Gallus gallus isolate bGalGal1 chromosome 38, bGalGal1.mat.broiler.GRCg7b, whole genome shotgun sequence.
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Galloanserae; Galliformes; Phasianidae; Phasianinae; Gallus.
REFSEQ INFORMATION: The reference sequence is identical to\nCM028519.1.\nAssembly name: bGalGal1.mat.broiler.GRCg7b\nThe genomic sequence for this RefSeq record is from the\nwhole-genome assembly released by the Vertebrate Genomes Project on\n2021/01/19. The original whole-genome shotgun project has the\naccession JAENSK000000000.1.\n\n##Genome-Assembly-Data-START##\nAssembly Provider :: Vertebrate Genomes Project\nAssembly Date :: 22-JUL-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 SMRTLink7.0.1; Freebayes v. 1.3.1; gEVAL\n manual curation v. 2020-07-22; VGP trio\n assembly pipeline v. 1.6\nAssembly Name :: bGalGal1.mat.broiler.GRCg7b\nDiploid :: Principal pseudohaplotype\nGenome Representation :: Full\nExpected Final Version :: No\nGenome Coverage :: 102.01x\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 :: Gallus gallus Annotation Release 106\nAnnotation Version :: 106\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##
SPT5 homolog, DSIF elongation factor subunit; Derived by automated computational analysis using gene prediction method: BestRefSeq.
SPT5 homolog, DSIF elongation factor subunit
similar to RNA sequence, mRNA (same species):RefSeq:NM_001031384.2
annotated by transcript or proteomic data
The RefSeq transcript has 3 substitutions and aligns at 95% coverage compared to this genomic sequence; Derived by automated computational analysis using gene prediction method: BestRefSeq.
similar to AA sequence (same species):RefSeq:NP_001026555.1
The RefSeq protein aligns at 98% coverage compared to this genomic sequence; Derived by automated computational analysis using gene prediction method: BestRefSeq.
propagated from UniProtKB/Swiss-Prot (Q5ZI08.1); Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite
propagated from UniProtKB/Swiss-Prot (Q5ZI08.1); Region: Interaction with SUPT4H1. /evidence=ECO:0000250
propagated from UniProtKB/Swiss-Prot (Q5ZI08.1); Region: Interaction with RNA polymerase II. /evidence=ECO:0000250
propagated from UniProtKB/Swiss-Prot (Q5ZI08.1); Region: 9 X 7 AA approximate tandem repeats of G-S-[QR]-T-P-X-[YQ], motif CTR1
Phosphothreonine, by CDK9. /evidence=ECO:0000250; propagated from UniProtKB/Swiss-Prot (Q5ZI08.1); phosphorylation site
propagated from UniProtKB/Swiss-Prot (Q5ZI08.1); Region: 10 X 8 AA approximate tandem repeats of P-[TS]-P-S-P-[QA]-[SG]-Y, motif CTR2
Derived by automated computational analysis using gene prediction method: Gnomon.
tristetraprolin-like, transcript variant X1
mRNA decay activator protein ZFP36-like isoform X1
COORDINATES: cap analysis [ECO:0007248] and polyA evidence [ECO:0006239]
mediator of RNA polymerase II transcription subunit 29
PAF1 homolog, Paf1/RNA polymerase II complex component
RNA polymerase II-associated factor 1 homolog
sterile alpha motif domain containing 4B, transcript variant X1
The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: deleted 2 bases in 2 codons
The sequence of the model RefSeq protein was modified relative to this genomic sequence to represent the inferred CDS: deleted 2 bases in 2 codons; Derived by automated computational analysis using gene prediction method: Gnomon.
LOW QUALITY PROTEIN: protein Smaug homolog 2 isoform X1
leucine rich repeat and fibronectin type III domain containing 1, transcript variant X1
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: leucine-rich repeat and fibronectin type III domain-containing protein 1 isoform X1
p21 (RAC1) activated kinase 4, transcript variant X2
p21 (RAC1) activated kinase 4, transcript variant X1
p21 (RAC1) activated kinase 4, transcript variant X5
p21 (RAC1) activated kinase 4, transcript variant X6
p21 (RAC1) activated kinase 4, transcript variant X9
p21 (RAC1) activated kinase 4, transcript variant X11
p21 (RAC1) activated kinase 4, transcript variant X13
p21 (RAC1) activated kinase 4, transcript variant X4
p21 (RAC1) activated kinase 4, transcript variant X7
p21 (RAC1) activated kinase 4, transcript variant X3
p21 (RAC1) activated kinase 4, transcript variant X12
p21 (RAC1) activated kinase 4, transcript variant X10
p21 (RAC1) activated kinase 4, transcript variant X8
serine/threonine-protein kinase PAK 4 isoform X4
serine/threonine-protein kinase PAK 4 isoform X3
serine/threonine-protein kinase PAK 4 isoform X2
serine/threonine-protein kinase PAK 4 isoform X1
28S ribosomal protein S12, mitochondrial
seryl-tRNA synthetase 2, mitochondrial, transcript variant X1
seryl-tRNA synthetase 2, mitochondrial, transcript variant X2
sirtuin 2; Derived by automated computational analysis using gene prediction method: BestRefSeq.
Derived by automated computational analysis using gene prediction method: BestRefSeq.
NAD-dependent protein deacetylase sirtuin-2 isoform 2; Derived by automated computational analysis using gene prediction method: BestRefSeq.
NAD-dependent protein deacetylase sirtuin-2
isoform 1 is encoded by transcript variant 1; Derived by automated computational analysis using gene prediction method: BestRefSeq.
NAD-dependent protein deacetylase sirtuin-2 isoform 1
heterogeneous nuclear ribonucleoprotein L-like, transcript variant X3
heterogeneous nuclear ribonucleoprotein L-like, transcript variant X1
heterogeneous nuclear ribonucleoprotein L-like, transcript variant X2
heterogeneous nuclear ribonucleoprotein L isoform X3
heterogeneous nuclear ribonucleoprotein L isoform X1
heterogeneous nuclear ribonucleoprotein L isoform X2
enoyl-CoA hydratase 1, transcript variant X1
enoyl-CoA hydratase 1, transcript variant X2
delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial isoform X1
delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial isoform X2
actinin, alpha 4; Derived by automated computational analysis using gene prediction method: BestRefSeq.
similar to RNA sequence, mRNA (same species):RefSeq:NM_001396037.1
The RefSeq transcript has 3 substitutions, 4 frameshifts compared to this genomic sequence; Derived by automated computational analysis using gene prediction method: BestRefSeq.
similar to AA sequence (same species):RefSeq:NP_001382966.1
The RefSeq protein has 1 substitution, 4 frameshifts compared to this genomic sequence; Derived by automated computational analysis using gene prediction method: BestRefSeq.
propagated from UniProtKB/Swiss-Prot (Q90734.1); Region: Actin-binding
propagated from UniProtKB/Swiss-Prot (Q90734.1); Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite
propagated from UniProtKB/Swiss-Prot (Q90734.1); Region: Spectrin 1. /evidence=ECO:0000255
propagated from UniProtKB/Swiss-Prot (Q90734.1); Region: Spectrin 2. /evidence=ECO:0000255
propagated from UniProtKB/Swiss-Prot (Q90734.1); Region: Spectrin 3. /evidence=ECO:0000255
propagated from UniProtKB/Swiss-Prot (Q90734.1); Region: Spectrin 4. /evidence=ECO:0000255
eukaryotic translation initiation factor 3 subunit K; Derived by automated computational analysis using gene prediction method: BestRefSeq.
eukaryotic translation initiation factor 3 subunit K
mitogen-activated protein kinase kinase kinase kinase 1-like, transcript variant X1
mitogen-activated protein kinase kinase kinase kinase 1-like, transcript variant X2
mitogen-activated protein kinase kinase kinase kinase 1-like, transcript variant X3
mitogen-activated protein kinase kinase kinase kinase 1 isoform X1
mitogen-activated protein kinase kinase kinase kinase 1 isoform X2
mitogen-activated protein kinase kinase kinase kinase 1 isoform X3
ryanodine receptor 1-like, transcript variant X1
COORDINATES: polyA evidence [ECO:0006239]
The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: deleted 3 bases in 3 codons
The sequence of the model RefSeq protein was modified relative to this genomic sequence to represent the inferred CDS: deleted 3 bases in 3 codons; Derived by automated computational analysis using gene prediction method: Gnomon.
LOW QUALITY PROTEIN: ryanodine receptor 1 isoform X1
solute carrier family 8 member A2, transcript variant X1
kaptin, actin binding protein; Derived by automated computational analysis using gene prediction method: BestRefSeq,Gnomon.
kaptin, actin binding protein, transcript variant X5
kaptin, actin binding protein, transcript variant X2
kaptin, actin binding protein, transcript variant X1
KICSTOR complex protein kaptin isoform X2
KICSTOR complex protein kaptin isoform X1
kaptin, actin binding protein, transcript variant X4
kaptin, actin binding protein, transcript variant X3
KICSTOR complex protein kaptin isoform X5
KICSTOR complex protein kaptin isoform X4
KICSTOR complex protein kaptin isoform X3
uncharacterized LOC112530471, transcript variant X1
uncharacterized LOC112530471, transcript variant X2
uncharacterized protein LOC112530471 isoform X1
uncharacterized protein LOC112530471 isoform X2
uncharacterized LOC112530471, transcript variant X3
uncharacterized LOC112530471, transcript variant X4
zinc finger protein 541, transcript variant X3
zinc finger protein 541, transcript variant X2
zinc finger protein 541, transcript variant X6
zinc finger protein 541, transcript variant X1
zinc finger protein 541, transcript variant X7
zinc finger protein 541, transcript variant X5
zinc finger protein 541, transcript variant X4
glioma tumor suppressor candidate region gene 1, transcript variant X4
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 2 ESTs, 2 long SRA reads, 1 Protein, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 5 samples with support for all annotated introns
glioma tumor suppressor candidate region gene 1, transcript variant X2
glioma tumor suppressor candidate region gene 1, transcript variant X1
glioma tumor suppressor candidate region gene 1, transcript variant X3
BRD4-interacting chromatin-remodeling complex-associated protein isoform X1
BRD4-interacting chromatin-remodeling complex-associated protein isoform X2
glioma tumor suppressor candidate region gene 2, transcript variant X1
ribosome biogenesis protein NOP53 isoform X1
gap junction delta-2 protein-like, 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 77 samples with support for all annotated introns
selenoprotein W; Derived by automated computational analysis using gene prediction method: BestRefSeq.
similar to RNA sequence, mRNA (same species):RefSeq:NM_001166327.2
The RefSeq transcript has 5 substitutions, 1 non-frameshifting indel compared to this genomic sequence; Derived by automated computational analysis using gene prediction method: BestRefSeq.
similar to RNA sequence, mRNA (same species):RefSeq:NM_001351374.1
similar to AA sequence (same species):RefSeq:NP_001338303.1
UGA stop codon recoded as selenocysteine; The RefSeq protein has 2 substitutions compared to this genomic sequence; Derived by automated computational analysis using gene prediction method: BestRefSeq.
similar to AA sequence (same species):RefSeq:NP_001159799.1
uncharacterized LOC107049828, transcript variant X1
orthodenticle-related homeobox 5; Derived by automated computational analysis using gene prediction method: BestRefSeq,Gnomon.
orthodenticle-related homeobox 5, transcript variant X1
uncharacterized LOC124416939, transcript variant X1
uncharacterized protein LOC124416939 isoform X1
distal membrane-arm assembly complex protein 2 isoform X1
branched chain keto acid dehydrogenase E1, alpha polypeptide
2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial
transforming growth factor beta 1; Derived by automated computational analysis using gene prediction method: BestRefSeq.
similar to RNA sequence, mRNA (same species):RefSeq:NM_001318456.1
The RefSeq transcript has 4 substitutions, 1 frameshift, 2 non-frameshifting indels compared to this genomic sequence; Derived by automated computational analysis using gene prediction method: BestRefSeq.
similar to AA sequence (same species):RefSeq:NP_001305385.1
The RefSeq protein has 1 substitution, 1 frameshift compared to this genomic sequence; Derived by automated computational analysis using gene prediction method: BestRefSeq.
transforming growth factor beta-1 proprotein precursor
COORDINATES: ab initio prediction:SignalP:4.0
propagated from UniProtKB/Swiss-Prot (P09531.3); Region: Straightjacket domain. /evidence=ECO:0000250|UniProtKB:P07200
propagated from UniProtKB/Swiss-Prot (P09531.3); Region: Arm domain. /evidence=ECO:0000250|UniProtKB:P07200
N-linked (GlcNAc...) asparagine. /evidence=ECO:0000255; propagated from UniProtKB/Swiss-Prot (P09531.3); glycosylation site
propagated from UniProtKB/Swiss-Prot (P09531.3); Region: Bowtie tail. /evidence=ECO:0000250|UniProtKB:P01137
propagated from UniProtKB/Swiss-Prot (P09531.3); Region: Cell attachment site. /evidence=ECO:0000255
coiled-coil domain-containing protein 97
heterogeneous nuclear ribonucleoprotein U like 1, transcript variant X1
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
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: heterogeneous nuclear ribonucleoprotein U-like protein 1 isoform 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
WAS/WASL-interacting protein family member 3 isoform 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 16 samples with support for all annotated introns
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 29 samples with support for all annotated introns
actin cytoskeleton-regulatory complex protein PAN1 isoform X1
actin cytoskeleton-regulatory complex protein PAN1 isoform X2
phospholipase D family member 3, transcript variant X1
phospholipase D family member 3, transcript variant X2
uncharacterized LOC101748353, transcript variant X1
uncharacterized LOC101748353, transcript variant X2
uncharacterized protein C19orf47 homolog isoform X1
uncharacterized protein C19orf47 homolog isoform X2
RAC-beta serine/threonine-protein kinase
26S proteasome non-ATPase regulatory subunit 8-like, transcript variant X1
26S proteasome non-ATPase regulatory subunit 8 isoform X1
SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4; Derived by automated computational analysis using gene prediction method: BestRefSeq.
SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4
similar to RNA sequence, mRNA (same species):RefSeq:NM_205059.1
The RefSeq transcript has 27 substitutions, 1 non-frameshifting indel and aligns at 79% coverage compared to this genomic sequence; Derived by automated computational analysis using gene prediction method: BestRefSeq.
similar to AA sequence (same species):RefSeq:NP_990390.1
The RefSeq protein has 13 substitutions, 1 non-frameshifting indel and aligns at 79% coverage compared to this genomic sequence; Derived by automated computational analysis using gene prediction method: BestRefSeq.
latent-transforming growth factor beta-binding protein 4-like, transcript variant X1
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 2 ESTs, 7 long SRA reads, 11 Proteins, and 92% coverage of the annotated genomic feature by RNAseq alignments
latent-transforming growth factor beta-binding protein 4 isoform X1
Yip1 interacting factor homolog B, membrane trafficking protein
kunitz-type protease inhibitor 2-like, transcript variant X1
kunitz-type protease inhibitor 2 isoform X1
LOW QUALITY PROTEIN: zinc finger CCCH domain-containing protein 4
coiled-coil domain containing 9, transcript variant X1
LOW QUALITY PROTEIN: SUMO-activating enzyme subunit 1 isoform X1
complement C5a receptor 1, transcript variant X1
C5a anaphylatoxin chemotactic receptor 1 isoform X1
DExH-box helicase 34, transcript variant X1
DExH-box helicase 34, transcript variant X2
DExH-box helicase 34, transcript variant X4
DExH-box helicase 34, transcript variant X3
probable ATP-dependent RNA helicase DHX34 isoform X1
probable ATP-dependent RNA helicase DHX34 isoform X2
leucine rich repeat and fibronectin type III domain containing 3, transcript variant X2
leucine rich repeat and fibronectin type III domain containing 3, transcript variant X1
leucine rich repeat and fibronectin type III domain containing 3, transcript variant X3
leucine-rich repeat and fibronectin type-III domain-containing protein 3 isoform X1
leucine-rich repeat and fibronectin type-III domain-containing protein 3 isoform X3
leucine-rich repeat and fibronectin type-III domain-containing protein 3 isoform X2
glutaminyl-peptide cyclotransferase like, transcript variant X2
glutaminyl-peptide cyclotransferase like, transcript variant X1
glutaminyl-peptide cyclotransferase-like protein isoform X1
glutaminyl-peptide cyclotransferase-like protein isoform X2
gastric inhibitory polypeptide receptor, transcript variant X1
optic atrophy 3 (autosomal recessive, with chorea and spastic paraplegia)
vasodilator-stimulated phosphoprotein isoform X1
NTPase KAP family P-loop domain containing 1
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 2 ESTs, 4 long SRA reads, 1 Protein, and 92% coverage of the annotated genomic feature by RNAseq alignments
NTPase KAP family P-loop domain-containing protein 1
protein phosphatase 1 regulatory subunit 37, transcript variant X1
protein phosphatase 1 regulatory subunit 37 isoform X1
gem nuclear organelle associated protein 7
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 98% coverage of the annotated genomic feature by RNAseq alignments, including 17 samples with support for all annotated introns
tubulin folding cofactor B, transcript variant X3
tubulin folding cofactor B, transcript variant X1
tubulin folding cofactor B, transcript variant X2
succinate dehydrogenase complex assembly factor 1, transcript variant X1
succinate dehydrogenase assembly factor 1, mitochondrial
Rho GTPase activating protein 35, transcript variant X1
Rho GTPase activating protein 35, transcript variant X2
rho GTPase-activating protein 35 isoform X1
adaptor related protein complex 2 sigma 1 subunit
fukutin related protein, transcript variant X1
LOW QUALITY PROTEIN: fukutin-related protein
cytochrome c oxidase subunit 7A1, mitochondrial
basic helix-loop-helix and HMG-box containing 1
small nuclear ribonucleoprotein D2 polypeptide