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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
  • 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
  • Mi2-ALPHA 3
  • Mi2-Alpha 4
  • 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. Among its related pathways are Gene Expression 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 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
GH17J007833 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 660.1 -45.0 -45047 12.5 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF416 KDM6B CHD3 DVL2 PFAS CTC1 WRAP53 CNTROB POLR2A SNORD10 SNORA48
GH17J007882 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 654.1 +1.8 1835 7.3 HDGF PKNOX1 FOXA2 SMAD1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 NAA38 CHD3 KDM6B CNTROB WRAP53 CTC1 DVL2 ENSG00000262089 CYB5D1 TMEM88
GH17J007854 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 660.2 -27.8 -27811 5 HDGF PKNOX1 CLOCK FOXA2 SMAD1 ARNT ARID4B NEUROD1 SIN3A FEZF1 CYB5D1 CHD3 NAA38 GC17P007860 TMEM88 ENSG00000280046 SNORD10 DVL2 GPS2 PFAS
GH17J007931 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 WRAP53 CTC1 CYB5D1 SCARNA21 CHD3
GH17J007474 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 KIAA0753 DVL2 SNORD10 PFAS CTC1 SNORA48 WRAP53
- 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 UCSC Golden Path with GeneCards custom track

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

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)
Size:
27,956 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

Post-translational modifications for CHD3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CHD3 Gene

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

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.
UniProtKB/Swiss-Prot CatalyticActivity:
ATP + H(2)O = ADP + phosphate.
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:0003677 DNA binding IEA,TAS --
GO:0003723 RNA binding HDA 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

Animal Model Products

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, Activator, Full agonist, Antagonist, Potentiation, Pore Blocker 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
Full agonist, Agonist, Partial agonist, Antagonist, Gating inhibitor 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, 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 34 33
  • 99.77 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CHD3 34
  • 99 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia CHD3 34
  • 95 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CHD3 34 33
  • 92.18 (n)
OneToOne
cow
(Bos Taurus)
Mammalia CHD3 34 33
  • 90.56 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Chd3 16 34 33
  • 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 34 33
  • 72.12 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Chd3 34 35
  • 58 (a)
ManyToMany
Mi-2 34 35
  • 53 (a)
ManyToMany
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)
Aminode:
Evolutionary constrained regions (ECRs) for CHD3: view image

Paralogs for CHD3 Gene

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 from dbSNP and Humsavar for CHD3 Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs1064795892 uncertain-significance, not specified 7,900,649(+) C/T coding_sequence_variant, missense_variant
rs1064795926 uncertain-significance, not specified 7,911,499(+) G/C coding_sequence_variant, genic_downstream_transcript_variant, missense_variant
rs1000028601 -- 7,889,171(+) G/A intron_variant
rs1000078283 -- 7,909,959(+) C/T genic_downstream_transcript_variant, intron_variant
rs1000221615 -- 7,895,476(+) G/A coding_sequence_variant, intron_variant, synonymous_variant

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