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HDAC2 histone deacetylase 2 [ Homo sapiens (human) ]

Gene ID: 3066, updated on 9-Feb-2020

Summary

Official Symbol
HDAC2provided by HGNC
Official Full Name
histone deacetylase 2provided by HGNC
Primary source
HGNC:HGNC:4853
See related
Ensembl:ENSG00000196591 MIM:605164
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
HD2; RPD3; YAF1; KDAC2
Summary
This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. Thus, it plays an important role in transcriptional regulation, cell cycle progression and developmental events. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2010]
Expression
Ubiquitous expression in testis (RPKM 14.8), endometrium (RPKM 10.6) and 25 other tissues See more
Orthologs

Genomic context

See HDAC2 in Genome Data Viewer
Location:
6q21
Exon count:
17
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (113933028..113971148, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (114257320..114292359, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene MARCKS cis regulating lncRNA promoter of cytokines and inflammation Neighboring gene long intergenic non-protein coding RNA 2880 Neighboring gene HDAC2 and HS3ST5 antisense RNA 2 Neighboring gene nudix hydrolase 19 pseudogene 3 Neighboring gene heparan sulfate-glucosamine 3-sulfotransferase 5 Neighboring gene ribosomal protein SA pseudogene 43

Genomic regions, transcripts, and products

Expression

  • 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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Tat tat HIV-1 Tat induces upregulation of HDAC2 expression and downregulation of CREB and CaMKIIa expression in human neuroblastoma SK-N-MC cells PubMed
tat The SIN3/HDAC complex, composed of SIN3A, SAP30, SAP18, HDAC-1 AND -2 and RbAp46/48 except SAP30, are identified to interact with HIV-1 Tat in Jurkat cell PubMed
Vpr vpr HIV-1 Vpr depletes HDAC1, 2, 3 and 8 to overcome HIV-1 proviral latency in macrophages PubMed
vpr COUP-TF-interacting protein 2 (CTIP2) abolishes Vpr-mediated stimulation of p21 by cooperating with SUV39H1 and HDAC1/HDAC2 to silence the p21 gene transcription PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
NAD-dependent histone deacetylase activity (H3-K14 specific) IEA
Inferred from Electronic Annotation
more info
 
NF-kappaB binding IPI
Inferred from Physical Interaction
more info
PubMed 
RNA binding HDA PubMed 
contributes_to RNA polymerase II distal enhancer sequence-specific DNA binding HDA PubMed 
contributes_to RNA polymerase II proximal promoter sequence-specific DNA binding HDA PubMed 
RNA polymerase II repressing transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
chromatin binding ISS
Inferred from Sequence or Structural Similarity
more info
 
deacetylase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
heat shock protein binding IEA
Inferred from Electronic Annotation
more info
 
histone deacetylase activity IBA
Inferred from Biological aspect of Ancestor
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 
contributes_to nucleosomal DNA binding HDA PubMed 
promoter-specific chromatin 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 
sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
ATP-dependent chromatin remodeling HDA PubMed 
behavioral response to ethanol IEA
Inferred from Electronic Annotation
more info
 
blood coagulation TAS
Traceable Author Statement
more info
 
cardiac muscle hypertrophy IEA
Inferred from Electronic Annotation
more info
 
cellular response to dopamine IEA
Inferred from Electronic Annotation
more info
 
cellular response to heat IEA
Inferred from Electronic Annotation
more info
 
cellular response to hydrogen peroxide IEA
Inferred from Electronic Annotation
more info
 
cellular response to retinoic acid IEA
Inferred from Electronic Annotation
more info
 
cellular response to transforming growth factor beta stimulus IEA
Inferred from Electronic Annotation
more info
 
chromatin remodeling IC
Inferred by Curator
more info
PubMed 
circadian regulation of gene expression ISS
Inferred from Sequence or Structural Similarity
more info
 
dendrite development ISS
Inferred from Sequence or Structural Similarity
more info
 
embryonic digit morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
epidermal cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
eyelid development in camera-type eye ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
fungiform papilla formation ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
hair follicle placode formation ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
histone H3 deacetylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone H3 deacetylation ISS
Inferred from Sequence or Structural Similarity
more info
 
histone H4 deacetylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone H4 deacetylation ISS
Inferred from Sequence or Structural Similarity
more info
 
histone deacetylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
maintenance of chromatin silencing IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of DNA binding IEA
Inferred from Electronic Annotation
more info
 
negative regulation of DNA-binding transcription factor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of MHC class II biosynthetic process IC
Inferred by Curator
more info
PubMed 
negative regulation of apoptotic process ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
negative regulation of dendritic spine development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of neuron projection development ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
negative regulation of peptidyl-lysine acetylation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription, DNA-templated IC
Inferred by Curator
more info
PubMed 
negative regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
odontogenesis of dentin-containing tooth ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
positive regulation of cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of collagen biosynthetic process IC
Inferred by Curator
more info
PubMed 
positive regulation of epithelial to mesenchymal transition IEA
Inferred from Electronic Annotation
more info
 
positive regulation of interleukin-1 production IEA
Inferred from Electronic Annotation
more info
 
positive regulation of male mating behavior IEA
Inferred from Electronic Annotation
more info
 
positive regulation of oligodendrocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of proteolysis IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of receptor biosynthetic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription, DNA-templated IC
Inferred by Curator
more info
PubMed 
positive regulation of tumor necrosis factor production IEA
Inferred from Electronic Annotation
more info
 
positive regulation of tyrosine phosphorylation of STAT protein IEA
Inferred from Electronic Annotation
more info
 
regulation of signal transduction by p53 class mediator TAS
Traceable Author Statement
more info
 
response to amphetamine IEA
Inferred from Electronic Annotation
more info
 
response to caffeine IEA
Inferred from Electronic Annotation
more info
 
response to cocaine IEA
Inferred from Electronic Annotation
more info
 
response to hyperoxia IEA
Inferred from Electronic Annotation
more info
 
response to lipopolysaccharide IEA
Inferred from Electronic Annotation
more info
 
response to nicotine IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
ESC/E(Z) complex IDA
Inferred from Direct Assay
more info
PubMed 
NuRD complex IDA
Inferred from Direct Assay
more info
PubMed 
Sin3 complex IDA
Inferred from Direct Assay
more info
PubMed 
Sin3-type complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm TAS
Traceable Author Statement
more info
PubMed 
histone deacetylase complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear chromatin HDA PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
protein-containing complex HDA PubMed 
protein-containing complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
histone deacetylase 2
Names
YY1-associated factor 1
transcriptional regulator homolog RPD3
NP_001518.3
XP_016866288.1

NCBI Reference Sequences (RefSeq)

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_001527.4NP_001518.3  histone deacetylase 2

    See identical proteins and their annotated locations for NP_001518.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the functional protein.
    Source sequence(s)
    AK296856, BC031055, FO393415
    Consensus CDS
    CCDS43493.2
    UniProtKB/Swiss-Prot
    Q92769
    Related
    ENSP00000430432.1, ENST00000519065.6
    Conserved Domains (2) summary
    cd10011
    Location:9374
    HDAC2; Histone deacetylase 2 (HDAC2)
    pfam14797
    Location:393487
    SEEEED; Serine-rich region of AP3B1, clathrin-adaptor complex

RNA

  1. NR_033441.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) includes an additional internal exon in the 5' region, compared to variant 1. This variant is represented as non-coding due to the presence of upstream ORFs that are predicted to interfere with the translation of the longest ORF.
    Source sequence(s)
    AK097376, AK296856, AL590398, FO393415
  2. NR_073443.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate 5' exon, compared to variant 1. This variant is represented as non-coding due to the presence of an upstream ORF that is predicted to interfere with translation of the longest ORF; translation of the upstream ORF renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK092156, FO393415

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    113933028..113971148 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017010799.1XP_016866288.1  histone deacetylase 2 isoform X1

    UniProtKB/Swiss-Prot
    Q92769
    Related
    ENSP00000430008.1, ENST00000519108.5
    Conserved Domains (2) summary
    pfam14797
    Location:363457
    SEEEED; Serine-rich region of AP3B1, clathrin-adaptor complex
    cl17011
    Location:1344
    Arginase_HDAC; Arginase-like and histone-like hydrolases
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