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HDAC5 (histone deacetylase 5)

Identity

Alias_symbol (synonym)KIAA0600
NY-CO-9
FLJ90614
Other aliasHD5
HGNC (Hugo) HDAC5
LocusID (NCBI) 10014
Atlas_Id 40806
Location 17q21.31  [Link to chromosome band 17q21]
Location_base_pair Starts at 44076753 and ends at 44123646 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
AFF3 (2q11.2) / HDAC5 (17q21.31)HDAC5 (17q21.31) / HDAC5 (17q21.31)HDAC5 (17q21.31) / PTPN11 (12q24.13)
WSB1 (17q11.1) / HDAC5 (17q21.31)AFF3 2q11.2 / HDAC5 17q21.31

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


External links

Nomenclature
HGNC (Hugo)HDAC5   14068
Cards
Entrez_Gene (NCBI)HDAC5  10014  histone deacetylase 5
AliasesHD5; NY-CO-9
GeneCards (Weizmann)HDAC5
Ensembl hg19 (Hinxton)ENSG00000108840 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000108840 [Gene_View]  chr17:44076753-44123646 [Contig_View]  HDAC5 [Vega]
ICGC DataPortalENSG00000108840
TCGA cBioPortalHDAC5
AceView (NCBI)HDAC5
Genatlas (Paris)HDAC5
WikiGenes10014
SOURCE (Princeton)HDAC5
Genetics Home Reference (NIH)HDAC5
Genomic and cartography
GoldenPath hg38 (UCSC)HDAC5  -     chr17:44076753-44123646 -  17q21.31   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)HDAC5  -     17q21.31   [Description]    (hg19-Feb_2009)
EnsemblHDAC5 - 17q21.31 [CytoView hg19]  HDAC5 - 17q21.31 [CytoView hg38]
Mapping of homologs : NCBIHDAC5 [Mapview hg19]  HDAC5 [Mapview hg38]
OMIM605315   
Gene and transcription
Genbank (Entrez)AB011172 AB177853 AF039691 AF132608 AK027734
RefSeq transcript (Entrez)NM_001015053 NM_005474 NM_139205
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)HDAC5
Cluster EST : UnigeneHs.438782 [ NCBI ]
CGAP (NCI)Hs.438782
Alternative Splicing GalleryENSG00000108840
Gene ExpressionHDAC5 [ NCBI-GEO ]   HDAC5 [ EBI - ARRAY_EXPRESS ]   HDAC5 [ SEEK ]   HDAC5 [ MEM ]
Gene Expression Viewer (FireBrowse)HDAC5 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)10014
GTEX Portal (Tissue expression)HDAC5
Human Protein AtlasENSG00000108840-HDAC5 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9UQL6   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9UQL6  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9UQL6
Splice isoforms : SwissVarQ9UQL6
Catalytic activity : Enzyme3.5.1.98 [ Enzyme-Expasy ]   3.5.1.983.5.1.98 [ IntEnz-EBI ]   3.5.1.98 [ BRENDA ]   3.5.1.98 [ KEGG ]   
PhosPhoSitePlusQ9UQL6
Domains : Interpro (EBI)His_deacetylse    His_deacetylse_dom    Hist_deacetylase_Gln_rich_N    Histone_deAcase_II_euk    Histone_deacetylase_5   
Domain families : Pfam (Sanger)HDAC4_Gln (PF12203)    Hist_deacetyl (PF00850)   
Domain families : Pfam (NCBI)pfam12203    pfam00850   
Conserved Domain (NCBI)HDAC5
DMDM Disease mutations10014
Blocks (Seattle)HDAC5
SuperfamilyQ9UQL6
Human Protein Atlas [tissue]ENSG00000108840-HDAC5 [tissue]
Peptide AtlasQ9UQL6
HPRD09246
IPIIPI00217801   IPI00328289   IPI00556288   IPI00386868   
Protein Interaction databases
DIP (DOE-UCLA)Q9UQL6
IntAct (EBI)Q9UQL6
FunCoupENSG00000108840
BioGRIDHDAC5
STRING (EMBL)HDAC5
ZODIACHDAC5
Ontologies - Pathways
QuickGOQ9UQL6
Ontology : AmiGOhistone deacetylase complex  negative regulation of transcription from RNA polymerase II promoter  negative regulation of transcription from RNA polymerase II promoter  RNA polymerase III transcription factor binding  core promoter binding  chromatin binding  histone deacetylase activity  protein kinase C binding  protein binding  nucleus  nucleoplasm  cytoplasm  Golgi apparatus  cytosol  chromatin organization  chromatin remodeling  chromatin silencing  transcription, DNA-templated  protein deacetylation  inflammatory response  transcription factor binding  regulation of myotube differentiation  negative regulation of myotube differentiation  response to activity  histone deacetylation  nuclear speck  neuron differentiation  B cell differentiation  NAD-dependent histone deacetylase activity (H3-K14 specific)  cellular response to insulin stimulus  protein deacetylase activity  regulation of gene expression, epigenetic  B cell activation  response to cocaine  response to drug  histone deacetylase binding  protein complex  regulation of protein binding  transcription regulatory region DNA binding  negative regulation of transcription, DNA-templated  positive regulation of transcription from RNA polymerase II promoter  metal ion binding  positive regulation of sequence-specific DNA binding transcription factor activity  repressing transcription factor binding  histone H3 deacetylation  cellular response to lipopolysaccharide  negative regulation of cell migration involved in sprouting angiogenesis  regulation of histone H3-K9 acetylation  
Ontology : EGO-EBIhistone deacetylase complex  negative regulation of transcription from RNA polymerase II promoter  negative regulation of transcription from RNA polymerase II promoter  RNA polymerase III transcription factor binding  core promoter binding  chromatin binding  histone deacetylase activity  protein kinase C binding  protein binding  nucleus  nucleoplasm  cytoplasm  Golgi apparatus  cytosol  chromatin organization  chromatin remodeling  chromatin silencing  transcription, DNA-templated  protein deacetylation  inflammatory response  transcription factor binding  regulation of myotube differentiation  negative regulation of myotube differentiation  response to activity  histone deacetylation  nuclear speck  neuron differentiation  B cell differentiation  NAD-dependent histone deacetylase activity (H3-K14 specific)  cellular response to insulin stimulus  protein deacetylase activity  regulation of gene expression, epigenetic  B cell activation  response to cocaine  response to drug  histone deacetylase binding  protein complex  regulation of protein binding  transcription regulatory region DNA binding  negative regulation of transcription, DNA-templated  positive regulation of transcription from RNA polymerase II promoter  metal ion binding  positive regulation of sequence-specific DNA binding transcription factor activity  repressing transcription factor binding  histone H3 deacetylation  cellular response to lipopolysaccharide  negative regulation of cell migration involved in sprouting angiogenesis  regulation of histone H3-K9 acetylation  
Pathways : BIOCARTAControl of skeletal myogenesis by HDAC & calcium/calmodulin-dependent kinase (CaMK) [Genes]    CARM1 and Regulation of the Estrogen Receptor [Genes]    Regulation of PGC-1a [Genes]    METS affect on Macrophage Differentiation [Genes]   
Pathways : KEGGAlcoholism    Epstein-Barr virus infection    Viral carcinogenesis   
NDEx NetworkHDAC5
Atlas of Cancer Signalling NetworkHDAC5
Wikipedia pathwaysHDAC5
Orthology - Evolution
OrthoDB10014
GeneTree (enSembl)ENSG00000108840
Phylogenetic Trees/Animal Genes : TreeFamHDAC5
HOVERGENQ9UQL6
HOGENOMQ9UQL6
Homologs : HomoloGeneHDAC5
Homology/Alignments : Family Browser (UCSC)HDAC5
Gene fusions - Rearrangements
Fusion : MitelmanAFF3/HDAC5 [2q11.2/17q21.31]  [t(2;17)(q11;q21)]  
Fusion: TCGA_MDACCAFF3 2q11.2 HDAC5 17q21.31 PRAD
Tumor Fusion PortalHDAC5
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerHDAC5 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)HDAC5
dbVarHDAC5
ClinVarHDAC5
1000_GenomesHDAC5 
Exome Variant ServerHDAC5
ExAC (Exome Aggregation Consortium)ENSG00000108840
GNOMAD BrowserENSG00000108840
Genetic variants : HAPMAP10014
Genomic Variants (DGV)HDAC5 [DGVbeta]
DECIPHERHDAC5 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisHDAC5 
Mutations
ICGC Data PortalHDAC5 
TCGA Data PortalHDAC5 
Broad Tumor PortalHDAC5
OASIS PortalHDAC5 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICHDAC5  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDHDAC5
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch HDAC5
DgiDB (Drug Gene Interaction Database)HDAC5
DoCM (Curated mutations)HDAC5 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)HDAC5 (select a term)
intoGenHDAC5
Cancer3DHDAC5(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM605315   
Orphanet
DisGeNETHDAC5
MedgenHDAC5
Genetic Testing Registry HDAC5
NextProtQ9UQL6 [Medical]
TSGene10014
GENETestsHDAC5
Target ValidationHDAC5
Huge Navigator HDAC5 [HugePedia]
snp3D : Map Gene to Disease10014
BioCentury BCIQHDAC5
ClinGenHDAC5
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD10014
Chemical/Pharm GKB GenePA29230
Clinical trialHDAC5
Miscellaneous
canSAR (ICR)HDAC5 (select the gene name)
Probes
Litterature
PubMed159 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineHDAC5
EVEXHDAC5
GoPubMedHDAC5
iHOPHDAC5
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Nov 21 14:15:52 CET 2017

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