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Aliases for CHD5 Gene

Aliases for CHD5 Gene

  • Chromodomain Helicase DNA Binding Protein 5 2 3 5
  • 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

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. Among its related pathways are Chromatin Regulation / Acetylation. Gene Ontology (GO) annotations related to this gene include hydrolase activity and hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides. An important paralog of this gene is CHD3.

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

Additional gene information for CHD5 Gene

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

Genomics for CHD5 Gene

GeneHancer (GH) Regulatory Elements for CHD5 Gene

Promoters and enhancers for CHD5 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
GH01J006180 Promoter 0.7 EPDnew 650.7 0.0 -10 0.1 CTCF RFX1 GLIS1 CHD5 GC01M006194
GH01J006182 Enhancer 0.6 ENCODE 650.7 -0.9 -881 0.2 SCRT1 USF1 ZNF10 ZNF335 ZFHX2 NFIC ZNF692 SCRT2 ZNF600 ZBTB26 CHD5 GC01M006194
GH01J006181 Enhancer 0.6 ENCODE 650.7 -1.4 -1398 0.5 ZBTB10 ZNF146 ZFP69B ZNF335 GLIS2 NFIC GLIS1 PATZ1 KLF9 PRDM10 CHD5 GC01M006194 RPL22
GH01J006259 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10.5 -81.9 -81864 4.6 PKNOX1 ATF1 ARID4B SIN3A BRCA1 YY1 GLIS2 KLF7 ATF7 ZNF263 GPR153 GC01P006262 NOL9 ICMT THAP3 LINC00337 ZBTB48 RPL22 RNF207 LOC102724450
GH01J006170 Enhancer 0.9 FANTOM5 Ensembl 21.3 +8.7 8713 1.6 CTCF MAX CEBPG ZIC2 RAD21 HIC1 ZFHX2 POLR2A SMC3 HLF CHD5 KCNAB2 RNF207 ICMT PLEKHG5 LOC105376687
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CHD5 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CHD5 gene promoter:

Genomic Locations for CHD5 Gene

Genomic Locations for CHD5 Gene
chr1:6,101,787-6,180,134
(GRCh38/hg38)
Size:
78,348 bases
Orientation:
Minus strand
chr1:6,161,847-6,240,194
(GRCh37/hg19)

Genomic View for CHD5 Gene

Genes around CHD5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CHD5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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

Post-translational modifications for CHD5 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CHD5 Gene

No data available for DME Specific Peptides for CHD5 Gene

Domains & Families for CHD5 Gene

Gene Families for CHD5 Gene

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

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 :
  • The PHD domains mediate specific binding to histone H3 unmethylated at Lys-4 and may preferentially recruit the protein to transcriptionally inactive genes.
  • Belongs to the SNF2/RAD54 helicase family.
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.
Family:
  • Belongs to the SNF2/RAD54 helicase family.
genes like me logo Genes that share domains with CHD5: view

Function for CHD5 Gene

Molecular function for CHD5 Gene

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.
UniProtKB/Swiss-Prot CatalyticActivity:
ATP + H(2)O = ADP + phosphate.

Enzyme Numbers (IUBMB) for CHD5 Gene

Phenotypes From GWAS Catalog 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:0004386 helicase activity IEA --
GO:0005524 ATP binding IEA --
GO:0016787 hydrolase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with CHD5: view
genes like me logo Genes that share phenotypes with CHD5: view

Animal Models for CHD5 Gene

MGI Knock Outs for CHD5:
  • Chd5 Chd5<tm1.2Gmbr>

Animal Model Products

Clone Products

  • Addgene plasmids for CHD5

No data available for Human Phenotype Ontology , Transcription Factor Targets 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
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 CHD5 gene
Compartment Confidence
nucleus 5
cytosol 4

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (3)
  • Nucleoplasm (3)
  • Cytosol (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CHD5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000792 heterochromatin ISS --
GO:0005634 nucleus IDA,IEA 21931736
GO:0005654 nucleoplasm IDA --
GO:0005829 cytosol IDA --
GO:0016020 membrane HDA 19946888
genes like me logo Genes that share ontologies with CHD5: view

Pathways & Interactions for CHD5 Gene

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

Pathways by source for CHD5 Gene

1 Cell Signaling Technology pathway for CHD5 Gene

Gene Ontology (GO) - Biological Process for CHD5 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:0007283 spermatogenesis IEA --
GO:0007399 nervous system development IEA --
genes like me logo Genes that share ontologies with CHD5: view

No data available for SIGNOR curated interactions for CHD5 Gene

Drugs & Compounds for CHD5 Gene

(3) Drugs for CHD5 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 CHD5 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 CHD5: view

Transcripts for CHD5 Gene

mRNA/cDNA for CHD5 Gene

Unigene Clusters for CHD5 Gene

Chromodomain helicase DNA binding protein 5:
Representative Sequences:

Clone Products

  • Addgene plasmids for CHD5

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 from GTEx, Illumina, BioGPS, and CGAP SAGE for CHD5 Gene

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

This gene is overexpressed in Brain - Cortex (x8.6), Pituitary (x7.1), Brain - Frontal Cortex (BA9) (x6.7), and Brain - Anterior cingulate cortex (BA24) (x5.9).

Protein differential expression in normal tissues from HIPED for CHD5 Gene

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

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CHD5 Gene



NURSA nuclear receptor signaling pathways regulating expression of CHD5 Gene:

CHD5

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.

Evidence on tissue expression from TISSUES for CHD5 Gene

  • Nervous system(4.9)
  • Pancreas(2.2)
genes like me logo Genes that share expression patterns with CHD5: view

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
chimpanzee
(Pan troglodytes)
Mammalia CHD5 34
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia CHD5 34 33
  • 92.21 (n)
OneToOne
dog
(Canis familiaris)
Mammalia CHD5 34 33
  • 91.59 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Chd5 33
  • 88.67 (n)
mouse
(Mus musculus)
Mammalia Chd5 16 34 33
  • 88.18 (n)
oppossum
(Monodelphis domestica)
Mammalia CHD5 34
  • 75 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CHD5 34
  • 74 (a)
OneToOne
chicken
(Gallus gallus)
Aves CHD5 34 33
  • 81.18 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CHD5 34
  • 83 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia chd5 33
  • 72.34 (n)
zebrafish
(Danio rerio)
Actinopterygii chd5 33
  • 73.22 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.11169 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012009 33
  • 69.29 (n)
fruit fly
(Drosophila melanogaster)
Insecta Mi-2 34 33
  • 65.2 (n)
ManyToMany
Chd3 34
  • 58 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea chd-3 34
  • 51 (a)
ManyToMany
let-418 34
  • 49 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CHD1 34
  • 25 (a)
OneToMany
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.4332 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8509 34
  • 56 (a)
OneToMany
Species where no ortholog for CHD5 was found in the sources mined by GeneCards:
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for CHD5: view image

Paralogs for CHD5 Gene

Paralogs for CHD5 Gene

(18) SIMAP similar genes for CHD5 Gene using alignment to 7 proteins:

  • CHD5_HUMAN
  • F2Z2R5_HUMAN
  • F6T542_HUMAN
  • K7EMC0_HUMAN
  • K7EMY3_HUMAN
  • K7ESA5_HUMAN
  • Q5TG85_HUMAN
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 Variation AA Info Type
VAR_035475 A breast cancer sample p.Val45Met
VAR_035476 A breast cancer sample p.Asp119Asn
VAR_035477 A breast cancer sample p.Arg667Gly
rs1000066166 -- 6,166,820(-) T/C intron_variant
rs1000147571 -- 6,170,661(-) G/A intron_variant

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

Variant ID Type Subtype PubMed ID
dgv75n54 CNV loss 21841781
dgv76n54 CNV gain 21841781
esv21998 CNV gain 19812545
esv2676924 CNV deletion 23128226
esv2739139 CNV deletion 23290073
esv2739250 CNV deletion 23290073
esv2739361 CNV deletion 23290073
esv2739473 CNV deletion 23290073
esv2739584 CNV deletion 23290073
esv3383496 CNV duplication 20981092
nsv1076981 CNV deletion 25765185
nsv1115334 CNV duplication 24896259
nsv1143431 CNV deletion 24896259
nsv1148543 CNV duplication 26484159
nsv1149305 CNV duplication 26484159
nsv461283 CNV loss 19166990
nsv470689 CNV loss 18288195
nsv545229 CNV loss 21841781
nsv545232 CNV gain 21841781
nsv545235 CNV loss 21841781
nsv545236 CNV loss 21841781
nsv818555 CNV loss 17921354
nsv825697 CNV gain 20364138
nsv831425 CNV loss 17160897
nsv854 CNV deletion 18451855

Variation tolerance for CHD5 Gene

Residual Variation Intolerance Score: 0.825% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.58; 44.76% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CHD5 Gene

Human Gene Mutation Database (HGMD)
CHD5
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CHD5

SNP Genotyping and Copy Number Assay Products

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

Disorders for CHD5 Gene

MalaCards: The human disease database

(1) MalaCards diseases for CHD5 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
neuroblastoma
  • neuroblastoma, susceptibility to
- elite association - COSMIC cancer census association via MalaCards
Search CHD5 in MalaCards View complete list of genes associated with diseases

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}.

Additional Disease Information for CHD5

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 CHD5: view

No data available for 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 PM … Brodeur GM (Oncogene 2003) 2 3 4 58
  2. CHD5 is required for neurogenesis and has a dual role in facilitating gene expression and polycomb gene repression. (PMID: 23948251) Egan CM … Bracken AP (Developmental cell 2013) 3 4 58
  3. CHD5, a brain-specific paralog of Mi2 chromatin remodeling enzymes, regulates expression of neuronal genes. (PMID: 21931736) Potts RC … Pazin MJ (PloS one 2011) 3 4 58
  4. CHD5 is down-regulated through promoter hypermethylation in gastric cancer. (PMID: 19840376) Wang X … Lam YW (Journal of biomedical science 2009) 3 22 58
  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 22 58

Products for CHD5 Gene

Sources for CHD5 Gene

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