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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 56
  • 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 Gene Expression and Regulation of TP53 Activity. Gene Ontology (GO) annotations related to this gene include 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

Additional gene information for CHD3 Gene

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

Genomics for CHD3 Gene

GeneHancer (GH) Regulatory Elements for CHD3 Gene

Promoters and enhancers for CHD3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17I007882 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 554.1 +1.8 1835 7.3 HDGF PKNOX1 FOXA2 SMAD1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 NAA38 CHD3 KDM6B NLGN2 WRAP53 CYB5D1 TMEM88 KCNAB3 TRAPPC1 CNTROB
GH17I007931 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 21.4 +47.7 47716 2.8 HDGF PKNOX1 SMAD1 FOXA2 ARID4B NEUROD1 SIN3A ZNF2 ZBTB7B YY1 CNTROB TRAPPC1 ENSG00000262730 PFAS DVL2 CYB5D1 SCARNA21 CHD3 SENP3 CTC1
GH17I007833 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10.1 -45.0 -45047 12.5 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF416 KDM6B DVL2 PFAS CTC1 WRAP53 CNTROB POLR2A SNORD10 SNORA48 PER1
GH17I007474 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 9.6 -404.2 -404187 12.5 FEZF1 DMAP1 YBX1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 NFYC POLR2A ZBTB4 SLC35G6 DVL2 PFAS SNORD10 CTC1 WRAP53 SNORA48 CNTROB
GH17I007010 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 9.9 -867.1 -867062 13.7 CLOCK MLX ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 MIR497HG RNASEK BCL6B C17orf49 MIR497 MIR195 ENSG00000267047 DVL2 SNORD10 CNTROB
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CHD3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CHD3 gene promoter:

Genomic Locations for CHD3 Gene

Genomic Locations for CHD3 Gene
chr17:7,884,776-7,912,760
(GRCh38/hg38)
Size:
27,985 bases
Orientation:
Plus strand
chr17:7,788,123-7,816,078
(GRCh37/hg19)

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

Domains & Families for CHD3 Gene

Gene Families for CHD3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Plasma proteins
  • Predicted intracellular proteins

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 :
  • Belongs to the SNF2/RAD54 helicase family.
Family:
  • Belongs to the SNF2/RAD54 helicase family.
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

Phenotypes From GWAS Catalog for CHD3 Gene

Gene Ontology (GO) - Molecular Function for CHD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding TAS,IEA --
GO:0003723 RNA binding HDA,IDA 22658674
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

Clone 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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CHD3 gene
Compartment Confidence
cytoskeleton 5
nucleus 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Microtubule organizing center (2)
  • Nucleoli (2)
  • Nucleus (2)
See all subcellular structures

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,IEA 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 NAS 9688266
GO:0006357 regulation of transcription by RNA polymerase II 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
ATP Investigational Nutra Agonist 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:

Clone 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 CGAP 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.

Evidence on tissue expression from TISSUES for CHD3 Gene

  • Nervous system(4.6)
  • Liver(4.1)
  • Lung(3)
genes like me logo Genes that share expression patterns with CHD3: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 33 34
  • 99.77 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia CHD3 34
  • 99 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia CHD3 34
  • 95 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CHD3 33 34
  • 92.18 (n)
cow
(Bos Taurus)
Mammalia CHD3 33 34
  • 90.56 (n)
mouse
(Mus musculus)
Mammalia Chd3 33 16 34
  • 90.54 (n)
rat
(Rattus norvegicus)
Mammalia Chd3 33
  • 90.45 (n)
lizard
(Anolis carolinensis)
Reptilia CHD3 34
  • 84 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia chd3 33
  • 72.77 (n)
zebrafish
(Danio rerio)
Actinopterygii chd3 33 34
  • 72.12 (n)
fruit fly
(Drosophila melanogaster)
Insecta Mi-2 35 34
  • 61 (a)
Chd3 35 34
  • 52 (a)
worm
(Caenorhabditis elegans)
Secernentea chd-3 34
  • 49 (a)
ManyToMany
let-418 34
  • 48 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CHD1 34
  • 25 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8509 34
  • 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