U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 1105, updated on 17-Jun-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 
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