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HDAC5 histone deacetylase 5 [ Homo sapiens (human) ]

Gene ID: 10014, updated on 5-Nov-2017
Official Symbol
HDAC5provided by HGNC
Official Full Name
histone deacetylase 5provided by HGNC
Primary source
HGNC:HGNC:14068
See related
Ensembl:ENSG00000108840 MIM:605315; Vega:OTTHUMG00000181806
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HD5; NY-CO-9
Summary
Histones play a critical role in transcriptional regulation, cell cycle progression, and developmental events. Histone acetylation/deacetylation alters chromosome structure and affects transcription factor access to DNA. The protein encoded by this gene belongs to the class II histone deacetylase/acuc/apha family. It possesses histone deacetylase activity and represses transcription when tethered to a promoter. It coimmunoprecipitates only with HDAC3 family member and might form multicomplex proteins. It also interacts with myocyte enhancer factor-2 (MEF2) proteins, resulting in repression of MEF2-dependent genes. This gene is thought to be associated with colon cancer. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in skin (RPKM 14.0), ovary (RPKM 13.4) and 25 other tissues See more
Orthologs
Location:
17q21.31
Exon count:
30
Annotation release Status Assembly Chr Location
108 current GRCh38.p7 (GCF_000001405.33) 17 NC_000017.11 (44076753..44123646, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (42154121..42201014, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene LSM12 homolog Neighboring gene glucose-6-phosphatase catalytic subunit 3 Neighboring gene uncharacterized LOC105371789 Neighboring gene RNA, U6 small nuclear 131, pseudogene Neighboring gene chromosome 17 open reading frame 53

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

NHGRI GWAS Catalog

Description
Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies.
NHGRI GWA Catalog
  • Alcoholism, organism-specific biosystem (from KEGG)
    Alcoholism, organism-specific biosystemAlcoholism, also called dependence on alcohol (ethanol), is a chronic relapsing disorder that is progressive and has serious detrimental health outcomes. As one of the primary mediators of the reward...
  • Alcoholism, conserved biosystem (from KEGG)
    Alcoholism, conserved biosystemAlcoholism, also called dependence on alcohol (ethanol), is a chronic relapsing disorder that is progressive and has serious detrimental health outcomes. As one of the primary mediators of the reward...
  • Apelin signaling pathway, organism-specific biosystem (from KEGG)
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  • Cardiac Hypertrophic Response, organism-specific biosystem (from WikiPathways)
    Cardiac Hypertrophic Response, organism-specific biosystemIntegrated schematic of the more extensively characterized intracellular signal-transduction pathways that coordinate the cardiac hypertrophic response. During development and in response to physiolo...
  • Cell Cycle, organism-specific biosystem (from WikiPathways)
    Cell Cycle, organism-specific biosystemThe cell cycle is the series of events that takes place in a cell leading to its division and duplication (replication). Regulation of the cell cycle involves processes crucial to the survival of a c...
  • Cell Differentiation - Index, organism-specific biosystem (from WikiPathways)
    Cell Differentiation - Index, organism-specific biosystemProteins and miRNAs associated with major cell type differentiation pathways.
  • Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants, organism-specific biosystem (from REACTOME)
    Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants, organism-specific biosystemWhen found in cis, HD and PEST domain mutations act synergistically, increasing NOTCH1 transcriptional activity up to ~40-fold, compared with up to ~10-fold and up to ~2-fold increase with HD mutatio...
  • Constitutive Signaling by NOTCH1 PEST Domain Mutants, organism-specific biosystem (from REACTOME)
    Constitutive Signaling by NOTCH1 PEST Domain Mutants, organism-specific biosystemAs NOTCH1 PEST domain is intracellular, NOTCH1 PEST domain mutants are expected to behave as the wild-type NOTCH1 with respect to ligand binding and proteolytic cleavage mediated activation of signal...
  • Disease, organism-specific biosystem (from REACTOME)
    Disease, organism-specific biosystemBiological processes are captured in Reactome by identifying the molecules (DNA, RNA, protein, small molecules) involved in them and describing the details of their interactions. From this molecular ...
  • Diseases of signal transduction, organism-specific biosystem (from REACTOME)
    Diseases of signal transduction, organism-specific biosystemSignaling processes are central to human physiology (e.g., Pires-da Silva & Sommer 2003), and their disruption by either germ-line and somatic mutation can lead to serious disease. Here, the molecula...
  • Epstein-Barr virus infection, organism-specific biosystem (from KEGG)
    Epstein-Barr virus infection, organism-specific biosystemEpstein-Barr virus (EBV) is a ubiquitous human herpesvirus that is associated with oncogenesis. EBV infection to primary human B lymphocytes leads to induction of EBV-specific HLA-restricted cytotoxi...
  • Epstein-Barr virus infection, conserved biosystem (from KEGG)
    Epstein-Barr virus infection, conserved biosystemEpstein-Barr virus (EBV) is a ubiquitous human herpesvirus that is associated with oncogenesis. EBV infection to primary human B lymphocytes leads to induction of EBV-specific HLA-restricted cytotoxi...
  • Initiation of transcription and translation elongation at the HIV-1 LTR, organism-specific biosystem (from WikiPathways)
    Initiation of transcription and translation elongation at the HIV-1 LTR, organism-specific biosystemFollowing cellular activation or drug treatment, NFAT and NF-kB translocate to the nucleus and bind sites at the HIV-1 LTR. NFAT and NF-kB recruit p300/CBP to the LTR, resulting in acetylation of his...
  • MicroRNAs in cardiomyocyte hypertrophy, organism-specific biosystem (from WikiPathways)
    MicroRNAs in cardiomyocyte hypertrophy, organism-specific biosystemThis pathway shows the role of microRNAs in the process of cardiac hypertrophy. MicroRNA targets were predicted by the TargetScan algorithm, and the predicted interactions are shown in red dashed lin...
  • NOTCH1 Intracellular Domain Regulates Transcription, organism-specific biosystem (from REACTOME)
    NOTCH1 Intracellular Domain Regulates Transcription, organism-specific biosystemNICD1 produced by activation of NOTCH1 in response to Delta and Jagged ligands (DLL/JAG) presented in trans, traffics to the nucleus where it acts as a transcription regulator. In the nucleus, NICD1 ...
  • Neural Crest Differentiation, organism-specific biosystem (from WikiPathways)
    Neural Crest Differentiation, organism-specific biosystemGene regulatory network model of cranial neural crest cell (CNCC) development, adaped from PMID: 19575671. Most interactions in the model are proposed to regulate transcription of core factors involv...
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Signaling by NOTCH, organism-specific biosystem (from REACTOME)
    Signaling by NOTCH, organism-specific biosystemThe Notch Signaling Pathway (NSP) is a highly conserved pathway for cell-cell communication. NSP is involved in the regulation of cellular differentiation, proliferation, and specification. For exam...
  • Signaling by NOTCH1, organism-specific biosystem (from REACTOME)
    Signaling by NOTCH1, organism-specific biosystemNOTCH1 functions as both a transmembrane receptor presented on the cell surface and as a transcriptional regulator in the nucleus.NOTCH1 receptor presented on the plasma membrane is activated by a me...
  • Signaling by NOTCH1 HD+PEST Domain Mutants in Cancer, organism-specific biosystem (from REACTOME)
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  • Signaling by NOTCH1 PEST Domain Mutants in Cancer, organism-specific biosystem (from REACTOME)
    Signaling by NOTCH1 PEST Domain Mutants in Cancer, organism-specific biosystemNOTCH1 PEST domain mutations are frequently found in T-cell acute lymphoblastic leukemia (T-ALL). PEST domain mutations interfere with ubiquitination-mediated NOTCH1 downregulation and result in prol...
  • Signaling by NOTCH1 in Cancer, organism-specific biosystem (from REACTOME)
    Signaling by NOTCH1 in Cancer, organism-specific biosystemHuman NOTCH1 was cloned as a chromosome 9 gene, translocated to the T-cell beta receptor (TCBR) promoter on chromosome 7 in T-cell acute lymphoblastic leukemia (T-ALL) (Ellisen et al. 1991). This tra...
  • Signaling events mediated by HDAC Class I, organism-specific biosystem (from Pathway Interaction Database)
    Signaling events mediated by HDAC Class I, organism-specific biosystem
    Signaling events mediated by HDAC Class I
  • Signaling events mediated by HDAC Class II, organism-specific biosystem (from Pathway Interaction Database)
    Signaling events mediated by HDAC Class II, organism-specific biosystem
    Signaling events mediated by HDAC Class II
  • Viral carcinogenesis, organism-specific biosystem (from KEGG)
    Viral carcinogenesis, organism-specific biosystemThere is a strong association between viruses and the development of human malignancies. We now know that at least six human viruses, Epstein-Barr virus (EBV), hepatitis B virus (HBV), hepatitis C vi...
  • Viral carcinogenesis, conserved biosystem (from KEGG)
    Viral carcinogenesis, conserved biosystemThere is a strong association between viruses and the development of human malignancies. We now know that at least six human viruses, Epstein-Barr virus (EBV), hepatitis B virus (HBV), hepatitis C vi...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • FLJ90614

Gene Ontology Provided by GOA

Function Evidence Code Pubs
NAD-dependent histone deacetylase activity (H3-K14 specific) IEA
Inferred from Electronic Annotation
more info
 
RNA polymerase III transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
chromatin binding IEA
Inferred from Electronic Annotation
more info
 
core promoter binding IDA
Inferred from Direct Assay
more info
PubMed 
histone deacetylase activity IDA
Inferred from Direct Assay
more info
PubMed 
histone deacetylase binding IPI
Inferred from Physical Interaction
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein deacetylase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein kinase C binding IPI
Inferred from Physical Interaction
more info
PubMed 
repressing transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
contributes_to transcription regulatory region DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
B cell activation TAS
Traceable Author Statement
more info
PubMed 
B cell differentiation TAS
Traceable Author Statement
more info
PubMed 
cellular response to insulin stimulus NAS
Non-traceable Author Statement
more info
PubMed 
cellular response to lipopolysaccharide IEA
Inferred from Electronic Annotation
more info
 
chromatin organization TAS
Traceable Author Statement
more info
PubMed 
chromatin remodeling TAS
Traceable Author Statement
more info
PubMed 
chromatin silencing TAS
Traceable Author Statement
more info
PubMed 
histone H3 deacetylation IEA
Inferred from Electronic Annotation
more info
 
histone deacetylation IDA
Inferred from Direct Assay
more info
PubMed 
inflammatory response TAS
Traceable Author Statement
more info
PubMed 
negative regulation of cell migration involved in sprouting angiogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of myotube differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription from RNA polymerase II promoter IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription from RNA polymerase II promoter IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription, DNA-templated TAS
Traceable Author Statement
more info
PubMed 
neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of DNA binding transcription factor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription from RNA polymerase II promoter IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein deacetylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of gene expression, epigenetic IMP
Inferred from Mutant Phenotype
more info
PubMed 
NOT regulation of histone H3-K9 acetylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of myotube differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of protein binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
response to activity IEA
Inferred from Electronic Annotation
more info
 
response to cocaine IEA
Inferred from Electronic Annotation
more info
 
response to drug IEA
Inferred from Electronic Annotation
more info
 
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
Golgi apparatus IDA
Inferred from Direct Assay
more info
 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
histone deacetylase complex TAS
Traceable Author Statement
more info
PubMed 
nuclear speck IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
protein complex IEA
Inferred from Electronic Annotation
more info
 
Preferred Names
histone deacetylase 5
Names
antigen NY-CO-9
NP_001015053.1
NP_005465.2
XP_005256962.1
XP_005256963.1
XP_011522451.1
XP_011522452.1
XP_016879477.1
XP_016879478.1
XP_016879479.1
XP_016879480.1
XP_016879481.1
XP_016879482.1
XP_016879483.1
XP_016879484.1
XP_016879485.1

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001015053.1NP_001015053.1  histone deacetylase 5 isoform 3

    See identical proteins and their annotated locations for NP_001015053.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) represents the longer transcript and encodes the longer isoform (3).
    Source sequence(s)
    AB011172, AC023855, BC051824, CN290533
    Consensus CDS
    CCDS32663.1
    UniProtKB/Swiss-Prot
    Q9UQL6
    Related
    ENSP00000225983.5, OTTHUMP00000267505, ENST00000225983.10, OTTHUMT00000457683
    Conserved Domains (2) summary
    cd10164
    Location:69165
    ClassIIa_HDAC5_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC5, a Class IIa histone deacetylase
    cd10007
    Location:6801096
    HDAC5; Histone deacetylase 5
  2. NM_005474.4NP_005465.2  histone deacetylase 5 isoform 1

    See identical proteins and their annotated locations for NP_005465.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) uses an alternate in-frame splice site compared to variant 3. The resulting isoform (1) has the same N- and C-termini but is 1 aa shorter compared to isoform 3.
    Source sequence(s)
    AB011172, AC023855, BC051824, BM564861, CN290533
    Consensus CDS
    CCDS45696.1
    UniProtKB/Swiss-Prot
    Q9UQL6
    Related
    ENSP00000337290.4, OTTHUMP00000267506, ENST00000336057.9, OTTHUMT00000457684
    Conserved Domains (2) summary
    cd10164
    Location:68164
    ClassIIa_HDAC5_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC5, a Class IIa histone deacetylase
    cd10007
    Location:6791095
    HDAC5; Histone deacetylase 5

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p7 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p7 Primary Assembly

    Range
    44076753..44123646 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011524149.1XP_011522451.1  histone deacetylase 5 isoform X9

    Conserved Domains (2) summary
    cd10007
    Location:6711087
    HDAC5; Histone deacetylase 5
    cl23765
    Location:69156
    iSH2_PI3K_IA_R; Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits
  2. XM_005256905.1XP_005256962.1  histone deacetylase 5 isoform X7

    Conserved Domains (2) summary
    cd10164
    Location:69164
    ClassIIa_HDAC5_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC5, a Class IIa histone deacetylase
    cd10007
    Location:6791095
    HDAC5; Histone deacetylase 5
  3. XM_017023992.1XP_016879481.1  histone deacetylase 5 isoform X4

  4. XM_017023995.1XP_016879484.1  histone deacetylase 5 isoform X10

  5. XM_017023993.1XP_016879482.1  histone deacetylase 5 isoform X5

  6. XM_017023991.1XP_016879480.1  histone deacetylase 5 isoform X3

  7. XM_017023988.1XP_016879477.1  histone deacetylase 5 isoform X1

  8. XM_017023996.1XP_016879485.1  histone deacetylase 5 isoform X12

    Conserved Domains (2) summary
    cd10164
    Location:27123
    ClassIIa_HDAC5_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC5, a Class IIa histone deacetylase
    cd10007
    Location:6381054
    HDAC5; Histone deacetylase 5
  9. XM_017023990.1XP_016879479.1  histone deacetylase 5 isoform X2

  10. XM_011524150.1XP_011522452.1  histone deacetylase 5 isoform X11

    Conserved Domains (2) summary
    cd10164
    Location:59155
    ClassIIa_HDAC5_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC5, a Class IIa histone deacetylase
    cd10007
    Location:6701086
    HDAC5; Histone deacetylase 5
  11. XM_017023989.1XP_016879478.1  histone deacetylase 5 isoform X1

  12. XM_005256906.4XP_005256963.1  histone deacetylase 5 isoform X6

    See identical proteins and their annotated locations for XP_005256963.1

    UniProtKB/Swiss-Prot
    Q9UQL6
    Related
    ENSP00000468004.1, OTTHUMP00000267507, ENST00000586802.5, OTTHUMT00000457686
    Conserved Domains (2) summary
    cd10164
    Location:68164
    ClassIIa_HDAC5_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC5, a Class IIa histone deacetylase
    cd10007
    Location:6791095
    HDAC5; Histone deacetylase 5
  13. XM_017023994.1XP_016879483.1  histone deacetylase 5 isoform X8

Alternate CHM1_1.1

Genomic

  1. NC_018928.2 Alternate CHM1_1.1

    Range
    42389491..42436420 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_139205.1: Suppressed sequence

    Description
    NM_139205.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
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