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Aliases for HDAC3 Gene

Aliases for HDAC3 Gene

  • Histone Deacetylase 3 2 3 5
  • EC 3.5.1.98 4 63
  • RPD3-2 3 4
  • SMAP45 3 4
  • HD3 3 4
  • RPD3 3

External Ids for HDAC3 Gene

Previous GeneCards Identifiers for HDAC3 Gene

  • GC05U990082
  • GC05M140983
  • GC05M141028
  • GC05M140980
  • GC05M136145

Summaries for HDAC3 Gene

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. Among its related pathways are p75 NTR receptor-mediated signalling and Macrophage Differentiation and Growth Inhibition by METS. GO annotations related to this gene include chromatin binding and hydrolase activity. An important paralog of this gene is HDAC8.

UniProtKB/Swiss-Prot for HDAC3 Gene

  • 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. Participates in the BCL6 transcriptional repressor activity by deacetylating the H3 Lys-27 (H3K27) on enhancer elements, antagonizing EP300 acetyltransferase activity and repressing proximal gene expression. 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 (PubMed:21444723, PubMed:23911289). Contributes, together with XBP1 isoform 1, to the activation of NFE2L2-mediated HMOX1 transcription factor gene expression in a PI(3)K/mTORC2/Akt-dependent signaling pathway leading to endothelial cell (EC) survival under disturbed flow/oxidative stress (PubMed:25190803).

Tocris Summary for HDAC3 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 HDAC3 Gene

No data available for PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HDAC3 Gene

Genomics for HDAC3 Gene

Regulatory Elements for HDAC3 Gene

Enhancers for HDAC3 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 HDAC3 on UCSC Golden Path with GeneCards custom track

Promoters for HDAC3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around HDAC3 on UCSC Golden Path with GeneCards custom track

Genomic Location for HDAC3 Gene

Chromosome:
5
Start:
141,620,876 bp from pter
End:
141,636,870 bp from pter
Size:
15,995 bases
Orientation:
Minus strand

Genomic View for HDAC3 Gene

Genes around HDAC3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HDAC3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HDAC3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HDAC3 Gene

Proteins for HDAC3 Gene

  • Protein details for HDAC3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O15379-HDAC3_HUMAN
    Recommended name:
    Histone deacetylase 3
    Protein Accession:
    O15379
    Secondary Accessions:
    • D3DQE1
    • O43268
    • Q9UEI5
    • Q9UEV0

    Protein attributes for HDAC3 Gene

    Size:
    428 amino acids
    Molecular mass:
    48848 Da
    Quaternary structure:
    • 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. 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. Interact with SMRT/NCOR2 and BCL6 on DNA enhancer elements. Interacts with INSM1 (PubMed:10655483, PubMed:10669754, PubMed:10860984, PubMed:10898795, PubMed:11006275, PubMed:11466315, PubMed:11533236, PubMed:11861901, PubMed:14525983, PubMed:14633989, PubMed:15297880, PubMed:15927959, PubMed:16569215, PubMed:18417529, PubMed:19409814, PubMed:23911289). Interacts with XBP1 isoform 1; the interaction occurs in endothelial cell (EC) under disturbed flow (PubMed:25190803). Interacts (via C-terminus) with CCAR2 (via N-terminus). Interacts with and deacetylates MEF2D. Interacts with BEND3.

    Three dimensional structures from OCA and Proteopedia for HDAC3 Gene

    Alternative splice isoforms for HDAC3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for HDAC3 Gene

Proteomics data for HDAC3 Gene at MOPED

Post-translational modifications for HDAC3 Gene

Other Protein References for HDAC3 Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for HDAC3 Gene

Gene Families for HDAC3 Gene

Suggested Antigen Peptide Sequences for HDAC3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O15379

UniProtKB/Swiss-Prot:

HDAC3_HUMAN :
  • Belongs to the histone deacetylase family. HD type 1 subfamily.
Family:
  • Belongs to the histone deacetylase family. HD type 1 subfamily.
genes like me logo Genes that share domains with HDAC3: view

Function for HDAC3 Gene

Molecular function for HDAC3 Gene

GENATLAS Biochemistry:
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)
UniProtKB/Swiss-Prot CatalyticActivity:
Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone.
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), 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. Participates in the BCL6 transcriptional repressor activity by deacetylating the H3 Lys-27 (H3K27) on enhancer elements, antagonizing EP300 acetyltransferase activity and repressing proximal gene expression. 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 (PubMed:21444723, PubMed:23911289). Contributes, together with XBP1 isoform 1, to the activation of NFE2L2-mediated HMOX1 transcription factor gene expression in a PI(3)K/mTORC2/Akt-dependent signaling pathway leading to endothelial cell (EC) survival under disturbed flow/oxidative stress (PubMed:25190803).
UniProtKB/Swiss-Prot Induction:
Up-regulated by disturbed flow in umbilical vein endothelial cells in vitro (PubMed:25190803).

Enzyme Numbers (IUBMB) for HDAC3 Gene

Gene Ontology (GO) - Molecular Function for HDAC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with HDAC3: view
genes like me logo Genes that share phenotypes with HDAC3: view

Animal Models for HDAC3 Gene

MGI Knock Outs for HDAC3:

Animal Model Products

  • Taconic Biosciences Mouse Models for HDAC3

miRNA for HDAC3 Gene

miRTarBase miRNAs that target HDAC3

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for HDAC3 Gene

Localization for HDAC3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HDAC3 Gene

Nucleus. Cytoplasm. Cytoplasm, cytosol. Note=Colocalizes with XBP1 and AKT1 in the cytoplasm (PubMed:25190803). Predominantly expressed in the nucleus in the presence of CCAR2. {ECO:0000269 PubMed:21030595, ECO:0000269 PubMed:25190803}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for HDAC3 Gene COMPARTMENTS Subcellular localization image for HDAC3 gene
Compartment Confidence
cytoskeleton 5
cytosol 5
golgi apparatus 5
nucleus 5
plasma membrane 5

No data available for Gene Ontology (GO) - Cellular Components for HDAC3 Gene

Pathways & Interactions for HDAC3 Gene

SuperPathways for HDAC3 Gene

genes like me logo Genes that share pathways with HDAC3: view

SIGNOR curated interactions for HDAC3 Gene

Activates:
Is activated by:

Gene Ontology (GO) - Biological Process for HDAC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter IMP 12628926
GO:0006351 transcription, DNA-templated IEA --
GO:0006476 protein deacetylation IDA 17172643
GO:0007219 Notch signaling pathway TAS --
GO:0007623 circadian rhythm TAS --
genes like me logo Genes that share ontologies with HDAC3: view

Drugs & Compounds for HDAC3 Gene

(55) Drugs for HDAC3 Gene - From: DrugBank, ApexBio, DGIdb, HMDB, Tocris, and Novoseek

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

(8) Additional Compounds for HDAC3 Gene - From: Tocris and Novoseek

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

(5) Tocris Compounds for HDAC3 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

(20) ApexBio Compounds for HDAC3 Gene

Compound Action Cas Number
AR-42 (OSU-HDAC42) HDAC inhibitor,novel and potent 935881-37-1
Belinostat (PXD101) Hydroxamate-type HDAC inhibitor 414864-00-9
CI994 (Tacedinaline) HDAC inhibitor 112522-64-2
CUDC-101 Multitargeted HDAC inhibitor 1012054-59-9
CUDC-907 Potent PI3K/HDAC inhibitor 1339928-25-4
Droxinostat Selective HDAC inhibitor 99873-43-5
Entinostat (MS-275,SNDX-275) HDAC1 and HDAC3 inhibitor 209783-80-2
ITF2357 (Givinostat) HDAC inhibitor 732302-99-7
LAQ824 (NVP-LAQ824,Dacinostat) HDAC inhibitor,potent and novel 404951-53-7
M344 HDAC inhibitor,potent and cell-permeable 251456-60-7
Mocetinostat (MGCD0103, MG0103) HDAC inhibitor,isotype-selective and potent 726169-73-9
Panobinostat (LBH589) HDAC inhibitor 404950-80-7
PCI-24781 (CRA-024781) Pan-HDAC inhibitor 783355-60-2
Pracinostat (SB939) Pan-HDAC inhibitor 929016-96-6
Resminostat (RAS2410) Potent HDAC inhibitor 864814-88-0
RG2833 Brain-penetrant HDAC inhibitor 1215493-56-3
RGFP966 Specific HDAC3 inhibitor 1357389-11-7
Scriptaid HDAC inhibitor,novel and cell-permeable 287383-59-9
Trichostatin A (TSA) HDAC inhibitor 58880-19-6
Vorinostat (SAHA, MK0683) HDAC inhibitor 149647-78-9
genes like me logo Genes that share compounds with HDAC3: view

Drug Products

Transcripts for HDAC3 Gene

Unigene Clusters for HDAC3 Gene

Histone deacetylase 3:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for HDAC3 Gene

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: - - -
SP6: - -
SP7: - - - - - -
SP8:
SP9: -
SP10:
SP11:
SP12:

ExUns: 15 ^ 16
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:

Relevant External Links for HDAC3 Gene

GeneLoc Exon Structure for
HDAC3
ECgene alternative splicing isoforms for
HDAC3

Expression for HDAC3 Gene

mRNA expression in normal human tissues for HDAC3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for HDAC3 Gene

This gene is overexpressed in Retina (9.9), Peripheral blood mononuclear cells (9.7), and Monocytes (7.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for HDAC3 Gene



SOURCE GeneReport for Unigene cluster for HDAC3 Gene Hs.519632

mRNA Expression by UniProt/SwissProt for HDAC3 Gene

O15379-HDAC3_HUMAN
Tissue specificity: Widely expressed.
genes like me logo Genes that share expression patterns with HDAC3: view

Protein tissue co-expression partners for HDAC3 Gene

- Elite partner

Primer Products

No data available for mRNA differential expression in normal tissues for HDAC3 Gene

Orthologs for HDAC3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for HDAC3 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia HDAC3 35
  • 94.47 (n)
  • 100 (a)
HDAC3 36
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia HDAC3 35
  • 94.31 (n)
  • 100 (a)
HDAC3 36
  • 100 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Hdac3 35
  • 92.37 (n)
  • 99.77 (a)
Hdac3 16
Hdac3 36
  • 100 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia HDAC3 35
  • 99.77 (n)
  • 100 (a)
HDAC3 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Hdac3 35
  • 92.76 (n)
  • 99.77 (a)
oppossum
(Monodelphis domestica)
Mammalia HDAC3 36
  • 98 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 49 (a)
ManyToMany
chicken
(Gallus gallus)
Aves HDAC3 35
  • 81.78 (n)
  • 97.43 (a)
HDAC3 36
  • 98 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia HDAC3 36
  • 97 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia hdac3 35
  • 79.67 (n)
  • 95.56 (a)
Str.20485 35
zebrafish
(Danio rerio)
Actinopterygii hdac3 35
  • 77.8 (n)
  • 92.06 (a)
zgc55927 35
hdac3 36
  • 93 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta HDAC3 37
  • 65 (a)
Hdac3 35
  • 66.59 (n)
  • 67.06 (a)
Hdac3 36
  • 65 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001143 35
  • 67.45 (n)
  • 70.52 (a)
worm
(Caenorhabditis elegans)
Secernentea hda-1 37
  • 54 (a)
hda-2 37
  • 51 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RPD3 36
  • 55 (a)
OneToMany
HOS2 38
thale cress
(Arabidopsis thaliana)
eudicotyledons HDA9 35
  • 57.77 (n)
  • 58.17 (a)
soybean
(Glycine max)
eudicotyledons Gma.12683 35
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.2985 35
barley
(Hordeum vulgare)
Liliopsida Hv.1657 35
rice
(Oryza sativa)
Liliopsida Os04g0409600 35
  • 58.85 (n)
  • 56.54 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.837 35
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 70 (a)
OneToOne
Species with no ortholog for HDAC3:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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 blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for HDAC3 Gene

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

Paralogs for HDAC3 Gene

Paralogs for HDAC3 Gene

(5) SIMAP similar genes for HDAC3 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with HDAC3: view

Variants for HDAC3 Gene

Sequence variations from dbSNP and Humsavar for HDAC3 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
VAR_033988 -
rs2735187 -- 141,633,549(-) cgcac(C/T)cagct intron-variant
rs2735188 -- 141,631,309(-) AAACT(A/G)TAAAA intron-variant
rs1005666 -- 141,629,627(-) GGTCT(C/T)TCAGT intron-variant
rs250793 -- 141,631,620(+) acaga(C/T)gaaga intron-variant

Structural Variations from Database of Genomic Variants (DGV) for HDAC3 Gene

Variant ID Type Subtype PubMed ID
nsv516495 CNV Gain+Loss 19592680
nsv5033 CNV Insertion 18451855

Variation tolerance for HDAC3 Gene

Residual Variation Intolerance Score: 22.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.15; 39.02% of all genes are more intolerant (likely to be disease-causing)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Relevant External Links for HDAC3 Gene

Disorders for HDAC3 Gene

Relevant External Links for HDAC3

Genetic Association Database (GAD)
HDAC3
Human Genome Epidemiology (HuGE) Navigator
HDAC3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HDAC3

No disorders were found for HDAC3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HDAC3 Gene

Publications for HDAC3 Gene

  1. Differential display cloning of a novel human histone deacetylase (HDAC3) cDNA from PHA-activated immune cells. (PMID: 9464271) Dangond F. … Gullans S.R. (Biochem. Biophys. Res. Commun. 1998) 2 3 4 23 67
  2. Characterization of a human RPD3 ortholog, HDAC3. (PMID: 9501169) Emiliani S. … Verdin E. (Proc. Natl. Acad. Sci. U.S.A. 1998) 2 3 23
  3. Anti-tumor effect of apicidin on Ishikawa human endometrial cancer cells both in vitro and in vivo by blocking histone deacetylase 3 and 4. (PMID: 19956841) Ahn M.Y. … Kim H.S. (Int. J. Oncol. 2010) 3 23
  4. Histone deacetylase 3 is selectively involved in L3MBTL2-mediated transcriptional repression. (PMID: 20385135) Yoo J.Y. … Yoon H.G. (FEBS Lett. 2010) 3 23
  5. Colon cancer cells maintain low levels of pyruvate to avoid cell death caused by inhibition of HDAC1/HDAC3. (PMID: 18789002) Thangaraju M. … Ganapathy V. (Biochem. J. 2009) 3 23

Products for HDAC3 Gene

Sources for HDAC3 Gene

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