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CHD5 chromodomain helicase DNA binding protein 5 [ Sus scrofa (pig) ]

Gene ID: 100738053, updated on 17-Aug-2024

Summary

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Official Symbol
CHD5provided by VGNC
Official Full Name
chromodomain helicase DNA binding protein 5provided by VGNC
Primary source
VGNC:VGNC:86632
See related
Ensembl:ENSSSCG00000003366
Gene type
protein coding
RefSeq status
MODEL
Organism
Sus scrofa
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Artiodactyla; Suina; Suidae; Sus
Expression
Biased expression in mixtures (RPKM 2.2), spleen (RPKM 0.9) and 3 other tissues See more
Orthologs
human mouse all
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Genomic context

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See CHD5 in Genome Data Viewer
Location:
chromosome: 6
Exon count:
42
Annotation release Status Assembly Chr Location
106 current Sscrofa11.1 (GCF_000003025.6) 6 NC_010448.4 (67017410..67086685, complement)
105 previous assembly Sscrofa10.2 (GCF_000003025.5) 6 NC_010448.3 (61940486..62084194, complement)

Chromosome 6 - NC_010448.4Genomic Context describing neighboring genes Neighboring gene nephrocystin 4 Neighboring gene potassium voltage-gated channel subfamily A regulatory beta subunit 2 Neighboring gene ribosomal protein L22 Neighboring gene ring finger protein 207 Neighboring gene isoprenylcysteine carboxyl methyltransferase

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Transcriptome data used for gene annotation Transcriptome data used for gene annotation
  • Description: Nine kinds of tissues and a mixture of multiple tissues were sequenced for genome annotation
  • BioProject: PRJNA311523
  • Publication: PMID 27646534
  • Analysis date: Thu Dec 14 17:10:49 2017

Bibliography

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Related articles in PubMed

  1. Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. Burge S, et al. Database (Oxford), 2012. PMID 22301074, Free PMC Article
  2. TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations. Tang H, et al. Bioinformatics, 2019 Feb 1. PMID 30032202, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

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Homology

Gene Ontology Provided by RefSeq

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
 PubMed 
enables ATP hydrolysis activity IEA
Inferred from Electronic Annotation
more info
 PubMed 
enables ATP-dependent chromatin remodeler activity IEA
Inferred from Electronic Annotation
more info
 PubMed 
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 PubMed 
enables chromatin binding IEA
Inferred from Electronic Annotation
more info
 PubMed 
enables histone binding IEA
Inferred from Electronic Annotation
more info
 PubMed 
Process Evidence Code Pubs
involved_in chromatin remodeling IEA
Inferred from Electronic Annotation
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 PubMed 
Component Evidence Code Pubs
part_of NuRD complex IEA
Inferred from Electronic Annotation
more info
 PubMed 
part_of chromatin IEA
Inferred from Electronic Annotation
more info
 PubMed 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
 PubMed 

General protein information

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Preferred Names
chromodomain-helicase-DNA-binding protein 5

NCBI Reference Sequences (RefSeq)

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RefSeqs of Annotated Genomes: Sus scrofa Annotation Release 106 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference Sscrofa11.1 Primary Assembly

Genomic

  1. NC_010448.4 Reference Sscrofa11.1 Primary Assembly

    Range
    67017410..67086685 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_021095234.1 → XP_020950893.1  chromodomain-helicase-DNA-binding protein 5 isoform X1

    UniProtKB/TrEMBL
    A0A4X1W8M7
    Conserved Domains (8) summary
    smart00298
    Location:592 → 625
    CHROMO; Chromatin organization modifier domain
    cd15531
    Location:345 → 387
    PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
    cd15532
    Location:418 → 460
    PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
    pfam06461
    Location:1388 → 1529
    DUF1086; Domain of Unknown Function (DUF1086)
    pfam06465
    Location:1298 → 1358
    DUF1087; Domain of Unknown Function (DUF1087)
    pfam08073
    Location:150 → 200
    CHDNT; CHDNT (NUC034) domain
    pfam08074
    Location:1728 → 1899
    CHDCT2; CHDCT2 (NUC038) domain
    cl26465
    Location:698 → 1214
    SNF2_N; SNF2 family N-terminal domain

  2. XM_021095238.1 → XP_020950897.1  chromodomain-helicase-DNA-binding protein 5 isoform X5

    UniProtKB/TrEMBL
    A0A286ZJ13, A0A4X1W8X3, A0A8D1NFE1
    Related
    ENSSSCP00000031438.2, ENSSSCT00000042706.3
    Conserved Domains (8) summary
    smart00298
    Location:592 → 625
    CHROMO; Chromatin organization modifier domain
    cd15531
    Location:345 → 387
    PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
    cd15532
    Location:418 → 460
    PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
    pfam06461
    Location:1388 → 1529
    DUF1086; Domain of Unknown Function (DUF1086)
    pfam06465
    Location:1298 → 1358
    DUF1087; Domain of Unknown Function (DUF1087)
    pfam08073
    Location:150 → 200
    CHDNT; CHDNT (NUC034) domain
    pfam08074
    Location:1728 → 1899
    CHDCT2; CHDCT2 (NUC038) domain
    cl26465
    Location:698 → 1214
    SNF2_N; SNF2 family N-terminal domain

  3. XM_021095237.1 → XP_020950896.1  chromodomain-helicase-DNA-binding protein 5 isoform X4

    UniProtKB/TrEMBL
    A0A4X1W2Y4, A0A8D1NAG5, F1SSZ2
    Related
    ENSSSCP00000019043.4, ENSSSCT00000019561.5
    Conserved Domains (8) summary
    smart00298
    Location:592 → 625
    CHROMO; Chromatin organization modifier domain
    cd15531
    Location:345 → 387
    PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
    cd15532
    Location:418 → 460
    PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
    pfam06461
    Location:1388 → 1529
    DUF1086; Domain of Unknown Function (DUF1086)
    pfam06465
    Location:1298 → 1358
    DUF1087; Domain of Unknown Function (DUF1087)
    pfam08073
    Location:150 → 200
    CHDNT; CHDNT (NUC034) domain
    pfam08074
    Location:1728 → 1899
    CHDCT2; CHDCT2 (NUC038) domain
    cl26465
    Location:698 → 1214
    SNF2_N; SNF2 family N-terminal domain

  4. XM_021095236.1 → XP_020950895.1  chromodomain-helicase-DNA-binding protein 5 isoform X3

    UniProtKB/TrEMBL
    A0A286ZJ13, A0A4X1W8X3
    Conserved Domains (8) summary
    smart00298
    Location:592 → 625
    CHROMO; Chromatin organization modifier domain
    cd15531
    Location:345 → 387
    PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
    cd15532
    Location:418 → 460
    PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
    pfam06461
    Location:1387 → 1528
    DUF1086; Domain of Unknown Function (DUF1086)
    pfam06465
    Location:1297 → 1357
    DUF1087; Domain of Unknown Function (DUF1087)
    pfam08073
    Location:150 → 200
    CHDNT; CHDNT (NUC034) domain
    pfam08074
    Location:1727 → 1898
    CHDCT2; CHDCT2 (NUC038) domain
    cl26465
    Location:698 → 1214
    SNF2_N; SNF2 family N-terminal domain

  5. XM_021095235.1 → XP_020950894.1  chromodomain-helicase-DNA-binding protein 5 isoform X2

    UniProtKB/TrEMBL
    A0A286ZJ13, A0A4X1W8X3
    Conserved Domains (8) summary
    smart00298
    Location:592 → 625
    CHROMO; Chromatin organization modifier domain
    cd15531
    Location:345 → 387
    PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
    cd15532
    Location:418 → 460
    PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
    pfam06461
    Location:1388 → 1529
    DUF1086; Domain of Unknown Function (DUF1086)
    pfam06465
    Location:1298 → 1358
    DUF1087; Domain of Unknown Function (DUF1087)
    pfam08073
    Location:150 → 200
    CHDNT; CHDNT (NUC034) domain
    pfam08074
    Location:1728 → 1899
    CHDCT2; CHDCT2 (NUC038) domain
    cl26465
    Location:698 → 1214
    SNF2_N; SNF2 family N-terminal domain
Nucleotide Protein
Heading Accession and Version

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