in taxon
checksum mapping
Checksums provided by some of our providers are used in lieu of sequence matching to indicate identity
dependant mapping
Mapping dependent upon another mapping in Ensembl.
direct mapping
A direct mapping between to an external database entry.
inferred mapping from transcript
This is a mapping between an ensembl identifier and external identifiers that has been inferred via transcription. Typically this is a mapping from a gene to one of it's transcripts xrefs
inferred mapping from translation
This is a mapping between an ensembl identifier and external identifiers that has been inferred via translation. Typically this is a mapping from a gene to one of it's translated products. A good example is the mapping of a Ensembl gene id to a UniProt protein id.
inferred pair mapping
This is a low quality assertion based on a transcript mapping to RefSeq. We infer the association of the Refseq protein to our Ensembl protein.
misc mapping
projection mapping
A mapping taken from one species and applied to another, due to homology.
sequence match mapping
Mapping based on an exact sequence match.
3prime_overlapping_ncrna
Transcripts where ditag and/or published experimental data strongly supports the existence of short non-coding transcripts transcribed from the 3'UTR.
A cytogenetic band is a region of chromosome that can be seen using a microscope and special stains. The cytogenetic bands are labeled p1, p2, p3, q1, q2, q3, etc., counting from the centromere out toward the telomeres. At higher resolutions, sub-bands can be seen within the bands. The sub-bands are also numbered from the centromere out toward the telomere.
Ensembl genomic feature
IG_C_gene
IG_C_pseudogene
IG_D_gene
IG_J_gene
IG_J_pseudogene
IG_V_gene
IG_V_pseudogene
Immunoglobulin (Ig) variable chain gene
Immunoglobulin (Ig) variable chain gene imported or annotated according to the IMGT
LRG_gene
Gene in a "Locus Reference Genomic" region known to have disease-related sequence variations.
Mt_rRNA
Mt_tRNA
Mt_tRNA_pseudogene
Non-coding RNA
Non-coding RNA predicted using sequences from RFAM and miRBase
Non-coding RNAs pseudogene
Non-coding RNAs predicted to be pseudogenes by the Ensembl pipeline
T-cell receptor (TcrR) gene
TR_C_gene
TR_D_gene
TR_J_gene
TR_J_pseudogene
TR_V_gene
TR_V_pseudogene
ambiguous_orf
Transcript believed to be protein coding, but with more than one possible open reading frame.
antisense
Has transcripts that overlap the genomic span (i.e. exon or introns) of a protein-coding locus on the opposite strand.
artifact
Used to tag mistakes in the public databases (Ensembl/SwissProt/Trembl)
disrupted_domain
Otherwise viable coding region omitted from this alternatively spliced transcript because the splice variation affects a region coding for a protein domain.
exon
An exon is a nucleotide sequence encoded by a gene that remains present within the final mature RNA product of that gene after introns have been removed by RNA splicing.
inactivated immunoglobulin gene
lincRNA
Long, intervening noncoding (linc) RNAs, that can be found in evolutionarily conserved, intergenic regions.
miRNA
miRNA_pseudogene
misc_RNA
misc_RNA_pseudogene
non_coding
Transcript which is known from the literature to not be protein coding.
non_stop_decay
Transcripts that have polyA features (including signal) without a prior stop codon in the CDS, i.e. a non-genomic polyA tail attached directly to the CDS without 3' UTR. These transcripts are subject to degradation.
If the coding sequence (following the appropriate reference) of a transcript finishes >50bp from a downstream splice site then it is tagged as NMD. If the variant does not cover the full reference coding sequence then it is annotated as NMD if NMD is unavoidable i.e. no matter what the exon structure of the missing portion is the transcript will be subject to NMD.
polymorphic_pseudogene
Pseudogene owing to a SNP/DIP but in other individuals/haplotypes/strains the gene is translated.
processed_pseudogene
Pseudogene that lack introns and is thought to arise from reverse transcription of mRNA followed by reinsertion of DNA into the genome.
processed_transcript
protein
A protein is an organic polymer that is composed of one or more linear polymers of amino acids.
protein_coding
pseudogene
Have homology to proteins but generally suffer from a disrupted coding sequence and an active homologous gene can be found at another locus. Sometimes these entries have an intact coding sequence or an open but truncated ORF, in which case there is other evidence used (for example genomic polyA stretches at the 3' end) to classify them as a pseudogene. Can be further classified as one of the following.
rRNA
rRNA_pseudogene
Alternatively spliced transcript believed to contain intronic sequence relative to other, coding, variants.
retrotransposed
Pseudogene owing to a reverse transcribed and re-inserted sequence.
scRNA_pseudogene
sense_intronic
Long non-coding transcript in introns of a coding gene that does not overlap any exons.
sense_overlapping
Long non-coding transcript that contains a coding gene in its intron on the same strand.
snRNA
snRNA_pseudogene
snoRNA
snoRNA_pseudogene
tRNA_pseudogene
transcribed_processed_pseudogene
Pseudogene where protein homology or genomic structure indicates a pseudogene, but the presence of locus-specific transcripts indicates expression.
transcribed_unprocessed_pseudogene
transcript
An RNA transcript is an RNA molecule that is produced from transcription of a nucleic acid template.
unitary_pseudogene
A species specific unprocessed pseudogene without a parent gene, as it has an active orthologue in another species.
unprocessed_pseudogene
Pseudogene that can contain introns since produced by gene duplication.