Human Gene CHD3 (ENST00000330494.12_11) from GENCODE V47lift37
  Description: chromodomain helicase DNA binding protein 3, transcript variant 1 (from RefSeq NM_001005273.3)
Gencode Transcript: ENST00000330494.12_11
Gencode Gene: ENSG00000170004.19_21
Transcript (Including UTRs)
   Position: hg19 chr17:7,792,107-7,816,073 Size: 23,967 Total Exon Count: 40 Strand: +
Coding Region
   Position: hg19 chr17:7,792,319-7,814,903 Size: 22,585 Coding Exon Count: 40 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:7,792,107-7,816,073)mRNA (may differ from genome)Protein (2000 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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UniProtKBWikipediaBioGrid CRISPR DB

-  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;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  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
5' UTR -57.70212-0.272 Picture PostScript Text
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:
PF00176 - SNF2-related domain
PF00271 - Helicase conserved C-terminal domain
PF00385 - Chromo (CHRromatin Organisation MOdifier) domain
PF00628 - PHD-finger
PF04851 - Type III restriction enzyme, res subunit
PF06461 - Domain of Unknown Function (DUF1086)
PF06465 - Domain of Unknown Function (DUF1087)
PF08073 - CHDNT (NUC034) domain
PF08074 - CHDCT2 (NUC038) domain
PF11496 - Class II histone deacetylase complex subunits 2 and 3

SCOP Domains:
47095 - HMG-box
109854 - DinB/YfiT-like putative metalloenzymes
46689 - Homeodomain-like
54160 - Chromo domain-like
52540 - P-loop containing nucleoside triphosphate hydrolases
57850 - RING/U-box
57903 - FYVE/PHD zinc finger

ModBase Predicted Comparative 3D Structure on Q12873
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  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
  BC156472 - Synthetic construct Homo sapiens clone IMAGE:100062993, MGC:190656 chromodomain helicase DNA binding protein 3 (CHD3) mRNA, encodes complete protein.
AF006515 - Homo sapiens CHD3 mRNA, complete cds.
JD565791 - Sequence 546815 from Patent EP1572962.
U91543 - Homo sapiens zinc-finger helicase (hZFH) mRNA, complete cds.
JD210331 - Sequence 191355 from Patent EP1572962.
JD126569 - Sequence 107593 from Patent EP1572962.
JD554448 - Sequence 535472 from Patent EP1572962.
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, E9PG89, ENST00000330494.1, ENST00000330494.10, ENST00000330494.11, ENST00000330494.2, ENST00000330494.3, ENST00000330494.4, ENST00000330494.5, ENST00000330494.6, ENST00000330494.7, ENST00000330494.8, ENST00000330494.9, NM_001005273, Q12873, Q9Y4I0, uc317sze.1, uc317sze.2
UCSC ID: ENST00000330494.12_11
RefSeq Accession: NM_001005273.3
Protein: Q12873 (aka CHD3_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

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