Hdac3 (histone deacetylase 3) - Rat Genome Database

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Gene: Hdac3 (histone deacetylase 3) Rattus norvegicus
Symbol: Hdac3
Name: histone deacetylase 3
RGD ID: 619977
Description: Enables several functions, including chromatin binding activity; enzyme binding activity; and transcription corepressor binding activity. Contributes to histone deacetylase activity. Involved in several processes, including cellular response to mechanical stimulus; negative regulation of cytokine production; and positive regulation of apoptotic process. Located in nucleus. Part of chromatin. Biomarker of acute kidney failure and impotence. Human ortholog(s) of this gene implicated in lung non-small cell carcinoma. Orthologous to human HDAC3 (histone deacetylase 3); PARTICIPATES IN histone modification pathway; INTERACTS WITH 1,2,4-trimethylbenzene; 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: HD3
RGD Orthologs
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Rat AssemblyChrPosition (strand)SourceGenome Browsers
GRCr81830,021,847 - 30,041,061 (-)NCBIGRCr8
mRatBN7.21829,770,637 - 29,789,850 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1829,770,636 - 29,793,856 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1829,874,943 - 29,894,123 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01830,636,921 - 30,656,319 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01829,972,266 - 29,991,665 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01831,073,057 - 31,094,347 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1831,073,058 - 31,094,303 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01830,764,344 - 30,782,387 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41830,857,209 - 30,875,986 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11830,883,855 - 30,902,632 (-)NCBI
Celera1829,414,681 - 29,434,382 (-)NCBICelera
Cytogenetic Map18p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(1->4)-beta-D-glucan  (ISO)
1,2,4-trimethylbenzene  (EXP)
1,2-dimethylhydrazine  (ISO)
15-deoxy-Delta(12,14)-prostaglandin J2  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4-phenylbutyric acid  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
8-Br-cAMP  (ISO)
acetylsalicylic acid  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
amitrole  (EXP)
ammonium chloride  (EXP)
benzamide  (ISO)
benzo[a]pyrene  (EXP)
bezafibrate  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
butyric acid  (EXP,ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
calcium oxalate  (EXP)
carbamazepine  (ISO)
chlorpyrifos  (ISO)
cisplatin  (ISO)
clobetasol  (ISO)
cobalt dichloride  (EXP)
copper(II) sulfate  (ISO)
curcumin  (ISO)
dexamethasone  (ISO)
diazinon  (ISO)
Dibutyl phosphate  (ISO)
dibutyl phthalate  (EXP)
disodium selenite  (ISO)
doxorubicin  (ISO)
endosulfan  (ISO)
epoxiconazole  (ISO)
ethanol  (EXP)
ethylene glycol  (EXP)
fenthion  (ISO)
folic acid  (ISO)
genistein  (ISO)
gentamycin  (EXP,ISO)
glyphosate  (ISO)
Honokiol  (ISO)
inulin  (ISO)
ivermectin  (ISO)
lead(0)  (ISO)
mancozeb  (ISO)
maneb  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (EXP,ISO)
melatonin  (ISO)
methidathion  (ISO)
methimazole  (EXP)
methoxyacetic acid  (ISO)
methylmercury chloride  (ISO)
metiram  (ISO)
mocetinostat  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
nickel dichloride  (EXP)
ochratoxin A  (EXP)
oxalic acid  (ISO)
ozone  (ISO)
p-toluidine  (EXP)
pelargonidin  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
resveratrol  (ISO)
RGFP966  (ISO)
rifampicin  (ISO)
sodium arsenite  (EXP,ISO)
streptozocin  (ISO)
sulfadimethoxine  (EXP)
sulforaphane  (ISO)
sunitinib  (ISO)
tangeretin  (ISO)
Tanshinone I  (ISO)
tauroursodeoxycholic acid  (EXP)
theophylline  (ISO)
thiram  (ISO)
Trapoxin B  (ISO)
Tributyltin oxide  (EXP)
trichostatin A  (ISO)
triphenyl phosphate  (ISO)
valproic acid  (ISO)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
cellular response to fluid shear stress  (ISO,ISS)
cellular response to mechanical stimulus  (IEP)
cellular response to parathyroid hormone stimulus  (IEP)
chromatin remodeling  (IEA)
circadian regulation of gene expression  (ISO,ISS)
cornified envelope assembly  (ISO)
DNA repair-dependent chromatin remodeling  (ISO)
epidermis development  (ISO)
epigenetic regulation of gene expression  (IBA)
establishment of mitotic spindle orientation  (ISO)
establishment of skin barrier  (ISO)
gene expression  (ISO)
in utero embryonic development  (ISO)
negative regulation of cardiac muscle cell differentiation  (ISO)
negative regulation of DNA-templated transcription  (ISO)
negative regulation of interleukin-1 production  (IMP)
negative regulation of JNK cascade  (ISO)
negative regulation of myotube differentiation  (ISO)
negative regulation of protein export from nucleus  (IMP)
negative regulation of transcription by RNA polymerase II  (ISO,ISS)
negative regulation of tumor necrosis factor production  (IMP)
neural precursor cell proliferation  (ISO)
positive regulation of cold-induced thermogenesis  (ISO,ISS)
positive regulation of neuron apoptotic process  (IMP)
positive regulation of protein import into nucleus  (ISO,ISS)
positive regulation of protein phosphorylation  (ISO,ISS)
positive regulation of protein ubiquitination  (ISO,ISS)
positive regulation of TOR signaling  (ISO,ISS)
positive regulation of transcription by RNA polymerase II  (ISO,ISS)
positive regulation of type B pancreatic cell apoptotic process  (IMP)
protein modification process  (IDA)
regulation of circadian rhythm  (ISO,ISS)
regulation of mitotic cell cycle  (ISO)
regulation of multicellular organism growth  (ISO)
regulation of protein stability  (ISO,ISS)
response to dexamethasone  (IEP)
response to nutrient levels  (IEP)
response to xenobiotic stimulus  (IEP)
spindle assembly  (ISO)
transcription by RNA polymerase II  (ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View

References - curated
# Reference Title Reference Citation
1. Sepsis and glucocorticoids upregulate p300 and downregulate HDAC6 expression and activity in skeletal muscle. Alamdari N, etal., Am J Physiol Regul Integr Comp Physiol. 2010 Aug;299(2):R509-20. doi: 10.1152/ajpregu.00858.2009. Epub 2010 Jun 10.
2. Selective toxicity by HDAC3 in neurons: regulation by Akt and GSK3beta. Bardai FH and D'Mello SR, J Neurosci. 2011 Feb 2;31(5):1746-51. doi: 10.1523/JNEUROSCI.5704-10.2011.
3. Histone deacetylase-1 (HDAC1) is a molecular switch between neuronal survival and death. Bardai FH, etal., J Biol Chem. 2012 Oct 12;287(42):35444-53. doi: 10.1074/jbc.M112.394544. Epub 2012 Aug 23.
4. Cloning and expression of a murine histone deacetylase 3 (mHdac3) cDNA and mapping to a region of conserved synteny between murine chromosome 18 and human chromosome 5. Dangond F, etal., Mol Cell Biol Res Commun 1999 Aug;2(2):91-6.
5. Transcriptional repression of histone deacetylase 3 by the histone demethylase KDM2A is coupled to tumorigenicity of lung cancer cells. Dhar SS, etal., J Biol Chem. 2014 Mar 14;289(11):7483-96. doi: 10.1074/jbc.M113.521625. Epub 2014 Jan 30.
6. Histone deacetylase 3 prepares brown adipose tissue for acute thermogenic challenge. Emmett MJ, etal., Nature. 2017 Jun 22;546(7659):544-548. doi: 10.1038/nature22819. Epub 2017 Jun 14.
7. Histone deacetylase-3 mediates positive feedback relationship between anaphylaxis and tumor metastasis. Eom S, etal., J Biol Chem. 2014 Apr 25;289(17):12126-44. doi: 10.1074/jbc.M113.521245. Epub 2014 Mar 11.
8. Ataxin-3 represses transcription via chromatin binding, interaction with histone deacetylase 3, and histone deacetylation. Evert BO, etal., J Neurosci. 2006 Nov 1;26(44):11474-86.
9. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
10. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
11. Valproic acid prevents penile fibrosis and erectile dysfunction in cavernous nerve-injured rats. Hannan JL, etal., J Sex Med. 2014 Jun;11(6):1442-51. doi: 10.1111/jsm.12522. Epub 2014 Mar 18.
12. Selective histone deacetylase (HDAC) inhibition imparts beneficial effects in Huntington's disease mice: implications for the ubiquitin-proteasomal and autophagy systems. Jia H, etal., Hum Mol Genet. 2012 Dec 15;21(24):5280-93. doi: 10.1093/hmg/dds379. Epub 2012 Sep 10.
13. HDAC inhibition suppresses cardiac hypertrophy and fibrosis in DOCA-salt hypertensive rats via regulation of HDAC6/HDAC8 enzyme activity. Kee HJ, etal., Kidney Blood Press Res. 2013;37(4-5):229-39. doi: 10.1159/000350148. Epub 2013 Jul 8.
14. Drug-induced inactivation or gene silencing of class I histone deacetylases suppresses ovarian cancer cell growth: implications for therapy. Khabele D, etal., Cancer Biol Ther. 2007 May;6(5):795-801. Epub 2007 Feb 14.
15. Clinically relevant concentrations of valproic acid modulate melatonin MT(1) receptor, HDAC and MeCP2 mRNA expression in C6 glioma cells. Kim B, etal., Eur J Pharmacol. 2008 Jul 28;589(1-3):45-8. Epub 2008 May 7.
16. Histone deacetylase 3 mediates allergic skin inflammation by regulating expression of MCP1 protein. Kim Y, etal., J Biol Chem. 2012 Jul 27;287(31):25844-59. doi: 10.1074/jbc.M112.348284. Epub 2012 Jun 7.
17. High expression of liver histone deacetylase 3 contributes to high-fat-diet-induced metabolic syndrome by suppressing the PPAR-gamma and LXR-alpha-pathways in E3 rats. Li D, etal., Mol Cell Endocrinol. 2011 Sep 15;344(1-2):69-80. doi: 10.1016/j.mce.2011.06.028. Epub 2011 Jul 8.
18. Histone deacetylases 1 and 3 but not 2 mediate cytokine-induced beta cell apoptosis in INS-1 cells and dispersed primary islets from rats and are differentially regulated in the islets of type 1 diabetic children. Lundh M, etal., Diabetologia. 2012 Sep;55(9):2421-31. doi: 10.1007/s00125-012-2615-0. Epub 2012 Jul 7.
19. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
20. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
21. Physical and functional HAT/HDAC interplay regulates protein acetylation balance. Peserico A and Simone C, J Biomed Biotechnol. 2011;2011:371832. doi: 10.1155/2011/371832. Epub 2010 Dec 5.
22. HDAC3 interacts with sumoylated C/EBPalpha to negatively regulate the LXRalpha expression in rat hepatocytes. Ren J, etal., Mol Cell Endocrinol. 2013 Jul 15;374(1-2):35-45. doi: 10.1016/j.mce.2013.04.013. Epub 2013 Apr 29.
23. GOA pipeline RGD automated data pipeline
24. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
25. Cisplatin induces Sirt1 in association with histone deacetylation and increased Werner syndrome protein in the kidney. Sakao Y, etal., Clin Exp Nephrol. 2011 Jun;15(3):363-72. doi: 10.1007/s10157-011-0421-5. Epub 2011 Mar 18.
26. Effect of Histone Deacetylase HDAC3 on Cytokines IL-18, IL-12 and TNF-α in Patients with Intrahepatic Cholestasis of Pregnancy. Shao Y, etal., Cell Physiol Biochem. 2017;42(4):1294-1302. doi: 10.1159/000478958. Epub 2017 Jul 11.
27. HDAC4 represses matrix metalloproteinase-13 transcription in osteoblastic cells, and parathyroid hormone controls this repression. Shimizu E, etal., J Biol Chem. 2010 Mar 26;285(13):9616-26. doi: 10.1074/jbc.M109.094862. Epub 2010 Jan 22.
28. In cortical neurons HDAC3 activity suppresses RD4-dependent SMRT export. Soriano FX and Hardingham GE, PLoS One. 2011;6(6):e21056. doi: 10.1371/journal.pone.0021056. Epub 2011 Jun 9.
29. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
30. HDAC up-regulation in early colon field carcinogenesis is involved in cell tumorigenicity through regulation of chromatin structure. Stypula-Cyrus Y, etal., PLoS One. 2013 May 28;8(5):e64600. doi: 10.1371/journal.pone.0064600. Print 2013.
31. Histone deacetylases 1, 2 and 3 are highly expressed in prostate cancer and HDAC2 expression is associated with shorter PSA relapse time after radical prostatectomy. Weichert W, etal., Br J Cancer. 2008 Feb 12;98(3):604-10. Epub 2008 Jan 22.
32. Expression of class I histone deacetylases indicates poor prognosis in endometrioid subtypes of ovarian and endometrial carcinomas. Weichert W, etal., Neoplasia. 2008 Sep;10(9):1021-7.
33. Chronic cerebrovascular hypoperfusion affects global DNA methylation and histone acetylation in rat brain. Wu X, etal., Neurosci Bull. 2013 Dec;29(6):685-92. doi: 10.1007/s12264-013-1345-8. Epub 2013 May 28.
34. Nuclear corepressor is required for inhibition of phosphoenolpyruvate carboxykinase expression by tumor necrosis factor-alpha. Yan J, etal., Mol Endocrinol. 2007 Jul;21(7):1630-41. Epub 2007 Apr 24.
35. Histone deacetylases modulate vascular smooth muscle cell migration induced by cyclic mechanical strain. Yan ZQ, etal., J Biomech. 2009 May 11;42(7):945-8. doi: 10.1016/j.jbiomech.2009.01.012. Epub 2009 Mar 3.
36. Histone deacetylation inhibition in pulmonary hypertension: therapeutic potential of valproic acid and suberoylanilide hydroxamic acid. Zhao L, etal., Circulation. 2012 Jul 24;126(4):455-67. doi: 10.1161/CIRCULATIONAHA.112.103176. Epub 2012 Jun 18.
37. Inhibited HDAC3 or Elevated MicroRNA-494-3p Plays a Protective Role in Myocardial Ischemia-Reperfusion Injury via Suppression of BRD4. Zheng W, etal., Mol Neurobiol. 2021 Sep;58(9):4268-4279. doi: 10.1007/s12035-021-02369-y. Epub 2021 May 12.
38. Histone deacetylase 3 implicated in the pathogenesis of children glioma by promoting glioma cell proliferation and migration. Zhu J, etal., Brain Res. 2013 Jul 3;1520:15-22. doi: 10.1016/j.brainres.2013.04.061. Epub 2013 May 15.
Additional References at PubMed
PMID:10869435   PMID:10983972   PMID:11641274   PMID:11804585   PMID:11931768   PMID:12403844   PMID:12590135   PMID:12628926   PMID:14980219   PMID:15051733   PMID:15489334   PMID:15681609  
PMID:15832170   PMID:16033423   PMID:16569215   PMID:16924111   PMID:17158926   PMID:17172643   PMID:17464331   PMID:17785205   PMID:18326024   PMID:18347167   PMID:18417529   PMID:18458156  
PMID:18483244   PMID:18854353   PMID:19037247   PMID:19463978   PMID:21030595   PMID:22297488   PMID:22349439   PMID:22395468   PMID:23867755   PMID:23980619   PMID:24565863   PMID:25190803  
PMID:25241747   PMID:25592718   PMID:26776516   PMID:26890755   PMID:27798112   PMID:28300292   PMID:28957873   PMID:29571524   PMID:31000586   PMID:31883511   PMID:32679145   PMID:33217223  
PMID:33932446   PMID:34971719   PMID:35025700   PMID:36201274  


Comparative Map Data
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
GRCr81830,021,847 - 30,041,061 (-)NCBIGRCr8
mRatBN7.21829,770,637 - 29,789,850 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1829,770,636 - 29,793,856 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1829,874,943 - 29,894,123 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01830,636,921 - 30,656,319 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01829,972,266 - 29,991,665 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01831,073,057 - 31,094,347 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1831,073,058 - 31,094,303 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01830,764,344 - 30,782,387 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41830,857,209 - 30,875,986 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11830,883,855 - 30,902,632 (-)NCBI
Celera1829,414,681 - 29,434,382 (-)NCBICelera
Cytogenetic Map18p11NCBI
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
GRCh385141,620,881 - 141,636,849 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5141,620,876 - 141,636,849 (-)EnsemblGRCh38hg38GRCh38
GRCh375141,000,448 - 141,016,416 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 365140,980,627 - 140,996,607 (-)NCBINCBI36Build 36hg18NCBI36
Build 345140,980,626 - 140,996,596NCBI
Celera5137,077,171 - 137,093,151 (-)NCBICelera
Cytogenetic Map5q31.3NCBI
HuRef5136,145,083 - 136,160,930 (-)NCBIHuRef
CHM1_15140,433,725 - 140,449,704 (-)NCBICHM1_1
T2T-CHM13v2.05142,146,886 - 142,162,855 (-)NCBIT2T-CHM13v2.0
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
GRCm391838,070,024 - 38,088,073 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1838,068,897 - 38,088,069 (-)EnsemblGRCm39 Ensembl
GRCm381837,936,971 - 37,955,015 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1837,935,844 - 37,955,016 (-)EnsemblGRCm38mm10GRCm38
MGSCv371838,096,625 - 38,114,642 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361838,062,953 - 38,080,909 (-)NCBIMGSCv36mm8
Celera1839,280,295 - 39,298,302 (-)NCBICelera
Cytogenetic Map18B3NCBI
cM Map1819.81NCBI
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
ChiLan1.0 EnsemblNW_00495541512,138,870 - 12,154,234 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541512,138,520 - 12,154,234 (+)NCBIChiLan1.0ChiLan1.0
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
NHGRI_mPanPan1-v24136,869,766 - 136,885,755 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan15135,009,317 - 135,025,306 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v05136,981,790 - 136,997,786 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.15143,094,406 - 143,110,322 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5143,094,406 - 143,110,322 (-)Ensemblpanpan1.1panPan2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
CanFam3.1236,583,283 - 36,598,121 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl236,583,283 - 36,597,682 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha233,635,234 - 33,650,086 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0237,037,462 - 37,052,393 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl237,037,381 - 37,052,025 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1234,112,034 - 34,126,890 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0234,923,559 - 34,938,422 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0235,730,823 - 35,745,706 (-)NCBIUU_Cfam_GSD_1.0
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
HiC_Itri_2NW_024407213150,956,557 - 150,972,579 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493650412,530,528 - 12,546,556 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493650412,530,546 - 12,546,556 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
Sscrofa11.1 Ensembl2143,273,192 - 143,287,399 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.12143,273,188 - 143,287,421 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.22149,475,764 - 149,490,030 (-)NCBISscrofa10.2Sscrofa10.2susScr3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
ChlSab1.12344,246,296 - 44,263,127 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603433,589,487 - 33,606,357 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
HetGla_female_1.0 EnsemblNW_004624774845,358 - 863,809 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624774845,970 - 864,080 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Variants in Hdac3
141 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:74
Count of miRNA genes:55
Interacting mature miRNAs:68
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2312598Bp340Blood pressure QTL 3400.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)18130558703Rat
2300180Bmd67Bone mineral density QTL 674.80.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)18134291613Rat
2293661Bss50Bone structure and strength QTL 504.640.0003lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)18134291613Rat
61388Bp2Blood pressure QTL 23.23arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)18135374722Rat
9589153Insul31Insulin level QTL 317.150.05blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)18142547119Rat
2299160Iddm35Insulin dependent diabetes mellitus QTL 352.79blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)18420794160377792Rat
2312568Glom21Glomerulus QTL 2120.005kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)18518585840503530Rat
2293708Bss46Bone structure and strength QTL 468.80.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)181179151863636873Rat
1578661Bss20Bone structure and strength QTL 203.7femur morphology trait (VT:0000559)femoral neck cross-sectional area (CMO:0001697)181179151883218561Rat
1578667Bss21Bone structure and strength QTL 213.5femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)181179151883218561Rat
61382Bp46Blood pressure QTL 4618.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181194179131393320Rat
631264Scl22Serum cholesterol level QTL 226.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)181194179131393320Rat
1331766Bp236Blood pressure QTL 2363.022arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)181194429931359530Rat
61375Bp41Blood pressure QTL 412.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)181194429941122201Rat
1331753Bp231Blood pressure QTL 2313.643arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181194429952293055Rat
1358358Sradr6Stress Responsive Adrenal Weight QTL 62.49adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)181194429959330563Rat
6903359Bp355Blood pressure QTL 3553.6arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181194454459796478Rat
2313082Bss85Bone structure and strength QTL 850.80.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)181495133759951337Rat
1358193Emca2Estrogen-induced mammary cancer QTL 21.6mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)181800759963571040Rat
1331735Rf44Renal function QTL 442.981urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)181823456431359530Rat
1331775Bp235Blood pressure QTL 2353.201arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)181823456431359530Rat
1600373Mamtr6Mammary tumor resistance QTL 6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)181927890183218561Rat
1331741Bp232Blood pressure QTL 2323.59112arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)182137289383213037Rat
1641923Colcr8Colorectal carcinoma resistance QTL 83.10.0014intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)182206624252293055Rat
1331733Bp233Blood pressure QTL 2333.97196arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182479697779788953Rat
2325839Bp348Blood pressure QTL 3480.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182557098570570985Rat
12904673Cm127Cardiac mass QTL 1270.005heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)182654808246969551Rat
12904675Am19Aortic mass QTL 190.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)182654808246969551Rat
12904677Kidm72Kidney mass QTL 720.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)182654808246969551Rat
12904668Bw188Body weight QTL 1880.03body mass (VT:0001259)body weight (CMO:0000012)182654808246969551Rat
12904669Cm125Cardiac mass QTL 1250.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)182654808246969551Rat
12904670Cm126Cardiac mass QTL 1260.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)182654808246969551Rat
2301413Bp318Blood pressure QTL 3180.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182654808246969551Rat
2293704Bss35Bone structure and strength QTL 354.590.0002femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)182896485373964853Rat
2300157Bmd66Bone mineral density QTL 6613.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)182896485373964853Rat
2300177Bmd65Bone mineral density QTL 6519.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)182896485373964853Rat

Markers in Region
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21829,770,659 - 29,770,857 (+)MAPPERmRatBN7.2
Rnor_6.01831,072,987 - 31,073,184NCBIRnor6.0
Rnor_5.01830,764,274 - 30,764,471UniSTSRnor5.0
RGSC_v3.41830,857,139 - 30,857,336UniSTSRGSC3.4
Celera1829,414,611 - 29,414,808UniSTS
RH 3.4 Map18444.2UniSTS
Cytogenetic Map18p11UniSTS


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
Medium 3 41 57 41 19 41 8 11 74 35 41 11 8
Low 2
Below cutoff


RefSeq Acc Id: ENSRNOT00000060417   ⟹   ENSRNOP00000057161
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1829,770,731 - 29,779,888 (-)Ensembl
Rnor_6.0 Ensembl1831,073,058 - 31,082,101 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000078667   ⟹   ENSRNOP00000071791
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1829,770,636 - 29,789,811 (-)Ensembl
Rnor_6.0 Ensembl1831,073,569 - 31,094,303 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000084735   ⟹   ENSRNOP00000074429
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1829,770,637 - 29,793,856 (-)Ensembl
Rnor_6.0 Ensembl1831,073,058 - 31,082,101 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000109932   ⟹   ENSRNOP00000091923
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1829,770,719 - 29,789,797 (-)Ensembl
RefSeq Acc Id: NM_053448   ⟹   NP_445900
RefSeq Status: VALIDATED
Rat AssemblyChrPosition (strand)Source
GRCr81830,021,847 - 30,041,025 (-)NCBI
mRatBN7.21829,770,637 - 29,789,817 (-)NCBI
Rnor_6.01831,073,057 - 31,094,347 (-)NCBI
Rnor_5.01830,764,344 - 30,782,387 (-)NCBI
RGSC_v3.41830,857,209 - 30,875,986 (-)RGD
Celera1829,414,681 - 29,434,382 (-)RGD
RefSeq Acc Id: XM_063277633   ⟹   XP_063133703
Rat AssemblyChrPosition (strand)Source
GRCr81830,026,802 - 30,041,061 (-)NCBI
RefSeq Acc Id: NP_445900   ⟸   NM_053448
- UniProtKB: Q6P6W3 (UniProtKB/Swiss-Prot),   Q99PA0 (UniProtKB/Swiss-Prot),   A6J3D3 (UniProtKB/TrEMBL),   A0A0G2K1C8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000074429   ⟸   ENSRNOT00000084735
RefSeq Acc Id: ENSRNOP00000057161   ⟸   ENSRNOT00000060417
RefSeq Acc Id: ENSRNOP00000071791   ⟸   ENSRNOT00000078667
RefSeq Acc Id: ENSRNOP00000091923   ⟸   ENSRNOT00000109932
RefSeq Acc Id: XP_063133703   ⟸   XM_063277633
- Peptide Label: isoform X1
- UniProtKB: A6J3D7 (UniProtKB/TrEMBL)
Protein Domains
Histone deacetylase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6P6W3-F1-model_v2 AlphaFold Q6P6W3 1-428 view protein structure


eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

RGD ID:13700741
Promoter ID:EPDNEW_R11261
Type:initiation region
Description:histone deacetylase 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Rat AssemblyChrPosition (strand)Source
Rnor_6.01831,094,357 - 31,094,417EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:619977 AgrOrtholog
BioCyc Gene G2FUF-7789 BioCyc
Ensembl Genes ENSRNOG00000019618 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00055024500 UniProtKB/Swiss-Prot
  ENSRNOG00060021231 UniProtKB/Swiss-Prot
  ENSRNOG00065013286 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000060417.5 UniProtKB/TrEMBL
  ENSRNOT00000078667.2 UniProtKB/TrEMBL
  ENSRNOT00000084735.2 UniProtKB/TrEMBL
  ENSRNOT00000109932.1 UniProtKB/TrEMBL
  ENSRNOT00055042176 UniProtKB/Swiss-Prot
  ENSRNOT00055042191 UniProtKB/Swiss-Prot
  ENSRNOT00060036929 UniProtKB/Swiss-Prot
  ENSRNOT00060036994 UniProtKB/Swiss-Prot
  ENSRNOT00065021830 UniProtKB/Swiss-Prot
  ENSRNOT00065021835 UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.800.20 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro His_deacetylse UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  His_deacetylse_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  His_deacetylse_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  His_deacetylse_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ureohydrolase_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:84578 UniProtKB/Swiss-Prot
Pfam Hist_deacetyl UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Hdac3 PhenoGen
PIRSF His_deacetylse_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000019618 RatGTEx
  ENSRNOG00055024500 RatGTEx
  ENSRNOG00060021231 RatGTEx
  ENSRNOG00065013286 RatGTEx
Superfamily-SCOP SSF52768 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  A0A0G2K814_RAT UniProtKB/TrEMBL
UniProt Secondary Q99PA0 UniProtKB/Swiss-Prot

Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Hdac3  histone deacetylase 3      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Hdac3  histone deacetylase 3      Symbol and Name status set to provisional 70820 PROVISIONAL