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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

HDAC3 Gene

protein-coding   GIFtS: 73
GCID: GC05M140980

Histone Deacetylase 3

Microbiology & Infectious Diseases Congress
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Histone Deacetylase 31 2
HD32 3
RPD3-22 3
SMAP452 3
EC 3.5.1.983 8
RPD32

External Ids:    HGNC: 48541   Entrez Gene: 88412   Ensembl: ENSG000001717207   OMIM: 6051665   UniProtKB: O153793   

Export aliases for HDAC3 gene to outside databases

Previous GC identifers: GC05U990082 GC05M141583 GC05M140983 GC05M141028 GC05M136145


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for HDAC3 Gene:
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 histone deacetylase/acuc/apha family. It has histone deacetylase
activity and represses transcription when tethered to a promoter. It may participate in the regulation of
transcription through its binding with the zinc-finger transcription factor YY1. This protein can also
down-regulate p53 function and thus modulate cell growth and apoptosis. This gene is regarded as a potential
tumor suppressor gene. (provided by RefSeq, Jul 2008)

GeneCards Summary for HDAC3 Gene: 
HDAC3 (histone deacetylase 3) is a protein-coding gene. Diseases associated with HDAC3 include hair loss, and friedreich ataxia, and among its related super-pathways are Constitutive Signaling by NOTCH1 PEST Domain Mutants and p53 Signaling. GO annotations related to this gene include transcription corepressor activity and transcription factor binding. An important paralog of this gene is HDAC1.

UniProtKB/Swiss-Prot: HDAC3_HUMAN, O15379
Function: Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A,
H2B, H3 and H4), and some other non-histone substrates. Histone deacetylation gives a tag for epigenetic
repression and plays an important role in transcriptional regulation, cell cycle progression and developmental
events. Histone deacetylases act via the formation of large multiprotein complexes. Probably participates in the
regulation of transcription through its binding to the zinc-finger transcription factor YY1; increases YY1
repression activity. Required to repress transcription of the POU1F1 transcription factor. Acts as a molecular
chaperone for shuttling phosphorylated NR2C1 to PML bodies for sumoylation (By similarity)

summary for HDAC3 Gene:
Histone Deacetylases (HDACs) are a group of enzymes closely related to sirtuins. They catalyze the removal
of acetyl groups from lysine residues in histones and non-histone proteins, resulting in transcriptional
repression. In general, they do not act autonomously but as components of large multiprotein complexes, such
as pRb-E2F and mSin3A, that mediate important transcription regulatory pathways. There are three classes of
HDACs; classes 1, 2 and 4, which are closely related Zn2+-dependent enzymes. HDACs are ubiquitously
expressed and they can exist in the nucleus or cytosol. Their subcellular localization is effected by
protein-protein interactions (for example HDAC-14.3.3 complexes are retained in the cytosol) and by the
class to which they belong (class 1 HDACs are predominantly nuclear whilst class 2 HDACs shuttle between the
nucleus and cytosol). HDACs have a role in cell growth arrest, differentiation and death and this has led to
substantial interest in HDAC inhibitors as possible antineoplastic agents.

Gene Wiki entry for HDAC3 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000005.9  NC_018916.2  NT_029289.11  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the HDAC3 gene promoter:
         AP-2alpha isoform 3   AP-1   AP-2alpha isoform 4   AP-2alpha isoform 2   AP-2alpha   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): HDAC3 promoter sequence
   Search SABiosciences Chromatin IP Primers for HDAC3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat HDAC3


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 5q31   Ensembl cytogenetic band:  5q31.3   HGNC cytogenetic band: 5q31.1-q31.2

HDAC3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HDAC3 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05M140980:  view genomic region     (about GC identifiers)

Start:
141,000,443 bp from pter      End:
141,016,437 bp from pter
Size:
15,995 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: HDAC3_HUMAN, O15379 (See protein sequence)
Recommended Name: Histone deacetylase 3  
Size: 428 amino acids; 48848 Da
Subunit: Interacts with HDAC7 and HDAC9. Forms a heterologous complex at least with YY1. Interacts with DAXX,
HDAC10 and DACH1. Found in a complex with NCOR1 and NCOR2. Component of the N-Cor repressor complex, at least
composed of NCOR1, NCOR2, HDAC3, TBL1X, TBL1R, CORO2A and GPS2. Interacts with BCOR, MJD2A/JHDM3A, NRIP1, PRDM6
and SRY. Interacts with BTBD14B. Interacts with GLIS2. Interacts (via the DNA-binding domain) with NR2C1; the
interaction recruits phosphorylated NR2C1 to PML bodies for sumoylation (By similarity). Component of the Notch
corepressor complex. Interacts with CBFA2T3 and NKAP. Interacts with APEX1; the interaction is not dependent on
the acetylated status of APEX1. Interacts with and deacetylates MAPK14. Interacts with ZMYND15 (By similarity)
Subcellular location: Nucleus
1 PDB 3D structure from and Proteopedia for HDAC3:
4A69 (3D)    
Secondary accessions: D3DQE1 O43268 Q9UEI5 Q9UEV0
Alternative splicing: 2 isoforms:  O15379-1   O15379-2   

Explore the universe of human proteins at neXtProt for HDAC3: NX_O15379

Explore proteomics data for HDAC3 at MOPED 

Post-translational modifications:

  • UniProtKB: Sumoylated in vitro
  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_O15379

  • 4/18 DME Specific Peptides for HDAC3 (O15379) (see all 18)
     HPMKPHR  QCGADSL  VSFHKYG  RCWTYET 

    HDAC3 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    HDAC3 Protein Expression
    REFSEQ proteins: NP_003874.2  
    ENSEMBL proteins: 
     ENSP00000302967   ENSP00000430667   ENSP00000429099   ENSP00000430782  
    Reactome Protein details: O15379
    Human Recombinant Protein Products for HDAC3: 
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    Sino Biological Cell Lysate for HDAC3 
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for HDAC3 

    Gene Ontology (GO): 5/6 cellular component terms (GO ID links to tree view) (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000118histone deacetylase complex TAS12711221
    GO:0005634nucleus TAS12711221
    GO:0005654nucleoplasm TAS--
    GO:0005737cytoplasm TAS12711221
    GO:0005876spindle microtubule IDA18326024

    HDAC3 for ontologies           About GeneDecksing



    HDAC3 Antibody Products: 
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    LSBio Antibodies in human, mouse, rat for HDAC3 

    Assay Products for HDAC3: 
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    Enzo Life Sciences assays for HDAC3
    Cloud-Clone Corp. ELISAs for HDAC3 
    Cloud-Clone Corp. CLIAs for HDAC3


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    3 InterPro protein domains:
     IPR000286 His_deacetylse
     IPR003084 His_deacetylse_1
     IPR023801 His_deacetylse_dom

    Graphical View of Domain Structure for InterPro Entry O15379

    ProtoNet protein and cluster: O15379

    2 Blocks protein domains:
    IPB000286 Histone deacetylase superfamily signature
    IPB003084 Histone deacetylase signature


    UniProtKB/Swiss-Prot: HDAC3_HUMAN, O15379
    Similarity: Belongs to the histone deacetylase family. HD type 1 subfamily


    HDAC3 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: HDAC3_HUMAN, O15379
    Function: Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A,
    H2B, H3 and H4), and some other non-histone substrates. Histone deacetylation gives a tag for epigenetic
    repression and plays an important role in transcriptional regulation, cell cycle progression and developmental
    events. Histone deacetylases act via the formation of large multiprotein complexes. Probably participates in the
    regulation of transcription through its binding to the zinc-finger transcription factor YY1; increases YY1
    repression activity. Required to repress transcription of the POU1F1 transcription factor. Acts as a molecular
    chaperone for shuttling phosphorylated NR2C1 to PML bodies for sumoylation (By similarity)
    Catalytic activity: Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone

         Genatlas biochemistry entry for HDAC3:
    histone deacetyltransferase 3,49kDa,ubiquitously expressed,binding to YY1,involved in negative regulation of
    transcription,modulator of chromatine structure,putatively involved in the pathogenesis of myeloproliferative
    disorders (potential tumor suppressor)

         Enzyme Number (IUBMB): EC 3.5.1.981 2

         Gene Ontology (GO): 5/14 molecular function terms (GO ID links to tree view) (see all 14):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding ----
    GO:0003682chromatin binding ----
    GO:0003714transcription corepressor activity IMP12628926
    GO:0004407histone deacetylase activity TAS12711221
    GO:0005515protein binding IPI10898795
         
    HDAC3 for ontologies           About GeneDecksing


    Phenotypes:
         8 GenomeRNAi human phenotypes for HDAC3:
     Decreased Salmonella enterica   Decreased Salmonella enterica   Decreased Salmonella enterica   Decreased Salmonella enterica  
     Decreased Salmonella-containin  Decreased viability  G0/1 arrest  Increased G1 DNA content 

         11 MGI mutant phenotypes (inferred from 8 alleles(MGI details for Hdac3):
     adipose tissue  behavior/neurological  cardiovascular system  cellular  embryogenesis 
     growth/size  homeostasis/metabolism  liver/biliary system  mortality/aging  muscle 
     no phenotypic analysis 

    HDAC3 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-outs for HDAC3: Hdac3tm1.1Swh Hdac3tm1.2Eno Hdac3tm1.2Xen

       inGenious Targeting Laboratory - Custom generated mouse model solutions for HDAC3 
       inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for HDAC3

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for HDAC3 
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for HDAC3 

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    hsa-miR-548d-3p hsa-miR-548am hsa-miR-3613-3p hsa-miR-548x hsa-miR-1261 hsa-miR-3662 hsa-miR-362-5p
    SwitchGear 3'UTR luciferase reporter plasmidHDAC3 3' UTR sequence
    Inhib. RNA
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    Sirion Biotech Customized adenovirus for overexpression of HDAC3

    Clone
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    Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore
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    OriGene ORF clones in mouse, rat for HDAC3
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    GenScript: all cDNA clones in your preferred vector: HDAC3 (NM_003883)
    Sino Biological Human cDNA Clone for HDAC3
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                         Customized lentivirus expression plasmids for stable overexpression of HDAC3 

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HDAC3


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for HDAC3 About   (see all 36)                                                                                              See pathways by source

    SuperPathSelected contained pathways About (see all per SuperPath)
    1Signaling by NOTCH1 t(7 9)(NOTCH1:M1580 K2555) Translocation Mutant
    Constitutive Signaling by NOTCH1 PEST Domain Mutants0.89
    Signaling by NOTCH1 in Cancer0.79
    Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants0.89
    Signaling by NOTCH10.79
    Signaling by NOTCH1 HD+PEST Domain Mutants in Cancer0.79
    Signaling by NOTCH1 t(7 9)(NOTCH1:M1580 K2555) Translocation Mutant0.79
    Signaling by NOTCH1 PEST Domain Mutants in Cancer0.79
    Signaling by NOTCH0.74
    2p53 Pathway
    p53 Signaling0.38
    p53 Pathway0.38
    3Cyclins and Cell Cycle Regulation
    Cyclins and Cell Cycle Regulation0.67
    G1-S Phase Transition0.67
    4Regulation of Lipid Metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)
    Regulation of Lipid Metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)0.74
    Fatty acid, triacylglycerol, and ketone body metabolism0.52
    5Metabolism
    Metabolism0.40
    Metabolism of lipids and lipoproteins0.34

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    1 EMD Millipore Pathway for HDAC3
        Histone modification

    5/16 Downloadable PowerPoint Slides of QIAGEN Pathway Central Maps for HDAC3 (see all 16)
        NF-KappaB (p50-p65) Pathway
    DNA Methylation and Transcriptional Repression
    Protein Acetylation and Deacetylation
    BRCA1 Pathway
    Glucocorticoid Receptor Signaling

    1 Cell Signaling Technology (CST) Pathway for HDAC3
        Chromatin Regulation / Acetylation

    5/7 BioSystems Pathways for HDAC3 (see all 7)
        Cell cycle
    Neural Crest Differentiation
    Signaling events mediated by HDAC Class I
    Retinoic acid receptors-mediated signaling
    Signaling events mediated by HDAC Class II

    2 Sino Biological Pathways for HDAC3 
        Notch Signaling Pathway
    p53 Pathway

    5/23        Reactome Pathways for HDAC3 (see all 23)
        Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants
    NOTCH1 Intracellular Domain Regulates Transcription
    Developmental Biology
    Transcriptional Regulation of White Adipocyte Differentiation
    FBXW7 Mutants and NOTCH1 in Cancer


    2         Kegg Pathways  (Kegg details for HDAC3):
        Alcoholism
    Viral carcinogenesis


    HDAC3 for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for HDAC3

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/427 Interacting proteins for HDAC3 (O153791, 2, 3 ENSP000003029674) via UniProtKB, MINT, STRING, and/or I2D (see all 427)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST1H4AP628053, ENSP000003529804I2D: score=1 STRING: ENSP00000352980
    HIST1H4BP628053I2D: score=1 
    HIST1H4CP628053I2D: score=1 
    HIST1H4DP628053I2D: score=1 
    HIST1H4EP628053I2D: score=1 
    About this table

    Gene Ontology (GO): 5/18 biological process terms (GO ID links to tree view) (see all 18):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000122negative regulation of transcription from RNA polymerase II promoter IMP12628926
    GO:0006351transcription, DNA-dependent IEA--
    GO:0006476protein deacetylation IDA17172643
    GO:0007219Notch signaling pathway TAS--
    GO:0007346regulation of mitotic cell cycle IEA--

    HDAC3 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section

    HDAC3 for compounds           About GeneDecksing

    EMD Millipore small molecules for HDAC3:
    Small Molecule - inhibitor
    Enzo Life Sciences drugs & compounds for HDAC3

    Compounds for HDAC3 available from Tocris Bioscience    About this table
    CompoundAction CAS #
    TCS HDAC6 20bSelective HDAC6 inhibitor[956154-63-5]
    LMK 235Selective HDAC4/HDAC5 inhibitor[1418033-25-6]
    Trichostatin AHistone deacetylase inhibitor[58880-19-6]
    TubacinHDAC6 inhibitor; inhibits alpha-tubulin deacetylation[1350555-93-9]
    Sodium 4-PhenylbutyrateHistone deacetylase inhibitor[1716-12-7]

    1 HMDB Compound for HDAC3    About this table
    CompoundSynonyms CAS #PubMed Ids
    Butyric acid1-Butyrate (see all 25)107-92-617258775

    1 DrugBank Compound for HDAC3    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    VorinostatMK0683 (see all 7)149647-78-9targetinhibitor17694093

    10/14 Novoseek inferred chemical compound relationships for HDAC3 gene (see all 14)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    suberoylanilide hydroxamic acid 74.5 3 17671692 (1), 15583844 (1), 20460513 (1)
    trapoxin 67.4 3 9520398 (1)
    butyrate 43.9 4 17849419 (3), 16849648 (1)
    lysine 35.8 2 15837933 (2)
    retinoic acid 34.8 12 19204783 (2), 14510502 (1), 17456789 (1), 11278635 (1) (see all 7)
    retinoid 24.1 1 19952854 (1)
    dopamine 6.2 8 10431754 (2), 9765337 (1), 10455259 (1), 9849894 (1) (see all 5)
    atp 0 2 17242407 (1), 11777905 (1)
    forskolin 0 1 16528103 (1)
    tyrosine 0 1 19171783 (1)

    Search CenterWatch for drugs/clinical trials and news about HDAC3

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
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    About This Section

    REFSEQ mRNAs for HDAC3 gene: 
    NM_003883.3  

    Unigene Cluster for HDAC3:

    Histone deacetylase 3
    Hs.519632  [show with all ESTs]
    Unigene Representative Sequence: AF005482
    17 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000469550(uc003lle.1) ENST00000305264(uc003llf.2 uc010jgd.1 uc010jge.1)
    ENST00000469207 ENST00000459727 ENST00000491581 ENST00000486618 ENST00000467533
    ENST00000492407 ENST00000523353 ENST00000475549 ENST00000523088 ENST00000519474
    ENST00000476739 ENST00000495485 ENST00000490808 ENST00000471968 ENST00000492506

    Congresses - knowledge worth sharing:  
    European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) 10 - 13 May 2014

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    DNA2.0 Custom Codon Optimized Gene Synthesis Service for HDAC3
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat HDAC3
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      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat HDAC3

    Additional mRNA sequence: 

    AF005482.1 AF039703.1 AY429537.1 AY429538.1 BC000614.1 U66914.1 U75696.1 U75697.1 

    23 DOTS entries:

    DT.100785686  DT.443260  DT.95297791  DT.120855392  DT.75137917  DT.100785687  DT.100785696  DT.97854585 
    DT.91777204  DT.75190334  DT.91777155  DT.95207505  DT.100744185  DT.100785692  DT.100785694  DT.120855407 
    DT.120855433  DT.75112484  DT.95293677  DT.95297854  DT.95297862  DT.120855314  DT.95297860 

    24/315 AceView cDNA sequences (see all 315):

    CR618922 AI339444 T34171 AA831038 BI759887 BG475337 BQ690104 AA862566 
    BM975400 AI283758 BE857995 BG755703 BQ957706 AW170369 AI032140 AI220114 
    BF940597 BM468317 BQ015435 BG419426 BM054838 CR615606 AI034260 AA810217 

    GeneLoc Exon Structure

    5/12 Alternative Splicing Database (ASD) splice patterns (SP) for HDAC3 (see all 12)    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3a · 3b · 3c · 3d ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10a · 10b ^ 11a · 11b ^ 12a · 12b · 12c · 12d ^ 13a · 13b ^ 14 ^
    SP1:                    -                             -                                         -                       -     -                                 
    SP2:                                                  -                                         -                       -     -                                 
    SP3:                    -     -     -     -           -                                         -                       -     -                                 
    SP4:                    -     -     -     -     -     -                                         -                       -     -                                 
    SP5:                                                  -                                                                 -     -                                 

    ExUns: 15 ^ 16
    SP1:            
    SP2:            
    SP3:            
    SP4:            
    SP5:            


    ECgene alternative splicing isoforms for HDAC3

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    HDAC3 expression in normal human tissues (normalized intensities)      HDAC3 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ACAATGACAA
    HDAC3 Expression
    About this image


    HDAC3 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/13 selected tissues (see all 13) fully expand
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex
     
     Testis (Reproductive System)    fully expand to see all 3 entries
             seminal vesicle ; glandular cells   
     
     Colon (Gastrointestinal Tract)    fully expand to see all 2 entries
             rectum ; glandular cells   
     
     Intestine (Gastrointestinal Tract)    fully expand to see all 2 entries
             small intestine ; glandular cells   
     
     Lymph (Hematopoietic System)    fully expand to see all 2 entries
             lymph node ; non-germinal center cells   

    See HDAC3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for HDAC3

    SOURCE GeneReport for Unigene cluster: Hs.519632

    UniProtKB/Swiss-Prot: HDAC3_HUMAN, O15379
    Tissue specificity: Widely expressed

        SABiosciences Expression via Pathway-Focused PCR Arrays including HDAC3: 
              Epigenetic Chromatin Modification Enzymes in human mouse rat
              Cancer Drug Targets in human mouse rat
              Nuclear Receptors & Coregulators in human mouse rat
              Apoptosis 384HT in human mouse rat

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of eukaryotes.

    Orthologs for HDAC3 gene from 9/20 species (see all 20)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Hdac31 , 5 histone deacetylase 31, 5 92.37(n)1
    99.77(a)1
      18 (19.81 cM)5
    151831  NM_010411.21  NP_034541.21 
     379358445 
    chicken
    (Gallus gallus)
    Aves HDAC31 histone deacetylase 3 81.78(n)
    97.43(a)
      395506  NM_204747.1  NP_990078.1 
    lizard
    (Anolis carolinensis)
    Reptilia HDAC36
    Histone deacetylase
    97(a)
    1 ↔ 1
    4(76327863-76358556)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia Str.204852 Transcribed sequence with strong similarity to protein more 79.01(n)    AL873085.2 
    zebrafish
    (Danio rerio)
    Actinopterygii zgc559272 similar to histone deacetylase 3 78.1(n)   393965  BC044543.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta HDAC33
    Hdac31
    histone deacetylase3
    Histone deacetylase 31
    65(a)3
    66.51(n)1
    67.06(a)1
      83A43
    444461  NM_143721.31  NP_651978.21 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes HOS2(YGL194C)4 Histone deacetylase required for gene activation via more   --   7(141726-140368) 852681  NP_011321.1 
    soybean
    (Glycine max)
    eudicotyledons Gma.126832 Transcribed sequence with moderate similarity to protein more 73.16(n)  
    rice
    (Oryza sativa)
    Liliopsida AF513384.12   -- 75.27(n)    AF513384.1 


    ENSEMBL Gene Tree for HDAC3 (if available)
    TreeFam Gene Tree for HDAC3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for HDAC3 gene
    HDAC12  HDAC22  HDAC82  
    5 SIMAP similar genes for HDAC3 using alignment to 5 protein entries:     HDAC3_HUMAN (see all proteins):
    HDAC2    HDAC8    HDAC1    DKFZp686H12203    HDAC9

    HDAC3 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/399 SNPs in HDAC3 are shown (see all 399)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs727923321,2
    C,F--141000660(+) CCCAGG/AGGAGG 1 -- ut312Minor allele frequency- A:0.05NA EA 240
    rs10436701,2
    C--141000743(+) GGGAAG/AAAATA 1 -- ut31 ese3 trp31Minor allele frequency- A:0.00NA 2
    rs1905737851,2
    --141000860(+) TTGGGA/GGAGAG 1 -- ut310--------
    rs37497641,2
    C,F,H--141000945(-) TGGGGG/TTCACC 1 -- ut31 ese315Minor allele frequency- T:0.03EA MN NS NA 3660
    rs2012118721,2
    --141001009(+) ATTCCC/TTGGGA 1 -- ut310--------
    rs349017431,2,4
    C,F,H--141001090(-) ACCCAA/GTGAGT 2 N S mis113Minor allele frequency- G:0.01NS NA EA CSA WA 5780
    rs1460626031,2
    C--141001149(+) GTTCTA/GATCTT 1 -- int10--------
    rs1158193081,2
    F--141001335(+) AGGTTG/ATCTAT 1 -- int11Minor allele frequency- A:0.03WA 118
    rs1389784411,2
    --141001491(+) CTATTA/GGGACA 1 -- int10--------
    rs1929841361,2
    --141001505(+) GACCTA/GAAGTC 1 -- int10--------

    HapMap Linkage Disequilibrium report for HDAC3 (141000443 - 141016437 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for HDAC3:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv5033CNV Insertion18451855
    nsv516495CNV Gain+Loss19592680

    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 605166    OMIM disorders: --

    20/37 diseases for HDAC3 (see all 37):    About MalaCards
    hair loss    friedreich ataxia    nonsyndromic deafness    hyperandrogenism
    colon cancer    chronic myeloid leukemia    myeloid leukemia    medulloblastoma
    acute leukemia    polycystic ovary syndrome    endometrial carcinoma    retinoblastoma
    huntington's disease    ataxia    acute myeloid leukemia    pancreatitis
    b-cell lymphomas    nasopharyngitis    hodgkin's lymphoma    atherosclerosis

    1 disease from the University of Copenhagen DISEASES database for HDAC3:
    Cancer

    HDAC3 for disorders           About GeneDecksing


    Congresses - knowledge worth sharing:  
    Alzheimer's & Parkinson's Diseases Congress (ADPD) 18 - 22 March 2015

    10/11 Novoseek inferred disease relationships for HDAC3 gene (see all 11)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    colon cancer 38.1 23 15981215 (3), 17849419 (3), 16533812 (3), 18769117 (3) (see all 6)
    cancer 31.1 16 19471575 (3), 16044157 (2), 19430493 (2), 20417177 (2) (see all 7)
    tumors 29.3 20 10575214 (2), 16309230 (1), 18027850 (1), 10491319 (1) (see all 13)
    colon tumor 11 1 16533812 (1)
    leukemia 10.9 2 17694085 (1), 19121623 (1)
    leukemia promyelocytic acute 8.83 1 16432238 (1)
    necrosis 4.84 4 15811852 (1), 16371367 (1), 20097764 (1)
    shock 0 2 16044157 (1), 12691522 (1)
    lung carcinoma 0 3 16022908 (1), 17650409 (1)
    carcinoma 0 1 18714364 (1)

    Genetic Association Database (GAD): HDAC3
    Human Genome Epidemiology (HuGE) Navigator: HDAC3 (5 documents)

    Export disorders for HDAC3 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for HDAC3 gene, integrated from 9 sources (see all 405):
    (articles sorted by number of sources associating them with HDAC3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Differential display cloning of a novel human histone deacetylase (HDAC3) cDNA from PHA-activated immune cells. (PubMed id 9464271)1, 2, 3, 9 Dangond F....Gullans S.R. (1998)
    2. Characterization of a human RPD3 ortholog, HDAC3. (PubMed id 9501169)1, 2, 3, 9 Emiliani S.... Verdin E. (1998)
    3. The histone deacetylase-3 complex contains nuclear receptor corepressors. (PubMed id 10860984)1, 2, 9 Wen Y.-D.... Seto E. (2000)
    4. Human HDAC7 histone deacetylase activity is associated with HDAC3 in vivo. (PubMed id 11466315)1, 2, 9 Fischle W....Verdin E. (2001)
    5. Both corepressor proteins SMRT and N-CoR exist in large protein complexes containing HDAC3. (PubMed id 10944117)1, 2, 9 Li J.... Wong J. (2000)
    6. Isolation and characterization of cDNAs corresponding to an additional member of the human histone deacetylase gene family. (PubMed id 9346952)1, 2, 9 Yang W.-M.... Seto E. (1997)
    7. Purification and functional characterization of the human N-CoR complex: the roles of HDAC3, TBL1 and TBLR1. (PubMed id 12628926)1, 2, 9 Yoon H.-G....Wong J. (2003)
    8. A core SMRT corepressor complex containing HDAC3 and TBL1, a WD40- repeat protein linked to deafness. (PubMed id 10809664)1, 2, 9 Guenther M.G....Shiekhattar R. (2000)
    9. Regulation of human SRY subcellular distribution by its acetylation/deacetylation. (PubMed id 15297880)1, 2, 9 Thevenet L....Boizet-Bonhoure B. (2004)
    10. Identification of HDAC10, a novel class II human histone deacetylase containing a leucine-rich domain. (PubMed id 11861901)1, 2, 9 Tong J.J.... Yang X.-J. (2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 8841 HGNC: 4854 AceView: HDAC3 Ensembl:ENSG00000171720 euGenes: HUgn8841
    ECgene: HDAC3 Kegg: 8841 H-InvDB: HDAC3

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for HDAC3 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for HDAC3 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for HDAC3 gene:
    Search GeneIP for patents involving HDAC3

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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    About This Section

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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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