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. Chro... See more...

Aliases for CHD3 Gene

Aliases for CHD3 Gene

  • Chromodomain Helicase DNA Binding Protein 3 2 3 5
  • Chromodomain-Helicase-DNA-Binding Protein 3 3 4
  • Mi-2 Autoantigen 240 KDa Protein 3 4
  • ATP-Dependent Helicase CHD3 3 4
  • Zinc Finger Helicase 3 4
  • Mi2-ALPHA 2 3
  • Mi-2a 2 3
  • CHD-3 3 4
  • HZFH 3 4
  • ZFH 2 3
  • Zinc-Finger Helicase (Snf2-Like) 3
  • EC 3.6.4.12 4
  • Mi2-Alpha 4
  • EC 3.6.1 51
  • SNIBCPS 3
  • CHD3 5

External Ids for CHD3 Gene

Previous GeneCards Identifiers for CHD3 Gene

  • GC17P008257
  • GC17P008659
  • GC17P007730
  • GC17P007988
  • GC17P007992
  • GC17P007732
  • GC17U900584
  • GC17P007788
  • GC17P007886
  • GC17P007913
  • GC17P007966
  • GC17P008060

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 Snijders Blok-Campeau Syndrome and Agenesis Of Corpus Callosum, Cardiac, Ocular, And Genital Syndrome. Among its related pathways are RNA Polymerase I Promoter Escape and Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3. Gene Ontology (GO) annotations related to this gene include helicase activity. An important paralog of this gene is CHD5.

UniProtKB/Swiss-Prot Summary for CHD3 Gene

  • Component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones (PubMed:9804427, PubMed:30397230). Involved in transcriptional repressiobn as part of the NuRD complex (PubMed:27068747). Required for anchoring centrosomal pericentrin in both interphase and mitosis, for spindle organization and centrosome integrity (PubMed:17626165).

Gene Wiki entry for CHD3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CHD3 Gene

Genomics for CHD3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CHD3 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CHD3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CHD3

Top Transcription factor binding sites by QIAGEN in the CHD3 gene promoter:
  • AREB6
  • Egr-3
  • HFH-1
  • Pax-5
  • PPAR-alpha

Genomic Locations for CHD3 Gene

Latest Assembly
chr17:7,884,764-7,912,760
(GRCh38/hg38)
Size:
27,997 bases
Orientation:
Plus strand

Previous Assembly
chr17:7,788,114-7,816,073
(GRCh37/hg19 by Entrez Gene)
Size:
27,960 bases
Orientation:
Plus strand

chr17:7,788,124-7,816,078
(GRCh37/hg19 by Ensembl)
Size:
27,955 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 (PubMed:9804427, PubMed:27068747). Interacts with TRIM28 (PubMed:11230151). Interacts with SERBP1 (PubMed:12505151). Interacts (via its C-terminal) with HABP4 (PubMed:12505151). Interacts with PCNT; the interaction regulates centrosome integrity (PubMed:17626165). Interacts with ZBED1/hDREF (PubMed:27068747).
    SequenceCaution:
    • Sequence=AAB87383.1; Type=Miscellaneous discrepancy; Note=Differs from position 1967 onward for unknown reasons.; Evidence={ECO:0000305};
    Miscellaneous:
    • One of the main antigens reacting with anti-MI-2 positive sera of dermatomyositis.

    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

  • Sumoylation at Lys-1971 results in dissociation from chromatin and suppression of transcriptional repression.
  • 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

Protein Domains for CHD3 Gene

InterPro:
Blocks:
  • Zn-finger, RING
  • Zn-finger-like, PHD finger
  • Chromo domain
  • ATP-dependent helicase, DEAH-box
  • SNF2 related domain
  • CHD, C-terminal 2
  • CHD, N-terminal
ProtoNet:

Suggested Antigen Peptide Sequences for CHD3 Gene

GenScript: Design optimal peptide antigens:
  • Zinc finger helicase (CHD3_HUMAN)
  • CHD3 protein (Q2TAZ1_HUMAN)

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

UniProtKB/Swiss-Prot Function:
Component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones (PubMed:9804427, PubMed:30397230). Involved in transcriptional repressiobn as part of the NuRD complex (PubMed:27068747). Required for anchoring centrosomal pericentrin in both interphase and mitosis, for spindle organization and centrosome integrity (PubMed:17626165).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.12; Evidence={ECO:0000269|PubMed:30397230};.
GENATLAS Biochemistry:
DNA binding protein with two chromatin organization (chromo) domains,and a helicase domain,3,component of the chromatin remodeling complex

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:0000166 nucleotide binding IEA --
GO:0000976 transcription regulatory region sequence-specific DNA binding IDA 27068747
GO:0003677 DNA binding TAS 9326634
GO:0003678 DNA helicase activity TAS 9326634
GO:0003723 RNA binding HDA 22658674
genes like me logo Genes that share ontologies with CHD3: view
genes like me logo Genes that share phenotypes with CHD3: view

Human Phenotype Ontology for CHD3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CHD3

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, PML body. Nucleus. Cytoplasm, cytoskeleton, microtubule organizing center, centrosome. Note=Associates with centrosomes in interphase and mitosis. {ECO:0000269 PubMed:17626165}.

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
plasma membrane 1
extracellular 1
mitochondrion 1
endoplasmic reticulum 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Centriolar satellite (2)
  • Nucleoli (2)
  • Nucleoplasm (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 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

1 GeneGo (Thomson Reuters) pathway for CHD3 Gene
  • Transcription Sin3 and NuRD in transcription regulation
1 Cell Signaling Technology pathway for CHD3 Gene

Gene Ontology (GO) - Biological Process for CHD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IDA 27068747
GO:0006325 chromatin organization IEA --
GO:0006333 chromatin assembly or disassembly 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
Water Approved Pharma 0
Phosphate Experimental Pharma 0
ATP Investigational Nutra 0

(1) Additional Compounds for CHD3 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • 5'-Adenylphosphoric acid
  • Adenosine 5'-diphosphate
  • ADENOSINE-5'-diphosphATE
  • H3ADP
  • 5'-Adenylphosphate
58-64-0
genes like me logo Genes that share compounds with CHD3: view

Transcripts for CHD3 Gene

mRNA/cDNA for CHD3 Gene

3 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
20 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CHD3

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

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, MaxQB, and MOPED for CHD3 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for 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(4.7)
  • Liver(4.3)
  • Lung(3.4)
  • Skin(2.5)
  • Intestine(2.5)
  • Kidney(2.4)
  • Eye(2.3)
  • Lymph node(2.2)
  • Spleen(2.2)
  • Blood(2.1)
  • Bone marrow(2.1)
  • Heart(2)
genes like me logo Genes that share expression patterns with CHD3: view

Primer products for research

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 30 31
  • 99.77 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia CHD3 31
  • 99 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia CHD3 31
  • 95 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia CHD3 30 31
  • 92.18 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia CHD3 30 31
  • 90.56 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Chd3 30 17 31
  • 90.54 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Chd3 30
  • 90.45 (n)
Lizard
(Anolis carolinensis)
Reptilia CHD3 31
  • 84 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia chd3 30
  • 72.77 (n)
Zebrafish
(Danio rerio)
Actinopterygii chd3 30 31
  • 72.12 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta Chd3 31 32
  • 58 (a)
ManyToMany
Mi-2 31 32
  • 53 (a)
ManyToMany
Worm
(Caenorhabditis elegans)
Secernentea chd-3 31
  • 49 (a)
ManyToMany
let-418 31
  • 48 (a)
ManyToMany
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CHD1 31
  • 25 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.8509 31
  • 56 (a)
OneToMany
Species where no ortholog for CHD3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for CHD3: view image

Paralogs for CHD3 Gene

(9) SIMAP similar genes for CHD3 Gene using alignment to 8 proteins:

  • CHD3_HUMAN
  • H7C0J3_HUMAN
  • H7C2H0_HUMAN
  • H7C3H7_HUMAN
  • I3L1I4_HUMAN
  • I3L229_HUMAN
  • K7EPV1_HUMAN
  • Q2TAZ1_HUMAN
genes like me logo Genes that share paralogs with CHD3: view

Variants for CHD3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CHD3 Gene