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HDAC9 Gene

protein-coding   GIFtS: 69
GCID: GC07P018179

Histone Deacetylase 9

Microbiology & Infectious Diseases Congress
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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Histone Deacetylase 91 2     EC 3.5.1.983 8
HDAC7B2 3 5     KIAA07443 5
MITR2 3 5     HDAC2
Histone Deacetylase 7B2 3     HDAC9B2
HD72 3     HDAC9FL2
HD7b2 3     Histone Deacetylase 4/5-Related Protein2
HD92 3     MEF-2 Interacting Transcription Repressor (MITR) Protein2
HDAC72 3     Histone Deacetylase-Related Protein3
HDRP2 3     MEF2-Interacting Transcription Repressor MITR3

External Ids:    HGNC: 140651   Entrez Gene: 97342   Ensembl: ENSG000000480527   OMIM: 6065435   UniProtKB: Q9UKV03   

Export aliases for HDAC9 gene to outside databases

Previous GC identifers: GC07P018279 GC07P018308 GC07P018501


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for HDAC9 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 has sequence homology to members of the histone deacetylase family. This gene is
orthologous to the Xenopus and mouse MITR genes. The MITR protein lacks the histone deacetylase catalytic domain.
It represses MEF2 activity through recruitment of multicomponent corepressor complexes that include CtBP and
HDACs. This encoded protein may play a role in hematopoiesis. Multiple alternatively spliced transcripts have
been described for this gene but the full-length nature of some of them has not been determined. (provided by
RefSeq, Jul 2008)

GeneCards Summary for HDAC9 Gene:
HDAC9 (histone deacetylase 9) is a protein-coding gene. Diseases associated with HDAC9 include hiv-1 viremia, and peters plus syndrome. GO annotations related to this gene include histone deacetylase binding and transcription factor binding. An important paralog of this gene is HDAC6.

UniProtKB/Swiss-Prot: HDAC9_HUMAN, Q9UKV0
Function: Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A,
H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in
transcriptional regulation, cell cycle progression and developmental events. Represses MEF2-dependent
transcription
Function: Isoform 3 lacks active site residues and therefore is catalytically inactive. Represses MEF2-dependent
transcription by recruiting HDAC1 and/or HDAC3. Seems to inhibit skeletal myogenesis and to be involved in heart
development. Protects neurons from apoptosis, both by inhibiting JUN phosphorylation by MAPK10 and by repressing
JUN transcription via HDAC1 recruitment to JUN promoter

summary for HDAC9 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 HDAC9 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000007.14  NT_007819.18  NC_018918.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the HDAC9 gene promoter:
         MEF-2A   aMEF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 4): HDAC9 promoter sequence
   Search Chromatin IP Primers for HDAC9

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat HDAC9


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

Entrez Gene cytogenetic band: 7p21.1   Ensembl cytogenetic band:  7p21.1   HGNC cytogenetic band: 7p21.1

HDAC9 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HDAC9 gene location

GeneLoc information about chromosome 7         GeneLoc Exon Structure

GeneLoc location for GC07P018179:  view genomic region     (about GC identifiers)

Start:
18,126,572 bp from pter      End:
19,042,039 bp from pter
Size:
915,468 bases      Orientation:
plus strand

1 alternative location:
Chr7+,CRA_TCAG 18,179,953-19,088,496     

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: HDAC9_HUMAN, Q9UKV0 (See protein sequence)
Recommended Name: Histone deacetylase 9  
Size: 1011 amino acids; 111297 Da
Subunit: Homodimer. Interacts with CTBP1. The phosphorylated form interacts with 14-3-3 (By similarity). Interacts
with HDAC1 and HDAC3, and probably with HDAC4 and HDAC5. Interacts with MEF2, MAPK10, ETV6, NCOR1 and BCL6
Sequence caution: Sequence=BAA34464.2; Type=Erroneous initiation;
Secondary accessions: A7E2F3 B7Z4I4 B7Z917 B7Z928 B7Z940 C9JS87 E7EX34 F8W9E0 O94845 O95028
Q2M2R6 Q86SL1 Q86US3
Alternative splicing: 11 isoforms:  Q9UKV0-1   Q9UKV0-2   Q9UKV0-3   Q9UKV0-4   Q9UKV0-5   Q9UKV0-6   Q9UKV0-7   Q9UKV0-8   
Q9UKV0-9   Q9UKV0-10   Q9UKV0-11   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for HDAC9: NX_Q9UKV0

Explore proteomics data for HDAC9 at MOPED

Post-translational modifications: 

  • Phosphorylated on Ser-220 and Ser-450; which promotes 14-3-3-binding, impairs interaction with MEF2, and
    antagonizes antimyogenic activity. Phosphorylated on Ser-240; which impairs nuclear accumulation (By similarity).
    Isoform 7 is phosphorylated on Tyr-1010. Phosphorylated by the PKC kinases PKN1 and PKN2, impairing nuclear
    import1
  • Sumoylated1
  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for HDAC9 (Q9UKV0) (see all 24)
     SGPSSPN  HHGNGTQ  FLEKQKQ  HRPLNRT 


    See HDAC9 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (9 alternative transcripts): 
    NP_001191073.1  NP_001191074.1  NP_001191075.1  NP_001191076.1  NP_001191077.1  NP_055522.1  NP_478056.1  NP_848510.1  
    NP_848512.1  

    ENSEMBL proteins: 
     ENSP00000401669   ENSP00000409003   ENSP00000412497   ENSP00000392564   ENSP00000411422  
     ENSP00000384382   ENSP00000384657   ENSP00000395655   ENSP00000384017   ENSP00000415095  
     ENSP00000383912   ENSP00000410337   ENSP00000408617   ENSP00000404763   ENSP00000388568  
     ENSP00000430036  
    Reactome Protein details: Q9UKV0

    HDAC9 Human Recombinant Protein Products:

    Browse Purified and Recombinant Proteins at EMD Millipore
    Browse R&D Systems for human recombinant proteins
    Browse recombinant and purified proteins available from Enzo Life Sciences
    OriGene Purified Protein for HDAC9
    OriGene Protein Over-expression Lysate for HDAC9
    OriGene MassSpec for HDAC9
    OriGene Custom Protein Services for HDAC9
    GenScript Custom Purified and Recombinant Proteins Services for HDAC9
    Novus Biologicals HDAC9 Proteins
    Novus Biologicals HDAC9 Lysates
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for HDAC9

    HDAC9 Antibody Products:

    EMD Millipore Mono- and Polyclonal Antibodies for the study of HDAC9
    Browse R&D Systems for Antibodies
    OriGene Antibodies for HDAC9
    OriGene Custom Antibody Services for HDAC9
    Novus Biologicals HDAC9 Antibodies
    Abcam antibodies for HDAC9
    Cloud-Clone Corp. Antibodies for HDAC9
    ThermoFisher Antibodies for HDAC9
    LSBio Antibodies in human, mouse, rat for HDAC9

    HDAC9 Assay Products:

    EMD Millipore Kits and Assays for the Analysis of HDAC9
    OriGene Custom Assay Services for HDAC9
    Browse R&D Systems for biochemical assays
    GenScript Custom Assay Services for HDAC9
    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for HDAC9
    Cloud-Clone Corp. CLIAs for HDAC9


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    4 InterPro protein domains:
     IPR024643 Hist_deacetylase_Gln_rich_N
     IPR017320 Histone_deAcase_II_euk
     IPR000286 His_deacetylse
     IPR023801 His_deacetylse_dom

    Graphical View of Domain Structure for InterPro Entry Q9UKV0

    ProtoNet protein and cluster: Q9UKV0

    1 Blocks protein domain: IPB000286 Histone deacetylase superfamily signature

    UniProtKB/Swiss-Prot: HDAC9_HUMAN, Q9UKV0
    Similarity: Belongs to the histone deacetylase family. HD type 2 subfamily


    HDAC9 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,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: HDAC9_HUMAN, Q9UKV0
    Function: Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A,
    H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in
    transcriptional regulation, cell cycle progression and developmental events. Represses MEF2-dependent
    transcription
    Function: Isoform 3 lacks active site residues and therefore is catalytically inactive. Represses MEF2-dependent
    transcription by recruiting HDAC1 and/or HDAC3. Seems to inhibit skeletal myogenesis and to be involved in heart
    development. Protects neurons from apoptosis, both by inhibiting JUN phosphorylation by MAPK10 and by repressing
    JUN transcription via HDAC1 recruitment to JUN promoter
    Catalytic activity: Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone
    Enzyme regulation: Inhibited by Trichostatin A (TSA) and suberoylanilide hydroxamic acid

         Enzyme Number (IUBMB): EC 3.5.1.981 2

         Gene Ontology (GO): Selected molecular function terms (see all 13):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003714transcription corepressor activity ISS--
    GO:0004407NOT histone deacetylase activity IDA10655483
    GO:0005080protein kinase C binding IPI--
    GO:0005515protein binding IPI12590135
    GO:0008134transcription factor binding IPI10748098
         
    HDAC9 for ontologies           About GeneDecksing


    Phenotypes:
         2 GenomeRNAi human phenotypes for HDAC9:
     Increased S DNA content  Synthetic lethal with Ras 

         4 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Hdac9):
     cardiovascular system  growth/size/body  mortality/aging  muscle 

    HDAC9 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Hdac9tm1Lex for HDAC9

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for HDAC9
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for HDAC9

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for HDAC9
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for HDAC9

    miRNA
    Products:
        
    miRTarBase miRNAs that target HDAC9:
    hsa-mir-615-3p (MIRT040075), hsa-mir-149-5p (MIRT045413)

    Block miRNA regulation of human, mouse, rat HDAC9 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate HDAC9 (see all 54):
    hsa-miR-124* hsa-miR-579 hsa-miR-19b-2* hsa-miR-188-5p hsa-miR-376b hsa-miR-218-1* hsa-miR-374a hsa-miR-30d
    SwitchGear 3'UTR luciferase reporter plasmidHDAC9 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for HDAC9
    Predesigned siRNA for gene silencing in human, mouse, rat HDAC9

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for HDAC9

    Clone
    Products:
         
    OriGene clones in human, mouse for HDAC9 (see all 26)
    OriGene ORF clones in mouse, rat for HDAC9
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 9): HDAC9 (NM_001204145)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for HDAC9
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat HDAC9

    Cell Line
    Products:
         
    GenScript Custom overexpressing Cell Line Services for HDAC9
    Browse ESI BIO Cell Lines and PureStem Progenitors for HDAC9 
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HDAC9


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    HDAC9_HUMAN, Q9UKV0: Nucleus (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytoskeleton2
    extracellular2
    mitochondrion2
    cytosol1
    endoplasmic reticulum1
    plasma membrane1

    Gene Ontology (GO): Selected cellular component terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000118histone deacetylase complex TAS12711221
    GO:0005634nucleus IDA12590135
    GO:0005654nucleoplasm TAS--
    GO:0005667transcription factor complex IDA15567413
    GO:0005737cytoplasm TAS12711221

    HDAC9 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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    SuperPaths for HDAC9 About   (see all 27)  
    See pathways by source

    SuperPathSelected contained pathways About (see all per SuperPath)
    1Signaling by NOTCH1 PEST Domain Mutants in Cancer
    Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants0.79
    Constitutive Signaling by NOTCH1 PEST Domain Mutants0.79
    Signaling by NOTCH1 PEST Domain Mutants in Cancer0.79
    Signaling by NOTCH1 t(7;9)(NOTCH1-M1580 K2555) Translocation Mutant0.79
    Signaling by NOTCH1 in Cancer0.79
    FBXW7 Mutants and NOTCH1 in Cancer0.79
    Signaling by NOTCH10.79
    NOTCH1 Intracellular Domain Regulates Transcription0.68
    2Cyclins and Cell Cycle Regulation
    Cyclins and Cell Cycle Regulation0.67
    G1-S Phase Transition0.67
    3CREB Pathway
    IP3 Pathway0.68
    Intracellular Calcium Signaling0.50
    4Immune response Function of MEF2 in T lymphocytes
    Development Role of HDAC and calcium calmodulin dependent kinase CaMK in control of skeletal myogenesis0.38
    Immune response Function of MEF2 in T lymphocytes0.38
    5Macrophage Differentiation and Growth Inhibition by METS
    Macrophage Differentiation and Growth Inhibition by METS0.30
    DNA Methylation and Transcriptional Repression0.30

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    Selected Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for HDAC9 (see all 17)
        DNA Methylation and Transcriptional Repression
    Nur77 Signaling in T-Cell
    BRCA1 Pathway
    Intracellular Calcium Signaling
    Notch Signaling

    2 GeneGo (Thomson Reuters) Pathways for HDAC9
        Development Role of HDAC and calcium/calmodulin-dependent kinase (CaMK) in control of skeletal myogenesis
    Immune response Function of MEF2 in T lymphocytes

    5 BioSystems Pathways for HDAC9
        MicroRNAs in cardiomyocyte hypertrophy
    SIDS Susceptibility Pathways
    Neural Crest Differentiation
    Signaling events mediated by HDAC Class I
    Signaling events mediated by HDAC Class II

    3 Reactome Pathways for HDAC9
        Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants
    NOTCH1 Intracellular Domain Regulates Transcription
    Constitutive Signaling by NOTCH1 PEST Domain Mutants

    1 PharmGKB Pathway for HDAC9
        Valproic Acid Pathway, Pharmacodynamics

    2 Kegg Pathways  (Kegg details for HDAC9):
        Alcoholism
    Viral carcinogenesis


    HDAC9 for pathways           About GeneDecksing

        Pathway & Disease-focused RT2 Profiler PCR Arrays including HDAC9: 
              Epigenetic Chromatin Modification Enzymes in human mouse rat
              T-Cell Anergy & Immune Tolerance in human mouse rat
              Inflammatory Response & Autoimmunity 384HT in human mouse rat
              Hematopoiesis in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for HDAC9

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

    Selected Interacting proteins for HDAC9 (Q9UKV01, 3 ENSP000004086174) via UniProtKB, MINT, STRING, and/or I2D (see all 227)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST4H4P628053, ENSP000003507674I2D: score=1 STRING: ENSP00000350767
    HIST1H4AP628053I2D: score=1 
    HIST1H4BP628053I2D: score=1 
    HIST1H4CP628053I2D: score=1 
    HIST1H4DP628053I2D: score=1 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 17):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000122negative regulation of transcription from RNA polymerase II promoter IDA10655483
    GO:0006351transcription, DNA-templated IEA--
    GO:0006954inflammatory response TAS12711221
    GO:0007219Notch signaling pathway TAS--
    GO:0007507heart development ISS--

    HDAC9 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
    Selected ApexBio Compounds for HDAC9 (see all 29)     About this table
    CompoundAction CAS #
    AR-42 (OSU-HDAC42)Pan-HDAC inhibitor[935881-37-1]
    Belinostat (PXD101)Novel and potent hydroxamate-type HDAC inhibitor[414864-00-9]
    CI994 (Tacedinaline)HDAC1 and 3 inhibitor[112522-64-2]
    CUDC-101Multitargeted HDAC inhibitor[1012054-59-9]
    CUDC-907PI3K and HDAC inhibitor[1339928-25-4]
    DroxinostatSelective HDAC inhibitor[99873-43-5]
    Entinostat (MS-275,SNDX-275)Entinostat inhibits HDAC1 and HDAC3 but not HDAC8[209783-80-2]
    ITF2357 (Givinostat)HDAC inhibitor, inhibits class I and class II HDACs[732302-99-7]
    JNJ-26481585Potent pan-HDAC inhibitor[875320-29-9]
    LAQ824 (NVP-LAQ824,Dacinostat)Novel and potent HDAC inhibitor[404951-53-7]

    Compounds for HDAC9 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 HDAC9    About this table
    CompoundSynonyms CAS #PubMed Ids
    Butyric acid1-Butyrate (see all 25)107-92-617258775

    1 DrugBank Compound for HDAC9    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    Valproic Acid2-Propylpentanoic Acid (see all 8)99-66-1targetinhibitor15685243 17514356 15166525 20811699 15289798 15850602 15242819

    Selected Novoseek inferred chemical compound relationships for HDAC9 gene (see all 110)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    suberoylanilide hydroxamic acid 96.8 232 20479100 (3), 17876049 (3), 20167479 (3), 17160079 (2) (see all 99)
    depsipeptide 92.9 132 19322073 (3), 15063388 (2), 15466934 (2), 18205373 (2) (see all 73)
    apicidin 91.2 35 10893438 (3), 11085529 (2), 19407971 (2), 14985106 (2) (see all 23)
    lbh-589 90.3 29 19322073 (2), 17145876 (2), 17317822 (2), 19176386 (1) (see all 20)
    ms 275 89 10 15069698 (1), 17929017 (1), 16432198 (1), 17868634 (1) (see all 8)
    hydroxamate 88.4 51 16305476 (3), 17307359 (2), 17218485 (2), 15171260 (2) (see all 39)
    valproic acid 87.5 277 16123451 (4), 17892546 (3), 15289798 (3), 15870934 (3) (see all 99)
    scriptaid 86.7 13 14620913 (3), 16844092 (3), 14529479 (1), 15043813 (1) (see all 8)
    trapoxin 86.1 11 13679859 (2), 18416310 (2), 16146885 (1), 9520369 (1) (see all 8)
    pxd-101 86 2 17428794 (1), 17982680 (1)



    HDAC9 for compounds           About GeneDecksing



    (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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for HDAC9 gene (10 alternative transcripts): 
    NM_001204144.1  NM_001204145.1  NM_001204146.1  NM_001204147.1  NM_001204148.1  NM_014707.1  NM_058176.2  NM_178423.1  
    NM_178425.2  NM_058177.2  

    Unigene Cluster for HDAC9:

    Histone deacetylase 9
    Hs.196054  [show with all ESTs]
    Unigene Representative Sequence: AJ459808
    Selected Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 28):
    ENST00000417496 ENST00000455069 ENST00000425071 ENST00000433709 ENST00000411993
    ENST00000413509 ENST00000461159(uc003sua.1) ENST00000474742 ENST00000413380
    ENST00000430454 ENST00000476135(uc003sub.4) ENST00000405010(uc003sud.2 uc011jyc.2 uc011jyb.2 uc003suf.2 uc010kud.2 uc011jye.2)
    ENST00000406451(uc003sue.3 uc003suj.3 uc003sui.3) ENST00000428307
    ENST00000461409 ENST00000406072(uc011jya.2 uc011jyf.2) ENST00000446646
    ENST00000401921
    Congresses - knowledge worth sharing:
    European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) 10 - 13 May 2014

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    Selected qRT-PCR Assays for microRNAs that regulate HDAC9 (see all 54):
    hsa-miR-124* hsa-miR-579 hsa-miR-19b-2* hsa-miR-188-5p hsa-miR-376b hsa-miR-218-1* hsa-miR-374a hsa-miR-30d
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    GenScript: all cDNA clones in your preferred vector (see all 9): HDAC9 (NM_001204145)
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      QuantiTect SYBR Green Assays in human, mouse, rat HDAC9
      QuantiFast Probe-based Assays in human, mouse, rat HDAC9

    Additional mRNA sequence: 

    AB018287.1 AF124924.1 AJ459808.1 AK095820.1 AK097178.1 AK296214.1 AK297404.1 AK304298.1 
    AK304343.1 AK304410.1 AK316109.1 AY032737.1 AY032738.1 AY197371.1 AY429540.1 BC092441.1 
    BC111735.1 BC150328.1 BC152405.1 CR749550.1 

    12 DOTS entries:

    DT.40200536  DT.121045675  DT.102828405  DT.402151  DT.95084955  DT.40281430  DT.100782788  DT.100020985 
    DT.100782783  DT.86835732  DT.100700546  DT.121045647 

    Selected AceView cDNA sequences (see all 95):

    BQ048866 NM_058177 AA884094 AK097178 AA629911 AI522005 AA488817 AI274776 
    AA701346 AA489065 BQ433721 AI608745 AI911740 BE889828 AY032737 AA360179 
    AB018287 AA504568 NM_058176 AY032738 BQ218937 AI419981 AI005442 NM_014707 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for HDAC9    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^
    SP1:              -           -                                                                 -                                                               
    SP2:              -           -                                                                                                                                 
    SP3:                                                                                                                                                            

    ExUns: 24 ^ 25 ^ 26 ^ 27
    SP1:                        
    SP2:                        
    SP3:                        


    ECgene alternative splicing isoforms for HDAC9

    (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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

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    HDAC9 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TGGCTGAGCA
    HDAC9 Expression
    About this image

    HDAC9 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    HDAC9 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.196054

    UniProtKB/Swiss-Prot: HDAC9_HUMAN, Q9UKV0
    Tissue specificity: Broadly expressed, with highest levels in brain, heart, muscle and testis. Isoform 3 is
    present in human bladder carcinoma cells (at protein level)

        Pathway & Disease-focused RT2 Profiler PCR Arrays including HDAC9: 
              Epigenetic Chromatin Modification Enzymes in human mouse rat
              T-Cell Anergy & Immune Tolerance in human mouse rat
              Inflammatory Response & Autoimmunity 384HT in human mouse rat
              Hematopoiesis in human mouse rat

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    In Situ
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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

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    This gene was present in the common ancestor of animals and fungi.

    Orthologs for HDAC9 gene from Selected species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Hdac91 , 5 histone deacetylase 91, 5 89.74(n)1
    92.4(a)1
      12 (15.06 cM)5
    792211  NM_001271386.11  NP_001258315.11 
     343715035 
    chicken
    (Gallus gallus)
    Aves HDAC91 histone deacetylase 9 81.69(n)
    84.79(a)
      420599  NM_001030981.2  NP_001026152.2 
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    (see all 3)
    Uncharacterized protein
    (see all 3)
    82(a)
    77(a)
    (see all 3)
    1 ↔ many
    1 ↔ many
    (see all 3)
    6(28325300-28366358)
    6(28418230-28465826)
    African clawed frog
    (Xenopus laevis)
    Amphibia hdac9-A2 histone deacetylase 9, MITR protein 76.22(n)    Z97214.1 
    zebrafish
    (Danio rerio)
    Actinopterygii hdac92 histone deacetylase 9 75.43(n)   393789  BC059696.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta HDAC46
    HDAC4
    32(a)
    1 → many
    X(13156720-13179354)
    worm
    (Caenorhabditis elegans)
    Secernentea hda-46
    Protein HDA-4, isoform a
    34(a)
    1 → many
    X(16729559-16744698) WBGene00001837
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes HDA16
    Putative catalytic subunit of a class II histone d...
    10(a)
    1 → many
    XIV(593227-595347) YNL021W


    ENSEMBL Gene Tree for HDAC9 (if available)
    TreeFam Gene Tree for HDAC9 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for HDAC9 gene
    HDAC62  HDAC52  HDAC72  HDAC42  HDAC102  
    13 SIMAP similar genes for HDAC9 using alignment to 15 protein entries:     HDAC9_HUMAN (see all proteins):
    DKFZp779K1053    HDAC4    KIAA0600    MGC16025    DKFZp566E044    HDAC6
    HDAC10    HDAC5    HDAC7    HDAC2    HDAC8    HDAC3
    HDAC1

    HDAC9 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for HDAC9 (see all 19036)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 7 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1459616751,2
    --18124578(+) CAAAAA/GCCAAA 1 -- us2k10--------
    rs1864419401,2
    --18124584(+) CCAAAA/CCCAAA 1 -- us2k10--------
    rs1421198591,2
    --18124687(+) CTAGA-/TAGT  
            
    TATAT
    1 -- us2k10--------
    rs1918636751,2
    --18124703(+) GGCATA/GTATAC 1 -- us2k10--------
    rs606034071,2
    C,F--18124877(+) TATTTT/CTAAAT 1 -- us2k14Minor allele frequency- C:0.15WA NA EA 360
    rs558991421,2
    C--18124879(+) TTTTTA/GAATTT 1 -- us2k14Minor allele frequency- G:0.15WA NA EA 360
    rs1415177301,2
    C--18124933(+) TTAGAA/GCAAAG 1 -- us2k10--------
    rs1829045151,2
    --18125008(+) ACAGCC/TACCAT 1 -- us2k10--------
    rs789015341,2
    C,F--18125077(+) TGAGGT/GTTTTG 1 -- us2k12Minor allele frequency- G:0.07NA 122
    rs766974981,2
    C,F--18125200(+) GCTACC/TGGGCC 1 -- us2k11Minor allele frequency- T:0.07WA 118

    HapMap Linkage Disequilibrium report for HDAC9 (18126572 - 18376572 bp, first 250kb of HDAC9)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for HDAC9 (see all 43):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2476785CNV Deletion19546169
    esv2734076CNV Deletion23290073
    esv2582410CNV Deletion19546169
    esv2442723CNV Deletion19546169
    esv2734077CNV Deletion23290073
    esv2734072CNV Deletion23290073
    esv999263CNV Deletion20482838
    esv2668991CNV Deletion23128226
    esv2664987CNV Deletion23128226
    esv2660622CNV Deletion23128226

    Human Gene Mutation Database (HGMD): HDAC9
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing HDAC9
    DNA2.0 Custom Variant and Variant Library Synthesis for HDAC9

    (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.)
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    OMIM gene information: 606543    OMIM disorders: --

    UniProtKB/Swiss-Prot: HDAC9_HUMAN, Q9UKV0
  • Note=A chromosomal aberration involving HDAC9 is found in a family with Peters anomaly. Translocation
    t(1;7)(q41;p21) with TGFB2 resulting in lack of HDAC9 protein

  • Selected diseases for HDAC9 (see all 118):    
    About MalaCards
    hiv-1 viremia    peters plus syndrome    gastrointestinal neuroendocrine tumor    rubinstein-taybi syndrome
    cytomegalovirus retinitis    autoimmune lymphoproliferative syndrome    friedreich ataxia    hemoglobinopathy
    endometrial stromal sarcoma    glucocorticoid resistance    polyploidy    muscular atrophy
    estrogen-receptor negative breast cancer    mood disorder    hiv-1    childhood leukemia
    rhabdoid tumor    neuroendocrine tumor    adrenoleukodystrophy    thyroid cancer

    6 diseases from the University of Copenhagen DISEASES database for HDAC9:
    Leukemia     Lymphoma     Huntington's disease     Lung cancer
    Breast cancer     Retinoblastoma

    HDAC9 for disorders           About GeneDecksing


    Congresses - knowledge worth sharing:
    The International Symposium on Pneumococci and Pneumococcal Diseases (ISPPD) 9 - 13 March 2014
    Alzheimer's & Parkinson's Diseases Congress (ADPD) 18 - 22 March 2015

    Selected Novoseek inferred disease relationships for HDAC9 gene (see all 92)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    cancer 73.4 473 14763127 (4), 16267097 (4), 16462761 (3), 20207580 (3) (see all 99)
    lymphoma t-cell cutaneous 72.4 14 19747008 (1), 17504226 (1), 18671804 (1), 20361469 (1) (see all 14)
    tumors 64.1 321 16782459 (4), 16338224 (4), 18201278 (4), 17121924 (4) (see all 99)
    colon cancer 54 36 19528666 (3), 15059516 (2), 18789002 (2), 16982769 (2) (see all 26)
    retinoblastoma 51.9 3 11596110 (1), 15003538 (1), 11752153 (1)
    leukemia 49.8 43 16273296 (3), 16219908 (3), 16424655 (3), 14707268 (2) (see all 33)
    hematologic malignancies 49.7 22 19549415 (3), 19861438 (1), 12649266 (1), 19546476 (1) (see all 19)
    solid tumor 46.3 17 19318486 (2), 17827453 (1), 19861438 (1), 11504668 (1) (see all 14)
    muscular atrophy spinal 46.2 5 18230051 (1), 17998807 (1), 19388875 (1), 16805808 (1) (see all 5)
    lymphoma t-cell 45.2 12 15655420 (1), 19689202 (1), 15078940 (1), 19438744 (1) (see all 9)

    Genetic Association Database (GAD): HDAC9
    Human Genome Epidemiology (HuGE) Navigator: HDAC9 (8 documents)

    Export disorders for HDAC9 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)
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    PubMed articles for HDAC9 gene, integrated from 10 sources (see all 1239):
    (articles sorted by number of sources associating them with HDAC9)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. HDAC4, a human histone deacetylase related to yeast HDA1, is a transcriptional corepressor. (PubMed id 10523670)1, 2, 3 Wang A.H.... Yang X.-J. (Mol. Cell. Biol. 1999)
    2. MEF-2 function is modified by a novel co-repressor, MITR. (PubMed id 10487760)1, 2, 3 Sparrow D.B.... Mohun T.J. (EMBO J. 1999)
    3. Cloning and characterization of a histone deacetylase, HDAC9. (PubMed id 11535832)1, 2, 9 Zhou X.... Richon V.M. (Proc. Natl. Acad. Sci. U.S.A. 2001)
    4. Identification of a transcriptional repressor related to the noncatalytic domain of histone deacetylases 4 and 5. (PubMed id 10655483)1, 2, 9 Zhou X.... Marks P.A. (Proc. Natl. Acad. Sci. U.S.A. 2000)
    5. The histone deacetylase 9 gene encodes multiple protein isoforms. (PubMed id 12590135)1, 2, 9 Petrie K....Zelent A. (J. Biol. Chem. 2003)
    6. Genome-wide association study identifies a variant in HDAC9 associated with large vessel ischemic stroke. (PubMed id 22306652)1, 4  ....Markus H.S. (Nat. Genet. 2012)
    7. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    8. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1, 4 Bailey S.D....Anand S. (Diabetes Care 2010)
    9. Single nucleotide polymorphisms in the Wnt and BMP pathways and colorectal cancer risk in a Spanish cohort. (PubMed id 20844743)1, 4 FernA!ndez-Rozadilla C....Ruiz-Ponte C. (PLoS ONE 2010)
    10. Association of regions on chromosomes 6 and 7 with blood pressure in Nigerian families. (PubMed id 20031566)1, 4 Tayo B.O....Cooper R.S. (Circ Cardiovasc Genet 2009)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     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)
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    Entrez Gene: 9734 HGNC: 14065 AceView: HDAC9 Ensembl:ENSG00000048052 euGenes: HUgn9734
    ECgene: HDAC9 Kegg: 9734 H-InvDB: HDAC9

    (According to HUGE)
    About This Section

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    HUGE: KIAA0744

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for HDAC9 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for HDAC9 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for HDAC9 gene:
    Search GeneIP for patents involving HDAC9

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



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