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Aliases for HDAC9 Gene

Aliases for HDAC9 Gene

  • Histone Deacetylase 9 2 3 5
  • Histone Deacetylase 7B 3 4
  • EC 3.5.1.98 4 63
  • HDAC7B 3 4
  • HDAC7 3 4
  • HD7b 3 4
  • HDRP 3 4
  • MITR 3 4
  • HD7 3 4
  • HD9 3 4
  • MEF-2 Interacting Transcription Repressor (MITR) Protein 3
  • MEF2-Interacting Transcription Repressor MITR 4
  • Histone Deacetylase 4/5-Related Protein 3
  • Histone Deacetylase-Related Protein 4
  • KIAA0744 4
  • HDAC9FL 3
  • HDAC9B 3
  • HDAC 3

External Ids for HDAC9 Gene

Previous GeneCards Identifiers for HDAC9 Gene

  • GC07P018279
  • GC07P018308
  • GC07P018501

Summaries for HDAC9 Gene

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 Peters Anomaly and Gastrointestinal Neuroendocrine Tumor. Among its related pathways are Macrophage Differentiation and Growth Inhibition by METS and Signaling by NOTCH1. GO annotations related to this gene include transcription factor binding and histone deacetylase binding. An important paralog of this gene is HDAC10.

UniProtKB/Swiss-Prot for HDAC9 Gene

  • 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.

  • 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.

Tocris Summary for HDAC9 Gene

  • Histone deacetylases (HDACs) are a group of enzymes closely related to sirtuins. They catalyze acetyl group removal from lysine residues in histones and non-histone proteins, causing transcriptional repression. HDACs are usually components of multiprotein complexes.

Gene Wiki entry for HDAC9 Gene

No data available for PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HDAC9 Gene

Genomics for HDAC9 Gene

Regulatory Elements for HDAC9 Gene

Enhancers for HDAC9 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around HDAC9 on UCSC Golden Path with GeneCards custom track

Promoters for HDAC9 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around HDAC9 on UCSC Golden Path with GeneCards custom track

Transcription factor binding sites by QIAGEN in the HDAC9 gene promoter:

Genomic Location for HDAC9 Gene

Chromosome:
7
Start:
18,086,942 bp from pter
End:
19,002,416 bp from pter
Size:
915,475 bases
Orientation:
Plus strand

Genomic View for HDAC9 Gene

Genes around HDAC9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HDAC9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HDAC9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HDAC9 Gene

Proteins for HDAC9 Gene

  • Protein details for HDAC9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UKV0-HDAC9_HUMAN
    Recommended name:
    Histone deacetylase 9
    Protein Accession:
    Q9UKV0
    Secondary Accessions:
    • A7E2F3
    • B7Z4I4
    • B7Z917
    • B7Z928
    • B7Z940
    • C9JS87
    • E7EX34
    • F8W9E0
    • O94845
    • O95028
    • Q2M2R6
    • Q86SL1
    • Q86US3

    Protein attributes for HDAC9 Gene

    Size:
    1011 amino acids
    Molecular mass:
    111297 Da
    Quaternary structure:
    • 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. Interacts with FOXP3 in the absence of T-cell stimulation.
    SequenceCaution:
    • Sequence=BAA34464.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for HDAC9 Gene

neXtProt entry for HDAC9 Gene

Proteomics data for HDAC9 Gene at MOPED

Post-translational modifications for HDAC9 Gene

  • 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 import.
  • Sumoylated.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for HDAC9 Gene

Gene Families for HDAC9 Gene

Suggested Antigen Peptide Sequences for HDAC9 Gene

Graphical View of Domain Structure for InterPro Entry

Q9UKV0

UniProtKB/Swiss-Prot:

HDAC9_HUMAN :
  • Belongs to the histone deacetylase family. HD type 2 subfamily.
Family:
  • Belongs to the histone deacetylase family. HD type 2 subfamily.
genes like me logo Genes that share domains with HDAC9: view

Function for HDAC9 Gene

Molecular function for HDAC9 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone.
UniProtKB/Swiss-Prot EnzymeRegulation:
Inhibited by Trichostatin A (TSA) and suberoylanilide hydroxamic acid.
UniProtKB/Swiss-Prot 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.
UniProtKB/Swiss-Prot 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.

Enzyme Numbers (IUBMB) for HDAC9 Gene

Gene Ontology (GO) - Molecular Function for HDAC9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005080 protein kinase C binding IPI 20188095
GO:0008134 transcription factor binding IPI 10748098
GO:0032041 NAD-dependent histone deacetylase activity (H3-K14 specific) IEA --
GO:0033558 protein deacetylase activity IDA 11535832
genes like me logo Genes that share ontologies with HDAC9: view
genes like me logo Genes that share phenotypes with HDAC9: view

Human Phenotype Ontology for HDAC9 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for HDAC9 Gene

MGI Knock Outs for HDAC9:

Animal Model Products

  • Taconic Biosciences Mouse Models for HDAC9

miRNA for HDAC9 Gene

miRTarBase miRNAs that target HDAC9

Flow Cytometry Products

No data available for Transcription Factor Targets and HOMER Transcription for HDAC9 Gene

Localization for HDAC9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HDAC9 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for HDAC9 Gene COMPARTMENTS Subcellular localization image for HDAC9 gene
Compartment Confidence
nucleus 5

Gene Ontology (GO) - Cellular Components for HDAC9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm TAS 12711221
genes like me logo Genes that share ontologies with HDAC9: view

Pathways & Interactions for HDAC9 Gene

genes like me logo Genes that share pathways with HDAC9: view

SIGNOR curated interactions for HDAC9 Gene

Inactivates:
Is inactivated by:

Gene Ontology (GO) - Biological Process for HDAC9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter IDA 10655483
GO:0006351 transcription, DNA-templated IEA --
GO:0007219 Notch signaling pathway TAS --
GO:0007507 heart development ISS --
GO:0016568 chromatin modification IEA --
genes like me logo Genes that share ontologies with HDAC9: view

Drugs & Compounds for HDAC9 Gene

(93) Drugs for HDAC9 Gene - From: DrugBank, ApexBio, DGIdb, HMDB, Tocris, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Valproic Acid Approved, Investigational Pharma inhibitor, Target HDAC1 inhibitor, Histone deacetylase (HDAC)inhibitors 312
Belinostat Approved, Investigational Pharma Inhibitor Histone deacetylase (HDAC)inhibitors 41
Vorinostat Approved, Investigational Pharma inhibitor HDAC inhibitor, Histone deacetylase (HDAC)inhibitors 240
butyric acid Experimental Pharma Full agonist, Agonist 348
MGCD-0103 Investigational Pharma inhibitor 0

(50) Additional Compounds for HDAC9 Gene - From: Novoseek, Tocris, and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
4-ene-Valproic acid
NSC 3852
3565-26-2
Sodium 4-Phenylbutyrate
1716-12-7

(5) Tocris Compounds for HDAC9 Gene

Compound Action Cas Number
M 344 Histone deacetylase inhibitor 251456-60-7
NSC 3852 Histone deacetylase inhibitor 3565-26-2
Scriptaid Histone deacetylase inhibitor 287383-59-9
Sodium 4-Phenylbutyrate Histone deacetylase inhibitor 1716-12-7
Trichostatin A Potent histone deacetylase inhibitor 58880-19-6

(10) ApexBio Compounds for HDAC9 Gene

Compound Action Cas Number
BMS-345541(free base) IKK-1/IKK-2 inhibitor,potent and selective 445430-58-0
HPOB HDAC6 inhibitor, potent and selective 1429651-50-2
MC1568 Class II HDAC inhibitor,potent and 852475-26-4
Parthenolide 20554-84-1
Pracinostat (SB939) Pan-HDAC inhibitor 929016-96-6
Santacruzamate A (CAY10683) 1477949-42-0
Sodium Phenylbutyrate Histone deacetylase inhibitor 1716-12-7
TMP269 HDAC 4/5/7/9 inhibitor 1314890-29-3
Tubacin HDAC6 inhibitor,potent,selective,reversible,cell-permeable 1350555-93-9
Valproic acid sodium salt (Sodium valproate) HDAC inhibitor 1069-66-5
genes like me logo Genes that share compounds with HDAC9: view

Drug Products

Transcripts for HDAC9 Gene

Unigene Clusters for HDAC9 Gene

Histone deacetylase 9:
Representative Sequences:

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for HDAC9 Gene

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:

Relevant External Links for HDAC9 Gene

GeneLoc Exon Structure for
HDAC9
ECgene alternative splicing isoforms for
HDAC9

Expression for HDAC9 Gene

mRNA expression in normal human tissues for HDAC9 Gene

Protein differential expression in normal tissues from HIPED for HDAC9 Gene

This gene is overexpressed in Heart (41.1) and Prostate (24.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for HDAC9 Gene



SOURCE GeneReport for Unigene cluster for HDAC9 Gene Hs.196054

mRNA Expression by UniProt/SwissProt for HDAC9 Gene

Q9UKV0-HDAC9_HUMAN
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).
genes like me logo Genes that share expression patterns with HDAC9: view

Protein tissue co-expression partners for HDAC9 Gene

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for HDAC9 Gene

Orthologs for HDAC9 Gene

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

Orthologs for HDAC9 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia HDAC9 35
  • 94.26 (n)
  • 96.72 (a)
HDAC9 36
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia HDAC9 35
  • 95.07 (n)
  • 98.03 (a)
HDAC9 36
  • 98 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Hdac9 35
  • 89.74 (n)
  • 92.4 (a)
Hdac9 16
Hdac9 36
  • 93 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia HDAC9 35
  • 99.69 (n)
  • 99.72 (a)
HDAC9 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Hdac9 35
  • 89.94 (n)
  • 92.5 (a)
oppossum
(Monodelphis domestica)
Mammalia HDAC9 36
  • 79 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia HDAC9 36
  • 84 (a)
OneToOne
chicken
(Gallus gallus)
Aves HDAC9 35
  • 81.69 (n)
  • 84.79 (a)
HDAC9 36
  • 79 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia -- 36
  • 82 (a)
OneToMany
-- 36
  • 77 (a)
OneToMany
-- 36
  • 75 (a)
OneToMany
African clawed frog
(Xenopus laevis)
Amphibia hdac9-A 35
zebrafish
(Danio rerio)
Actinopterygii hdac9 35
hdac9b 36
  • 54 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta HDAC4 36
  • 32 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea hda-4 36
  • 34 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes HDA1 36
  • 10 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 53 (a)
ManyToMany
CSA.5129 36
  • 32 (a)
ManyToMany
Species with no ortholog for HDAC9:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for HDAC9 Gene

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

Paralogs for HDAC9 Gene

Paralogs for HDAC9 Gene

genes like me logo Genes that share paralogs with HDAC9: view

Variants for HDAC9 Gene

Sequence variations from dbSNP and Humsavar for HDAC9 Gene

SNP ID Clin Chr 07 pos Sequence Context AA Info Type
VAR_064719 -
rs768830 -- 18,930,984(+) GTTCA(A/G)TAGTG intron-variant
rs768957 -- 18,182,274(-) GTATA(A/T)ATCAA intron-variant
rs768958 -- 18,182,598(-) ATTCA(C/T)TGACA intron-variant
rs769132 -- 18,699,147(-) CTTGG(G/T)TCTCA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for HDAC9 Gene

Variant ID Type Subtype PubMed ID
nsv887808 CNV Gain 21882294
nsv887809 CNV Loss 21882294
esv2734072 CNV Deletion 23290073
nsv366882 CNV Loss 16902084
esv999263 CNV Deletion 20482838
esv2734074 CNV Deletion 23290073
nsv887810 CNV Gain 21882294
nsv830914 CNV Gain 17160897
esv2476785 CNV Deletion 19546169
nsv830916 CNV Gain 17160897
nsv482942 CNV Gain 15286789
esv270583 CNV Insertion 20981092
nsv887811 CNV Loss 21882294
esv271208 CNV Insertion 20981092
esv32771 CNV Gain 17666407
esv272796 CNV Insertion 20981092
esv269171 CNV Insertion 20981092
esv2442723 CNV Deletion 19546169
esv2676378 CNV Deletion 23128226
nsv887812 CNV Loss 21882294
esv2582410 CNV Deletion 19546169
nsv5648 CNV Insertion 18451855
nsv516893 CNV Loss 19592680
nsv830917 CNV Gain 17160897
esv2664987 CNV Deletion 23128226
esv270803 CNV Insertion 20981092
esv29862 CNV Loss 19812545
nsv887813 CNV Gain 21882294
nsv483058 CNV Gain 15286789
nsv887814 CNV Loss 21882294
dgv2068e1 CNV Complex 17122850
esv2734075 CNV Deletion 23290073
esv2734076 CNV Deletion 23290073
esv2660622 CNV Deletion 23128226
esv2668991 CNV Deletion 23128226
esv2734077 CNV Deletion 23290073
nsv8065 CNV Loss 18304495
nsv528759 CNV Loss 19592680
nsv523497 CNV Loss 19592680
dgv7225n71 CNV Loss 21882294
nsv523468 CNV Loss 19592680
esv2734078 CNV Deletion 23290073
nsv887817 CNV Gain 21882294

Variation tolerance for HDAC9 Gene

Residual Variation Intolerance Score: 11.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.87; 35.04% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HDAC9 Gene

Human Gene Mutation Database (HGMD)
HDAC9

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HDAC9 Gene

Disorders for HDAC9 Gene

MalaCards: The human disease database

(17) MalaCards diseases for HDAC9 Gene - From: Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
peters anomaly
  • peters-plus syndrome
gastrointestinal neuroendocrine tumor
  • malignant gastrointestinal neuroendocrine tumor
corneal staphyloma
cutaneous t cell lymphoma
  • cutaneous t-cell lymphoma
jaw-winking syndrome
  • abnormal innervation syndrome of eyelid
- elite association - COSMIC cancer census association via MalaCards
Search HDAC9 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

HDAC9_HUMAN
  • 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. {ECO:0000269 PubMed:12706107}.

Relevant External Links for HDAC9

Genetic Association Database (GAD)
HDAC9
Human Genome Epidemiology (HuGE) Navigator
HDAC9
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HDAC9
genes like me logo Genes that share disorders with HDAC9: view

No data available for Genatlas for HDAC9 Gene

Publications for HDAC9 Gene

  1. MEF-2 function is modified by a novel co-repressor, MITR. (PMID: 10487760) Sparrow D.B. … Mohun T.J. (EMBO J. 1999) 2 3 4 67
  2. Carbamazepine is an inhibitor of histone deacetylases. (PMID: 15850602) Beutler A.S. … Walsh M.J. (Life Sci. 2005) 23 25 26
  3. Coaxing HIV-1 from resting CD4 T cells: histone deacetylase inhibition allows latent viral expression. (PMID: 15166525) Ylisastigui L. … Margolis D.M. (AIDS 2004) 23 25 26
  4. Increased human cytomegalovirus replication in fibroblasts after treatment with therapeutical plasma concentrations of valproic acid. (PMID: 15242819) Michaelis M. … Cinatl J. (Biochem. Pharmacol. 2004) 23 25 26
  5. Valproic acid inhibits histone deacetylase activity and suppresses excitotoxicity-induced GAPDH nuclear accumulation and apoptotic death in neurons. (PMID: 15289798) Kanai H. … Chuang D.M. (Pharmacogenomics J. 2004) 23 25 26

Products for HDAC9 Gene

Sources for HDAC9 Gene

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