Free for academic non-profit institutions. Other users need a Commercial license

CHD1 Gene(Protein Coding)

Chromodomain Helicase DNA Binding Protein 1

GCID:
GC05M098853
GIFtS:
63
Genes Participants
UDN Logo

Aliases for CHD1 Gene

Aliases for CHD1 Gene

  • Chromodomain Helicase DNA Binding Protein 1 2 3 5
  • ATP-Dependent Helicase CHD1 3 4
  • CHD-1 3 4
  • EC 3.6.4.12 4
  • EC 3.6.1 63

External Ids for CHD1 Gene

Previous GeneCards Identifiers for CHD1 Gene

  • GC05M097537
  • GC05M098601
  • GC05M098222
  • GC05M098267
  • GC05M098219
  • GC05M093378
  • GC05M098190

Summaries for CHD1 Gene

Entrez Gene Summary for CHD1 Gene

  • 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]

GeneCards Summary for CHD1 Gene

CHD1 (Chromodomain Helicase DNA Binding Protein 1) is a Protein Coding gene. Diseases associated with CHD1 include Photosensitive Epilepsy. Among its related pathways are Chromatin Regulation / Acetylation. GO annotations related to this gene include methylated histone binding and ATP-dependent DNA helicase activity. An important paralog of this gene is CHD3.

UniProtKB/Swiss-Prot for CHD1 Gene

  • ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. Regulates polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. Regulates negatively DNA replication. Not only involved in transcription-related chromatin-remodeling, but also required to maintain a specific chromatin configuration across the genome. Is also associated with histone deacetylase (HDAC) activity (By similarity). Required for the bridging of SNF2, the FACT complex, the PAF complex as well as the U2 snRNP complex to H3K4me3. Functions to modulate the efficiency of pre-mRNA splicing in part through physical bridging of spliceosomal components to H3K4me3. Required for maintaining open chromatin and pluripotency in embryonic stem cells.

Gene Wiki entry for CHD1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CHD1 Gene

Genomics for CHD1 Gene

Products:

  1. Regulatory Element

Regulatory Elements for CHD1 Gene

Enhancers for CHD1 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around CHD1 on UCSC Golden Path with GeneCards custom track

Promoters for CHD1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around CHD1 on UCSC Golden Path with GeneCards custom track

Transcription factor binding sites by QIAGEN in the CHD1 gene promoter:

Genomic Location for CHD1 Gene

Chromosome:
5
Start:
98,853,985 bp from pter
End:
98,928,957 bp from pter
Size:
74,973 bases
Orientation:
Minus strand

Genomic View for CHD1 Gene

Genes around CHD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CHD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CHD1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for CHD1 Gene

Proteins for CHD1 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for CHD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O14646-CHD1_HUMAN
    Recommended name:
    Chromodomain-helicase-DNA-binding protein 1
    Protein Accession:
    O14646
    Secondary Accessions:
    • Q17RZ3

    Protein attributes for CHD1 Gene

    Size:
    1710 amino acids
    Molecular mass:
    196688 Da
    Quaternary structure:
    • Component of the SAGA complex (By similarity). Interacts with BCLAF1, NCoR, SRP20 and SAFB (By similarity). Specifically interacts with methylated H3K4me2 and H3K4me3. Interacts with the FACT complex, the PAF complex and the U2 snRNP. Interacts directly with PAF1, SFA3A1, SFA3A2, SFA3A3, SNF2 and SSRP1.

    Three dimensional structures from OCA and Proteopedia for CHD1 Gene

    Alternative splice isoforms for CHD1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CHD1 Gene

Proteomics data for CHD1 Gene at MOPED

Protein Expression for CHD1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Selected DME Specific Peptides for CHD1 Gene

O14646:

Post-translational modifications for CHD1 Gene

  • Ubiquitination at Lys 364
  • Modification sites at PhosphoSitePlus

Other Protein References for CHD1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for CHD1 (CHD-1)

Domains & Families for CHD1 Gene

Protein Domains for CHD1 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for CHD1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O14646

UniProtKB/Swiss-Prot:

CHD1_HUMAN :
  • The 2 chromodomains are involved in the binding to the histone H3 methyllysine at position 4 (H3K4me3).
  • Belongs to the SNF2/RAD54 helicase family.
Domain:
  • The 2 chromodomains are involved in the binding to the histone H3 methyllysine at position 4 (H3K4me3).
  • Contains 2 chromo domains.
  • Contains 1 helicase ATP-binding domain.
  • Contains 1 helicase C-terminal domain.
Family:
  • Belongs to the SNF2/RAD54 helicase family.
genes like me logo Genes that share domains with CHD1: view

No data available for Gene Families for CHD1 Gene

Function for CHD1 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

Molecular function for CHD1 Gene

GENATLAS Biochemistry:
DNA binding protein with two chromatin organization (chromo) domains and a helicase ATPase domain,1,binding A.T tracts, released into cytoplasm during mitosis,component of the chromatin remodeling complex
UniProtKB/Swiss-Prot CatalyticActivity:
ATP + H(2)O = ADP + phosphate.
UniProtKB/Swiss-Prot Function:
ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. Regulates polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. Regulates negatively DNA replication. Not only involved in transcription-related chromatin-remodeling, but also required to maintain a specific chromatin configuration across the genome. Is also associated with histone deacetylase (HDAC) activity (By similarity). Required for the bridging of SNF2, the FACT complex, the PAF complex as well as the U2 snRNP complex to H3K4me3. Functions to modulate the efficiency of pre-mRNA splicing in part through physical bridging of spliceosomal components to H3K4me3. Required for maintaining open chromatin and pluripotency in embryonic stem cells.

Enzyme Numbers (IUBMB) for CHD1 Gene

Gene Ontology (GO) - Molecular Function for CHD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0004003 ATP-dependent DNA helicase activity TAS 9326634
genes like me logo Genes that share ontologies with CHD1: view

Phenotypes for CHD1 Gene

MGI mutant phenotypes for CHD1:
inferred from 3 alleles
GenomeRNAi human phenotypes for CHD1:
genes like me logo Genes that share phenotypes with CHD1: view

Animal Models for CHD1 Gene

MGI Knock Outs for CHD1:
  • Chd1 tm1b(KOMP)Wtsi
  • Chd1 tm1b(KOMP)Rsan

Animal Model Products

  • Taconic Biosciences Mouse Models for CHD1

miRNA for CHD1 Gene

miRTarBase miRNAs that target CHD1

Inhibitory RNA Products

Flow Cytometry Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CHD1 Gene

Localization for CHD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CHD1 Gene

Nucleus. Cytoplasm. Note=Is released into the cytoplasm when cells enter mitosis and is reincorporated into chromatin during telophase-cytokinesis. {ECO:0000250 UniProtKB:P40201}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for CHD1 Gene COMPARTMENTS Subcellular localization image for CHD1 gene
Compartment Confidence
nucleus 5

No data available for Gene Ontology (GO) - Cellular Components for CHD1 Gene

Pathways & Interactions for CHD1 Gene

genes like me logo Genes that share pathways with CHD1: view

Pathways by source for CHD1 Gene

1 Cell Signaling Technology pathway for CHD1 Gene

Gene Ontology (GO) - Biological Process for CHD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0032508 DNA duplex unwinding TAS 9326634
genes like me logo Genes that share ontologies with CHD1: view

No data available for SIGNOR curated interactions for CHD1 Gene

Drugs & Compounds for CHD1 Gene

Products:

  1. Drug

(4) Drugs for CHD1 Gene - From: DrugBank, DGIdb, FDA Approved Drugs, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Epirubicin Approved Pharma inhibitor, Target, antagonist 366
Ellence Approved September 1999 Pharma 0
Adenosine triphosphate Approved Nutra 0

(3) Additional Compounds for CHD1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • Adenosindiphosphorsaeure
  • Adenosine 5'-pyrophosphate
  • Adenosine diphosphate
  • Adenosine pyrophosphate
  • Adenosine-5'-diphosphate
 Full agonist, Agonist 58-64-0
phosphoric acid
  • Acide phosphorique (FRENCH)
  • Acido fosforico [Italian]
  • Acidum phosphoricum
  • Diphosphate tetrasodium
  • Fosforzuuroplossingen [Dutch]
 7664-38-2
Water
  • Dihydrogen oxide
  • Steam
 7732-18-5
genes like me logo Genes that share compounds with CHD1: view

Transcripts for CHD1 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for CHD1 Gene

(4) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(137) Selected AceView cDNA sequences:
(12) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CHD1 Gene

Chromodomain helicase DNA binding protein 1:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CHD1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16a · 16b ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:

ExUns: 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30a · 30b ^ 31 ^ 32 ^ 33a · 33b ^ 34 ^ 35 ^ 36 ^ 37a · 37b ^ 38
SP1:
SP2: - -
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12: -
SP13: -
SP14:

Relevant External Links for CHD1 Gene

GeneLoc Exon Structure for
CHD1
ECgene alternative splicing isoforms for
CHD1

Expression for CHD1 Gene

Products:

  1. Primer

mRNA expression in normal human tissues for CHD1 Gene

mRNA expression in normal human tissues for CHD1 Gene
mRNA expression by BioGPS for CHD1 GenemRNA expression by GTEx for CHD1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for CHD1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (19.3), Breast (12.3), Lung (9.5), and Adrenal (6.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for CHD1 Gene



SOURCE GeneReport for Unigene cluster for CHD1 Gene Hs.643465

genes like me logo Genes that share expression patterns with CHD1: view

Protein tissue co-expression partners for CHD1 Gene

- Elite partner

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for CHD1 Gene

Orthologs for CHD1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for CHD1 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
 Mammalia CHD1 35
  • 93.54 (n)
  • 97.43 (a)
CHD1 36
  • 92 (a)
 OneToOne
dog
(Canis familiaris)
 Mammalia CHD1 35
  • 95.02 (n)
  • 98.36 (a)
CHD1 36
  • 93 (a)
 OneToOne
mouse
(Mus musculus)
 Mammalia Chd1 35
  • 88.02 (n)
  • 95.73 (a)
Chd1 16
Chd1 36
  • 96 (a)
 OneToOne
chimpanzee
(Pan troglodytes)
 Mammalia CHD1 35
  • 99.65 (n)
  • 99.65 (a)
CHD1 36
  • 100 (a)
 OneToOne
rat
(Rattus norvegicus)
 Mammalia Chd1 35
  • 88.37 (n)
  • 95.2 (a)
oppossum
(Monodelphis domestica)
 Mammalia CHD1 36
  • 96 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia CHD1 36
  • 94 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves CHD1 35
  • 81.93 (n)
  • 90.72 (a)
CHDZ 36
  • 96 (a)
 OneToMany
CHDZ 36
  • 88 (a)
 OneToMany
lizard
(Anolis carolinensis)
 Reptilia CHD1 36
  • 86 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia Str.17448 35
zebrafish
(Danio rerio)
 Actinopterygii zgc:173506 35
  • 70.86 (n)
  • 80.49 (a)
CHD1 36
  • 75 (a)
 OneToOne
fruit fly
(Drosophila melanogaster)
 Insecta Chd1 37
  • 54 (a)
Chd1 36
  • 44 (a)
 OneToMany
worm
(Caenorhabditis elegans)
 Secernentea H06O01.2 37
  • 48 (a)
chd-1 36
  • 46 (a)
 OneToMany
A. gosspyii yeast
(Ashbya gossypii)
 Saccharomycetes AGOS_AGR123C 35
  • 50.33 (n)
  • 43.33 (a)
K. lactis yeast
(Kluyveromyces lactis)
 Saccharomycetes KLLA0C17578g 35
  • 50.56 (n)
  • 42.72 (a)
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes CHD1 35
  • 49.92 (n)
  • 41.11 (a)
CHD1 36
  • 34 (a)
 OneToMany
fission yeast
(Schizosaccharomyces pombe)
 Schizosaccharomycetes hrp1 35
  • 52.66 (n)
  • 46.99 (a)
sea squirt
(Ciona savignyi)
 Ascidiacea -- 36
  • 54 (a)
 OneToMany
Species with no ortholog for CHD1:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for CHD1 Gene

ENSEMBL:
Gene Tree for CHD1 (if available)
TreeFam:
Gene Tree for CHD1 (if available)

Paralogs for CHD1 Gene

Paralogs for CHD1 Gene

(3) SIMAP similar genes for CHD1 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with CHD1: view

Variants for CHD1 Gene

Sequence variations from dbSNP and Humsavar for CHD1 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs10062803 - 98,900,880(+) TTGAG(A/G/T)AACAT nc-transcript-variant, reference, missense
rs727637 -- 98,878,287(-) TGGCA(A/G)GGCTT intron-variant
rs819025 -- 98,881,513(+) AATCC(C/T)TTTTT intron-variant
rs34487 -- 98,872,725(+) GTGAT(A/T)ATAAT intron-variant
rs150935 -- 98,887,108(-) tcagt(A/G)gtttt intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CHD1 Gene

Variant ID Type Subtype PubMed ID
nsv882414 CNV Gain 21882294
dgv6224n71 CNV Loss 21882294
nsv507277 CNV Insertion 20534489

Variation tolerance for CHD1 Gene

Residual Variation Intolerance Score: 1.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.72; 83.11% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CHD1 Gene

Human Gene Mutation Database (HGMD)
CHD1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CHD1 Gene

Disorders for CHD1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for CHD1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
photosensitive epilepsy
  • photoparoxysmal response 1
- elite association - COSMIC cancer census association via MalaCards
Search CHD1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for CHD1

Genetic Association Database (GAD)
CHD1
Human Genome Epidemiology (HuGE) Navigator
CHD1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CHD1
genes like me logo Genes that share disorders with CHD1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CHD1 Gene

Publications for CHD1 Gene

  1. Characterization of the CHD family of proteins. (PMID: 9326634) Woodage T. … Collins F.S. (Proc. Natl. Acad. Sci. U.S.A. 1997) 2 3 4 67
  2. Structural polymorphism of chromodomains in Chd1. (PMID: 17098252) Okuda M. … Nishimura Y. (J. Mol. Biol. 2007) 3 23
  3. Human but not yeast CHD1 binds directly and selectively to histone H3 methylated at lysine 4 via its tandem chromodomains. (PMID: 16263726) Sims R.J. III … Reinberg D. (J. Biol. Chem. 2005) 3 23
  4. CHD1 interacts with SSRP1 and depends on both its chromodomain and its ATPase/helicase-like domain for proper association with chromatin. (PMID: 10199952) Kelley D.E. … Perry R.P. (Chromosoma 1999) 3 23
  5. DNA-binding and chromatin localization properties of CHD1. (PMID: 7739555) Stokes D.G. … Perry R.P. (Mol. Cell. Biol. 1995) 3 23

Products for CHD1 Gene

Sources for CHD1 Gene

Content