence

ss_RNA_viral_sequence
type: Class
subclass of: viral_sequence
IAO_0000115: A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA.
IAO id: SO:0001199
IAO_0000118: single strand RNA virus
IAO_0000118: ss RNA viral sequence

Axiom
IAO scope: EXACT
annotated target: single strand RNA virus
annotated property: IAO_0000118
annotated source: ss_RNA_viral_sequence

Axiom
IAO scope: EXACT
annotated target: ss RNA viral sequence
annotated property: IAO_0000118
annotated source: ss_RNA_viral_sequence

Axiom
annotated target: A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: ss_RNA_viral_sequence

negative_sense_ssRNA_viral_sequence
type: Class
subclass of: ss_RNA_viral_sequence
IAO_0000115: A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation.
IAO id: SO:0001200
IAO_0000118: negative sense single stranded RNA virus
IAO_0000118: negative sense ssRNA viral sequence

Axiom
IAO scope: RELATED
annotated target: negative sense single stranded RNA virus
annotated property: IAO_0000118
annotated source: negative_sense_ssRNA_viral_sequence

Axiom
annotated target: A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: negative_sense_ssRNA_viral_sequence

Axiom
IAO scope: EXACT
annotated target: negative sense ssRNA viral sequence
annotated property: IAO_0000118
annotated source: negative_sense_ssRNA_viral_sequence

positive_sense_ssRNA_viral_sequence
type: Class
subclass of: ss_RNA_viral_sequence
IAO_0000115: A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host.
IAO id: SO:0001201
IAO_0000118: positive sense single stranded RNA virus
IAO_0000118: positive sense ssRNA viral sequence

Axiom
annotated target: A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: positive_sense_ssRNA_viral_sequence

Axiom
IAO scope: EXACT
annotated target: positive sense ssRNA viral sequence
annotated property: IAO_0000118
annotated source: positive_sense_ssRNA_viral_sequence

Axiom
IAO scope: RELATED
annotated target: positive sense single stranded RNA virus
annotated property: IAO_0000118
annotated source: positive_sense_ssRNA_viral_sequence

ambisense_ssRNA_viral_sequence
type: Class
subclass of: ss_RNA_viral_sequence
IAO_0000115: A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity.
IAO id: SO:0001202
IAO_0000118: ambisense single stranded RNA virus
IAO_0000118: ambisense ssRNA viral sequence

Axiom
annotated target: A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: ambisense_ssRNA_viral_sequence

Axiom
IAO scope: EXACT
annotated target: ambisense ssRNA viral sequence
annotated property: IAO_0000118
annotated source: ambisense_ssRNA_viral_sequence

Axiom
IAO scope: EXACT
annotated target: ambisense single stranded RNA virus
annotated property: IAO_0000118
annotated source: ambisense_ssRNA_viral_sequence

RNA_polymerase_promoter
type: Class
subclass of: promoter
IAO_0000115: A region (DNA) to which RNA polymerase binds, to begin transcription.
IAO_0000118: RNA polymerase promoter
IAO id: SO:0001203

Axiom
IAO scope: EXACT
annotated target: RNA polymerase promoter
annotated property: IAO_0000118
annotated source: RNA_polymerase_promoter

Axiom
annotated target: A region (DNA) to which RNA polymerase binds, to begin transcription.
IAO xref: xenbase:jb
annotated property: IAO_0000115
annotated source: RNA_polymerase_promoter

Phage_RNA_Polymerase_Promoter
type: Class
subclass of: RNA_polymerase_promoter
IAO_0000115: A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription.
IAO_0000118: Phage RNA Polymerase Promoter
IAO id: SO:0001204

Axiom
annotated target: A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription.
IAO xref: xenbase:jb
annotated property: IAO_0000115
annotated source: Phage_RNA_Polymerase_Promoter

Axiom
IAO scope: EXACT
annotated target: Phage RNA Polymerase Promoter
annotated property: IAO_0000118
annotated source: Phage_RNA_Polymerase_Promoter

SP6_RNA_Polymerase_Promoter
type: Class
subclass of: Phage_RNA_Polymerase_Promoter
IAO_0000115: A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription.
IAO id: SO:0001205
IAO_0000118: SP6 RNA Polymerase Promoter

Axiom
annotated target: A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription.
IAO xref: xenbase:jb
annotated property: IAO_0000115
annotated source: SP6_RNA_Polymerase_Promoter

Axiom
IAO scope: EXACT
annotated target: SP6 RNA Polymerase Promoter
annotated property: IAO_0000118
annotated source: SP6_RNA_Polymerase_Promoter

T3_RNA_Polymerase_Promoter
type: Class
subclass of: Phage_RNA_Polymerase_Promoter
IAO_0000115: A DNA sequence to which the T3 RNA polymerase binds, to begin transcription.
IAO id: SO:0001206
IAO_0000118: T3 RNA Polymerase Promoter

Axiom
annotated target: A DNA sequence to which the T3 RNA polymerase binds, to begin transcription.
IAO xref: xenbase:jb
annotated property: IAO_0000115
annotated source: T3_RNA_Polymerase_Promoter

Axiom
IAO scope: EXACT
annotated target: T3 RNA Polymerase Promoter
annotated property: IAO_0000118
annotated source: T3_RNA_Polymerase_Promoter

T7_RNA_Polymerase_Promoter
type: Class
subclass of: Phage_RNA_Polymerase_Promoter
IAO_0000115: A region (DNA) to which the T7 RNA polymerase binds, to begin transcription.
IAO id: SO:0001207
IAO_0000118: T7 RNA Polymerase Promoter

Axiom
annotated target: A region (DNA) to which the T7 RNA polymerase binds, to begin transcription.
IAO xref: xenbase:jb
annotated property: IAO_0000115
annotated source: T7_RNA_Polymerase_Promoter

Axiom
IAO scope: EXACT
annotated target: T7 RNA Polymerase Promoter
annotated property: IAO_0000118
annotated source: T7_RNA_Polymerase_Promoter

five_prime_EST
type: Class
subclass of: EST
IAO_0000118: 5' EST
IAO_0000115: An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family.
IAO id: SO:0001208
IAO_0000118: five prime EST

Axiom
annotated target: An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family.
IAO xref: http://www.ncbi.nlm.nih.gov/About/primer/est.html
annotated property: IAO_0000115
annotated source: five_prime_EST

Axiom
IAO scope: EXACT
annotated target: five prime EST
annotated property: IAO_0000118
annotated source: five_prime_EST

Axiom
annotated target: 5' EST
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: five_prime_EST

three_prime_EST
type: Class
subclass of: EST
IAO_0000118: 3' EST
IAO_0000115: An EST read from the 3' end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs).
IAO id: SO:0001209
IAO_0000118: three prime EST

Axiom
IAO scope: EXACT
annotated target: three prime EST
annotated property: IAO_0000118
annotated source: three_prime_EST

Axiom
annotated target: 3' EST
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: three_prime_EST

Axiom
annotated target: An EST read from the 3' end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs).
IAO xref: http://www.ncbi.nlm.nih.gov/About/primer/est.html
annotated property: IAO_0000115
annotated source: three_prime_EST

translational_frameshift
type: Class
subclass of: mRNA_region
IAO id: SO:0001210
IAO_0000115: The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.
IAO xref: http://en.wikipedia.org/wiki/Translational_frameshift
IAO_0000118: ribosomal frameshift
IAO_0000118: translational frameshift

Axiom
IAO xref: SO:ke
annotated target: The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.
annotated property: IAO_0000115
annotated source: translational_frameshift

Axiom
IAO scope: EXACT
annotated target: translational frameshift
annotated property: IAO_0000118
annotated source: translational_frameshift

Axiom
IAO scope: EXACT
annotated target: ribosomal frameshift
annotated property: IAO_0000118
annotated source: translational_frameshift

plus_1_translational_frameshift
type: Class
subclass of: translational_frameshift
IAO id: SO:0001211
IAO_0000115: The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.
IAO_0000118: plus 1 ribosomal frameshift
IAO_0000118: plus 1 translational frameshift

Axiom
IAO xref: SO:ke
annotated target: The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.
annotated property: IAO_0000115
annotated source: plus_1_translational_frameshift

Axiom
IAO scope: EXACT
annotated target: plus 1 ribosomal frameshift
annotated property: IAO_0000118
annotated source: plus_1_translational_frameshift

Axiom
IAO scope: EXACT
annotated target: plus 1 translational frameshift
annotated property: IAO_0000118
annotated source: plus_1_translational_frameshift

plus_2_translational_frameshift
type: Class
subclass of: translational_frameshift
IAO id: SO:0001212
IAO_0000115: The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.
IAO_0000118: plus 2 ribosomal frameshift
IAO_0000118: plus 2 translational frameshift

Axiom
IAO scope: EXACT
annotated target: plus 2 ribosomal frameshift
annotated property: IAO_0000118
annotated source: plus_2_translational_frameshift

Axiom
IAO scope: EXACT
annotated target: plus 2 translational frameshift
annotated property: IAO_0000118
annotated source: plus_2_translational_frameshift

Axiom
IAO xref: SO:ke
annotated target: The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.
annotated property: IAO_0000115
annotated source: plus_2_translational_frameshift

group_III_intron
type: Class
subclass of: autocatalytically_spliced_intron
comment: GO:0000374.
IAO_0000115: Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile.
IAO id: SO:0001213
IAO_0000118: group III intron
IAO xref: http://en.wikipedia.org/wiki/Group_III_intron

Axiom
annotated target: Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile.
IAO xref: PMID:11377794
annotated property: IAO_0000115
annotated source: group_III_intron

Axiom
IAO scope: EXACT
annotated target: group III intron
annotated property: IAO_0000118
annotated source: group_III_intron

noncoding_region_of_exon
type: Class
subclass of: exon_region
comment: An exon either containing but not starting with a start codon or containing but not ending with a stop codon will be partially coding and partially non coding.
IAO id: SO:0001214
IAO subset: SOFA
IAO_0000115: The maximal intersection of exon and UTR.
IAO_0000118: noncoding region of exon

Axiom
IAO xref: SO:ke
annotated target: The maximal intersection of exon and UTR.
annotated property: IAO_0000115
annotated source: noncoding_region_of_exon

Axiom
IAO scope: EXACT
annotated target: noncoding region of exon
annotated property: IAO_0000118
annotated source: noncoding_region_of_exon

coding_region_of_exon
type: Class
subclass of: exon_region
comment: An exon containing either a start or stop codon will be partially coding and partially non coding.
IAO id: SO:0001215
IAO subset: SOFA
IAO_0000115: The region of an exon that encodes for protein sequence.
IAO_0000118: coding region of exon

Axiom
IAO scope: EXACT
annotated target: coding region of exon
annotated property: IAO_0000118
annotated source: coding_region_of_exon

Axiom
IAO xref: SO:ke
annotated target: The region of an exon that encodes for protein sequence.
annotated property: IAO_0000115
annotated source: coding_region_of_exon

endonuclease_spliced_intron
type: Class
subclass of: intron
IAO_0000115: An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification.
IAO id: SO:0001216
IAO_0000118: endonuclease spliced intron

Axiom
IAO scope: EXACT
annotated target: endonuclease spliced intron
annotated property: IAO_0000118
annotated source: endonuclease_spliced_intron

Axiom
annotated target: An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: endonuclease_spliced_intron

protein_coding_gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: protein_coding
subclass of: gene
IAO id: SO:0001217
IAO_0000118: protein coding gene

Axiom
IAO scope: EXACT
annotated target: protein coding gene
annotated property: IAO_0000118
annotated source: protein_coding_gene

transgenic_insertion
type: Class
equivalent class: Class
  intersection of: insertion
  intersection of: Restriction
    on property: has_quality
    some values from: transgenic
subclass of: insertion
IAO_0000115: An insertion that derives from another organism, via the use of recombinant DNA technology.
IAO id: SO:0001218
IAO_0000118: transgenic insertion

Axiom
IAO scope: EXACT
annotated target: transgenic insertion
annotated property: IAO_0000118
annotated source: transgenic_insertion

Axiom
annotated target: An insertion that derives from another organism, via the use of recombinant DNA technology.
IAO xref: SO:bm
annotated property: IAO_0000115
annotated source: transgenic_insertion

retrogene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: has_quality
    some values from: retrotransposed
subclass of: gene
IAO id: SO:0001219

silenced_by_RNA_interference
type: Class
subclass of: silenced
IAO_0000115: An attribute describing an epigenetic process where a gene is inactivated by RNA interference.
comment: RNA interference is GO:0016246.
IAO id: SO:0001220
IAO_0000118: silenced by RNA interference

Axiom
IAO scope: EXACT
annotated target: silenced by RNA interference
annotated property: IAO_0000118
annotated source: silenced_by_RNA_interference

Axiom
annotated target: An attribute describing an epigenetic process where a gene is inactivated by RNA interference.
IAO xref: RSC:cb
annotated property: IAO_0000115
annotated source: silenced_by_RNA_interference

silenced_by_histone_modification
type: Class
subclass of: silenced
IAO_0000115: An attribute describing an epigenetic process where a gene is inactivated by histone modification.
comment: Histone modification is GO:0016570.
IAO id: SO:0001221
IAO_0000118: silenced by histone modification

Axiom
IAO scope: EXACT
annotated target: silenced by histone modification
annotated property: IAO_0000118
annotated source: silenced_by_histone_modification

Axiom
annotated target: An attribute describing an epigenetic process where a gene is inactivated by histone modification.
IAO xref: RSC:cb
annotated property: IAO_0000115
annotated source: silenced_by_histone_modification

silenced_by_histone_methylation
type: Class
subclass of: silenced_by_histone_modification
IAO_0000115: An attribute describing an epigenetic process where a gene is inactivated by histone methylation.
comment: Histone methylation is GO:0016571.
IAO id: SO:0001222
IAO_0000118: silenced by histone methylation

Axiom
IAO scope: EXACT
annotated target: silenced by histone methylation
annotated property: IAO_0000118
annotated source: silenced_by_histone_methylation

Axiom
annotated target: An attribute describing an epigenetic process where a gene is inactivated by histone methylation.
IAO xref: RSC:cb
annotated property: IAO_0000115
annotated source: silenced_by_histone_methylation

silenced_by_histone_deacetylation
type: Class
subclass of: silenced_by_histone_modification
IAO_0000115: An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation.
comment: Histone deacetylation is GO:0016573.
IAO id: SO:0001223
IAO_0000118: silenced by histone deacetylation

Axiom
IAO scope: EXACT
annotated target: silenced by histone deacetylation
annotated property: IAO_0000118
annotated source: silenced_by_histone_deacetylation

Axiom
annotated target: An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation.
IAO xref: RSC:cb
annotated property: IAO_0000115
annotated source: silenced_by_histone_deacetylation

gene_silenced_by_RNA_interference
type: Class
equivalent class: Class
  intersection of: silenced_gene
  intersection of: Restriction
    on property: has_quality
    some values from: silenced_by_RNA_interference
subclass of: silenced_gene
IAO_0000115: A gene that is silenced by RNA interference.
IAO_0000118: RNA interference silenced gene
IAO_0000118: RNAi silenced gene
IAO id: SO:0001224
IAO_0000118: gene silenced by RNA interference

Axiom
IAO scope: EXACT
annotated target: RNA interference silenced gene
annotated property: IAO_0000118
annotated source: gene_silenced_by_RNA_interference

Axiom
IAO scope: EXACT
annotated target: gene silenced by RNA interference
annotated property: IAO_0000118
annotated source: gene_silenced_by_RNA_interference

Axiom
annotated target: A gene that is silenced by RNA interference.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: gene_silenced_by_RNA_interference

Axiom
IAO scope: EXACT
annotated target: RNAi silenced gene
annotated property: IAO_0000118
annotated source: gene_silenced_by_RNA_interference

gene_silenced_by_histone_modification
type: Class
equivalent class: Class
  intersection of: silenced_gene
  intersection of: Restriction
    on property: has_quality
    some values from: silenced_by_histone_modification
subclass of: silenced_gene
IAO_0000115: A gene that is silenced by histone modification.
IAO id: SO:0001225
IAO_0000118: gene silenced by histone modification

Axiom
annotated target: A gene that is silenced by histone modification.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: gene_silenced_by_histone_modification

Axiom
IAO scope: EXACT
annotated target: gene silenced by histone modification
annotated property: IAO_0000118
annotated source: gene_silenced_by_histone_modification

gene_silenced_by_histone_methylation
type: Class
equivalent class: Class
  intersection of: gene_silenced_by_histone_modification
  intersection of: Restriction
    on property: has_quality
    some values from: silenced_by_histone_methylation
subclass of: gene_silenced_by_histone_modification
IAO_0000115: A gene that is silenced by histone methylation.
IAO id: SO:0001226
IAO_0000118: gene silenced by histone methylation

Axiom
IAO scope: EXACT
annotated target: gene silenced by histone methylation
annotated property: IAO_0000118
annotated source: gene_silenced_by_histone_methylation

Axiom
annotated target: A gene that is silenced by histone methylation.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: gene_silenced_by_histone_methylation

gene_silenced_by_histone_deacetylation
type: Class
equivalent class: Class
  intersection of: gene_silenced_by_histone_modification
  intersection of: Restriction
    on property: has_quality
    some values from: silenced_by_histone_deacetylation
subclass of: gene_silenced_by_histone_modification
IAO_0000115: A gene that is silenced by histone deacetylation.
IAO id: SO:0001227
IAO_0000118: gene silenced by histone deacetylation

Axiom
IAO scope: EXACT
annotated target: gene silenced by histone deacetylation
annotated property: IAO_0000118
annotated source: gene_silenced_by_histone_deacetylation

Axiom
annotated target: A gene that is silenced by histone deacetylation.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: gene_silenced_by_histone_deacetylation

dihydrouridine
type: Class
subclass of: modified_uridine
IAO_0000115: A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring.
IAO_0000118: D
IAO xref: RNAMOD:051
IAO id: SO:0001228
IAO xref: http://en.wikipedia.org/wiki/Dihydrouridine

Axiom
annotated target: D
IAO scope: EXACT
IAO type: RNAMOD
annotated property: IAO_0000118
annotated source: dihydrouridine

Axiom
annotated target: A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring.
IAO xref: RSC:cb
annotated property: IAO_0000115
annotated source: dihydrouridine

pseudouridine
type: Class
subclass of: modified_uridine
IAO_0000115: A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position.
IAO xref: RNAMOD:050
IAO id: SO:0001229
comment: The free molecule is CHEBI:17802.
IAO_0000118: Y
IAO xref: http://en.wikipedia.org/wiki/Pseudouridine

Axiom
annotated target: A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position.
IAO xref: RSC:cb
annotated property: IAO_0000115
annotated source: pseudouridine

Axiom
IAO scope: EXACT
IAO type: RNAMOD
annotated target: Y
annotated property: IAO_0000118
annotated source: pseudouridine

inosine
type: Class
subclass of: modified_RNA_base_feature
IAO_0000115: A modified RNA base in which hypoxanthine is bound to the ribose ring.
IAO_0000118: I
IAO_0000118: RNAMOD:017
IAO id: SO:0001230
comment: The free molecule is CHEBI:17596.
IAO xref: http://en.wikipedia.org/wiki/Inosine

Axiom
annotated target: A modified RNA base in which hypoxanthine is bound to the ribose ring.
IAO xref: RSC:cb
IAO xref: http://library.med.utah.edu/RNAmods/
annotated property: IAO_0000115
annotated source: inosine

Axiom
annotated target: I
IAO scope: RELATED
annotated property: IAO_0000118
annotated source: inosine

Axiom
IAO scope: RELATED
annotated target: RNAMOD:017
annotated property: IAO_0000118
annotated source: inosine

seven_methylguanine
type: Class
subclass of: modified_RNA_base_feature
IAO_0000118: 7-methylguanine
IAO_0000115: A modified RNA base in which guanine is methylated at the 7- position.
IAO id: SO:0001231
comment: The free molecule is CHEBI:2274.
IAO_0000118: seven methylguanine

Axiom
IAO scope: EXACT
annotated target: seven methylguanine
annotated property: IAO_0000118
annotated source: seven_methylguanine

Axiom
annotated target: 7-methylguanine
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: seven_methylguanine

Axiom
annotated target: A modified RNA base in which guanine is methylated at the 7- position.
IAO xref: RSC:cb
annotated property: IAO_0000115
annotated source: seven_methylguanine

ribothymidine
type: Class
subclass of: modified_RNA_base_feature
IAO_0000115: A modified RNA base in which thymine is bound to the ribose ring.
IAO id: SO:0001232
comment: The free molecule is CHEBI:30832.

Axiom
annotated target: A modified RNA base in which thymine is bound to the ribose ring.
IAO xref: RSC:cb
annotated property: IAO_0000115
annotated source: ribothymidine

methylinosine
type: Class
subclass of: modified_inosine
IAO_0000115: A modified RNA base in which methylhypoxanthine is bound to the ribose ring.
IAO id: SO:0001233

Axiom
annotated target: A modified RNA base in which methylhypoxanthine is bound to the ribose ring.
IAO xref: RSC:cb
annotated property: IAO_0000115
annotated source: methylinosine

mobile
type: Class
subclass of: feature_attribute
IAO_0000115: An attribute describing a feature that has either intra-genome or intracellular mobility.
IAO id: SO:0001234
IAO xref: http://en.wikipedia.org/wiki/Mobile

Axiom
annotated target: An attribute describing a feature that has either intra-genome or intracellular mobility.
IAO xref: RSC:cb
annotated property: IAO_0000115
annotated source: mobile

replicon
type: Class
subclass of: SO_0001411
IAO_0000115: A region containing at least one unique origin of replication and a unique termination site.
IAO id: SO:0001235
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/Replicon_(genetics)

Axiom
annotated target: A region containing at least one unique origin of replication and a unique termination site.
IAO xref: ISBN:0716719207
annotated property: IAO_0000115
annotated source: replicon

base
type: Class
subclass of: SO_0001411
IAO_0000115: A base is a sequence feature that corresponds to a single unit of a nucleotide polymer.
IAO id: SO:0001236
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/Nucleobase

Axiom
annotated target: A base is a sequence feature that corresponds to a single unit of a nucleotide polymer.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: base

amino_acid
type: Class
subclass of: SO_0001411
subclass of: Restriction
  on property: part_of
  some values from: polypeptide
IAO_0000115: A sequence feature that corresponds to a single amino acid residue in a polypeptide.
comment: Probably in the future this will cross reference to Chebi.
IAO id: SO:0001237
IAO_0000118: amino acid
IAO xref: http://en.wikipedia.org/wiki/Amino_acid

Axiom
IAO scope: EXACT
annotated target: amino acid
annotated property: IAO_0000118
annotated source: amino_acid

Axiom
annotated target: A sequence feature that corresponds to a single amino acid residue in a polypeptide.
IAO xref: RSC:cb
annotated property: IAO_0000115
annotated source: amino_acid

major_TSS
type: Class
subclass of: TSS
IAO id: SO:0001238
IAO_0000118: major TSS
IAO_0000118: major transcription start site

Axiom
IAO scope: EXACT
annotated target: major transcription start site
annotated property: IAO_0000118
annotated source: major_TSS

Axiom
IAO scope: EXACT
annotated target: major TSS
annotated property: IAO_0000118
annotated source: major_TSS

minor_TSS
type: Class
subclass of: TSS
IAO id: SO:0001239
IAO_0000118: minor TSS

Axiom
IAO scope: EXACT
annotated target: minor TSS
annotated property: IAO_0000118
annotated source: minor_TSS

TSS_region
type: Class
subclass of: gene_component_region
subclass of: Restriction
  on property: has_part
  some values from: TSS
IAO id: SO:0001240
IAO_0000118: TSS region
IAO_0000115: The region of a gene from the 5' most TSS to the 3' TSS.

Axiom
IAO xref: BBOP:nw
annotated target: The region of a gene from the 5' most TSS to the 3' TSS.
annotated property: IAO_0000115
annotated source: TSS_region

Axiom
IAO scope: EXACT
annotated target: TSS region
annotated property: IAO_0000118
annotated source: TSS_region

encodes_alternate_transcription_start_sites
type: Class
subclass of: gene_attribute
IAO id: SO:0001241
IAO_0000118: encodes alternate transcription start sites

Axiom
IAO scope: EXACT
annotated target: encodes alternate transcription start sites
annotated property: IAO_0000118
annotated source: encodes_alternate_transcription_start_sites

miRNA_primary_transcript_region
type: Class
subclass of: primary_transcript_region
IAO_0000115: A part of an miRNA primary_transcript.
IAO id: SO:0001243
IAO_0000118: miRNA primary transcript region

Axiom
annotated target: A part of an miRNA primary_transcript.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: miRNA_primary_transcript_region

Axiom
IAO scope: EXACT
annotated target: miRNA primary transcript region
annotated property: IAO_0000118
annotated source: miRNA_primary_transcript_region

pre_miRNA
type: Class
subclass of: miRNA_primary_transcript_region
subclass of: Restriction
  on property: part_of
  some values from: miRNA_primary_transcript
IAO id: SO:0001244
IAO_0000115: The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin sructure.
IAO_0000118: pre-miRNA

Axiom
IAO xref: SO:ke
annotated target: The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin sructure.
annotated property: IAO_0000115
annotated source: pre_miRNA

Axiom
IAO scope: EXACT
annotated target: pre-miRNA
annotated property: IAO_0000118
annotated source: pre_miRNA

miRNA_stem
type: Class
subclass of: miRNA_primary_transcript_region
subclass of: Restriction
  on property: part_of
  some values from: pre_miRNA
IAO id: SO:0001245
IAO_0000115: The stem of the hairpin loop formed by folding of the pre-miRNA.
IAO_0000118: miRNA stem

Axiom
IAO scope: EXACT
annotated target: miRNA stem
annotated property: IAO_0000118
annotated source: miRNA_stem

Axiom
IAO xref: SO:ke
annotated target: The stem of the hairpin loop formed by folding of the pre-miRNA.
annotated property: IAO_0000115
annotated source: miRNA_stem

miRNA_loop
type: Class
subclass of: miRNA_primary_transcript_region
subclass of: Restriction
  on property: part_of
  some values from: pre_miRNA
IAO id: SO:0001246
IAO_0000115: The loop of the hairpin loop formed by folding of the pre-miRNA.
IAO_0000118: miRNA loop

Axiom
IAO scope: EXACT
annotated target: miRNA loop
annotated property: IAO_0000118
annotated source: miRNA_loop

Axiom
IAO xref: SO:ke
annotated target: The loop of the hairpin loop formed by folding of the pre-miRNA.
annotated property: IAO_0000115
annotated source: miRNA_loop

synthetic_oligo
type: Class
subclass of: oligo
IAO_0000115: An oligo composed of synthetic nucleotides.
IAO id: SO:0001247
IAO_0000118: synthetic oligo

Axiom
annotated target: An oligo composed of synthetic nucleotides.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: synthetic_oligo

Axiom
IAO scope: EXACT
annotated target: synthetic oligo
annotated property: IAO_0000118
annotated source: synthetic_oligo

assembly
type: Class
subclass of: SO_0001410
IAO_0000115: A region of the genome of known length that is composed by ordering and aligning two or more different regions.
IAO id: SO:0001248
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/Genome_assembly#Genome_assembly

Axiom
annotated target: A region of the genome of known length that is composed by ordering and aligning two or more different regions.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: assembly

fragment_assembly
type: Class
subclass of: assembly
IAO_0000115: A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths.
IAO id: SO:0001249
IAO_0000118: fragment assembly
IAO_0000118: physical map

Axiom
annotated target: A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: fragment_assembly

Axiom
IAO scope: EXACT
annotated target: physical map
annotated property: IAO_0000118
annotated source: fragment_assembly

Axiom
IAO scope: EXACT
annotated target: fragment assembly
annotated property: IAO_0000118
annotated source: fragment_assembly

fingerprint_map
type: Class
subclass of: fragment_assembly
subclass of: Restriction
  on property: has_part
  some values from: restriction_fragment
IAO_0000115: A fingerprint_map is a physical map composed of restriction fragments.
IAO_0000118: BACmap
IAO_0000118: FPC
IAO_0000118: FPCmap
IAO id: SO:0001250
IAO_0000118: fingerprint map
IAO_0000118: restriction map

Axiom
IAO scope: EXACT
annotated target: fingerprint map
annotated property: IAO_0000118
annotated source: fingerprint_map

Axiom
IAO scope: EXACT
annotated target: FPC
annotated property: IAO_0000118
annotated source: fingerprint_map

Axiom
IAO scope: EXACT
annotated target: restriction map
annotated property: IAO_0000118
annotated source: fingerprint_map

Axiom
annotated target: A fingerprint_map is a physical map composed of restriction fragments.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: fingerprint_map

Axiom
annotated target: BACmap
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: fingerprint_map

Axiom
IAO scope: EXACT
annotated target: FPCmap
annotated property: IAO_0000118
annotated source: fingerprint_map

STS_map
type: Class
subclass of: fragment_assembly
subclass of: Restriction
  on property: has_part
  some values from: STS
IAO_0000115: An STS map is a physical map organized by the unique STS landmarks.
IAO id: SO:0001251
IAO_0000118: STS map

Axiom
annotated target: An STS map is a physical map organized by the unique STS landmarks.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: STS_map

Axiom
IAO scope: EXACT
annotated target: STS map
annotated property: IAO_0000118
annotated source: STS_map

RH_map
type: Class
subclass of: fragment_assembly
subclass of: Restriction
  on property: has_part
  some values from: STS
IAO_0000115: A radiation hybrid map is a physical map.
IAO_0000118: RH map
IAO id: SO:0001252
IAO_0000118: radiation hybrid map

Axiom
IAO scope: EXACT
annotated target: radiation hybrid map
annotated property: IAO_0000118
annotated source: RH_map

Axiom
annotated target: A radiation hybrid map is a physical map.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: RH_map

Axiom
IAO scope: EXACT
annotated target: RH map
annotated property: IAO_0000118
annotated source: RH_map

sonicate_fragment
type: Class
subclass of: assembly_component
IAO_0000115: A DNA fragment generated by sonication. Sonication is a technique used to sheer DNA into smaller fragments.
IAO id: SO:0001253
IAO_0000118: sonicate fragment

Axiom
annotated target: A DNA fragment generated by sonication. Sonication is a technique used to sheer DNA into smaller fragments.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: sonicate_fragment

Axiom
IAO scope: EXACT
annotated target: sonicate fragment
annotated property: IAO_0000118
annotated source: sonicate_fragment

polyploid
type: Class
subclass of: SO_1000182
IAO_0000115: A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number.
IAO id: SO:0001254
IAO xref: http://en.wikipedia.org/wiki/Polyploid

Axiom
annotated target: A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: polyploid

autopolyploid
type: Class
subclass of: polyploid
IAO_0000115: A polyploid where the multiple chromosome set was derived from the same organism.
IAO id: SO:0001255
IAO xref: http://en.wikipedia.org/wiki/Autopolyploid

Axiom
annotated target: A polyploid where the multiple chromosome set was derived from the same organism.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: autopolyploid

allopolyploid
type: Class
subclass of: polyploid
IAO_0000115: A polyploid where the multiple chromosome set was derived from a different organism.
IAO id: SO:0001256
IAO xref: http://en.wikipedia.org/wiki/Allopolyploid

Axiom
annotated target: A polyploid where the multiple chromosome set was derived from a different organism.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: allopolyploid

homing_endonuclease_binding_site
type: Class
subclass of: nuclease_binding_site
IAO id: SO:0001257
IAO_0000115: The binding site (recognition site) of a homing endonuclease. The binding site is typically large.
IAO_0000118: homing endonuclease binding site

Axiom
IAO xref: SO:ke
annotated target: The binding site (recognition site) of a homing endonuclease. The binding site is typically large.
annotated property: IAO_0000115
annotated source: homing_endonuclease_binding_site

Axiom
IAO scope: EXACT
annotated target: homing endonuclease binding site
annotated property: IAO_0000118
annotated source: homing_endonuclease_binding_site

octamer_motif
type: Class
subclass of: DNA_motif
subclass of: Restriction
  on property: part_of
  some values from: RNApol_II_promoter
IAO_0000115: A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors.
comment: Nature. 1986 Oct 16-22;323(6089):640-3.
IAO id: SO:0001258
IAO_0000118: octamer motif

Axiom
IAO scope: EXACT
annotated target: octamer motif
annotated property: IAO_0000118
annotated source: octamer_motif

Axiom
annotated target: A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors.
IAO xref: GOC:dh
IAO xref: PMID:3095662
annotated property: IAO_0000115
annotated source: octamer_motif

apicoplast_chromosome
type: Class
equivalent class: Class
  intersection of: chromosome
  intersection of: Restriction
    on property: has_origin
    some values from: apicoplast_sequence
subclass of: chromosome
IAO_0000115: A chromosome originating in an apicoplast.
IAO id: SO:0001259
IAO_0000118: apicoplast chromosome

Axiom
annotated target: A chromosome originating in an apicoplast.
IAO xref: SO:xp
annotated property: IAO_0000115
annotated source: apicoplast_chromosome

Axiom
IAO scope: EXACT
annotated target: apicoplast chromosome
annotated property: IAO_0000118
annotated source: apicoplast_chromosome

sequence_collection
type: Class
IAO_0000115: A collection of discontinuous sequences.
IAO id: SO:0001260
IAO_0000118: sequence collection

Axiom
IAO scope: EXACT
annotated target: sequence collection
annotated property: IAO_0000118
annotated source: sequence_collection

Axiom
annotated target: A collection of discontinuous sequences.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: sequence_collection

overlapping_feature_set
type: Class
subclass of: experimental_result_region
IAO_0000115: A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature.
IAO id: SO:0001261
comment: This feature was requested by Nicole, tracker id 1911479. It is required to gather evidence together for annotation. An example would be overlapping ESTs that support an mRNA.
IAO_0000118: overlapping feature set

Axiom
IAO scope: EXACT
annotated target: overlapping feature set
annotated property: IAO_0000118
annotated source: overlapping_feature_set

Axiom
annotated target: A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: overlapping_feature_set

overlapping_EST_set
type: Class
subclass of: overlapping_feature_set
subclass of: Restriction
  on property: has_part
  some values from: EST
IAO_0000115: A continous experimental result region extending the length of multiple overlapping EST's.
IAO id: SO:0001262
IAO_0000118: overlapping EST set

Axiom
annotated target: A continous experimental result region extending the length of multiple overlapping EST's.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: overlapping_EST_set

Axiom
IAO scope: EXACT
annotated target: overlapping EST set
annotated property: IAO_0000118
annotated source: overlapping_EST_set

ncRNA_gene
type: Class
subclass of: gene
IAO id: SO:0001263
IAO_0000118: ncRNA gen
IAO_0000118: ncRNA gene
IAO_0000118: non-coding RNA gene

Axiom
IAO scope: RELATED
annotated target: non-coding RNA gene
annotated property: IAO_0000118
annotated source: ncRNA_gene

Axiom
IAO scope: EXACT
annotated target: ncRNA gene
annotated property: IAO_0000118
annotated source: ncRNA_gene

Axiom
IAO scope: EXACT
annotated target: ncRNA gen
annotated property: IAO_0000118
annotated source: ncRNA_gene

gRNA_gene
type: Class
equivalent class: Class
  intersection of: ncRNA_gene
  intersection of: Restriction
    on property: has_quality
    some values from: gRNA_encoding
subclass of: ncRNA_gene
IAO id: SO:0001264
IAO_0000118: gRNA gene

Axiom
IAO scope: EXACT
annotated target: gRNA gene
annotated property: IAO_0000118
annotated source: gRNA_gene

miRNA_gene
type: Class
equivalent class: Class
  intersection of: ncRNA_gene
  intersection of: Restriction
    on property: has_quality
    some values from: miRNA_encoding
subclass of: ncRNA_gene
IAO id: SO:0001265
IAO_0000118: miRNA gene

Axiom
IAO scope: EXACT
annotated target: miRNA gene
annotated property: IAO_0000118
annotated source: miRNA_gene

scRNA_gene
type: Class
equivalent class: Class
  intersection of: ncRNA_gene
  intersection of: Restriction
    on property: has_quality
    some values from: scRNA_encoding
subclass of: ncRNA_gene
IAO id: SO:0001266
IAO_0000118: scRNA gene

Axiom
IAO scope: EXACT
annotated target: scRNA gene
annotated property: IAO_0000118
annotated source: scRNA_gene

snoRNA_gene
type: Class
equivalent class: Class
  intersection of: ncRNA_gene
  intersection of: Restriction
    on property: has_quality
    some values from: snoRNA_encoding
subclass of: ncRNA_gene
IAO id: SO:0001267
IAO_0000118: snoRNA gene

Axiom
IAO scope: EXACT
annotated target: snoRNA gene
annotated property: IAO_0000118
annotated source: snoRNA_gene

snRNA_gene
type: Class
equivalent class: Class
  intersection of: ncRNA_gene
  intersection of: Restriction
    on property: has_quality
    some values from: ncRNA_gene
subclass of: ncRNA_gene
IAO id: SO:0001268
IAO_0000118: snRNA gene

Axiom
IAO scope: EXACT
annotated target: snRNA gene
annotated property: IAO_0000118
annotated source: snRNA_gene

SRP_RNA_gene
type: Class
equivalent class: Class
  intersection of: ncRNA_gene
  intersection of: Restriction
    on property: has_quality
    some values from: SRP_RNA_encoding
subclass of: ncRNA_gene
IAO id: SO:0001269
IAO_0000118: SRP RNA gene

Axiom
IAO scope: EXACT
annotated target: SRP RNA gene
annotated property: IAO_0000118
annotated source: SRP_RNA_gene

stRNA_gene
type: Class
equivalent class: Class
  intersection of: ncRNA_gene
  intersection of: Restriction
    on property: has_quality
    some values from: stRNA_encoding
subclass of: ncRNA_gene
IAO id: SO:0001270
IAO_0000118: stRNA gene

Axiom
IAO scope: EXACT
annotated target: stRNA gene
annotated property: IAO_0000118
annotated source: stRNA_gene

tmRNA_gene
type: Class
equivalent class: Class
  intersection of: ncRNA_gene
  intersection of: Restriction
    on property: has_quality
    some values from: tmRNA_encoding
subclass of: ncRNA_gene
IAO id: SO:0001271
IAO_0000118: tmRNA gene

Axiom
IAO scope: EXACT
annotated target: tmRNA gene
annotated property: IAO_0000118
annotated source: tmRNA_gene

tRNA_gene
type: Class
equivalent class: Class
  intersection of: ncRNA_gene
  intersection of: Restriction
    on property: has_quality
    some values from: tRNA_encoding
subclass of: ncRNA_gene
IAO id: SO:0001272
IAO_0000118: tRNA gene

Axiom
IAO scope: EXACT
annotated target: tRNA gene
annotated property: IAO_0000118
annotated source: tRNA_gene

modified_adenosine
type: Class
subclass of: modified_RNA_base_feature
IAO_0000115: A modified adenine is an adenine base feature that has been altered.
IAO id: SO:0001273
IAO_0000118: modified adenosine

Axiom
annotated target: A modified adenine is an adenine base feature that has been altered.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: modified_adenosine

Axiom
IAO scope: EXACT
annotated target: modified adenosine
annotated property: IAO_0000118
annotated source: modified_adenosine

modified_inosine
type: Class
subclass of: inosine
IAO_0000115: A modified inosine is an inosine base feature that has been altered.
IAO id: SO:0001274
IAO_0000118: modified inosine

Axiom
IAO scope: EXACT
annotated target: modified inosine
annotated property: IAO_0000118
annotated source: modified_inosine

Axiom
annotated target: A modified inosine is an inosine base feature that has been altered.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: modified_inosine

modified_cytidine
type: Class
subclass of: modified_RNA_base_feature
IAO_0000115: A modified cytidine is a cytidine base feature which has been altered.
IAO id: SO:0001275
IAO_0000118: modified cytidine

Axiom
annotated target: A modified cytidine is a cytidine base feature which has been altered.
IAO xref: SO:ke
annotated property: IAO_0000115
annotated source: modified_cytidine

Axiom
IAO scope: EXACT
annotated target: modified cytidine
annotated property: IAO_0000118
annotated source: modified_cytidine

modified_guanosine
type: Class
subclass of: modified_RNA_base_feature
IAO id: SO:0001276
IAO_0000118: modified guanosine

Axiom
IAO scope: EXACT
annotated target: modified guanosine
annotated property: IAO_0000118
annotated source: modified_guanosine

modified_uridine
type: Class
subclass of: modified_RNA_base_feature
IAO id: SO:0001277
IAO_0000118: modified uridine

Axiom
IAO scope: EXACT
annotated target: modified uridine
annotated property: IAO_0000118
annotated source: modified_uridine

one_methylinosine
type: Class
subclass of: modified_inosine
IAO_0000118: 1-methylinosine
IAO_0000115: 1-methylinosine is a modified insosine.
IAO xref: RNAMOD:018
IAO id: SO:0001278
IAO_0000118: m1I
IAO_0000118: one methylinosine

Axiom
annotated target: 1-methylinosine is a modified insosine.
IAO xref: http://library.med.utah.edu/RNAmods/
annotated property: IAO_0000115
annotated source: one_methylinosine

Axiom
annotated target: 1-methylinosine
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: one_methylinosine

Axiom
IAO scope: EXACT
annotated target: one methylinosine
annotated property: IAO_0000118
annotated source: one_methylinosine

Axiom
IAO scope: EXACT
IAO type: RNAMOD
annotated target: m1I
annotated property: IAO_0000118
annotated source: one_methylinosine

one_two_prime_O_dimethylinosine
type: Class
subclass of: modified_inosine
IAO_0000118: 1,2'-O-dimethylinosine
IAO_0000115: 1,2'-O-dimethylinosine is a modified inosine.
IAO xref: RNAMOD:019
IAO id: SO:0001279
IAO_0000118: m'Im
IAO_0000118: one two prime O dimethylinosine

Axiom
annotated target: 1,2'-O-dimethylinosine is a modified inosine.
IAO xref: http://library.med.utah.edu/RNAmods/
annotated property: IAO_0000115
annotated source: one_two_prime_O_dimethylinosine

Axiom
IAO scope: EXACT
IAO type: RNAMOD
annotated target: m'Im
annotated property: IAO_0000118
annotated source: one_two_prime_O_dimethylinosine

Axiom
IAO scope: EXACT
annotated target: one two prime O dimethylinosine
annotated property: IAO_0000118
annotated source: one_two_prime_O_dimethylinosine

Axiom
annotated target: 1,2'-O-dimethylinosine
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: one_two_prime_O_dimethylinosine

two_prime_O_methylinosine
type: Class
subclass of: modified_inosine
IAO_0000118: 2'-O-methylinosine
IAO_0000115: 2'-O-methylinosine is a modified inosine.
IAO_0000118: Im
IAO xref: RNAMOD:081
IAO id: SO:0001280
IAO_0000118: two prime O methylinosine

Axiom
annotated target: 2'-O-methylinosine
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: two_prime_O_methylinosine

Axiom
IAO scope: EXACT
annotated target: Im
IAO type: RNAMOD
annotated property: IAO_0000118
annotated source: two_prime_O_methylinosine

Axiom
annotated target: 2'-O-methylinosine is a modified inosine.
IAO xref: http://library.med.utah.edu/RNAmods/
annotated property: IAO_0000115
annotated source: two_prime_O_methylinosine

Axiom
IAO scope: EXACT
annotated target: two prime O methylinosine
annotated property: IAO_0000118
annotated source: two_prime_O_methylinosine

three_methylcytidine
type: Class
subclass of: modified_cytidine
IAO_0000118: 3-methylcytidine
IAO_0000115: 3-methylcytidine is a modified cytidine.
IAO xref: RNAMOD:020
IAO id: SO:0001281
IAO_0000118: m3C
IAO_0000118: three methylcytidine

Axiom
IAO scope: EXACT
annotated target: three methylcytidine
annotated property: IAO_0000118
annotated source: three_methylcytidine

Axiom
annotated target: 3-methylcytidine
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: three_methylcytidine

Axiom
annotated target: 3-methylcytidine is a modified cytidine.
IAO xref: http://library.med.utah.edu/RNAmods/
annotated property: IAO_0000115
annotated source: three_methylcytidine

Axiom
IAO scope: EXACT
IAO type: RNAMOD
annotated target: m3C
annotated property: IAO_0000118
annotated source: three_methylcytidine

five_methylcytidine
type: Class
subclass of: modified_cytidine
IAO_0000118: 5-methylcytidine
IAO_0000115: 5-methylcytidine is a modified cytidine.
IAO xref: RNAMOD:021
IAO id: SO:0001282
IAO_0000118: five methylcytidine
IAO_0000118: m5C

Axiom
IAO scope: EXACT
IAO type: RNAMOD
annotated target: m5C
annotated property: IAO_0000118
annotated source: five_methylcytidine

Axiom
annotated target: 5-methylcytidine
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: five_methylcytidine

Axiom
IAO scope: EXACT
annotated target: five methylcytidine
annotated property: IAO_0000118
annotated source: five_methylcytidine

Axiom
annotated target: 5-methylcytidine is a modified cytidine.
IAO xref: http://library.med.utah.edu/RNAmods/
annotated property: IAO_0000115
annotated source: five_methylcytidine

two_prime_O_methylcytidine
type: Class
subclass of: modified_cytidine
IAO_0000118: 2'-O-methylcytidine
IAO_0000115: 2'-O-methylcytidine is a modified cytidine.
IAO_0000118: Cm
IAO xref: RNAMOD:022
IAO id: SO:0001283
IAO_0000118: two prime O methylcytidine

Axiom
annotated target: 2'-O-methylcytidine
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: two_prime_O_methylcytidine

Axiom
IAO scope: EXACT
annotated target: two prime O methylcytidine
annotated property: IAO_0000118
annotated source: two_prime_O_methylcytidine

Axiom
annotated target: 2'-O-methylcytidine is a modified cytidine.
IAO xref: http://library.med.utah.edu/RNAmods/
annotated property: IAO_0000115
annotated source: two_prime_O_methylcytidine

Axiom
annotated target: Cm
IAO scope: EXACT
IAO type: RNAMOD
annotated property: IAO_0000118
annotated source: two_prime_O_methylcytidine

two_thiocytidine
type: Class
subclass of: modified_cytidine
IAO_0000118: 2-thiocytidine
IAO_0000115: 2-thiocytidine is a modified cytidine.
IAO xref: RNAMOD:023
IAO id: SO:0001284
IAO_0000118: s2C
IAO_0000118: two thiocytidine

Axiom
IAO scope: EXACT
IAO type: RNAMOD
annotated target: s2C
annotated property: IAO_0000118
annotated source: two_thiocytidine

Axiom
annotated target: 2-thiocytidine
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: two_thiocytidine

Axiom
annotated target: 2-thiocytidine is a modified cytidine.
IAO xref: http://library.med.utah.edu/RNAmods/
annotated property: IAO_0000115
annotated source: two_thiocytidine

Axiom
IAO scope: EXACT
annotated target: two thiocytidine
annotated property: IAO_0000118
annotated source: two_thiocytidine

N4_acetylcytidine
type: Class
subclass of: modified_cytidine
IAO_0000118: N4 acetylcytidine
IAO_0000118: N4-acetylcytidine
IAO_0000115: N4-acetylcytidine is a modified cytidine.
IAO xref: RNAMOD:024
IAO id: SO:0001285
IAO_0000118: ac4C

Axiom
IAO scope: EXACT
annotated target: N4 acetylcytidine
annotated property: IAO_0000118
annotated source: N4_acetylcytidine

Axiom
IAO scope: EXACT
annotated target: N4-acetylcytidine
annotated property: IAO_0000118
annotated source: N4_acetylcytidine

Axiom
annotated target: N4-acetylcytidine is a modified cytidine.
IAO xref: http://library.med.utah.edu/RNAmods/
annotated property: IAO_0000115
annotated source: N4_acetylcytidine

Axiom
IAO scope: EXACT
IAO type: RNAMOD
annotated target: ac4C
annotated property: IAO_0000118
annotated source: N4_acetylcytidine

five_formylcytidine
type: Class
subclass of: modified_cytidine
IAO_0000118: 5-formylcytidine
IAO_0000115: 5-formylcytidine is a modified cytidine.
IAO xref: RNAMOD:025
IAO id: SO:0001286
IAO_0000118: f5C
IAO_0000118: five formylcytidine

Axiom
IAO scope: EXACT
annotated target: five formylcytidine
annotated property: IAO_0000118
annotated source: five_formylcytidine

Axiom
annotated target: 5-formylcytidine
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: five_formylcytidine

Axiom
annotated target: 5-formylcytidine is a modified cytidine.
IAO xref: http://library.med.utah.edu/RNAmods/
annotated property: IAO_0000115
annotated source: five_formylcytidine

Axiom
IAO scope: EXACT
IAO type: RNAMOD
annotated target: f5C
annotated property: IAO_0000118
annotated source: five_formylcytidine

five_two_prime_O_dimethylcytidine
type: Class
subclass of: modified_cytidine
IAO_0000118: 5,2'-O-dimethylcytidine
IAO_0000115: 5,2'-O-dimethylcytidine is a modified cytidine.
IAO xref: RNAMOD:026
IAO id: SO:0001287
IAO_0000118: five two prime O dimethylcytidine
IAO_0000118: m5Cm

Axiom
IAO scope: EXACT
annotated target: five two prime O dimethylcytidine
annotated property: IAO_0000118
annotated source: five_two_prime_O_dimethylcytidine

Axiom
annotated target: 5,2'-O-dimethylcytidine is a modified cytidine.
IAO xref: http://library.med.utah.edu/RNAmods/
annotated property: IAO_0000115
annotated source: five_two_prime_O_dimethylcytidine

Axiom
annotated target: 5,2'-O-dimethylcytidine
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: five_two_prime_O_dimethylcytidine

Axiom
IAO scope: EXACT
IAO type: RNAMOD
annotated target: m5Cm
annotated property: IAO_0000118
annotated source: five_two_prime_O_dimethylcytidine

N4_acetyl_2_prime_O_methylcytidine
type: Class
subclass of: modified_cytidine
IAO_0000118: N4 acetyl 2 prime O methylcytidine
IAO_0000118: N4-acetyl-2'-O-methylcytidine
IAO_0000115: N4-acetyl-2'-O-methylcytidine is a modified cytidine.
IAO xref: RNAMOD:027
IAO id: SO:0001288
IAO_0000118: ac4Cm

Axiom
IAO scope: EXACT
IAO type: RNAMOD
annotated target: ac4Cm
annotated property: IAO_0000118
annotated source: N4_acetyl_2_prime_O_methylcytidine

Axiom
IAO scope: EXACT
annotated target: N4 acetyl 2 prime O methylcytidine
annotated property: IAO_0000118
annotated source: N4_acetyl_2_prime_O_methylcytidine

Axiom
annotated target: N4-acetyl-2'-O-methylcytidine is a modified cytidine.
IAO xref: http://library.med.utah.edu/RNAmods/
annotated property: IAO_0000115
annotated source: N4_acetyl_2_prime_O_methylcytidine

Axiom
IAO scope: EXACT
annotated target: N4-acetyl-2'-O-methylcytidine
annotated property: IAO_0000118
annotated source: N4_acetyl_2_prime_O_methylcytidine

lysidine
type: Class
subclass of: modified_cytidine
IAO_0000115: Lysidine is a modified cytidine.
IAO xref: RNAMOD:028
IAO id: SO:0001289
IAO xref: http://en.wikipedia.org/wiki/Lysidine
IAO_0000118: k2C

Axiom
annotated target: Lysidine is a modified cytidine.
IAO xref: http://library.med.utah.edu/RNAmods/
annotated property: IAO_0000115
annotated source: lysidine

Axiom
IAO scope: EXACT
IAO type: RNAMOD
annotated target: k2C
annotated property: IAO_0000118
annotated source: lysidine

N4_methylcytidine
type: Class
subclass of: modified_cytidine
IAO_0000118: N4 methylcytidine
IAO_0000118: N4-methylcytidine
IAO_0000115: N4-methylcytidine is a modified cytidine.
IAO xref: RNAMOD:082
IAO id: SO:0001290
IAO_0000118: m4C

Axiom
IAO scope: EXACT
annotated target: N4-methylcytidine
annotated property: IAO_0000118
annotated source: N4_methylcytidine

Axiom
IAO scope: EXACT
IAO type: RNAMOD
annotated target: m4C
annotated property: IAO_0000118
annotated source: N4_methylcytidine

Axiom
IAO scope: EXACT
annotated target: N4 methylcytidine
annotated property: IAO_0000118
annotated source: N4_methylcytidine

Axiom
annotated target: N4-methylcytidine is a modified cytidine.
IAO xref: http://library.med.utah.edu/RNAmods/
annotated property: IAO_0000115
annotated source: N4_methylcytidine

N4_2_prime_O_dimethylcytidine
type: Class
subclass of: modified_cytidine
IAO_0000118: N4 2 prime O dimethylcytidine
IAO_0000118: N4,2'-O-dimethylcytidine
IAO_0000115: N4,2'-O-dimethylcytidine is a modified cytidine.
IAO xref: RNAMOD:083
IAO id: SO:0001291
IAO_0000118: m4Cm

Axiom
IAO scope: EXACT
IAO type: RNAMOD
annotated target: m4Cm
annotated property: IAO_0000118
annotated source: N4_2_prime_O_dimethylcytidine

Axiom
IAO scope: EXACT
annotated target: N4,2'-O-dimethylcytidine
annotated property: IAO_0000118
annotated source: N4_2_prime_O_dimethylcytidine

Axiom
annotated target: N4,2'-O-dimethylcytidine is a modified cytidine.
IAO xref: http://library.med.utah.edu/RNAmods/
annotated property: IAO_0000115
annotated source: N4_2_prime_O_dimethylcytidine

Axiom
IAO scope: EXACT
annotated target: N4 2 prime O dimethylcytidine
annotated property: IAO_0000118
annotated source: N4_2_prime_O_dimethylcytidine

five_hydroxymethylcytidine
type: Class
subclass of: modified_cytidine
IAO_0000118: 5-hydroxymethylcytidine
IAO_0000115: 5-hydroxymethylcytidine is a modified cytidine.
IAO xref: RNAMOD:084
IAO id: SO:0001292
IAO_0000118: five hydroxymethylcytidine
IAO_0000118: hm5C

Axiom
annotated target: 5-hydroxymethylcytidine is a modified cytidine.
IAO xref: http://library.med.utah.edu/RNAmods/
annotated property: IAO_0000115
annotated source: five_hydroxymethylcytidine

Axiom
IAO scope: EXACT
annotated target: five hydroxymethylcytidine
annotated property: IAO_0000118
annotated source: five_hydroxymethylcytidine

Axiom
annotated target: 5-hydroxymethylcytidine
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: five_hydroxymethylcytidine

Axiom
IAO scope: EXACT
IAO type: RNAMOD
annotated target: hm5C
annotated property: IAO_0000118
annotated source: five_hydroxymethylcytidine

five_formyl_two_prime_O_methylcytidine
type: Class
subclass of: modified_cytidine
IAO_0000118: 5-formyl-2'-O-methylcytidine
IAO_0000115: 5-formyl-2'-O-methylcytidine is a modified cytidine.
IAO xref: RNAMOD:095
IAO id: SO:0001293
IAO_0000118: f5Cm
IAO_0000118: five formyl two prime O methylcytidine

Axiom
IAO scope: EXACT
annotated target: five formyl two prime O methylcytidine
annotated property: IAO_0000118
annotated source: five_formyl_two_prime_O_methylcytidine

Axiom
annotated target: 5-formyl-2'-O-methylcytidine is a modified cytidine.
IAO xref: http://library.med.utah.edu/RNAmods/
annotated property: IAO_0000115
annotated source: five_formyl_two_prime_O_methylcytidine

Axiom
annotated target: 5-formyl-2'-O-methylcytidine
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: five_formyl_two_prime_O_methylcytidine

Axiom
IAO scope: EXACT
IAO type: RNAMOD
annotated target: f5Cm
annotated property: IAO_0000118
annotated source: five_formyl_two_prime_O_methylcytidine

N4_N4_2_prime_O_trimethylcytidine
type: Class
subclass of: modified_cytidine
IAO_0000118: N4,N4,2'-O-trimethylcytidine
IAO_0000115: N4_N4_2_prime_O_trimethylcytidine is a modified cytidine.
IAO xref: RNAMOD:107
IAO id: SO:0001294
IAO_0000118: m42Cm

Axiom
annotated target: N4_N4_2_prime_O_trimethylcytidine is a modified cytidine.
IAO xref: http://library.med.utah.edu/RNAmods/
annotated property: IAO_0000115
annotated source: N4_N4_2_prime_O_trimethylcytidine

Axiom
IAO scope: EXACT
annotated target: N4,N4,2'-O-trimethylcytidine
annotated property: IAO_0000118
annotated source: N4_N4_2_prime_O_trimethylcytidine

Axiom
IAO scope: EXACT
IAO type: RNAMOD
annotated target: m42Cm
annotated property: IAO_0000118
annotated source: N4_N4_2_prime_O_trimethylcytidine

one_methyladenosine
type: Class
subclass of: modified_adenosine
IAO_0000118: 1-methyladenosine
IAO_0000115: 1_methyladenosine is a modified adenosine.
IAO xref: RNAMOD:001
IAO id: SO:0001295
IAO_0000118: m1A
IAO_0000118: one methyladenosine

Axiom
IAO scope: EXACT
IAO type: RNAMOD
annotated target: m1A
annotated property: IAO_0000118
annotated source: one_methyladenosine

Axiom
annotated target: 1_methyladenosine is a modified adenosine.
IAO xref: http://library.med.utah.edu/RNAmods/
annotated property: IAO_0000115
annotated source: one_methyladenosine

Axiom
IAO scope: EXACT
annotated target: one methyladenosine
annotated property: IAO_0000118
annotated source: one_methyladenosine

Axiom
annotated target: 1-methyladenosine
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: one_methyladenosine

two_methyladenosine
type: Class
subclass of: modified_adenosine
IAO_0000118: 2-methyladenosine
IAO_0000115: 2_methyladenosine is a modified adenosine.
IAO xref: RNAMOD:002
IAO id: SO:0001296
IAO_0000118: m2A
IAO_0000118: two methyladenosine

Axiom
IAO scope: EXACT
IAO type: RNAMOD
annotated target: m2A
annotated property: IAO_0000118
annotated source: two_methyladenosine

Axiom
IAO scope: EXACT
annotated target: two methyladenosine
annotated property: IAO_0000118
annotated source: two_methyladenosine

Axiom
annotated target: 2-methyladenosine
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: two_methyladenosine

Axiom
annotated target: 2_methyladenosine is a modified adenosine.
IAO xref: http://library.med.utah.edu/RNAmods/
annotated property: IAO_0000115
annotated source: two_methyladenosine

N6_methyladenosine
type: Class
subclass of: modified_adenosine
IAO_0000118: N6 methyladenosine
IAO_0000118: N6-methyladenosine
IAO_0000115: N6_methyladenosine is a modified adenosine.
IAO xref: RNAMOD:003
IAO id: SO:0001297
IAO_0000118: m6A

Axiom
IAO scope: EXACT
annotated target: N6-methyladenosine
annotated property: IAO_0000118
annotated source: N6_methyladenosine

Axiom
IAO scope: EXACT
IAO type: RNAMOD
annotated target: m6A
annotated property: IAO_0000118
annotated source: N6_methyladenosine

Axiom
annotated target: N6_methyladenosine is a modified adenosine.
IAO xref: http://library.med.utah.edu/RNAmods/
annotated property: IAO_0000115
annotated source: N6_methyladenosine

Axiom
IAO scope: EXACT
annotated target: N6 methyladenosine
annotated property: IAO_0000118
annotated source: N6_methyladenosine

two_prime_O_methyladenosine
type: Class
subclass of: modified_adenosine
IAO_0000118: 2'-O-methyladenosine
IAO_0000115: 2prime_O_methyladenosine is a modified adenosine.
IAO_0000118: Am
IAO xref: RNAMOD:004
IAO id: SO:0001298
IAO_0000118: two prime O methyladenosine

Axiom
annotated target: 2prime_O_methyladenosine is a modified adenosine.
IAO xref: http://library.med.utah.edu/RNAmods/
annotated property: IAO_0000115
annotated source: two_prime_O_methyladenosine

Axiom
IAO scope: EXACT
annotated target: two prime O methyladenosine
annotated property: IAO_0000118
annotated source: two_prime_O_methyladenosine

Axiom
annotated target: 2'-O-methyladenosine
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: two_prime_O_methyladenosine

Axiom
annotated target: Am
IAO scope: EXACT
IAO type: RNAMOD
annotated property: IAO_0000118
annotated source: two_prime_O_methyladenosine

two_methylthio_N6_methyladenosine
type: Class
subclass of: modified_adenosine
IAO_0000118: 2-methylthio-N6-methyladenosine
IAO_0000115: 2_methylthio_N6_methyladenosine is a modified adenosine.
IAO xref: RNAMOD:005
IAO id: SO:0001299
IAO_0000118: ms2m6A
IAO_0000118: two methylthio N6 methyladenosine

Axiom
annotated target: 2-methylthio-N6-methyladenosine
IAO scope: EXACT
annotated property: IAO_0000118
annotated source: two_methylthio_N6_methyladenosine

Axiom
IAO scope: EXACT
annotated target: two methylthio N6 methyladenosine
annotated property: IAO_0000118
annotated source: two_methylthio_N6_methyladenosine

Axiom
IAO scope: EXACT
IAO type: RNAMOD
annotated target: ms2m6A
annotated property: IAO_0000118
annotated source: two_methylthio_N6_methyladenosine

Axiom
annotated target: 2_methylthio_N6_methyladenosine is a modified adenosine.
IAO xref: http://library.med.utah.edu/RNAmods/
annotated property: IAO_0000115
annotated source: two_methylthio_N6_methyladenosine

N6_isopentenyladenosine
type: Class
subclass of: modified_adenosine
IAO_0000118: N6 isopentenyladenosine
IAO_0000118: N6-isopentenyladenosine
IAO_0000115: N6_isopentenyladenosine is a modified adenosine.
IAO xref: RNAMOD:006
IAO id: SO:0001300
IAO_0000118: i6A

Axiom
IAO scope: EXACT
IAO type: RNAMOD
annotated target: i6A
annotated property: IAO_0000118
annotated source: N6_isopentenyladenosine

Axiom
IAO scope: EXACT
annotated target: N6 isopentenyladenosine
annotated property: IAO_0000118
annotated source: N6_isopentenyladenosine