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    CHD4 chromodomain helicase DNA binding protein 4 [ Homo sapiens (human) ]

    Gene ID: 1108, updated on 20-Dec-2019

    Summary

    Official Symbol
    CHD4provided by HGNC
    Official Full Name
    chromodomain helicase DNA binding protein 4provided by HGNC
    Primary source
    HGNC:HGNC:1919
    See related
    Ensembl:ENSG00000111642 MIM:603277
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CHD-4; Mi-2b; SIHIWES; Mi2-BETA
    Summary
    The product of this gene belongs to the SNF2/RAD54 helicase family. It represents the main component of the nucleosome remodeling and deacetylase complex and plays an important role in epigenetic transcriptional repression. Patients with dermatomyositis develop antibodies against this protein. Somatic mutations in this gene are associated with serous endometrial tumors. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2014]
    Expression
    Ubiquitous expression in thyroid (RPKM 37.2), endometrium (RPKM 27.5) and 25 other tissues See more
    Orthologs

    Genomic context

    See CHD4 in Genome Data Viewer
    Location:
    12p13.31
    Exon count:
    40
    Annotation release Status Assembly Chr Location
    109.20191205 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (6570082..6607379, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (6679248..6716551, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene intermediate filament family orphan 1 Neighboring gene NOP2 nucleolar protein Neighboring gene Sharpr-MPRA regulatory region 3501 Neighboring gene small Cajal body-specific RNA 11 Neighboring gene CRISPRi-validated cis-regulatory element chr12.325 Neighboring gene uncharacterized LOC105369631 Neighboring gene lysophosphatidic acid receptor 5

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Sifrim-Hitz-Weiss syndrome
    MedGen: C4310688 OMIM: 617159 GeneReviews: Not available
    Compare labs

    NHGRI GWAS Catalog

    Description
    A genome-wide association study provides evidence for association of chromosome 8p23 (MYP10) and 10q21.1 (MYP15) with high myopia in the French Population.
    NHGRI GWA Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • DKFZp686E06161

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    NuRD complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    centrosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    membrane HDA PubMed 
    nuclear chromatin HDA PubMed 
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    protein-containing complex HDA PubMed 

    General protein information

    Preferred Names
    chromodomain-helicase-DNA-binding protein 4
    Names
    ATP-dependent helicase CHD4
    Mi-2 autoantigen 218 kDa protein
    NP_001264.2
    NP_001284482.1
    NP_001350535.1

    NCBI Reference Sequences (RefSeq)

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_052823.1 RefSeqGene

      Range
      5061..42358
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001273.5NP_001264.2  chromodomain-helicase-DNA-binding protein 4 isoform 1

      See identical proteins and their annotated locations for NP_001264.2

      Status: REVIEWED

      Source sequence(s)
      AC006064, BC038596, BP234473, X86691
      Consensus CDS
      CCDS8552.1
      UniProtKB/Swiss-Prot
      Q14839
      Related
      ENSP00000440542.2, ENST00000544040.6
      Conserved Domains (12) summary
      smart00298
      Location:622676
      CHROMO; Chromatin organization modifier domain
      cd00024
      Location:540577
      CHROMO; Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence ...
      cd00046
      Location:746904
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      cd15531
      Location:372414
      PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd15532
      Location:451493
      PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      pfam00176
      Location:7291025
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:10681164
      Helicase_C; Helicase conserved C-terminal domain
      pfam06461
      Location:13851521
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:13021352
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam06614
      Location:15171649
      Neuromodulin; Neuromodulin
      pfam08073
      Location:164216
      CHDNT; CHDNT (NUC034) domain
      pfam08074
      Location:17261896
      CHDCT2; CHDCT2 (NUC038) domain
    2. NM_001297553.2NP_001284482.1  chromodomain-helicase-DNA-binding protein 4 isoform 2

      See identical proteins and their annotated locations for NP_001284482.1

      Status: REVIEWED

      Source sequence(s)
      AC006064, BC038596, CR936680, X86691
      Consensus CDS
      CCDS76510.1
      UniProtKB/Swiss-Prot
      Q14839
      UniProtKB/TrEMBL
      F5GWX5
      Related
      ENSP00000496163.1, ENST00000645022.1
      Conserved Domains (12) summary
      smart00298
      Location:615669
      CHROMO; Chromatin organization modifier domain
      cd00024
      Location:533570
      CHROMO; Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence ...
      cd00046
      Location:739897
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      cd15531
      Location:365407
      PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd15532
      Location:444486
      PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      pfam00176
      Location:7221018
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:10611157
      Helicase_C; Helicase conserved C-terminal domain
      pfam06461
      Location:13781514
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:12951345
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam06614
      Location:15101642
      Neuromodulin; Neuromodulin
      pfam08073
      Location:157209
      CHDNT; CHDNT (NUC034) domain
      pfam08074
      Location:17191889
      CHDCT2; CHDCT2 (NUC038) domain
    3. NM_001363606.2NP_001350535.1  chromodomain-helicase-DNA-binding protein 4 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC006064
      Consensus CDS
      CCDS86267.1
      Related
      ENSP00000349508.3, ENST00000357008.7
      Conserved Domains (10) summary
      smart00298
      Location:609663
      CHROMO; Chromatin organization modifier domain
      cd00024
      Location:527564
      CHROMO; Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence ...
      cd15531
      Location:359401
      PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd15532
      Location:438480
      PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      pfam06461
      Location:13721508
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:12891339
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08073
      Location:164217
      CHDNT; CHDNT (NUC034) domain
      pfam08074
      Location:17151886
      CHDCT2; CHDCT2 (NUC038) domain
      cl25758
      Location:14981633
      DUF4775; Domain of unknown function (DUF4775)
      cl26465
      Location:7111268
      SNF2_N; SNF2 family N-terminal domain

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

      Range
      6570082..6607379 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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