Catharus ustulatus isolate bCatUst1 chromosome 39, bCatUst1.pri.v2, whole genome shotgun sequence.
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Passeriformes; Turdidae; Catharus.
REFSEQ INFORMATION: The reference sequence is identical to\nCM020374.1.\nAssembly name: bCatUst1.pri.v2\nThe genomic sequence for this RefSeq record is from the\nwhole-genome assembly released by the Vertebrate Genomes Project on\n2020/12/22. The original whole-genome shotgun project has the\naccession WNMQ00000000.2.\n\n##Genome-Assembly-Data-START##\nAssembly Provider :: Vertebrate Genomes Project\nAssembly Date :: 06-AUG-2020\nAssembly Method :: FALCON v. DX 1.9.0; FALCON-Unzip v.\n 6.0.0.47841; purge_dups github v.\n purge_haplotig (bitbucket v1.0.3+\n 1.Nov.2018); Scaff10x v. 2; Bionano Solve\n v. 3.2.1_04122018; Salsa2 HiC v. 2.2;\n Arrow 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. 2020-08-06; VGP assembly\n pipeline v. 1.5\nAssembly Name :: bCatUst1.pri.v2\nDiploid :: Principal pseudohaplotype\nGenome Representation :: Full\nExpected Final Version :: No\nGenome Coverage :: 60.58x\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 :: Catharus ustulatus Annotation\n Release 101\nAnnotation Version :: 101\nAnnotation Pipeline :: NCBI eukaryotic genome annotation\n pipeline\nAnnotation Software Version :: 9.0\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.
Rho guanine nucleotide exchange factor 1
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 11 Proteins, and 92% coverage of the annotated genomic feature by RNAseq alignments
COORDINATES: polyA evidence [ECO:0006239]
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 5 Proteins, and 81% coverage of the annotated genomic feature by RNAseq alignments
ETS domain-containing transcription factor ERF-like
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 1 Protein
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 6 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 100% coverage of the annotated genomic feature by RNAseq alignments, including 5 samples with support for all annotated introns
prenylated Rab acceptor protein 1 isoform X2
prenylated Rab acceptor protein 1 isoform X3
prenylated Rab acceptor protein 1 isoform X4
prenylated Rab acceptor protein 1 isoform X1
ATPase Na+/K+ transporting subunit alpha 3, transcript variant X3
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 8 ESTs, 3 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 19 samples with support for all annotated introns
ATPase Na+/K+ transporting subunit alpha 3, transcript variant X2
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 7 ESTs, 4 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 19 samples with support for all annotated introns
ATPase Na+/K+ transporting subunit alpha 3, transcript variant X1
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 2 mRNAs, 11 ESTs, 54 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 19 samples with support for all annotated introns
ATPase Na+/K+ transporting subunit alpha 3, transcript variant X4
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 5 ESTs, 2 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 19 samples with support for all annotated introns
ATPase Na+/K+ transporting subunit alpha 3, transcript variant X6
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 2 ESTs, 1 Protein, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 19 samples with support for all annotated introns
ATPase Na+/K+ transporting subunit alpha 3, transcript variant X5
ATPase Na+/K+ transporting subunit alpha 3, transcript variant X7
sodium/potassium-transporting ATPase subunit alpha-3 isoform X3
sodium/potassium-transporting ATPase subunit alpha-3 isoform X2
sodium/potassium-transporting ATPase subunit alpha-3 isoform X1
sodium/potassium-transporting ATPase subunit alpha-3 isoform X4
sodium/potassium-transporting ATPase subunit alpha-3 isoform X6
sodium/potassium-transporting ATPase subunit alpha-3 isoform X5
sodium/potassium-transporting ATPase subunit alpha-3 isoform X7
glutamate ionotropic receptor kainate type subunit 5
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 1 mRNA, 1 EST, 103 Proteins, and 95% coverage of the annotated genomic feature by RNAseq alignments
glutamate receptor ionotropic, kainate 5
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 3 Proteins, and 78% coverage of the annotated genomic feature by RNAseq alignments
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 4 Proteins, and 66% coverage of the annotated genomic feature by RNAseq alignments
POU domain, class 2, transcription factor 2
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 7 Proteins, and 92% coverage of the annotated genomic feature by RNAseq alignments
DNA-binding death effector domain-containing protein 2
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 11 Proteins, and 65% coverage of the annotated genomic feature by RNAseq alignments
ETS domain-containing transcription factor ERF
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
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: protein capicua homolog
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: 6 Proteins, and 97% coverage of the annotated genomic feature by RNAseq alignments
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
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 89% coverage of the annotated genomic feature by RNAseq alignments
plasminogen activator, urokinase receptor
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 93% coverage of the annotated genomic feature by RNAseq alignments
urokinase plasminogen activator surface receptor
ly6/PLAUR domain-containing protein 3-like
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 62% coverage of the annotated genomic feature by RNAseq alignments
pleckstrin homology like domain family B member 3, transcript variant X5
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 8 samples with support for all annotated introns
pleckstrin homology like domain family B member 3, transcript variant X3
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 12 samples with support for all annotated introns
pleckstrin homology-like domain family B member 3 isoform X3
pleckstrin homology-like domain family B member 3 isoform X5
pleckstrin homology like domain family B member 3, 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 9 samples with support for all annotated introns
pleckstrin homology like domain family B member 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 18 samples with support for all annotated introns
pleckstrin homology like domain family B member 3, transcript variant X2
pleckstrin homology-like domain family B member 3 isoform X4
pleckstrin homology-like domain family B member 3 isoform X1
pleckstrin homology-like domain family B member 3 isoform X2
persulfide dioxygenase ETHE1, mitochondrial
The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: deleted 2 bases in 1 codon; 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 4 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 2 bases in 1 codon; Derived by automated computational analysis using gene prediction method: Gnomon.
LOW QUALITY PROTEIN: DNA repair protein XRCC1
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 LOC117010206, transcript variant X1
uncharacterized LOC117010206, 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 3 samples with support for all annotated introns
SMG9 nonsense mediated mRNA decay factor, transcript variant X2
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 15 samples with support for all annotated introns
SMG9 nonsense mediated mRNA decay factor, transcript variant X1
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 8 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 16 samples with support for all annotated introns
protein phosphatase 2 scaffold subunit Aalpha, transcript variant X1
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 1 mRNA, 152 ESTs, 28 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 7 samples with support for all annotated introns
protein phosphatase 2 scaffold subunit Aalpha, transcript variant X4
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 149 ESTs, 2 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 2 samples with support for all annotated introns
protein phosphatase 2 scaffold subunit Aalpha, transcript variant X3
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 149 ESTs, 2 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 6 samples with support for all annotated introns
protein phosphatase 2 scaffold subunit Aalpha, transcript variant X2
serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform isoform X1
serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform isoform X4
serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform isoform X3
serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform isoform X2
protein phosphatase 2 scaffold subunit Aalpha, transcript variant X5
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 149 ESTs, 2 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 17 samples with support for all annotated introns
protein phosphatase 2 scaffold subunit Aalpha, transcript variant X7
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 149 ESTs, 2 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 3 samples with support for all annotated introns
protein phosphatase 2 scaffold subunit Aalpha, transcript variant X6
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 149 ESTs, 2 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 4 samples with support for all annotated introns
serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform isoform X5
serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform isoform X7
serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform isoform X6
protein phosphatase 2 scaffold subunit Aalpha, transcript variant X9
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 149 ESTs, 2 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 16 samples with support for all annotated introns
protein phosphatase 2 scaffold subunit Aalpha, transcript variant X11
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 149 ESTs, 2 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 5 samples with support for all annotated introns
protein phosphatase 2 scaffold subunit Aalpha, transcript variant X12
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 149 ESTs, 2 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 1 sample with support for all annotated introns
protein phosphatase 2 scaffold subunit Aalpha, transcript variant X13
protein phosphatase 2 scaffold subunit Aalpha, transcript variant X10
serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform isoform X9
serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform isoform X11
serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform isoform X12
serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform isoform X13
serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform isoform X10
protein phosphatase 2 scaffold subunit Aalpha, transcript variant X8
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 149 ESTs, 2 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 8 samples with support for all annotated introns
serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform isoform X8
uncharacterized LOC117010189, transcript variant X1
uncharacterized LOC117010189, 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 2 samples with support for all annotated introns
electron transfer flavoprotein subunit beta, transcript variant X7
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 18 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 1 sample with support for all annotated introns
electron transfer flavoprotein subunit beta, transcript variant X5
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 18 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 3 samples with support for all annotated introns
electron transfer flavoprotein subunit beta, transcript variant X3
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 18 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 5 samples with support for all annotated introns
electron transfer flavoprotein subunit beta, transcript variant X6
electron transfer flavoprotein subunit beta, transcript variant X4
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 18 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 4 samples with support for all annotated introns
electron transfer flavoprotein subunit beta, transcript variant X2
electron transfer flavoprotein subunit beta, transcript variant X1
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 18 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 12 samples with support for all annotated introns
electron transfer flavoprotein subunit beta
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 1 EST, 6 Proteins, and 94% coverage of the annotated genomic feature by RNAseq alignments, including 7 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: 1 Protein
upstream transcription factor 2, c-fos interacting
The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: inserted 1 base in 1 codon
The sequence of the model RefSeq protein was modified relative to this genomic sequence to represent the inferred CDS: inserted 1 base in 1 codon; Derived by automated computational analysis using gene prediction method: Gnomon.
LOW QUALITY PROTEIN: upstream stimulatory factor 2
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: 4 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 2 samples with support for all annotated introns
LOW QUALITY PROTEIN: myelin-associated glycoprotein
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 91% coverage of the annotated genomic feature by RNAseq alignments
proteasome 26S subunit, ATPase 4, transcript variant X1
proteasome 26S subunit, ATPase 4, transcript variant X2
26S proteasome regulatory subunit 6B isoform X1
26S proteasome regulatory subunit 6B isoform X2
proteasome 26S subunit, ATPase 4, transcript variant X4
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 2 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 3 samples with support for all annotated introns
26S proteasome regulatory subunit 6B isoform X4
proteasome 26S subunit, ATPase 4, transcript variant X3
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 2 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 9 samples with support for all annotated introns
26S proteasome regulatory subunit 6B isoform X3
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 1 Protein, and 98% coverage of the annotated genomic feature by RNAseq alignments
sodium voltage-gated channel beta subunit 1
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 15 Proteins, and 64% coverage of the annotated genomic feature by RNAseq alignments
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 19 Proteins
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 40 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments
histone-lysine N-methyltransferase 2B-like
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 19 samples with support for all annotated introns
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 63% coverage of the annotated genomic feature by RNAseq alignments
transmembrane immune signaling adaptor TYROBP
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 19 samples with support for all annotated introns
TYRO protein tyrosine kinase-binding protein
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 3 Proteins, and 79% coverage of the annotated genomic feature by RNAseq alignments
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 66% coverage of the annotated genomic feature by RNAseq alignments
synaptophysin-like protein 1, transcript variant X1
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 9 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 14 samples with support for all annotated introns
synaptophysin-like protein 1, transcript variant X2
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 9 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 12 samples with support for all annotated introns
synaptophysin-like protein 1, transcript variant X3
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 1 EST, 13 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 13 samples with support for all annotated introns
synaptophysin-like protein 1, transcript variant X4
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 14 samples with support for all annotated introns
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 26 Proteins, and 66% coverage of the annotated genomic feature by RNAseq alignments
rRNA 2'-O-methyltransferase fibrillarin-like
cytochrome c oxidase subunit 6B1-like, transcript variant X2
cytochrome c oxidase subunit 6B1-like, transcript variant X1
cytochrome c oxidase subunit 6B1-like isoform X2
cytochrome c oxidase subunit 6B1-like isoform X1