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Aliases for CHD5 Gene

Aliases for CHD5 Gene

  • Chromodomain Helicase DNA Binding Protein 5 2 3
  • ATP-Dependent Helicase CHD5 3 4
  • CHD-5 3 4
  • Chromodomain-Helicase-DNA-Binding Protein 5 3
  • EC 3.6.4.12 4
  • KIAA0444 4
  • EC 3.6.1 63

External Ids for CHD5 Gene

Previous GeneCards Identifiers for CHD5 Gene

  • GC01M005970
  • GC01M005758
  • GC01M005871
  • GC01M006096
  • GC03U900582
  • GC01M005310

Summaries for CHD5 Gene

Entrez Gene Summary for CHD5 Gene

  • This gene encodes a member of the chromodomain helicase DNA-binding protein family. Members of this family are characterized by a chromodomain, a helicase ATP-binding domain and an additional functional domain. This gene encodes a neuron-specific protein that may function in chromatin remodeling and gene transcription. This gene is a potential tumor suppressor gene that may play a role in the development of neuroblastoma. [provided by RefSeq, Feb 2012]

GeneCards Summary for CHD5 Gene

CHD5 (Chromodomain Helicase DNA Binding Protein 5) is a Protein Coding gene. Diseases associated with CHD5 include neuroblastoma. GO annotations related to this gene include ATP-dependent helicase activity. An important paralog of this gene is CHD1.

UniProtKB/Swiss-Prot for CHD5 Gene

  • Chromatin-remodeling protein that binds DNA through histones and regulates gene transcription. May specifically recognize and bind trimethylated Lys-27 (H3K27me3) and non-methylated Lys-4 of histone H3. Plays a role in the development of the nervous system by activating the expression of genes promoting neuron terminal differentiation. In parallel, it may also positively regulate the trimethylation of histone H3 at Lys-27 thereby specifically repressing genes that promote the differentiation into non-neuronal cell lineages. Tumor suppressor, it regulates the expression of genes involved in cell proliferation and differentiation. Downstream activated genes may include CDKN2A that positively regulates the p53/TP53 pathway, which in turn, prevents cell proliferation. In spermatogenesis, it probably regulates histone hyperacetylation and the replacement of histones by transition proteins in chromatin, a crucial step in the condensation of spermatid chromatin and the production of functional spermatozoa.

Gene Wiki entry for CHD5 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CHD5 Gene

Genomics for CHD5 Gene

Regulatory Elements for CHD5 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for CHD5 Gene

Start:
6,101,787 bp from pter
End:
6,180,134 bp from pter
Size:
78,348 bases
Orientation:
Minus strand

Genomic View for CHD5 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for CHD5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CHD5 Gene

Proteins for CHD5 Gene

  • Protein details for CHD5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8TDI0-CHD5_HUMAN
    Recommended name:
    Chromodomain-helicase-DNA-binding protein 5
    Protein Accession:
    Q8TDI0
    Secondary Accessions:
    • O75032
    • Q5TG89
    • Q7LGH2
    • Q9UFR9

    Protein attributes for CHD5 Gene

    Size:
    1954 amino acids
    Molecular mass:
    223050 Da
    Quaternary structure:
    • May be part of a nucleosome remodeling and histone deacetylation, NuRD-like, complex composed at least of GATAD2B, HDAC1, HDAC2 and MTA3.

neXtProt entry for CHD5 Gene

Proteomics data for CHD5 Gene at MOPED

Post-translational modifications for CHD5 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CHD5 Gene

Domains for CHD5 Gene

Gene Families for CHD5 Gene

HGNC:
  • PHF :Zinc fingers, PHD-type

Suggested Antigen Peptide Sequences for CHD5 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q8TDI0

UniProtKB/Swiss-Prot:

CHD5_HUMAN :
  • Q8TDI0
Domain:
  • The PHD domains mediate specific binding to histone H3 unmethylated at Lys-4 and may preferentially recruit the protein to transcriptionally inactive genes.
  • The chromo domains mediate specific binding to histone H3 trimethylated at Lys-27 (H3K27me3) and may be required in neuron differentiation for proper gene regulation.
  • Contains 2 chromo domains.
  • Contains 1 helicase ATP-binding domain.
  • Contains 1 helicase C-terminal domain.
Family:
  • Belongs to the SNF2/RAD54 helicase family.
Similarity:
  • Contains 2 PHD-type zinc fingers.
genes like me logo Genes that share domains with CHD5: view

Function for CHD5 Gene

Molecular function for CHD5 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
ATP + H(2)O = ADP + phosphate
UniProtKB/Swiss-Prot Function:
Chromatin-remodeling protein that binds DNA through histones and regulates gene transcription. May specifically recognize and bind trimethylated Lys-27 (H3K27me3) and non-methylated Lys-4 of histone H3. Plays a role in the development of the nervous system by activating the expression of genes promoting neuron terminal differentiation. In parallel, it may also positively regulate the trimethylation of histone H3 at Lys-27 thereby specifically repressing genes that promote the differentiation into non-neuronal cell lineages. Tumor suppressor, it regulates the expression of genes involved in cell proliferation and differentiation. Downstream activated genes may include CDKN2A that positively regulates the p53/TP53 pathway, which in turn, prevents cell proliferation. In spermatogenesis, it probably regulates histone hyperacetylation and the replacement of histones by transition proteins in chromatin, a crucial step in the condensation of spermatid chromatin and the production of functional spermatozoa.

Enzyme Numbers (IUBMB) for CHD5 Gene

Gene Ontology (GO) - Molecular Function for CHD5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0005515 protein binding --
GO:0005524 ATP binding IEA --
GO:0008026 ATP-dependent helicase activity IEA --
GO:0008270 zinc ion binding IEA --
genes like me logo Genes that share ontologies with CHD5: view

Phenotypes for CHD5 Gene

GenomeRNAi human phenotypes for CHD5:
genes like me logo Genes that share phenotypes with CHD5: view

Animal Model Products

miRNA for CHD5 Gene

miRTarBase miRNAs that target CHD5

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for CHD5

In Situ Assay Products

Flow Cytometry Products

No data available for Animal Models , Transcription Factor Targeting and HOMER Transcription for CHD5 Gene

Localization for CHD5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CHD5 Gene

Nucleus. Note=Associates with heterochromatin. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for CHD5 Gene COMPARTMENTS Subcellular localization image for CHD5 gene
Compartment Confidence
nucleus 3

Gene Ontology (GO) - Cellular Components for CHD5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin --
GO:0000792 heterochromatin ISS --
GO:0005634 nucleus IDA 21931736
GO:0016020 membrane IDA 19946888
GO:0016581 NuRD complex ISS --
genes like me logo Genes that share ontologies with CHD5: view

Pathways for CHD5 Gene

SuperPathways for CHD5 Gene

No Data Available

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays
    • Epigenetic Chromatin Remodeling Factors in human,mouse,rat

Gene Ontology (GO) - Biological Process for CHD5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006200 obsolete ATP catabolic process --
GO:0006351 transcription, DNA-templated --
GO:0006355 regulation of transcription, DNA-templated --
GO:0006366 transcription from RNA polymerase II promoter IEA --
GO:0008285 negative regulation of cell proliferation ISS --
genes like me logo Genes that share ontologies with CHD5: view

No data available for Pathways by source for CHD5 Gene

Transcripts for CHD5 Gene

Unigene Clusters for CHD5 Gene

Chromodomain helicase DNA binding protein 5:
Representative Sequences:

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for CHD5

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CHD5 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19a · 19b ^ 20a · 20b ^ 21 ^ 22 ^
SP1: - -
SP2: - -
SP3:
SP4:
SP5:

ExUns: 23 ^ 24 ^ 25a · 25b ^ 26 ^ 27 ^ 28a · 28b ^ 29 ^ 30 ^ 31 ^ 32a · 32b ^ 33 ^ 34 ^ 35 ^ 36 ^ 37 ^ 38 ^ 39 ^ 40 ^ 41a · 41b
SP1: -
SP2: - -
SP3: - -
SP4:
SP5:

Relevant External Links for CHD5 Gene

GeneLoc Exon Structure for
CHD5
ECgene alternative splicing isoforms for
CHD5

Expression for CHD5 Gene

mRNA expression in normal human tissues for CHD5 Gene

mRNA differential expression in normal tissues according to GTEx for CHD5 Gene

This gene is overexpressed in Brain - Cortex (8.6), Pituitary (7.1), Brain - Frontal Cortex (BA9) (6.7), and Brain - Anterior cingulate cortex (BA24) (5.9).

Protein differential expression in normal tissues for CHD5 Gene

This gene is overexpressed in Brain (38.7), Synovial fluid (10.1), and Gallbladder (7.6).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for CHD5 Gene

SOURCE GeneReport for Unigene cluster for CHD5 Gene Hs.522898

mRNA Expression by UniProt/SwissProt for CHD5 Gene

Q8TDI0-CHD5_HUMAN
Tissue specificity: Preferentially expressed in total brain, fetal brain, and cerebellum. It is also moderately expressed in the adrenal gland and detected in testis.
genes like me logo Genes that share expressions with CHD5: view

In Situ Assay Products

No data available for Expression partners for CHD5 Gene

Orthologs for CHD5 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for CHD5 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia CHD5 35
  • 92.21 (n)
  • 96.73 (a)
CHD5 36
  • 94 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CHD5 35
  • 91.59 (n)
  • 96.93 (a)
CHD5 36
  • 93 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Chd5 35
  • 88.18 (n)
  • 94.36 (a)
Chd5 16
Chd5 36
  • 95 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Chd5 35
  • 88.67 (n)
  • 95.07 (a)
oppossum
(Monodelphis domestica)
Mammalia CHD5 36
  • 75 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CHD5 36
  • 74 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia CHD5 36
  • 99 (a)
OneToOne
chicken
(Gallus gallus)
Aves CHD5 35
  • 81.18 (n)
  • 88.79 (a)
CHD5 36
  • 90 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CHD5 36
  • 83 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia chd5 35
  • 72.34 (n)
  • 84.97 (a)
zebrafish
(Danio rerio)
Actinopterygii chd5 35
  • 73.22 (n)
  • 81.51 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.11169 35
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012009 35
  • 69.29 (n)
  • 67.75 (a)
fruit fly
(Drosophila melanogaster)
Insecta Mi-2 35
  • 65.2 (n)
  • 64.01 (a)
Chd3 36
  • 58 (a)
ManyToMany
Mi-2 36
  • 53 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea chd-3 36
  • 51 (a)
ManyToMany
let-418 36
  • 49 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CHD1 36
  • 25 (a)
OneToMany
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.4332 35
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8509 36
  • 56 (a)
OneToMany
Species with no ortholog for CHD5:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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 CHD5 Gene

ENSEMBL:
Gene Tree for CHD5 (if available)
TreeFam:
Gene Tree for CHD5 (if available)

Paralogs for CHD5 Gene

Paralogs for CHD5 Gene

genes like me logo Genes that share paralogs with CHD5: view

Variants for CHD5 Gene

Sequence variations from dbSNP and Humsavar for CHD5 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type MAF
rs11587 -- 6,103,081(-) TGGTG(A/C/G)TGTCC utr-variant-3-prime
rs731975 -- 6,162,441(-) TCCCG(G/T)GTCAC intron-variant
rs745758 -- 6,104,620(-) GGGGG(C/G/T)GCAGC utr-variant-3-prime
rs745759 -- 6,104,611(-) GCACT(C/T)GCCTC utr-variant-3-prime
rs746122 -- 6,152,348(+) CTTGC(A/G)TGCTC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CHD5 Gene

Variant ID Type Subtype PubMed ID
nsv871082 CNV Loss 21882294
nsv871226 CNV Loss 21882294
nsv871698 CNV Loss 21882294
nsv461283 CNV Loss 19166990
dgv117n71 CNV Loss 21882294
dgv118n71 CNV Loss 21882294
nsv871817 CNV Loss 21882294
nsv870945 CNV Loss 21882294
nsv470689 CNV Loss 18288195
dgv119n71 CNV Loss 21882294
nsv871337 CNV Loss 21882294
nsv825697 CNV Gain 20364138
esv21998 CNV Gain 19812545
esv2739139 CNV Deletion 23290073
esv2676924 CNV Deletion 23128226
nsv870818 CNV Loss 21882294
nsv831425 CNV Loss 17160897
nsv818555 CNV Loss 17921354
nsv854 CNV Loss 18451855
nsv871123 CNV Loss 21882294
esv2739250 CNV Deletion 23290073
esv2739361 CNV Deletion 23290073
esv2739473 CNV Deletion 23290073
esv2739584 CNV Deletion 23290073

Relevant External Links for CHD5 Gene

HapMap Linkage Disequilibrium report
CHD5
Human Gene Mutation Database (HGMD)
CHD5

PCR Panel Products

  • Copy Number PCR Panels: for CHD5

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CHD5 Gene

Disorders for CHD5 Gene

MalaCards: The human disease database

MalaCards: The human disease database.

Search for CHD5 Gene in MalaCards »

(1) Diseases for CHD5 Gene including...

UniProtKB/Swiss-Prot

CHD5_HUMAN
  • Note=Defects in CHD5 may be a cause of the development of cancers from epithelial, neural and hematopoietic origin. CHD5 is one of the missing genes in the del(1p36), a deletion which is extremely common in this type of cancers. A decrease of its expression, results in increased susceptibility of cells to Ras-mediated transformation in vitro and in vivo (PubMed:17289567). {ECO:0000269 PubMed:17289567}.

Relevant External Links for CHD5

Genetic Association Database (GAD)
CHD5
Human Genome Epidemiology (HuGE) Navigator
CHD5
genes like me logo Genes that share disorders with CHD5: view

No data available for OMIM , University of Copenhagen DISEASES , Novoseek inferred disease relationships and Genatlas for CHD5 Gene

Publications for CHD5 Gene

  1. CHD5, a new member of the chromodomain gene family, is preferentially expressed in the nervous system. (PMID: 12592387) Thompson P.M. … Brodeur G.M. (Oncogene 2003) 2 3 4
  2. Characterization of cDNA clones in size-fractionated cDNA libraries from human brain. (PMID: 9455484) Seki N. … Ohara O. (DNA Res. 1997) 3 4
  3. The quest for the 1p36 tumor suppressor. (PMID: 18413720) Bagchi A. … Mills A.A. (Cancer Res. 2008) 3 23
  4. CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas. (PMID: 18577749) Fujita T. … Brodeur G.M. (J. Natl. Cancer Inst. 2008) 3 23
  5. Chromatin remodeling factor CHD5 is silenced by promoter CpG island hypermethylation in human cancer. (PMID: 18698156) Mulero-Navarro S. … Esteller M. (Epigenetics 2008) 3 23

Products for CHD5 Gene

Sources for CHD5 Gene

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