Melopsittacus undulatus isolate bMelUnd1 chromosome 25, bMelUnd1.mat.Z, whole genome shotgun sequence.
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Psittaciformes; Psittaculidae; Melopsittacus.
REFSEQ INFORMATION: The reference sequence is identical to\nCM022656.1.\nAssembly name: bMelUnd1.mat.Z\nThe genomic sequence for this RefSeq record is from the\nwhole-genome assembly released by the G10K on 2020/04/13. The\noriginal whole-genome shotgun project has the accession\nJAAVWG000000000.1.\n\n##Genome-Assembly-Data-START##\nAssembly Provider :: G10K\nAssembly Date :: 24-FEB-2020\nAssembly Method :: TrioCanu v. 1.8; purge_dups v. 1.0.0;\n Scaff 10x v. 4.1.0; Bionano solve v.\n 3.2.1_04122018; Salsa2 HiC v. 2.2; Arrow\n polishing and gap filling v.\n smrtlink_6.0.0.47841; Longranger Align v.\n 2.2.2; Freebayes v. 1.3.1; gEVAL manual\n curation v. 2020-02-24; VGP assembly\n pipeline v. 1.6\nAssembly Name :: bMelUnd1.mat.Z\nDiploid :: Principal pseudohaplotype\nGenome Representation :: Full\nExpected Final Version :: No\nGenome Coverage :: 61.11x\nSequencing Technology :: PacBio Sequel I CLR; Illumina NovaSeq;\n Arima Genomics Hi-C; Bionano Genomics DLS\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI\nAnnotation Status :: Full annotation\nAnnotation Name :: Melopsittacus undulatus Annotation\n Release 104\nAnnotation Version :: 104\nAnnotation Pipeline :: NCBI eukaryotic genome annotation\n pipeline\nAnnotation Software Version :: 8.4\nAnnotation Method :: Best-placed RefSeq; Gnomon\nFeatures Annotated :: Gene; mRNA; CDS; ncRNA\n##Genome-Annotation-Data-END##
Derived by automated computational analysis using gene prediction method: Gnomon.
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 100% coverage of the annotated genomic feature by RNAseq alignments, including 4 samples with support for all annotated introns
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 94% coverage of the annotated genomic feature by RNAseq alignments, including 2 samples with support for all annotated introns
adaptor related protein complex 1 subunit sigma 1, transcript variant X1
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 1 mRNA, 5 ESTs, 21 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 3 samples with support for all annotated introns
adaptor related protein complex 1 subunit sigma 1, transcript variant X2
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 1 mRNA, 5 ESTs, 21 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 2 samples with support for all annotated introns
adaptor related protein complex 1 subunit sigma 1, transcript variant X3
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 1 mRNA, 5 ESTs, 21 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 1 sample with support for all annotated introns
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
transfer RNA threonine (anticodon AGU); Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 100% coverage of the annotated genomic feature by RNAseq alignments, including 3 samples with support for all annotated introns
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 53% coverage of the annotated genomic feature by RNAseq alignments
RNA polymerase II subunit A, transcript variant X1
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 5 ESTs, 7 Proteins, and 98% coverage of the annotated genomic feature by RNAseq alignments, including 2 samples with support for all annotated introns
RNA polymerase II subunit A, transcript variant X3
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 5 ESTs, 1 Protein, and 98% coverage of the annotated genomic feature by RNAseq alignments, including 2 samples with support for all annotated introns
RNA polymerase II subunit A, transcript variant X2
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 5 ESTs, 1 Protein, and 98% coverage of the annotated genomic feature by RNAseq alignments, including 4 samples with support for all annotated introns
RNA polymerase II subunit A, transcript variant X4
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 4 ESTs, 1 Protein, and 98% coverage of the annotated genomic feature by RNAseq alignments, including 4 samples with support for all annotated introns
DNA-directed RNA polymerase II subunit RPB1 isoform X1
DNA-directed RNA polymerase II subunit RPB1 isoform X3
DNA-directed RNA polymerase II subunit RPB1 isoform X2
DNA-directed RNA polymerase II subunit RPB1 isoform X4
uncharacterized LOC117437669, transcript variant X1
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 100% coverage of the annotated genomic feature by RNAseq alignments, including 5 samples with support for all annotated introns
uncharacterized LOC117437669, transcript variant X2
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 2 Proteins, and 92% coverage of the annotated genomic feature by RNAseq alignments
zinc finger and BTB domain-containing protein 4
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 6 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 7 samples with support for all annotated introns
trafficking protein particle complex subunit 1
WD repeat containing antisense to TP53, transcript variant X1
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 1 Protein, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 5 samples with support for all annotated introns
WD repeat containing antisense to TP53, transcript variant X2
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 1 Protein, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 3 samples with support for all annotated introns
telomerase Cajal body protein 1 isoform X1
telomerase Cajal body protein 1 isoform X2
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 13 Proteins, and 86% coverage of the annotated genomic feature by RNAseq alignments
N-alpha-acetyltransferase 38, NatC auxiliary subunit, transcript variant X9
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 5 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 1 sample with support for all annotated introns
N-alpha-acetyltransferase 38, NatC auxiliary subunit, transcript variant X7
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 5 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 2 samples with support for all annotated introns
N-alpha-acetyltransferase 38, NatC auxiliary subunit, transcript variant X3
N-alpha-acetyltransferase 38, NatC auxiliary subunit, transcript variant X5
N-alpha-acetyltransferase 38, NatC auxiliary subunit, transcript variant X6
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 5 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 3 samples with support for all annotated introns
N-alpha-acetyltransferase 38, NatC auxiliary subunit, transcript variant X1
N-alpha-acetyltransferase 38, NatC auxiliary subunit, transcript variant X8
N-alpha-acetyltransferase 38, NatC auxiliary subunit, transcript variant X2
N-alpha-acetyltransferase 38, NatC auxiliary subunit, transcript variant X4
N-alpha-acetyltransferase 38, NatC auxiliary subunit isoform X3
N-alpha-acetyltransferase 38, NatC auxiliary subunit isoform X2
N-alpha-acetyltransferase 38, NatC auxiliary subunit isoform X1
chromodomain helicase DNA binding protein 3
The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: deleted 1 base in 1 codon; Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 1 mRNA, 28 ESTs, 15 Proteins, and 99% coverage of the annotated genomic feature by RNAseq alignments, including 7 samples with support for all annotated introns
The sequence of the model RefSeq protein was modified relative to this genomic sequence to represent the inferred CDS: deleted 1 base in 1 codon; Derived by automated computational analysis using gene prediction method: Gnomon.
LOW QUALITY PROTEIN: chromodomain-helicase-DNA-binding protein 3
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 95% coverage of the annotated genomic feature by RNAseq alignments, including 1 sample with support for all annotated introns
coiled-coil domain-containing protein 81
potassium voltage-gated channel subfamily A regulatory beta subunit 3, transcript variant X2
potassium voltage-gated channel subfamily A regulatory beta subunit 3, transcript variant X1
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 100% coverage of the annotated genomic feature by RNAseq alignments, including 7 samples with support for all annotated introns
voltage-gated potassium channel subunit beta-3 isoform X2
voltage-gated potassium channel subunit beta-3 isoform X1
ATPase Na+/K+ transporting subunit beta 2
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 4 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 4 samples with support for all annotated introns
sodium/potassium-transporting ATPase subunit beta-2
mannose-P-dolichol utilization defect 1, transcript variant X1
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 11 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 7 samples with support for all annotated introns
mannose-P-dolichol utilization defect 1 protein isoform X1
mannose-P-dolichol utilization defect 1, transcript variant X2
mannose-P-dolichol utilization defect 1 protein isoform X2
late endosomal/lysosomal adaptor, MAPK and MTOR activator 4
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 7 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 7 samples with support for all annotated introns
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 3 Proteins, and 95% coverage of the annotated genomic feature by RNAseq alignments
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 5 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 6 samples with support for all annotated introns
minichromosome maintenance complex component 7
The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: deleted 1 base in 1 codon; Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 12 Proteins, and 98% coverage of the annotated genomic feature by RNAseq alignments, including 2 samples with support for all annotated introns
LOW QUALITY PROTEIN: DNA replication licensing factor MCM7
adaptor related protein complex 4 subunit mu 1, transcript variant X1
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 3 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 7 samples with support for all annotated introns
adaptor related protein complex 4 subunit mu 1, transcript variant X4
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 100% coverage of the annotated genomic feature by RNAseq alignments, including 6 samples with support for all annotated introns
adaptor related protein complex 4 subunit mu 1, transcript variant X3
adaptor related protein complex 4 subunit mu 1, transcript variant X2
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 3 Proteins, and 70% coverage of the annotated genomic feature by RNAseq alignments
probable inactive tRNA-specific adenosine deaminase-like protein 3
discs large MAGUK scaffold protein 4, transcript variant X1
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 1 EST, 37 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 1 sample with support for all annotated introns
discs large MAGUK scaffold protein 4, transcript variant X2
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 1 EST, 9 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 2 samples with support for all annotated introns
The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: deleted 1 base in 1 codon; Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 11 Proteins, and 98% coverage of the annotated genomic feature by RNAseq alignments, including 7 samples with support for all annotated introns
LOW QUALITY PROTEIN: very long-chain specific acyl-CoA dehydrogenase, mitochondrial
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 3 ESTs, 35 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 7 samples with support for all annotated introns
gamma-aminobutyric acid receptor-associated protein
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 1 EST, 10 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 7 samples with support for all annotated introns
uncharacterized LOC117437688, transcript variant X1
uncharacterized LOC117437688, transcript variant X2
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 100% coverage of the annotated genomic feature by RNAseq alignments, including 1 sample with support for all annotated introns
uncharacterized protein LOC117437688 isoform X1
uncharacterized protein LOC117437688 isoform X2
mediator of RNA polymerase II transcription subunit 11
proline, glutamate and leucine rich protein 1
The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: deleted 1 base in 1 codon; Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 6 Proteins, and 88% coverage of the annotated genomic feature by RNAseq alignments
LOW QUALITY PROTEIN: proline-, glutamic acid- and leucine-rich protein 1
small nuclear RNA activating complex polypeptide 2
snRNA-activating protein complex subunit 2
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 15 Proteins, and 72% coverage of the annotated genomic feature by RNAseq alignments
Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: nucleotide motif:Rfam:12.0:RF00096
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 36 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 3 samples with support for all annotated introns
multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3-like, transcript variant X2
multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3-like, transcript variant X1
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 16 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 7 samples with support for all annotated introns
multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3-like, transcript variant X3
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 6 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 2 samples with support for all annotated introns
multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3-like isoform X2
multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3-like isoform X1
multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3-like isoform X3
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 5 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 7 samples with support for all annotated introns
zinc finger HIT domain-containing protein 1
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 7 Proteins