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    HDAC2 histone deacetylase 2 [ Homo sapiens (human) ]

    Gene ID: 3066, updated on 11-Jun-2017
    Official Symbol
    HDAC2provided by HGNC
    Official Full Name
    histone deacetylase 2provided by HGNC
    Primary source
    HGNC:HGNC:4853
    See related
    Ensembl:ENSG00000196591 MIM:605164; Vega:OTTHUMG00000015411
    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
    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]
    Orthologs
    Location:
    6q21
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 6 NC_000006.12 (113936156..113971195, 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 uncharacterized LOC105377958 Neighboring gene long intergenic non-protein coding RNA 1268 Neighboring gene uncharacterized FLJ34503 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

    • 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?

    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 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

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    Products Interactant Other Gene Complex Source Pubs Description

    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    contributes_to RNA polymerase II core promoter proximal region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    contributes_to RNA polymerase II distal enhancer sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    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
     
    core promoter binding IEA
    Inferred from Electronic Annotation
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    histone deacetylase activity TAS
    Traceable Author Statement
    more info
     
    contributes_to nucleosomal DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    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 ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    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 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 sequence-specific DNA binding transcription factor activity IMP
    Inferred from Mutant Phenotype
    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 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 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 from RNA polymerase II promoter 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 drug 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
     
    transcription, DNA-templated 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 
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoplasm TAS
    Traceable Author Statement
    more info
    PubMed 
    nuclear chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    histone deacetylase 2
    Names
    YY1-associated factor 1
    transcriptional regulator homolog RPD3
    NP_001518.3
    XP_011534090.1
    XP_016866288.1

    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_001527.3NP_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, OTTHUMP00000017046, ENST00000519065.5, OTTHUMT00000041909
      Conserved Domains (3) summary
      cd10011
      Location:9374
      HDAC2; Histone deacetylase 2 (HDAC2)
      PTZ00063
      Location:9398
      PTZ00063; histone deacetylase; Provisional
      pfam14797
      Location:393487
      SEEEED; Serine-rich region of AP3B1, clathrin-adaptor complex

    RNA

    1. NR_033441.1 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 Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p7 Primary Assembly

      Range
      113936156..113971195 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, OTTHUMP00000227077, ENST00000519108.5, OTTHUMT00000379478
      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
    2. XM_011535788.1XP_011534090.1  histone deacetylase 2 isoform X1

      See identical proteins and their annotated locations for XP_011534090.1

      UniProtKB/Swiss-Prot
      Q92769
      Related
      ENSP00000357621.2, OTTHUMP00000227078, ENST00000368632.6, OTTHUMT00000379479
      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

    Alternate CHM1_1.1

    Genomic

    1. NC_018917.2 Alternate CHM1_1.1

      Range
      114520179..114555225 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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