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Aliases for CHD3 Gene

Aliases for CHD3 Gene

  • Chromodomain Helicase DNA Binding Protein 3 2 3 5
  • Mi-2 Autoantigen 240 KDa Protein 3 4
  • ATP-Dependent Helicase CHD3 3 4
  • Zinc Finger Helicase 3 4
  • Mi2-ALPHA 3 4
  • CHD-3 3 4
  • HZFH 3 4
  • Chromodomain-Helicase-DNA-Binding Protein 3 3
  • Zinc-Finger Helicase (Snf2-Like) 3
  • EC 3.6.4.12 4
  • EC 3.6.1 61
  • Mi-2a 3
  • ZFH 3

External Ids for CHD3 Gene

Previous GeneCards Identifiers for CHD3 Gene

  • GC17P008257
  • GC17P008659
  • GC17P007730
  • GC17P007988
  • GC17P007992
  • GC17P007732
  • GC17U900584
  • GC17P007788

Summaries for CHD3 Gene

Entrez Gene Summary for CHD3 Gene

  • This gene encodes a member of the CHD family of proteins which are characterized by the presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. This protein is one of the components of a histone deacetylase complex referred to as the Mi-2/NuRD complex which participates in the remodeling of chromatin by deacetylating histones. Chromatin remodeling is essential for many processes including transcription. Autoantibodies against this protein are found in a subset of patients with dermatomyositis. Three alternatively spliced transcripts encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

GeneCards Summary for CHD3 Gene

CHD3 (Chromodomain Helicase DNA Binding Protein 3) is a Protein Coding gene. Diseases associated with CHD3 include Dermatomyositis. Among its related pathways are Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 and RNA Polymerase I Promoter Escape. GO annotations related to this gene include poly(A) RNA binding and helicase activity. An important paralog of this gene is CHD5.

UniProtKB/Swiss-Prot for CHD3 Gene

  • Component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. Required for anchoring centrosomal pericentrin in both interphase and mitosis, for spindle organization and centrosome integrity.

Gene Wiki entry for CHD3 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CHD3 Gene

Genomics for CHD3 Gene

Regulatory Elements for CHD3 Gene

Enhancers for CHD3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH17F007981 0.8 Ensembl ENCODE 11.9 +97.6 97625 1.2 PKNOX1 ARID4B SIN3A FEZF1 GLIS2 FOS SP3 TSHZ1 TBX21 MYNN KCNAB3 CNTROB TRAPPC1 SCARNA21 CHD3 ALOX15B GUCY2D LOC105371517
GH17F007988 1.1 Ensembl ENCODE 11.7 +105.1 105126 2.2 HDGF ZFP64 ARID4B SIN3A DMAP1 ZNF48 BRCA1 ZNF2 GLIS2 ZNF207 KCNAB3 CNTROB LOC105371523 SNORD10 SNORA48 DVL2 PFAS ALOX15B TRAPPC1 SCARNA21
GH17F007992 0.4 ENCODE 11.7 +107.9 107902 0.2 FOS ALOX15B TRAPPC1 CNTROB KCNAB3 SCARNA21 CHD3 NAA38 TMEM88 CYB5D1 GUCY2D
GH17F007991 0.5 ENCODE 11.7 +106.3 106342 0.2 ALOX15B TRAPPC1 CNTROB KCNAB3 SCARNA21 CHD3 NAA38 TMEM88 CYB5D1 GUCY2D
GH17F007931 0.6 ENCODE 11.6 +47.7 47717 2.8 MLX CREB3L1 FEZF1 DMAP1 YY1 ZNF143 ZNF263 SP3 NFYC TBX21 PFAS DVL2 CTC1 CNTROB LOC105371523 SNORD10 SNORA48 CYB5D1 NLGN2 SCARNA21
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around CHD3 on UCSC Golden Path with GeneCards custom track

Promoters for CHD3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001340321 1224 4801 HDGF PKNOX1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF263 SP3

Genomic Location for CHD3 Gene

Chromosome:
17
Start:
7,884,776 bp from pter
End:
7,912,760 bp from pter
Size:
27,985 bases
Orientation:
Plus strand

Genomic View for CHD3 Gene

Genes around CHD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CHD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CHD3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CHD3 Gene

Proteins for CHD3 Gene

  • Protein details for CHD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q12873-CHD3_HUMAN
    Recommended name:
    Chromodomain-helicase-DNA-binding protein 3
    Protein Accession:
    Q12873
    Secondary Accessions:
    • D3DTQ9
    • E9PG89
    • Q9Y4I0

    Protein attributes for CHD3 Gene

    Size:
    2000 amino acids
    Molecular mass:
    226592 Da
    Quaternary structure:
    • Central component of the nucleosome remodeling and histone deacetylase (NuRD) repressive complex. Interacts with TRIM28 and SERBP1. Interacts (via its C-terminal) with HABP4. Interacts with PCNT; the interaction regulates centrosome integrity.
    Miscellaneous:
    • One of the main antigens reacting with anti-MI-2 positive sera of dermatomyositis.
    SequenceCaution:
    • Sequence=AAB87383.1; Type=Miscellaneous discrepancy; Note=Differs from position 1967 onward for unknown reasons.; Evidence={ECO:0000305};

    Alternative splice isoforms for CHD3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CHD3 Gene

Selected DME Specific Peptides for CHD3 Gene

Q12873:
  • AGNKPANAVLHKVL
  • IFDSDWNP
  • RWQDIQND
  • DEMGLGKT
  • DEAHRLK
  • TGTPLQN
  • VLLTSYELI
  • KMMLTHLVVRPG
  • ETFADGVPREGLSRQ
  • GHRVLIF
  • MGLGKTIQ
  • NQSKFFR
  • FLLSTRA
  • YKYERIDGGITG
  • NEYLSSFKVA
  • AGGLGINL
  • LVVDEAH
  • FLYSLYKEGH
  • RVLIFSQM
  • PEGKWSCPHCE
  • RAHRIGQ
  • DSDWNPH
  • LSTRAGGLG

Post-translational modifications for CHD3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for CHD3 (CHD-3 iso3)

Domains & Families for CHD3 Gene

Gene Families for CHD3 Gene

Suggested Antigen Peptide Sequences for CHD3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q12873

UniProtKB/Swiss-Prot:

CHD3_HUMAN :
  • Contains 2 chromo domains.
  • Belongs to the SNF2/RAD54 helicase family.
  • Contains 2 PHD-type zinc fingers.
Domain:
  • Contains 2 chromo domains.
  • Contains 1 helicase ATP-binding domain.
  • Contains 1 helicase C-terminal domain.
Family:
  • Belongs to the SNF2/RAD54 helicase family.
Similarity:
  • Contains 2 PHD-type zinc fingers.
genes like me logo Genes that share domains with CHD3: view

Function for CHD3 Gene

Molecular function for CHD3 Gene

GENATLAS Biochemistry:
DNA binding protein with two chromatin organization (chromo) domains,and a helicase domain,3,component of the chromatin remodeling complex
UniProtKB/Swiss-Prot CatalyticActivity:
ATP + H(2)O = ADP + phosphate.
UniProtKB/Swiss-Prot Function:
Component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. Required for anchoring centrosomal pericentrin in both interphase and mitosis, for spindle organization and centrosome integrity.

Enzyme Numbers (IUBMB) for CHD3 Gene

Gene Ontology (GO) - Molecular Function for CHD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0004003 ATP-dependent DNA helicase activity TAS 9326634
GO:0004386 helicase activity NAS 9688266
GO:0004407 histone deacetylase activity TAS --
genes like me logo Genes that share ontologies with CHD3: view
genes like me logo Genes that share phenotypes with CHD3: view

Animal Model Products

miRNA for CHD3 Gene

Inhibitory RNA Products

Flow Cytometry Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CHD3 Gene

Localization for CHD3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CHD3 Gene

Nucleus. Cytoplasm, cytoskeleton, microtubule organizing center, centrosome. Note=Associates with centrosomes in interphase and mitosis.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for CHD3 Gene COMPARTMENTS Subcellular localization image for CHD3 gene
Compartment Confidence
cytoskeleton 5
nucleus 5

Gene Ontology (GO) - Cellular Components for CHD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,NAS 9688266
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IDA --
GO:0005737 cytoplasm IEA,IDA 17626165
GO:0005813 centrosome IDA 17626165
genes like me logo Genes that share ontologies with CHD3: view

Pathways & Interactions for CHD3 Gene

genes like me logo Genes that share pathways with CHD3: view

Pathways by source for CHD3 Gene

Gene Ontology (GO) - Biological Process for CHD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization IEA --
GO:0006333 chromatin assembly or disassembly IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA,NAS 9688266
GO:0006357 regulation of transcription from RNA polymerase II promoter TAS 9326634
genes like me logo Genes that share ontologies with CHD3: view

No data available for SIGNOR curated interactions for CHD3 Gene

Drugs & Compounds for CHD3 Gene

(3) Drugs for CHD3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
Adenosine triphosphate Approved Nutra 0

(1) Additional Compounds for CHD3 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
genes like me logo Genes that share compounds with CHD3: view

Transcripts for CHD3 Gene

mRNA/cDNA for CHD3 Gene

(20) REFSEQ mRNAs :
(9) Additional mRNA sequences :
(17) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CHD3 Gene

Chromodomain helicase DNA binding protein 3:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CHD3 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13a · 13b ^ 14 ^ 15a · 15b · 15c ^ 16a · 16b ^ 17a · 17b · 17c ^
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:
SP16:
SP17: - -
SP18:
SP19:
SP20:
SP21:
SP22: -
SP23:
SP24:
SP25:
SP26:
SP27:

ExUns: 18a · 18b ^ 19 ^ 20 ^ 21a · 21b · 21c ^ 22a · 22b ^ 23a · 23b · 23c · 23d ^ 24a · 24b · 24c ^ 25a · 25b ^ 26a · 26b ^ 27 ^ 28a · 28b · 28c ^ 29 ^ 30 ^
SP1: -
SP2:
SP3:
SP4:
SP5: - - -
SP6: - - -
SP7: - - -
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:
SP16:
SP17:
SP18:
SP19:
SP20:
SP21:
SP22:
SP23:
SP24:
SP25:
SP26:
SP27:

ExUns: 31a · 31b ^ 32a · 32b ^ 33a · 33b ^ 34a · 34b ^ 35a · 35b · 35c ^ 36a · 36b · 36c ^ 37a · 37b · 37c · 37d ^ 38 ^ 39a · 39b
SP1: - -
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8: - -
SP9: - - - -
SP10: - -
SP11: - - - - -
SP12:
SP13:
SP14: -
SP15: - - -
SP16: -
SP17:
SP18:
SP19:
SP20:
SP21: - - - - -
SP22:
SP23:
SP24:
SP25:
SP26:
SP27:

Relevant External Links for CHD3 Gene

GeneLoc Exon Structure for
CHD3
ECgene alternative splicing isoforms for
CHD3

Expression for CHD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CHD3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for CHD3 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (15.5), Bone marrow mesenchymal stem cell (8.7), and Fetal Brain (8.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for CHD3 Gene



NURSA nuclear receptor signaling pathways regulating expression of CHD3 Gene:

CHD3

SOURCE GeneReport for Unigene cluster for CHD3 Gene:

Hs.25601

mRNA Expression by UniProt/SwissProt for CHD3 Gene:

Q12873-CHD3_HUMAN
Tissue specificity: Widely expressed.
genes like me logo Genes that share expression patterns with CHD3: view

Primer Products

No data available for mRNA differential expression in normal tissues and Protein tissue co-expression partners for CHD3 Gene

Orthologs for CHD3 Gene

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

Orthologs for CHD3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CHD3 34 35
  • 99.77 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia CHD3 35
  • 99 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia CHD3 35
  • 95 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CHD3 34 35
  • 92.18 (n)
cow
(Bos Taurus)
Mammalia CHD3 34 35
  • 90.56 (n)
mouse
(Mus musculus)
Mammalia Chd3 34 16 35
  • 90.54 (n)
rat
(Rattus norvegicus)
Mammalia Chd3 34
  • 90.45 (n)
lizard
(Anolis carolinensis)
Reptilia CHD3 35
  • 84 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia chd3 34
  • 72.77 (n)
zebrafish
(Danio rerio)
Actinopterygii chd3 34 35
  • 72.12 (n)
fruit fly
(Drosophila melanogaster)
Insecta Mi-2 36 35
  • 61 (a)
Chd3 36 35
  • 52 (a)
worm
(Caenorhabditis elegans)
Secernentea chd-3 35
  • 49 (a)
ManyToMany
let-418 35
  • 48 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CHD1 35
  • 25 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8509 35
  • 56 (a)
OneToMany
Species where no ortholog for CHD3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • 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)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • 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 CHD3 Gene

ENSEMBL:
Gene Tree for CHD3 (if available)
TreeFam:
Gene Tree for CHD3 (if available)

Paralogs for CHD3 Gene

Paralogs for CHD3 Gene

genes like me logo Genes that share paralogs with CHD3: view

Variants for CHD3 Gene

Sequence variations from dbSNP and Humsavar for CHD3 Gene

SNP ID Clin Chr 17 pos Sequence Context AA Info Type
rs11078713 -- 7,892,654(+) ACTAC(A/G)CCCAG intron-variant
rs111368246 -- 7,904,955(+) CTTTG(G/T)GCAGT intron-variant, upstream-variant-2KB
rs111435916 -- 7,883,834(+) TATTC(-/A)AAAAA intron-variant, upstream-variant-2KB
rs111436114 -- 7,893,703(+) AGTGA(A/G)ACCAC intron-variant
rs111630031 -- 7,885,955(+) CAGAT(A/G)CCCCC intron-variant, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for CHD3 Gene

Variant ID Type Subtype PubMed ID
dgv510n67 CNV gain 20364138
esv2715608 CNV deletion 23290073
nsv1070385 CNV deletion 25765185
nsv1070805 CNV deletion 25765185
nsv1112701 CNV deletion 24896259
nsv1113845 CNV deletion 24896259
nsv1136227 CNV deletion 24896259
nsv457660 CNV loss 19166990
nsv574333 CNV loss 21841781
nsv833351 CNV loss 17160897
nsv952122 CNV deletion 24416366

Variation tolerance for CHD3 Gene

Residual Variation Intolerance Score: 1.26% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.18; 69.65% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CHD3 Gene

Human Gene Mutation Database (HGMD)
CHD3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CHD3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CHD3 Gene

Disorders for CHD3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for CHD3 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
dermatomyositis
  • amyopathic dermatomyositis
- elite association - COSMIC cancer census association via MalaCards
Search CHD3 in MalaCards View complete list of genes associated with diseases

Relevant External Links for CHD3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CHD3
genes like me logo Genes that share disorders with CHD3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CHD3 Gene

Publications for CHD3 Gene

  1. Characterization of a new family of proteins that interact with the C-terminal region of the chromatin-remodeling factor CHD-3. (PMID: 12505151) Lemos T.A. … Kobarg J. (FEBS Lett. 2003) 3 4 22 64
  2. Identification of a human 17p-located cDNA encoding a protein of the Snf2-like helicase family. (PMID: 9688266) Aubry F. … Galibert F. (Eur. J. Biochem. 1998) 3 4 22 64
  3. Chromatin deacetylation by an ATP-dependent nucleosome remodelling complex. (PMID: 9804427) Tong J.K. … Schreiber S.L. (Nature 1998) 3 4 22 64
  4. 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 64
  5. Molecular analysis of a major antigenic region of the 240 kD protein of Mi-2 autoantigen. (PMID: 7560064) Ge Q. … Targoff I.N. (J. Clin. Invest. 1995) 2 3 4 64

Products for CHD3 Gene

Sources for CHD3 Gene

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