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Aliases for CHD6 Gene

Aliases for CHD6 Gene

  • Chromodomain Helicase DNA Binding Protein 6 2 3 5
  • Radiation-Induced Gene B Protein 3 4
  • ATP-Dependent Helicase CHD6 3 4
  • CHD-6 3 4
  • CHD5 3 4
  • RIGB 3 4
  • Helicase C-Terminal Domain- And SNF2 N-Terminal Domain-Containing Protein 3
  • Chromodomain-Helicase-DNA-Binding Protein 6 3
  • EC 3.6.4.12 4
  • KIAA1335 4
  • EC 3.6.1 61

External Ids for CHD6 Gene

Previous GeneCards Identifiers for CHD6 Gene

  • GC20M039721
  • GC20M040669
  • GC20M040716
  • GC20M039464
  • GC20M040030
  • GC20M036768

Summaries for CHD6 Gene

Entrez Gene Summary for CHD6 Gene

  • This gene encodes a member of the SNF2/RAD54 helicase protein family. The encoded protein contains two chromodomains, a helicase domain, and an ATPase domain. Several multi-subunit protein complexes remodel chromatin to allow patterns of cell type-specific gene expression, and the encoded protein is thought to be a core member of one or more of these chromatin remodeling complexes. The encoded protein may function as a transcriptional repressor and is involved in the cellular repression of influenza virus replication. [provided by RefSeq, Jul 2013]

GeneCards Summary for CHD6 Gene

CHD6 (Chromodomain Helicase DNA Binding Protein 6) is a Protein Coding gene. Diseases associated with CHD6 include Developmental Coordination Disorder and Pitt-Hopkins Syndrome. GO annotations related to this gene include nucleic acid binding and hydrolase activity. An important paralog of this gene is CHD7.

UniProtKB/Swiss-Prot for CHD6 Gene

  • Probable chromatin-remodeling protein with a DNA-dependent ATPase activity. May play a role in transcription regulation, activating for instance, the transcription of specific genes in response to oxidative stress through interaction with NFE2L2.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CHD6 Gene

Genomics for CHD6 Gene

Regulatory Elements for CHD6 Gene

Enhancers for CHD6 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH20F041579 0.8 Ensembl ENCODE 11.3 +38.3 38334 1.9 ZNF316 ZNF133 CEBPA HLF NR2F6 MAFK CHD6 RPL12P11
GH20F041664 0.7 ENCODE 11.2 -46.3 -46273 0.2 ATF1 USF1 SUZ12 ZBTB40 NFYB ZNF143 FOS THAP11 HCFC1 NFYA LPIN3 CHD6 RNU6-1018P
GH20F041660 0.4 ENCODE 11.2 -41.8 -41783 0.2 GATA3 NFE2 CHD6 RNU6-1018P
GH20F041581 0.3 FANTOM5 11.3 +36.9 36941 0.4 CHD6 EMILIN3 RPL12P11
GH20F041145 1.7 FANTOM5 Ensembl ENCODE 1.6 +465.5 465531 15.5 PKNOX1 ATF1 SIN3A ARID4B YBX1 GATA2 FOS SP5 JUNB REST LPIN3 EMILIN3 ZHX3 PLCG1 CHD6 PLCG1-AS1 MIR6871
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CHD6 on UCSC Golden Path with GeneCards custom track

Promoters for CHD6 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000234654 294 2400 ATF1 PKNOX1 ARID4B SIN3A FEZF1 DMAP1 ZNF48 YY1 GLIS2 ZNF143

Genomic Location for CHD6 Gene

Chromosome:
20
Start:
41,402,101 bp from pter
End:
41,618,494 bp from pter
Size:
216,394 bases
Orientation:
Minus strand

Genomic View for CHD6 Gene

Genes around CHD6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CHD6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CHD6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CHD6 Gene

Proteins for CHD6 Gene

  • Protein details for CHD6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8TD26-CHD6_HUMAN
    Recommended name:
    Chromodomain-helicase-DNA-binding protein 6
    Protein Accession:
    Q8TD26
    Secondary Accessions:
    • Q5JYQ0
    • Q5TGZ9
    • Q5TH00
    • Q5TH01
    • Q8IZR2
    • Q8WTY0
    • Q9H4H6
    • Q9H6D4
    • Q9NTT7
    • Q9P2L1

    Protein attributes for CHD6 Gene

    Size:
    2715 amino acids
    Molecular mass:
    305412 Da
    Quaternary structure:
    • Interacts with NFE2L2; involved in activation of the transcription. May interact with PPARA.
    SequenceCaution:
    • Sequence=AAK56405.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAN59903.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAB15325.1; Type=Miscellaneous discrepancy; Note=The sequence differs from position 1528 onward for unknown reasons.; Evidence={ECO:0000305}; Sequence=CAI21743.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=CAI22254.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for CHD6 Gene

    Alternative splice isoforms for CHD6 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CHD6 Gene

Selected DME Specific Peptides for CHD6 Gene

Q8TD26:
  • VLIFSQMVR
  • INRLDNIC
  • PVPRGRKGK
  • GAEEKIL
  • ILKPMMLRRLK
  • IFDSDWNP
  • KASFVAS
  • KASLKLG
  • DEMGLGKT
  • SRQMIQQYEM
  • FCEEDIDQIL
  • DEAHRLK
  • TGTPLQN
  • ETIIEVELT
  • YRLITRNSYEREM
  • LDILEDY
  • ECFRVEKNLL
  • MGLGKTIQ
  • FLEPSQFPSE
  • GIHGPFL
  • DSDWNPQ
  • QKKYYRAILE
  • RADPALCFLE
  • FNPDYVE
  • ITTFEMIL
  • AGGLGINL
  • PSSFQES
  • RCHRIGQ
  • KAVKVYRL
  • YLVKWCSLPYE
  • RRTHTITI
  • CNKVLLRVRMLY
  • DKLLPKL
  • NWEREFRTWT
  • LLIGVFK
  • NTMMELRKCCNHPYLI
  • PLSTITNW

Post-translational modifications for CHD6 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for CHD6 Gene

Gene Families for CHD6 Gene

Suggested Antigen Peptide Sequences for CHD6 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q8TD26

UniProtKB/Swiss-Prot:

CHD6_HUMAN :
  • Contains 2 chromo domains.
  • Belongs to the SNF2/RAD54 helicase family.
Domain:
  • Contains 2 chromo domains.
  • Contains 1 helicase ATP-binding domain.
  • Contains 1 helicase C-terminal domain.
  • Contains 1 Myb-like domain.
Family:
  • Belongs to the SNF2/RAD54 helicase family.
genes like me logo Genes that share domains with CHD6: view

Function for CHD6 Gene

Molecular function for CHD6 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
ATP + H(2)O = ADP + phosphate.
UniProtKB/Swiss-Prot Function:
Probable chromatin-remodeling protein with a DNA-dependent ATPase activity. May play a role in transcription regulation, activating for instance, the transcription of specific genes in response to oxidative stress through interaction with NFE2L2.

Enzyme Numbers (IUBMB) for CHD6 Gene

Gene Ontology (GO) - Molecular Function for CHD6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001221 transcription cofactor binding IPI 16314513
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0004386 helicase activity IEA --
GO:0005524 ATP binding IEA --
genes like me logo Genes that share ontologies with CHD6: view
genes like me logo Genes that share phenotypes with CHD6: view

Animal Models for CHD6 Gene

MGI Knock Outs for CHD6:

Animal Model Products

miRNA for CHD6 Gene

miRTarBase miRNAs that target CHD6

Inhibitory RNA Products

Flow Cytometry Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CHD6 Gene

Localization for CHD6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CHD6 Gene

Nucleus, nucleoplasm. Note=Enriched at sites of mRNA synthesis.

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 CHD6 gene
Compartment Confidence
nucleus 5

Gene Ontology (GO) - Cellular Components for CHD6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IEA,IDA 17027977
GO:0005665 colocalizes_with DNA-directed RNA polymerase II, core complex IDA 17027977
genes like me logo Genes that share ontologies with CHD6: view

Pathways & Interactions for CHD6 Gene

No Data Available

Gene Ontology (GO) - Biological Process for CHD6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0016569 covalent chromatin modification IEA --
GO:0036091 positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress IMP 16314513
genes like me logo Genes that share ontologies with CHD6: view

No data available for Pathways by source and SIGNOR curated interactions for CHD6 Gene

Drugs & Compounds for CHD6 Gene

(3) Drugs for CHD6 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
Adenosine triphosphate Approved Nutra 0

(1) Additional Compounds for CHD6 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • Adenosindiphosphorsaeure
  • Adenosine 5'-pyrophosphate
  • Adenosine diphosphate
  • Adenosine pyrophosphate
  • Adenosine-5'-diphosphate
Full agonist, Agonist 58-64-0
genes like me logo Genes that share compounds with CHD6: view

Transcripts for CHD6 Gene

Unigene Clusters for CHD6 Gene

Chromodomain helicase DNA binding protein 6:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CHD6 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b · 6c · 6d ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^
SP1: - - - -
SP2: - - -
SP3: - -
SP4:
SP5: - - - - -
SP6: -
SP7: - - -
SP8:

ExUns: 20 ^ 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30 ^ 31 ^ 32 ^ 33 ^ 34 ^ 35 ^ 36 ^ 37 ^ 38a · 38b ^ 39 ^ 40a · 40b
SP1: -
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:

Relevant External Links for CHD6 Gene

GeneLoc Exon Structure for
CHD6
ECgene alternative splicing isoforms for
CHD6

Expression for CHD6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CHD6 Gene

Protein differential expression in normal tissues from HIPED for CHD6 Gene

This gene is overexpressed in Plasma (24.8), Monocytes (21.1), Peripheral blood mononuclear cells (11.8), and Lung (7.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for CHD6 Gene



Protein tissue co-expression partners for CHD6 Gene

NURSA nuclear receptor signaling pathways regulating expression of CHD6 Gene:

CHD6

SOURCE GeneReport for Unigene cluster for CHD6 Gene:

Hs.740645

mRNA Expression by UniProt/SwissProt for CHD6 Gene:

Q8TD26-CHD6_HUMAN
Tissue specificity: Widely expressed.
genes like me logo Genes that share expression patterns with CHD6: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for CHD6 Gene

Orthologs for CHD6 Gene

This gene was present in the common ancestor of animals.

Orthologs for CHD6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CHD6 34 35
  • 99.74 (n)
dog
(Canis familiaris)
Mammalia CHD6 34 35
  • 89.76 (n)
mouse
(Mus musculus)
Mammalia Chd6 34 16 35
  • 87.48 (n)
rat
(Rattus norvegicus)
Mammalia Chd6 34
  • 87.04 (n)
cow
(Bos Taurus)
Mammalia CHD6 34 35
  • 85.96 (n)
oppossum
(Monodelphis domestica)
Mammalia CHD6 35
  • 81 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CHD6 35
  • 71 (a)
OneToOne
chicken
(Gallus gallus)
Aves CHD6 34 35
  • 72.48 (n)
lizard
(Anolis carolinensis)
Reptilia CHD6 35
  • 68 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia chd6 34
  • 70.64 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.16257 34
zebrafish
(Danio rerio)
Actinopterygii chd6 34
  • 66.1 (n)
CHD6 35
  • 54 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta kis 35
  • 18 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea chd-7 35
  • 25 (a)
OneToMany
Species where no ortholog for CHD6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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 CHD6 Gene

ENSEMBL:
Gene Tree for CHD6 (if available)
TreeFam:
Gene Tree for CHD6 (if available)

Paralogs for CHD6 Gene

Paralogs for CHD6 Gene

(4) SIMAP similar genes for CHD6 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with CHD6: view

Variants for CHD6 Gene

Sequence variations from dbSNP and Humsavar for CHD6 Gene

SNP ID Clin Chr 20 pos Sequence Context AA Info Type
rs61752057 Benign 41,412,230(+) ACAGC(A/G)TGGCC reference, missense
rs1010304 -- 41,473,007(-) AATTC(C/T)TGATA intron-variant
rs1010305 -- 41,472,901(-) CATGG(C/T)GTGGC intron-variant
rs1010306 -- 41,470,029(-) ATATA(C/G)AATAT intron-variant
rs1010901 -- 41,500,590(-) CACCC(C/G)TTTCT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CHD6 Gene

Variant ID Type Subtype PubMed ID
nsv965875 CNV duplication 23825009
nsv833984 CNV loss 17160897
nsv510786 CNV deletion 20534489
nsv478389 CNV novel sequence insertion 20440878
nsv475887 CNV novel sequence insertion 20440878
nsv3382 CNV insertion 18451855
nsv3381 CNV deletion 18451855
nsv178957 CNV deletion 16902084
nsv1064246 CNV loss 25217958
esv3645841 CNV gain 21293372
esv3645840 CNV gain 21293372
esv3645839 CNV gain 21293372
esv3645838 CNV loss 21293372
esv3645837 CNV gain 21293372
esv3369351 CNV insertion 20981092
esv3304036 CNV mobile element insertion 20981092
esv2460578 CNV deletion 19546169

Variation tolerance for CHD6 Gene

Residual Variation Intolerance Score: 1.25% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.93; 74.48% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CHD6 Gene

Human Gene Mutation Database (HGMD)
CHD6
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CHD6

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CHD6 Gene

Disorders for CHD6 Gene

MalaCards: The human disease database

(2) MalaCards diseases for CHD6 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
developmental coordination disorder
  • motor skills disorders
pitt-hopkins syndrome
  • pallister-hall syndrome
- elite association - COSMIC cancer census association via MalaCards
Search CHD6 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

CHD6_HUMAN
  • Note=A chromosomal aberration disrupting CHD6 has been found in a patient with mild to moderate mental retardation and minor facial anomalies. Translocation t(18;20)(q21.1;q11.2) with TCF4 producing a CHD6-TCF4 fusion transcript (PubMed:18627065). {ECO:0000269 PubMed:18627065}.

Relevant External Links for CHD6

Genetic Association Database (GAD)
CHD6
Human Genome Epidemiology (HuGE) Navigator
CHD6
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CHD6
genes like me logo Genes that share disorders with CHD6: view

No data available for Genatlas for CHD6 Gene

Publications for CHD6 Gene

  1. CHD5 defines a new subfamily of chromodomain-SWI2/SNF2-like helicases. (PMID: 11889561) Schuster E.F. … Stoeger R.J. (Mamm. Genome 2002) 2 3 4 64
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  3. Disruption of the TCF4 gene in a girl with mental retardation but without the classical Pitt-Hopkins syndrome. (PMID: 18627065) Kalscheuer V.M. … Ropers H.H. (Am. J. Med. Genet. A 2008) 4 22 64
  4. CHD6 is a DNA-dependent ATPase and localizes at nuclear sites of mRNA synthesis. (PMID: 17027977) Lutz T. … Nieto A. (FEBS Lett. 2006) 3 4 64
  5. The carboxy-terminal Neh3 domain of Nrf2 is required for transcriptional activation. (PMID: 16314513) Nioi P. … Pickett C.B. (Mol. Cell. Biol. 2005) 3 4 64

Products for CHD6 Gene

Sources for CHD6 Gene

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