Human Gene CHD6 (ENST00000373233.8_7) from GENCODE V47lift37
  Description: chromodomain helicase DNA binding protein 6 (from RefSeq NM_032221.5)
Gencode Transcript: ENST00000373233.8_7
Gencode Gene: ENSG00000124177.16_12
Transcript (Including UTRs)
   Position: hg19 chr20:40,030,723-40,247,016 Size: 216,294 Total Exon Count: 37 Strand: -
Coding Region
   Position: hg19 chr20:40,033,233-40,179,976 Size: 146,744 Coding Exon Count: 36 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr20:40,030,723-40,247,016)mRNA (may differ from genome)Protein (2715 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MalacardsMGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CHD6_HUMAN
DESCRIPTION: RecName: Full=Chromodomain-helicase-DNA-binding protein 6; Short=CHD-6; EC=3.6.4.12; AltName: Full=ATP-dependent helicase CHD6; AltName: Full=Radiation-induced gene B protein;
FUNCTION: Probable transcription regulator.
CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
SUBCELLULAR LOCATION: Nucleus (Probable).
TISSUE SPECIFICITY: Ubiquitous.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
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.
SEQUENCE CAUTION: Sequence=AAK56405.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAN59903.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAB15325.1; Type=Miscellaneous discrepancy; Note=The sequence differs from position 1528 onward for unknown reasons; Sequence=CAI21743.1; Type=Erroneous gene model prediction; Sequence=CAI22254.1; Type=Erroneous gene model prediction;

-  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: CHD6
Diseases sorted by gene-association score: pitt-hopkins syndrome (12), developmental coordination disorder (9), charge syndrome (5)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • C016403 2,4-dinitrotoluene
  • C548651 2-(1'H-indolo-3'-carbonyl)thiazole-4-carboxylic acid methyl ester
  • C532162 2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine
  • D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide
  • C547126 AZM551248
  • D016604 Aflatoxin B1
  • D002509 Cephaloridine
  • D003375 Coumestrol
  • D007657 Ketone Bodies
  • D013749 Tetrachlorodibenzodioxin
          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: 8.42 RPKM in Thyroid
Total median expression: 237.93 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 -12.2061-0.200 Picture PostScript Text
3' UTR -581.102510-0.232 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
IPR006576 - BRK_domain
IPR023780 - Chromo_domain
IPR000953 - Chromo_domain/shadow
IPR016197 - Chromodomain-like
IPR002464 - DNA/RNA_helicase_DEAH_CS
IPR014001 - Helicase_ATP-bd
IPR001650 - Helicase_C
IPR001005 - SANT/Myb
IPR000330 - SNF2_N

Pfam Domains:
PF00176 - SNF2-related domain
PF00271 - Helicase conserved C-terminal domain
PF00385 - Chromo (CHRromatin Organisation MOdifier) domain
PF04851 - Type III restriction enzyme, res subunit

SCOP Domains:
54160 - Chromo domain-like
52540 - P-loop containing nucleoside triphosphate hydrolases
160481 - BRK domain-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2EPB - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q8TD26
FrontTopSide
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 Gene Details  
Gene SorterGene Sorter Gene Sorter  
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0001221 transcription cofactor binding
GO:0003677 DNA binding
GO:0004386 helicase activity
GO:0005524 ATP binding
GO:0008094 DNA-dependent ATPase activity
GO:0016787 hydrolase activity
GO:0016817 hydrolase activity, acting on acid anhydrides

Biological Process:
GO:0006325 chromatin organization
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0016032 viral process
GO:0036091 positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005665 DNA-directed RNA polymerase II, core complex


-  Descriptions from all associated GenBank mRNAs
  AB037756 - Homo sapiens mRNA for KIAA1335 protein, partial cds.
BC172397 - Synthetic construct Homo sapiens clone IMAGE:100069091, MGC:199102 chromodomain helicase DNA binding protein 6 (CHD6) mRNA, encodes complete protein.
AY034072 - Homo sapiens chromodomain helicase DNA binding protein 5 (CHD5) mRNA, complete cds.
AK026022 - Homo sapiens cDNA: FLJ22369 fis, clone HRC06676.
AK091551 - Homo sapiens cDNA FLJ34232 fis, clone FCBBF3026021, moderately similar to Drosophila melanogaster KISMET-L long isoform (kis) mRNA.
AX747054 - Sequence 579 from Patent EP1308459.
AF525085 - Homo sapiens RIGB (RIGB) mRNA, complete cds.
AK296955 - Homo sapiens cDNA FLJ59295 partial cds, highly similar to Chromodomain-helicase-DNA-binding protein 6 (EC 3.6.1.-).
BC039860 - Homo sapiens chromodomain helicase DNA binding protein 6, mRNA (cDNA clone IMAGE:5726781).
BC040016 - Homo sapiens chromodomain helicase DNA binding protein 6, mRNA (cDNA clone IMAGE:5495304), with apparent retained intron.
BC012516 - Homo sapiens chromodomain helicase DNA binding protein 6, mRNA (cDNA clone IMAGE:3875390).
JD261660 - Sequence 242684 from Patent EP1572962.
JD351309 - Sequence 332333 from Patent EP1572962.
BC021907 - Homo sapiens, clone IMAGE:4341355, mRNA, partial cds.
JD184411 - Sequence 165435 from Patent EP1572962.
JD082628 - Sequence 63652 from Patent EP1572962.
JD461151 - Sequence 442175 from Patent EP1572962.
JD367337 - Sequence 348361 from Patent EP1572962.
JD370167 - Sequence 351191 from Patent EP1572962.
JD563516 - Sequence 544540 from Patent EP1572962.
JD555449 - Sequence 536473 from Patent EP1572962.
JD290465 - Sequence 271489 from Patent EP1572962.
JD298467 - Sequence 279491 from Patent EP1572962.
JD246174 - Sequence 227198 from Patent EP1572962.
JD293802 - Sequence 274826 from Patent EP1572962.
JD507455 - Sequence 488479 from Patent EP1572962.
JD359875 - Sequence 340899 from Patent EP1572962.
JD437819 - Sequence 418843 from Patent EP1572962.
JD525012 - Sequence 506036 from Patent EP1572962.
JD130913 - Sequence 111937 from Patent EP1572962.
JD077901 - Sequence 58925 from Patent EP1572962.
JD247730 - Sequence 228754 from Patent EP1572962.
JD549486 - Sequence 530510 from Patent EP1572962.
JD298897 - Sequence 279921 from Patent EP1572962.
JD344919 - Sequence 325943 from Patent EP1572962.
AK098144 - Homo sapiens cDNA FLJ40825 fis, clone TRACH2011290.
CR749575 - Homo sapiens mRNA; cDNA DKFZp686O1331 (from clone DKFZp686O1331).

-  Other Names for This Gene
  Alternate Gene Symbols: CHD5, CHD6_HUMAN, ENST00000373233.1, ENST00000373233.2, ENST00000373233.3, ENST00000373233.4, ENST00000373233.5, ENST00000373233.6, ENST00000373233.7, KIAA1335, NM_032221, Q5JYQ0, Q5TGZ9, Q5TH00, Q5TH01, Q8IZR2, Q8TD26, Q8WTY0, Q9H4H6, Q9H6D4, Q9NTT7, Q9P2L1, RIGB, uc318kpl.1, uc318kpl.2
UCSC ID: ENST00000373233.8_7
RefSeq Accession: NM_032221.5
Protein: Q8TD26 (aka CHD6_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.