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    CHD1 chromodomain helicase DNA binding protein 1 [ Homo sapiens (human) ]

    Gene ID: 1105, updated on 4-Feb-2024

    Summary

    Official Symbol
    CHD1provided by HGNC
    Official Full Name
    chromodomain helicase DNA binding protein 1provided by HGNC
    Primary source
    HGNC:HGNC:1915
    See related
    Ensembl:ENSG00000153922 MIM:602118; AllianceGenome:HGNC:1915
    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-1; PILBOS
    Summary
    The CHD family of proteins is characterized by the presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in bone marrow (RPKM 30.4), appendix (RPKM 9.5) and 23 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CHD1 in Genome Data Viewer
    Location:
    5q15-q21.1
    Exon count:
    39
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (98853985..98929007, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (99357270..99432327, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (98189689..98264711, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:98175311-98175811 Neighboring gene casein kinase 1 alpha 1 pseudogene 3 Neighboring gene uncharacterized LOC105379099 Neighboring gene RNA, U6 small nuclear 402, pseudogene Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:98240158-98241357 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16204 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:98264728-98265626 Neighboring gene uncharacterized LOC100289230 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22838 Neighboring gene CHD1 divergent transcript Neighboring gene ribosomal protein S9 pseudogene 3

    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
    Pilarowski-Bjornsson syndrome
    MedGen: C4540131 OMIM: 617682 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association study of chronic periodontitis in a general German population.
    EBI GWAS Catalog
    Heritability and genome-wide association analysis of renal sinus fat accumulation in the Framingham Heart Study.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • DKFZp686E2337

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables ATP hydrolysis activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables ATP-dependent chromatin remodeler activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables helicase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables methylated histone binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables methylated histone binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in chromatin remodeling IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in nucleosome organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation by host of viral transcription IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    part_of chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in nuclear chromosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    chromodomain-helicase-DNA-binding protein 1
    Names
    ATP-dependent helicase CHD1
    NP_001261.2
    NP_001351042.1
    NP_001363123.1
    XP_024310112.1
    XP_024310113.1
    XP_047272625.1
    XP_047272626.1
    XP_047272628.1
    XP_047272629.1
    XP_054207481.1
    XP_054207482.1
    XP_054207483.1
    XP_054207484.1
    XP_054207485.1
    XP_054207486.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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.

    mRNA and Protein(s)

    1. NM_001270.4NP_001261.2  chromodomain-helicase-DNA-binding protein 1 isoform 2

      See identical proteins and their annotated locations for NP_001261.2

      Status: REVIEWED

      Source sequence(s)
      AC022121, KC877055
      Consensus CDS
      CCDS34204.1
      UniProtKB/Swiss-Prot
      O14646, Q17RZ3
      Related
      ENSP00000483667.1, ENST00000614616.5
      Conserved Domains (8) summary
      PLN03142
      Location:4641000
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd18661
      Location:387443
      CD2_tandem_CHD1-2_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and 2, and similar proteins
      cd18666
      Location:276354
      CD1_tandem_CHD1-2_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and 2, and similar proteins
      pfam05110
      Location:12811401
      AF-4; AF-4 proto-oncoprotein
      pfam13907
      Location:14091498
      DUF4208; Domain of unknown function (DUF4208)
      pfam15440
      Location:15541708
      THRAP3_BCLAF1; THRAP3/BCLAF1 family
      pfam18375
      Location:11241210
      CDH1_2_SANT_HL1; CDH1/2 SANT-Helical linker 1
      cl28899
      Location:460697
      DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily
    2. NM_001364113.3NP_001351042.1  chromodomain-helicase-DNA-binding protein 1 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC022121, KC877055
      Consensus CDS
      CCDS93752.1
      UniProtKB/TrEMBL
      A0A087WVF4
      Related
      ENSP00000479403.2, ENST00000511067.3
      Conserved Domains (5) summary
      cd00024
      Location:306355
      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 ...
      pfam00385
      Location:389443
      Chromo; Chromo (CHRromatin Organisation MOdifier) domain
      pfam08648
      Location:16721781
      DUF1777; Protein of unknown function (DUF1777)
      pfam13907
      Location:14961586
      DUF4208; Domain of unknown function (DUF4208)
      cl26465
      Location:4641000
      SNF2_N; SNF2 family N-terminal domain
    3. NM_001376194.2NP_001363123.1  chromodomain-helicase-DNA-binding protein 1 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC022121, KC877055
      Consensus CDS
      CCDS34204.1
      UniProtKB/Swiss-Prot
      O14646, Q17RZ3
      Conserved Domains (8) summary
      PLN03142
      Location:4641000
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd18661
      Location:387443
      CD2_tandem_CHD1-2_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and 2, and similar proteins
      cd18666
      Location:276354
      CD1_tandem_CHD1-2_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and 2, and similar proteins
      pfam05110
      Location:12811401
      AF-4; AF-4 proto-oncoprotein
      pfam13907
      Location:14091498
      DUF4208; Domain of unknown function (DUF4208)
      pfam15440
      Location:15541708
      THRAP3_BCLAF1; THRAP3/BCLAF1 family
      pfam18375
      Location:11241210
      CDH1_2_SANT_HL1; CDH1/2 SANT-Helical linker 1
      cl28899
      Location:460697
      DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily

    RNA

    1. NR_157078.3 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC022121, KC877055
    2. NR_157079.3 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC022121, KC877055

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      98853985..98929007 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047416670.1XP_047272626.1  chromodomain-helicase-DNA-binding protein 1 isoform X4

    2. XM_024454345.2XP_024310113.1  chromodomain-helicase-DNA-binding protein 1 isoform X3

      Conserved Domains (4) summary
      cd00024
      Location:306355
      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 ...
      pfam00385
      Location:389443
      Chromo; Chromo (CHRromatin Organisation MOdifier) domain
      pfam13907
      Location:14961586
      DUF4208; Domain of unknown function (DUF4208)
      cl26465
      Location:4641000
      SNF2_N; SNF2 family N-terminal domain
    3. XM_024454344.2XP_024310112.1  chromodomain-helicase-DNA-binding protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A087WVF4
      Conserved Domains (5) summary
      cd00024
      Location:306355
      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 ...
      pfam00385
      Location:389443
      Chromo; Chromo (CHRromatin Organisation MOdifier) domain
      pfam08648
      Location:16721781
      DUF1777; Protein of unknown function (DUF1777)
      pfam13907
      Location:14961586
      DUF4208; Domain of unknown function (DUF4208)
      cl26465
      Location:4641000
      SNF2_N; SNF2 family N-terminal domain
    4. XM_047416669.1XP_047272625.1  chromodomain-helicase-DNA-binding protein 1 isoform X2

      UniProtKB/Swiss-Prot
      O14646, Q17RZ3
    5. XM_047416672.1XP_047272628.1  chromodomain-helicase-DNA-binding protein 1 isoform X5

    6. XM_047416673.1XP_047272629.1  chromodomain-helicase-DNA-binding protein 1 isoform X6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      99357270..99432327 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054351509.1XP_054207484.1  chromodomain-helicase-DNA-binding protein 1 isoform X4

    2. XM_054351508.1XP_054207483.1  chromodomain-helicase-DNA-binding protein 1 isoform X3

    3. XM_054351506.1XP_054207481.1  chromodomain-helicase-DNA-binding protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A087WVF4
    4. XM_054351507.1XP_054207482.1  chromodomain-helicase-DNA-binding protein 1 isoform X2

      UniProtKB/Swiss-Prot
      O14646, Q17RZ3
    5. XM_054351510.1XP_054207485.1  chromodomain-helicase-DNA-binding protein 1 isoform X5

    6. XM_054351511.1XP_054207486.1  chromodomain-helicase-DNA-binding protein 1 isoform X6