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Aliases for CHD3 Gene

Aliases for CHD3 Gene

  • Chromodomain Helicase DNA Binding Protein 3 2 3
  • 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
  • Zinc-Finger Helicase (Snf2-Like) 3
  • EC 3.6.4.12 4
  • EC 3.6.1 63
  • 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 RNA Polymerase I Promoter Opening and Development NOTCH1-mediated pathway for NF-KB activity modulation. GO annotations related to this gene include poly(A) RNA binding and helicase activity. An important paralog of this gene is CHD1.

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

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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

Proteomics data for CHD3 Gene at MOPED

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 --
GO:0003677 DNA binding IEA --
GO:0004003 ATP-dependent DNA helicase activity TAS 9326634
GO:0004386 helicase activity NAS 9688266
GO:0005515 protein binding IPI 9804427
genes like me logo Genes that share ontologies with CHD3: view

Phenotypes for CHD3 Gene

GenomeRNAi human phenotypes for CHD3:
genes like me logo Genes that share phenotypes with CHD3: view

Animal Model Products

miRNA for CHD3 Gene

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for CHD3

In Situ Assay Products

Flow Cytometry Products

No data available for 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 NAS 9688266
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IDA --
GO:0005737 cytoplasm 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

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays

Gene Ontology (GO) - Biological Process for CHD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization TAS --
GO:0006333 chromatin assembly or disassembly IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated 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

(1) Drugs for CHD3 Gene - From: HMDB

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

(3) 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
Antagonist, Gating inhibitor 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 CHD3: view

Transcripts for CHD3 Gene

mRNA/cDNA for CHD3 Gene

(16) 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

  • Predesigned siRNA for gene silencing in human,mouse,rat for CHD3

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 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, MOPED, and MaxQB for CHD3 Gene



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

In Situ Assay 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
cow
(Bos Taurus)
Mammalia CHD3 35
  • 90.56 (n)
  • 95.9 (a)
CHD3 36
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CHD3 35
  • 92.18 (n)
  • 98.63 (a)
CHD3 36
  • 98 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Chd3 35
  • 90.54 (n)
  • 97.15 (a)
Chd3 16
Chd3 36
  • 97 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia CHD3 35
  • 99.77 (n)
  • 99.95 (a)
CHD3 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Chd3 35
  • 90.45 (n)
  • 96.86 (a)
oppossum
(Monodelphis domestica)
Mammalia CHD3 36
  • 95 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CHD3 36
  • 99 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CHD3 36
  • 84 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia chd3 35
  • 72.77 (n)
  • 80.23 (a)
zebrafish
(Danio rerio)
Actinopterygii chd3 35
  • 72.12 (n)
  • 78.29 (a)
chd3 36
  • 74 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Chd3 37
  • 52 (a)
Mi-2 37
  • 61 (a)
Chd3 36
  • 58 (a)
ManyToMany
Mi-2 36
  • 53 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea chd-3 36
  • 49 (a)
ManyToMany
let-418 36
  • 48 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CHD1 36
  • 25 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8509 36
  • 56 (a)
OneToMany
Species with no ortholog for CHD3:
  • 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 MAF
rs931543 - 7,889,008(-) CTGCC(A/G/T)CCTTC intron-variant, missense, reference
rs1804966 -- 7,912,157(+) AAGTC(A/G)ACTGC utr-variant-3-prime
rs2279620 -- 7,889,147(-) ACATC(C/G/T)TTTTG intron-variant
rs4239111 -- 7,908,680(+) GTTCC(C/T)TTTCC intron-variant
rs4321249 -- 7,892,211(+) CACCC(A/G)TGTCC intron-variant

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

Variant ID Type Subtype PubMed ID
nsv833351 CNV Loss 17160897
dgv510n67 CNV Gain 20364138
nsv907654 CNV Loss 21882294
nsv457660 CNV Loss 19166990
esv2715608 CNV Deletion 23290073

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

HapMap Linkage Disequilibrium report
CHD3
Human Gene Mutation Database (HGMD)
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
  • polymyositis with skin involvement
- elite association
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. CHD3 proteins and polycomb group proteins antagonistically determine cell identity in Arabidopsis. (PMID: 19680533) Aichinger E. … KAPhler C. (PLoS Genet. 2009) 23 67
  2. The CHD3 remodeler PICKLE promotes trimethylation of histone H3 lysine 27. (PMID: 18539592) Zhang H. … Ogas J. (J. Biol. Chem. 2008) 23 67
  3. The C-terminal region of CHD3/ZFH interacts with the CIDD region of the Ets transcription factor ERM and represses transcription of the human presenilin 1 gene. (PMID: 17489097) Pastorcic M. … Das H.K. (FEBS J. 2007) 23 67
  4. CGI-55 interacts with nuclear proteins and co-localizes to p80-coilin positive-coiled bodies in the nucleus. (PMID: 16679534) Lemos T.A. … Kobarg J. (Cell Biochem. Biophys. 2006) 23 67
  5. Ki-1/57 interacts with PRMT1 and is a substrate for arginine methylation. (PMID: 16879614) Passos D.O. … Kobarg J. (FEBS J. 2006) 23 67

Products for CHD3 Gene

Sources for CHD3 Gene

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