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

Gene ID: 1105, updated on 6-Jan-2019

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
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

Genomic context

See CHD1 in Genome Data Viewer
Location:
5q15-q21.1
Exon count:
40
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 5 NC_000005.10 (98855204..98929772, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (98189689..98264522, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986435 Neighboring gene uncharacterized LOC105379099 Neighboring gene casein kinase 1 alpha 1 pseudogene 3 Neighboring gene RNA, U6 small nuclear 402, pseudogene Neighboring gene uncharacterized LOC100289230 Neighboring gene long intergenic non-protein coding RNA 2062 Neighboring gene ribosomal protein S9 pseudogene 3 Neighboring gene uncharacterized LOC107986436

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 FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
PILAROWSKI-BJORNSSON SYNDROME
MedGen: C4540131 OMIM: 617682 GeneReviews: Not available
not available

NHGRI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • DKFZp686E2337

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
ATP-dependent DNA helicase activity TAS
Traceable Author Statement
more info
PubMed 
DNA binding IEA
Inferred from Electronic Annotation
more info
 
methylated histone binding IDA
Inferred from Direct Assay
more info
PubMed 
methylated histone binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
DNA duplex unwinding IEA
Inferred from Electronic Annotation
more info
 
chromatin remodeling IEA
Inferred from Electronic Annotation
more info
 
covalent chromatin modification IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation by host of viral transcription IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of transcription by RNA polymerase II TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
fibrillar center IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
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
XP_005271923.1
XP_005271924.1
XP_016864480.1
XP_016864481.1
XP_024310112.1
XP_024310113.1

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.

mRNA and Protein(s)

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

    See identical proteins and their annotated locations for NP_001261.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AC022121, AF006513, AK094871, BM698633, BQ436172, CN277742
    Consensus CDS
    CCDS34204.1
    UniProtKB/Swiss-Prot
    O14646
    UniProtKB/TrEMBL
    B3KT33
    Related
    ENSP00000284049.3, ENST00000284049.7
    Conserved Domains (9) summary
    PHA03420
    Location:15901680
    PHA03420; E4 protein; Provisional
    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 ...
    cd00046
    Location:500645
    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.
    pfam00176
    Location:484765
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:803902
    Helicase_C; Helicase conserved C-terminal domain
    pfam00385
    Location:390443
    Chromo; Chromo (CHRromatin Organization MOdifier) domain
    pfam08648
    Location:15551657
    DUF1777; Protein of unknown function (DUF1777)
    pfam11496
    Location:718971
    HDA2-3; Class II histone deacetylase complex subunits 2 and 3
    pfam13907
    Location:14071498
    DUF4208; Domain of unknown function (DUF4208)
  2. NM_001364113.1NP_001351042.1  chromodomain-helicase-DNA-binding protein 1 isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC022121
    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

RNA

  1. NR_157078.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate exon and lacks another alternate exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC022121
  2. NR_157079.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks alternate exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC022121

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p12 Primary Assembly

    Range
    98855204..98929772 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005271867.5XP_005271924.1  chromodomain-helicase-DNA-binding protein 1 isoform X2

    See identical proteins and their annotated locations for XP_005271924.1

    UniProtKB/Swiss-Prot
    O14646
    Related
    ENSP00000483667.1, ENST00000614616.4
    Conserved Domains (9) summary
    PHA03420
    Location:15901680
    PHA03420; E4 protein; Provisional
    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 ...
    cd00046
    Location:500645
    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.
    pfam00176
    Location:484765
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:803902
    Helicase_C; Helicase conserved C-terminal domain
    pfam00385
    Location:390443
    Chromo; Chromo (CHRromatin Organization MOdifier) domain
    pfam08648
    Location:15551657
    DUF1777; Protein of unknown function (DUF1777)
    pfam11496
    Location:718971
    HDA2-3; Class II histone deacetylase complex subunits 2 and 3
    pfam13907
    Location:14071498
    DUF4208; Domain of unknown function (DUF4208)
  2. XM_024454345.1XP_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_005271866.5XP_005271923.1  chromodomain-helicase-DNA-binding protein 1 isoform X1

    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_024454344.1XP_024310112.1  chromodomain-helicase-DNA-binding protein 1 isoform X1

    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
  5. XM_017008992.1XP_016864481.1  chromodomain-helicase-DNA-binding protein 1 isoform X4

  6. XM_017008991.1XP_016864480.1  chromodomain-helicase-DNA-binding protein 1 isoform X4

RNA

  1. XR_001741986.2 RNA Sequence

  2. XR_427702.4 RNA Sequence

  3. XR_002959841.1 RNA Sequence

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