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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

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 Influenza and Pitt-Hopkins Syndrome. Gene Ontology (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

  • DNA-dependent ATPase that plays a role in chromatin remodeling. Regulates transcription by disrupting nucleosomes in a largely non-sliding manner which strongly increases the accessibility of chromatin (PubMed:28533432). Activates transcription of specific genes in response to oxidative stress through interaction with NFE2L2.

  • (Microbial infection) Acts as a transcriptional repressor of different viruses including influenza virus or papillomavirus. During influenza virus infection, the viral polymerase complex localizes CHD6 to inactive chromatin where it gets degraded in a proteasome independent-manner.

Additional gene information for CHD6 Gene

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

Genomics for CHD6 Gene

GeneHancer (GH) Regulatory Elements for CHD6 Gene

Promoters and enhancers for CHD6 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
GH20J041616 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE 650.7 0.0 -20 3.7 PKNOX1 ARID4B NEUROD1 SIN3A DMAP1 YY1 ZNF143 FOS SP3 SP5 CHD6 RNU6-1018P
GH20J041001 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 30.8 +612.6 612555 9.1 CLOCK MLX YBX1 FEZF1 DMAP1 SLC30A9 ZNF143 NFYC MEF2D SSRP1 LOC105372621 CHD6 PLCG1 MAFB TOP1 PLCG1-AS1 LPIN3 EMILIN3 GC20M041019 LOC100128988
GH20J041136 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 20 +478.6 478568 7.5 HDGF PKNOX1 CLOCK MLX ARNT ARID4B NEUROD1 SIN3A DMAP1 ZBTB7B PLCG1 PLCG1-AS1 CHD6 LPIN3 GC20P041111 MIR6871
GH20J041692 Enhancer 1.3 Ensembl ENCODE 30.9 -75.1 -75111 2.8 CLOCK MLX ZFP64 YBX1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 TOP1 CHD6 LPIN3 PLCG1 RNU6-1018P GC20M041699
GH20J040686 Promoter/Enhancer 1.7 Ensembl ENCODE dbSUPER 14.9 +930.1 930118 4.8 PKNOX1 SIN3A ZBTB7B ZNF48 YY1 GLIS2 ZNF143 KLF7 SP3 RXRA GC20M040687 MAFB CHD6 PLCG1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CHD6 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CHD6 gene promoter:
  • Pax-4a
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • ER-alpha
  • TBP
  • Evi-1

Genomic Locations for CHD6 Gene

Genomic Locations for CHD6 Gene
chr20:41,402,101-41,618,494
(GRCh38/hg38)
Size:
216,394 bases
Orientation:
Minus strand
chr20:40,030,741-40,247,133
(GRCh37/hg19)
Size:
216,393 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.
    • (Microbial infection) Interacts with the influenza A polymerase complex composed fo PB1, PB2 and PA (PubMed:21899694). Interacts (via N-terminus) with human papillomavirus protein E8^E2C (via C-terminus); this interaction induces transcriptional repression of the viral genome (PubMed:20631145).
    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

Post-translational modifications for CHD6 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CHD6 Gene

Domains & Families for CHD6 Gene

Gene Families for CHD6 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Plasma proteins
  • Potential drug targets
  • Predicted intracellular proteins

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 :
  • Belongs to the SNF2/RAD54 helicase family.
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 Function:
DNA-dependent ATPase that plays a role in chromatin remodeling. Regulates transcription by disrupting nucleosomes in a largely non-sliding manner which strongly increases the accessibility of chromatin (PubMed:28533432). Activates transcription of specific genes in response to oxidative stress through interaction with NFE2L2.
UniProtKB/Swiss-Prot Function:
(Microbial infection) Acts as a transcriptional repressor of different viruses including influenza virus or papillomavirus. During influenza virus infection, the viral polymerase complex localizes CHD6 to inactive chromatin where it gets degraded in a proteasome independent-manner.
UniProtKB/Swiss-Prot CatalyticActivity:
ATP + H(2)O = ADP + phosphate.

Enzyme Numbers (IUBMB) for CHD6 Gene

Phenotypes From GWAS Catalog 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:0003677 DNA binding IEA --
GO:0004386 helicase activity IEA --
GO:0005515 protein binding 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:
  • Chd6 Chd6<tm1.2Fier>

Animal Model Products

miRNA for CHD6 Gene

miRTarBase miRNAs that target CHD6

Clone 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 (PubMed:17027977). During influenza A virus infection, localizes to inactive chromatin. {ECO:0000269 PubMed:17027977, ECO:0000269 PubMed:21899694}.

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

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for CHD6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA,IEA 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:0006325 chromatin organization IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0016032 viral process 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
ATP Investigational Nutra Agonist, Activator, Full agonist, Antagonist, Potentiation, Pore Blocker 0

(1) Additional Compounds for CHD6 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 CHD6: view

Transcripts for CHD6 Gene

Unigene Clusters for CHD6 Gene

Chromodomain helicase DNA binding protein 6:
Representative Sequences:

Clone 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 CGAP 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, 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.

Evidence on tissue expression from TISSUES for CHD6 Gene

  • Nervous system(4.7)
genes like me logo Genes that share expression patterns with CHD6: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 33
  • 99.74 (n)
OneToOne
dog
(Canis familiaris)
Mammalia CHD6 34 33
  • 89.76 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Chd6 16 34 33
  • 87.48 (n)
rat
(Rattus norvegicus)
Mammalia Chd6 33
  • 87.04 (n)
cow
(Bos Taurus)
Mammalia CHD6 34 33
  • 85.96 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia CHD6 34
  • 81 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CHD6 34
  • 71 (a)
OneToOne
chicken
(Gallus gallus)
Aves CHD6 34 33
  • 72.48 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CHD6 34
  • 68 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia chd6 33
  • 70.64 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.16257 33
zebrafish
(Danio rerio)
Actinopterygii chd6 33
  • 66.1 (n)
CHD6 34
  • 54 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta kis 34
  • 18 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea chd-7 34
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for CHD6: view image

Paralogs for CHD6 Gene

Paralogs for CHD6 Gene

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

  • CHD6_HUMAN
  • C9JFU2_HUMAN
  • H7C294_HUMAN
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 Variation AA Info Type
rs61752057 benign, not specified 41,412,230(-) G/A coding_sequence_variant, genic_downstream_transcript_variant, missense_variant
rs1000006849 -- 41,450,418(-) A/C genic_upstream_transcript_variant, intron_variant
rs1000007254 -- 41,618,149(-) G/C genic_upstream_transcript_variant, intron_variant
rs1000068173 -- 41,539,904(-) T/C genic_upstream_transcript_variant, intron_variant
rs1000075200 -- 41,580,140(-) T/C genic_upstream_transcript_variant, intron_variant

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

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

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)

Additional Variant Information for CHD6 Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for CHD6 Gene

MalaCards: The human disease database

(4) MalaCards diseases for CHD6 Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
influenza
  • flu
pitt-hopkins syndrome
  • phs
developmental coordination disorder
  • motor skills disorders
charge syndrome
  • charge association--coloboma, heart anomaly, choanal atresia, retardation, genital and ear anomalies
- 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}.

Additional Disease Information for CHD6

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 EF … Stöger R (Mammalian genome : official journal of the International Mammalian Genome Society 2002) 2 3 4 58
  2. The ATP-dependent chromatin remodeling enzymes CHD6, CHD7, and CHD8 exhibit distinct nucleosome binding and remodeling activities. (PMID: 28533432) Manning BJ … Yusufzai T (The Journal of biological chemistry 2017) 3 4 58
  3. CHD6, a cellular repressor of influenza virus replication, is degraded in human alveolar epithelial cells and mice lungs during infection. (PMID: 23408615) Alfonso R … Nieto A (Journal of virology 2013) 3 4 58
  4. CHD6 chromatin remodeler is a negative modulator of influenza virus replication that relocates to inactive chromatin upon infection. (PMID: 21899694) Alfonso R … Nieto A (Cellular microbiology 2011) 3 4 58
  5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58

Products for CHD6 Gene

Sources for CHD6 Gene

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