Human Gene CHD3 (ENST00000380358.9) Description and Page Index
  Description: Homo sapiens chromodomain helicase DNA binding protein 3 (CHD3), transcript variant 3, mRNA. (from RefSeq NM_001005271)
RefSeq Summary (NM_001005271): 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].
Gencode Transcript: ENST00000380358.9
Gencode Gene: ENSG00000170004.17
Transcript (Including UTRs)
   Position: hg38 chr17:7,884,796-7,912,755 Size: 27,960 Total Exon Count: 40 Strand: +
Coding Region
   Position: hg38 chr17:7,884,807-7,911,585 Size: 26,779 Coding Exon Count: 40 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:7,884,796-7,912,755)mRNA (may differ from genome)Protein (2059 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC
HPRDLynxMGImyGene2neXtProtOMIM
PubMedReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: CHD3_HUMAN
DESCRIPTION: RecName: Full=Chromodomain-helicase-DNA-binding protein 3; Short=CHD-3; EC=3.6.4.12; AltName: Full=ATP-dependent helicase CHD3; AltName: Full=Mi-2 autoantigen 240 kDa protein; AltName: Full=Mi2-alpha; AltName: Full=Zinc finger helicase; Short=hZFH;
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.
CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
SUBUNIT: 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.
INTERACTION: Q99728:BARD1; NbExp=2; IntAct=EBI-523590, EBI-473181; P17844:DDX5; NbExp=4; IntAct=EBI-523590, EBI-351962; Q9Y2X7:GIT1; NbExp=2; IntAct=EBI-523590, EBI-466061; P42858:HTT; NbExp=3; IntAct=EBI-523590, EBI-466029; O60341:KDM1A; NbExp=4; IntAct=EBI-523590, EBI-710124; O75400:PRPF40A; NbExp=2; IntAct=EBI-523590, EBI-473291; Q8NC51:SERBP1; NbExp=5; IntAct=EBI-523590, EBI-523558;
SUBCELLULAR LOCATION: Nucleus. Cytoplasm, cytoskeleton, centrosome. Note=Associates with centrosomes in interphase and mitosis.
TISSUE SPECIFICITY: Widely expressed.
MISCELLANEOUS: One of the main antigens reacting with anti-MI-2 positive sera of dermatomyositis.
SIMILARITY: Belongs to the SNF2/RAD54 helicase family.
SIMILARITY: Contains 2 chromo domains.
SIMILARITY: Contains 1 helicase ATP-binding domain.
SIMILARITY: Contains 1 helicase C-terminal domain.
SIMILARITY: Contains 2 PHD-type zinc fingers.
SEQUENCE CAUTION: Sequence=AAB87383.1; Type=Miscellaneous discrepancy; Note=Differs from position 1967 onward for unknown reasons;

-  MalaCards Disease Associations
  MalaCards Gene Search: CHD3
Diseases sorted by gene-association score: dermatomyositis (20)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 67.32 RPKM in Prostate
Total median expression: 1372.62 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
3' UTR -481.301170-0.411 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR012957 - CHD_C2
IPR012958 - CHD_N
IPR023780 - Chromo_domain
IPR000953 - Chromo_domain/shadow
IPR016197 - Chromodomain-like
IPR023779 - Chromodomain_CS
IPR002464 - DNA/RNA_helicase_DEAH_CS
IPR009462 - DUF1086
IPR009463 - DUF1087
IPR014001 - Helicase_ATP-bd
IPR001650 - Helicase_C
IPR009071 - HMG_superfamily
IPR000330 - SNF2_N
IPR019786 - Zinc_finger_PHD-type_CS
IPR011011 - Znf_FYVE_PHD
IPR001965 - Znf_PHD
IPR019787 - Znf_PHD-finger
IPR001841 - Znf_RING
IPR013083 - Znf_RING/FYVE/PHD

Pfam Domains:
PF08074 - CHDCT2 (NUC038) domain
PF08073 - CHDNT (NUC034) domain
PF00385 - Chromo (CHRromatin Organisation MOdifier) domain
PF06461 - Domain of Unknown Function (DUF1086)
PF06465 - Domain of Unknown Function (DUF1087)
PF00271 - Helicase conserved C-terminal domain
PF00628 - PHD-finger
PF00176 - SNF2 family N-terminal domain

ModBase Predicted Comparative 3D Structure on Q12873
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003677 DNA binding
GO:0003723 RNA binding
GO:0004003 ATP-dependent DNA helicase activity
GO:0004386 helicase activity
GO:0004407 histone deacetylase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008270 zinc ion binding
GO:0016787 hydrolase activity
GO:0046872 metal ion binding

Biological Process:
GO:0006325 chromatin organization
GO:0006333 chromatin assembly or disassembly
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0007051 spindle organization
GO:0007098 centrosome cycle
GO:0016575 histone deacetylation
GO:0032508 DNA duplex unwinding

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005815 microtubule organizing center
GO:0005856 cytoskeleton
GO:0016581 NuRD complex


-  Descriptions from all associated GenBank mRNAs
  LF209126 - JP 2014500723-A/16629: Polycomb-Associated Non-Coding RNAs.
MA444703 - JP 2018138019-A/16629: Polycomb-Associated Non-Coding RNAs.
LF212399 - JP 2014500723-A/19902: Polycomb-Associated Non-Coding RNAs.
MA447976 - JP 2018138019-A/19902: Polycomb-Associated Non-Coding RNAs.
LF213603 - JP 2014500723-A/21106: Polycomb-Associated Non-Coding RNAs.
MA449180 - JP 2018138019-A/21106: Polycomb-Associated Non-Coding RNAs.
LF326321 - JP 2014500723-A/133824: Polycomb-Associated Non-Coding RNAs.
MA561898 - JP 2018138019-A/133824: Polycomb-Associated Non-Coding RNAs.
BC156472 - Synthetic construct Homo sapiens clone IMAGE:100062993, MGC:190656 chromodomain helicase DNA binding protein 3 (CHD3) mRNA, encodes complete protein.
JD458495 - Sequence 439519 from Patent EP1572962.
JD458496 - Sequence 439520 from Patent EP1572962.
JD458485 - Sequence 439509 from Patent EP1572962.
AF006515 - Homo sapiens CHD3 mRNA, complete cds.
U91543 - Homo sapiens zinc-finger helicase (hZFH) mRNA, complete cds.
U08379 - Human Mi-2 autoantigen 240 kDa protein mRNA, partial cds.
AK296725 - Homo sapiens cDNA FLJ58804 complete cds, highly similar to Chromodomain helicase-DNA-binding protein 3 (EC 3.6.1.-).
AK296937 - Homo sapiens cDNA FLJ59330 complete cds, highly similar to Chromodomain helicase-DNA-binding protein 3 (EC 3.6.1.-).
AK308362 - Homo sapiens cDNA, FLJ98310.
AK125928 - Homo sapiens cDNA FLJ43940 fis, clone TESTI4014175, highly similar to Chromodomain helicase-DNA-binding protein 3 (EC 3.6.1.-).
BC110648 - Homo sapiens chromodomain helicase DNA binding protein 3, mRNA (cDNA clone IMAGE:4536556), partial cds.
AK096555 - Homo sapiens cDNA FLJ39236 fis, clone OCBBF2007892, highly similar to Homo sapiens zinc-finger helicase (hZFH) mRNA.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q12873 (Reactome details) participates in the following event(s):

R-HSA-8956365 ZBED1 (DREF) SUMOylates CHD3 with SUMO1
R-HSA-427404 Recruitment of ERCC6 (CSB), EHMT2 (G9a), and NuRD to the promoter of rRNA gene
R-HSA-8943780 SALL4 recruits NuRD to PTEN gene
R-HSA-6805650 MTA2-NuRD complex deacetylates TP53
R-HSA-427336 TTF1:rRNA promoter:ERCC6:EHMT2 complex dimethylates histone H3 at lysine-9.
R-HSA-3769447 HDAC1/2 containing-complexes deacetylate histones
R-HSA-4551638 SUMOylation of chromatin organization proteins
R-HSA-3108232 SUMO E3 ligases SUMOylate target proteins
R-HSA-427389 ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression
R-HSA-8943724 Regulation of PTEN gene transcription
R-HSA-2990846 SUMOylation
R-HSA-5250913 Positive epigenetic regulation of rRNA expression
R-HSA-6807070 PTEN Regulation
R-HSA-6804758 Regulation of TP53 Activity through Acetylation
R-HSA-597592 Post-translational protein modification
R-HSA-3214815 HDACs deacetylate histones
R-HSA-212165 Epigenetic regulation of gene expression
R-HSA-1257604 PIP3 activates AKT signaling
R-HSA-5633007 Regulation of TP53 Activity
R-HSA-392499 Metabolism of proteins
R-HSA-3247509 Chromatin modifying enzymes
R-HSA-74160 Gene expression (Transcription)
R-HSA-9006925 Intracellular signaling by second messengers
R-HSA-3700989 Transcriptional Regulation by TP53
R-HSA-4839726 Chromatin organization
R-HSA-162582 Signal Transduction
R-HSA-212436 Generic Transcription Pathway
R-HSA-73857 RNA Polymerase II Transcription

-  Other Names for This Gene
  Alternate Gene Symbols: CHD3_HUMAN, D3DTQ9, NM_001005271, Q12873, Q9Y4I0, uc002gjd.1, uc002gjd.2, uc002gjd.3, uc002gjd.4
UCSC ID: uc002gjd.4
RefSeq Accession: NM_001005271
Protein: Q12873 (aka CHD3_HUMAN)
CCDS: CCDS32554.1, CCDS32553.2

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.