HDAC3 (histone deacetylase 3) - Rat Genome Database

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Gene: HDAC3 (histone deacetylase 3) Homo sapiens
Analyze
Symbol: HDAC3
Name: histone deacetylase 3
RGD ID: 731326
HGNC Page HGNC
Description: Exhibits several functions, including cyclin binding activity; histone deacetylase binding activity; and transcription factor binding activity. Involved in several processes, including positive regulation of protein import into nucleus; regulation of intracellular signal transduction; and regulation of transcription by RNA polymerase II. Localizes to several cellular components, including Golgi apparatus; histone deacetylase complex; and mitotic spindle. Implicated in lung non-small cell carcinoma. Biomarker of several diseases, including colorectal cancer; intrahepatic cholestasis of pregnancy; pulmonary hypertension; reproductive organ cancer (multiple); and type 1 diabetes mellitus.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: HD3; KDAC3; RPD3; RPD3-2; SMAP45
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl5141,620,876 - 141,636,849 (-)EnsemblGRCh38hg38GRCh38
GRCh385141,620,881 - 141,636,849 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh375141,000,448 - 141,016,416 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 365140,980,627 - 140,996,607 (-)NCBINCBI36hg18NCBI36
Build 345140,980,626 - 140,996,596NCBI
Celera5137,077,171 - 137,093,151 (-)NCBI
Cytogenetic Map5q31.3NCBI
HuRef5136,145,083 - 136,160,930 (-)NCBIHuRef
CHM1_15140,433,725 - 140,449,704 (-)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
cellular response to fluid shear stress  (IDA)
cellular response to mechanical stimulus  (ISO)
cellular response to parathyroid hormone stimulus  (ISO)
chromatin organization  (TAS)
circadian regulation of gene expression  (ISO,ISS)
circadian rhythm  (TAS)
histone deacetylation  (ISO)
histone H3 deacetylation  (IBA,IEA,ISO)
histone H4 deacetylation  (IBA,ISO)
histone H4-K12 deacetylation  (ISO)
intracellular receptor signaling pathway  (TAS)
negative regulation of apoptotic process  (TAS)
negative regulation of cardiac muscle cell differentiation  (ISO)
negative regulation of DNA-binding transcription factor activity  (ISO)
negative regulation of interleukin-1 production  (ISO)
negative regulation of JNK cascade  (IMP)
negative regulation of myotube differentiation  (IMP)
negative regulation of protein export from nucleus  (ISO)
negative regulation of transcription by RNA polymerase II  (IDA,IMP,ISO)
negative regulation of transcription, DNA-templated  (IEA,IMP)
negative regulation of tumor necrosis factor production  (ISO)
positive regulation of cold-induced thermogenesis  (ISS)
positive regulation of neuron apoptotic process  (ISO)
positive regulation of protein import into nucleus  (IDA)
positive regulation of protein phosphorylation  (IDA)
positive regulation of protein ubiquitination  (ISS)
positive regulation of TOR signaling  (IMP)
positive regulation of transcription by RNA polymerase II  (IBA,IDA)
positive regulation of type B pancreatic cell apoptotic process  (ISO)
protein deacetylation  (IDA)
regulation of circadian rhythm  (ISS)
regulation of lipid metabolic process  (TAS)
regulation of mitotic cell cycle  (ISO)
regulation of multicellular organism growth  (ISO)
regulation of protein stability  (IDA)
response to dexamethasone  (ISO)
response to drug  (ISO)
response to nutrient levels  (ISO)
spindle assembly  (IMP)
transcription initiation from RNA polymerase II promoter  (TAS)

Cellular Component
chromatin  (ISO)
cytoplasm  (IDA,ISO,TAS)
cytosol  (IDA)
Golgi apparatus  (IDA)
histone deacetylase complex  (IBA,IDA,TAS)
mitotic spindle  (IDA)
nucleoplasm  (IDA,TAS)
nucleus  (IDA,IEA,ISO,TAS)
plasma membrane  (IDA)
transcription repressor complex  (IDA)

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
Ependymoma  (IAGP)
References

References - curated
1. Bardai FH, etal., J Biol Chem. 2012 Oct 12;287(42):35444-53. doi: 10.1074/jbc.M112.394544. Epub 2012 Aug 23.
2. Dhar SS, etal., J Biol Chem. 2014 Mar 14;289(11):7483-96. doi: 10.1074/jbc.M113.521625. Epub 2014 Jan 30.
3. Eom S, etal., J Biol Chem. 2014 Apr 25;289(17):12126-44. doi: 10.1074/jbc.M113.521245. Epub 2014 Mar 11.
4. GOA_HUMAN data from the GO Consortium
5. Hannan JL, etal., J Sex Med. 2014 Jun;11(6):1442-51. doi: 10.1111/jsm.12522. Epub 2014 Mar 18.
6. Jia H, etal., Hum Mol Genet. 2012 Dec 15;21(24):5280-93. doi: 10.1093/hmg/dds379. Epub 2012 Sep 10.
7. Khabele D, etal., Cancer Biol Ther. 2007 May;6(5):795-801. Epub 2007 Feb 14.
8. 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.
9. Lundh M, etal., Diabetologia. 2012 Sep;55(9):2421-31. doi: 10.1007/s00125-012-2615-0. Epub 2012 Jul 7.
10. Peserico A and Simone C, J Biomed Biotechnol. 2011;2011:371832. doi: 10.1155/2011/371832. Epub 2010 Dec 5.
11. RGD automated import pipeline for gene-chemical interactions
12. Sakao Y, etal., Clin Exp Nephrol. 2011 Jun;15(3):363-72. doi: 10.1007/s10157-011-0421-5. Epub 2011 Mar 18.
13. Shao Y, etal., Cell Physiol Biochem. 2017;42(4):1294-1302. doi: 10.1159/000478958. Epub 2017 Jul 11.
14. Stypula-Cyrus Y, etal., PLoS One. 2013 May 28;8(5):e64600. doi: 10.1371/journal.pone.0064600. Print 2013.
15. Weichert W, etal., Br J Cancer. 2008 Feb 12;98(3):604-10. Epub 2008 Jan 22.
16. Weichert W, etal., Neoplasia. 2008 Sep;10(9):1021-7.
17. Wu X, etal., Neurosci Bull. 2013 Dec;29(6):685-92. doi: 10.1007/s12264-013-1345-8. Epub 2013 May 28.
18. Zhao L, etal., Circulation. 2012 Jul 24;126(4):455-67. doi: 10.1161/CIRCULATIONAHA.112.103176. Epub 2012 Jun 18.
19. 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:9346952   PMID:9360932   PMID:9464271   PMID:9501169   PMID:9722949   PMID:10051405   PMID:10220385   PMID:10490602   PMID:10575214   PMID:10581039   PMID:10655483   PMID:10669754  
PMID:10777477   PMID:10809664   PMID:10860984   PMID:10869435   PMID:10898795   PMID:10944117   PMID:10958676   PMID:10983972   PMID:11006275   PMID:11013263   PMID:11022042   PMID:11046157  
PMID:11259576   PMID:11302704   PMID:11439334   PMID:11463856   PMID:11466315   PMID:11470869   PMID:11486036   PMID:11509652   PMID:11533236   PMID:11533489   PMID:11567998   PMID:11641274  
PMID:11641275   PMID:11777905   PMID:11779848   PMID:11788710   PMID:11804585   PMID:11861901   PMID:11867539   PMID:11867749   PMID:11889044   PMID:11923873   PMID:11931768   PMID:12015313  
PMID:12032081   PMID:12048199   PMID:12150997   PMID:12205093   PMID:12239342   PMID:12242670   PMID:12371150   PMID:12393887   PMID:12403844   PMID:12419806   PMID:12477932   PMID:12479814  
PMID:12502735   PMID:12535528   PMID:12590135   PMID:12628926   PMID:12711221   PMID:12853483   PMID:12861000   PMID:12943985   PMID:12972430   PMID:14521922   PMID:14525983   PMID:14527417  
PMID:14633989   PMID:14668799   PMID:14684825   PMID:14722073   PMID:15016912   PMID:15051733   PMID:15140878   PMID:15184363   PMID:15192014   PMID:15194749   PMID:15292260   PMID:15297880  
PMID:15333839   PMID:15356147   PMID:15467736   PMID:15469820   PMID:15489334   PMID:15494311   PMID:15558026   PMID:15561719   PMID:15572445   PMID:15601853   PMID:15619633   PMID:15653507  
PMID:15711539   PMID:15713663   PMID:15761026   PMID:15805470   PMID:15831498   PMID:15831516   PMID:15832170   PMID:15835920   PMID:15837933   PMID:15917248   PMID:15927959   PMID:16022908  
PMID:16033423   PMID:16055724   PMID:16129885   PMID:16186112   PMID:16195251   PMID:16204234   PMID:16227606   PMID:16249187   PMID:16288017   PMID:16298343   PMID:16371367   PMID:16432238  
PMID:16461912   PMID:16469706   PMID:16481466   PMID:16481475   PMID:16528103   PMID:16532030   PMID:16537907   PMID:16569215   PMID:16652147   PMID:16712523   PMID:16730330   PMID:16820529  
PMID:16847267   PMID:16849648   PMID:16917504   PMID:16919237   PMID:16924111   PMID:16943425   PMID:16980585   PMID:16987993   PMID:17007107   PMID:17008592   PMID:17015477   PMID:17053781  
PMID:17075044   PMID:17079677   PMID:17101790   PMID:17126328   PMID:17141982   PMID:17158926   PMID:17172643   PMID:17182846   PMID:17227585   PMID:17242407   PMID:17245431   PMID:17273746  
PMID:17311813   PMID:17353931   PMID:17620012   PMID:17621263   PMID:17675290   PMID:17699109   PMID:17785205   PMID:17786334   PMID:17849419   PMID:17873065   PMID:17895379   PMID:17908689  
PMID:17910034   PMID:17925399   PMID:17956871   PMID:17956988   PMID:17970752   PMID:18037959   PMID:18097041   PMID:18202150   PMID:18241676   PMID:18245468   PMID:18279852   PMID:18321663  
PMID:18326024   PMID:18347167   PMID:18377363   PMID:18403372   PMID:18417529   PMID:18439917   PMID:18483244   PMID:18523274   PMID:18542060   PMID:18558095   PMID:18585351   PMID:18619497  
PMID:18667423   PMID:18769117   PMID:18789002   PMID:18832068   PMID:18854353   PMID:18940814   PMID:18948102   PMID:19015268   PMID:19032343   PMID:19081374   PMID:19099586   PMID:19121623  
PMID:19204783   PMID:19244234   PMID:19279113   PMID:19341714   PMID:19409814   PMID:19453261   PMID:19463978   PMID:19583777   PMID:19738286   PMID:19855430   PMID:19912635   PMID:19956841  
PMID:19995069   PMID:20026773   PMID:20049841   PMID:20200160   PMID:20211142   PMID:20348541   PMID:20385135   PMID:20415600   PMID:20471694   PMID:20473547   PMID:20484017   PMID:20534529  
PMID:20547759   PMID:20563766   PMID:20663877   PMID:20691163   PMID:20705923   PMID:20731616   PMID:20826751   PMID:21030595   PMID:21059642   PMID:21081493   PMID:21081666   PMID:21143702  
PMID:21179472   PMID:21258344   PMID:21262769   PMID:21324898   PMID:21346816   PMID:21444723   PMID:21453528   PMID:21527249   PMID:21532573   PMID:21549311   PMID:21624135   PMID:21637537  
PMID:21670149   PMID:21685935   PMID:21868449   PMID:21873635   PMID:21884981   PMID:21914818   PMID:21972094   PMID:22002311   PMID:22027828   PMID:22116549   PMID:22190034   PMID:22190037  
PMID:22230954   PMID:22294699   PMID:22308472   PMID:22337871   PMID:22349439   PMID:22363205   PMID:22455388   PMID:22508987   PMID:22641068   PMID:22647876   PMID:22649097   PMID:22651256  
PMID:22685561   PMID:22730529   PMID:22763818   PMID:22792074   PMID:22796363   PMID:22939629   PMID:22989952   PMID:23079660   PMID:23395002   PMID:23402757   PMID:23615070   PMID:23667531  
PMID:23752268   PMID:23760262   PMID:23857786   PMID:23867755   PMID:23879963   PMID:23904210   PMID:24045946   PMID:24120624   PMID:24286308   PMID:24286324   PMID:24324066   PMID:24419085  
PMID:24449765   PMID:24565863   PMID:24722339   PMID:24760274   PMID:24811789   PMID:24821727   PMID:24919179   PMID:24939842   PMID:24943844   PMID:24982244   PMID:25070540   PMID:25136952  
PMID:25138213   PMID:25144594   PMID:25190803   PMID:25196196   PMID:25200321   PMID:25301942   PMID:25305081   PMID:25307283   PMID:25380050   PMID:25610877   PMID:25623232   PMID:25644061  
PMID:25678599   PMID:25892518   PMID:25940092   PMID:25959826   PMID:25973054   PMID:25997740   PMID:26186194   PMID:26221039   PMID:26305553   PMID:26356530   PMID:26359372   PMID:26420860  
PMID:26432290   PMID:26450925   PMID:26468294   PMID:26487511   PMID:26496610   PMID:26531724   PMID:26542778   PMID:26593974   PMID:26598521   PMID:26638075   PMID:26663086   PMID:26673895  
PMID:26679995   PMID:26704017   PMID:26728228   PMID:26745602   PMID:26883907   PMID:26918727   PMID:26972000   PMID:27012186   PMID:27109927   PMID:27177472   PMID:27248326   PMID:27279362  
PMID:27342975   PMID:27420561   PMID:27428650   PMID:27457515   PMID:27462923   PMID:27550312   PMID:27573569   PMID:27684187   PMID:27773593   PMID:27864346   PMID:27880911   PMID:27904654  
PMID:27956629   PMID:27986747   PMID:28074065   PMID:28152507   PMID:28348241   PMID:28514442   PMID:28614293   PMID:28718761   PMID:28985013   PMID:29115379   PMID:29395067   PMID:29453984  
PMID:29484387   PMID:29509190   PMID:29523594   PMID:29540666   PMID:29555935   PMID:29568061   PMID:29680858   PMID:29802126   PMID:30053564   PMID:30317579   PMID:30402512   PMID:30459282  
PMID:30626716   PMID:30804394   PMID:30804502   PMID:30824609   PMID:30866966   PMID:30912164   PMID:30945288   PMID:31040226   PMID:31097476   PMID:31155734   PMID:31253590   PMID:31268609  
PMID:31302139   PMID:31358320   PMID:31387873   PMID:31390528   PMID:31428774   PMID:31527615   PMID:31693860   PMID:31949131   PMID:32071087   PMID:32076268   PMID:32152128   PMID:32416067  
PMID:32455774   PMID:32513988   PMID:32694731   PMID:32731255   PMID:32877691  


Genomics

Comparative Map Data
HDAC3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl5141,620,876 - 141,636,849 (-)EnsemblGRCh38hg38GRCh38
GRCh385141,620,881 - 141,636,849 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh375141,000,448 - 141,016,416 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 365140,980,627 - 140,996,607 (-)NCBINCBI36hg18NCBI36
Build 345140,980,626 - 140,996,596NCBI
Celera5137,077,171 - 137,093,151 (-)NCBI
Cytogenetic Map5q31.3NCBI
HuRef5136,145,083 - 136,160,930 (-)NCBIHuRef
CHM1_15140,433,725 - 140,449,704 (-)NCBICHM1_1
Hdac3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391838,070,024 - 38,088,073 (-)NCBIGRCm39mm39
GRCm39 Ensembl1838,068,897 - 38,088,069 (-)Ensembl
GRCm381837,936,971 - 37,955,015 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1837,935,844 - 37,955,016 (-)EnsemblGRCm38mm10GRCm38
MGSCv371838,096,625 - 38,114,642 (-)NCBIGRCm37mm9NCBIm37
MGSCv361838,062,953 - 38,080,909 (-)NCBImm8
Celera1839,280,295 - 39,298,302 (-)NCBICelera
Cytogenetic Map18B3NCBI
cM Map1819.81NCBI
Hdac3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21829,770,637 - 29,789,850 (-)NCBI
Rnor_6.0 Ensembl1831,073,058 - 31,094,303 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01831,073,057 - 31,094,347 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01830,764,344 - 30,782,387 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41830,857,209 - 30,875,986 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11830,883,855 - 30,902,632 (-)NCBI
Celera1829,414,681 - 29,434,382 (-)NCBICelera
Cytogenetic Map18p11NCBI
Hdac3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541512,138,870 - 12,154,234 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541512,138,520 - 12,154,234 (+)NCBIChiLan1.0ChiLan1.0
HDAC3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.15143,094,406 - 143,110,322 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5143,094,406 - 143,110,322 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v05136,981,790 - 136,997,786 (-)NCBIMhudiblu_PPA_v0panPan3
HDAC3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 (-)NCBI
ROS_Cfam_1.0237,037,462 - 37,052,393 (-)NCBI
UMICH_Zoey_3.1234,112,034 - 34,126,890 (-)NCBI
UNSW_CanFamBas_1.0234,923,559 - 34,938,422 (-)NCBI
UU_Cfam_GSD_1.0235,730,823 - 35,745,706 (-)NCBI
Hdac3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213150,956,557 - 150,972,579 (+)NCBI
SpeTri2.0NW_00493650412,530,546 - 12,546,556 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HDAC3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl2143,273,191 - 143,287,387 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.12143,273,188 - 143,287,421 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.22149,475,764 - 149,490,030 (-)NCBISscrofa10.2Sscrofa10.2susScr3
HDAC3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12344,246,296 - 44,263,127 (-)NCBI
Vero_WHO_p1.0NW_02366603433,589,487 - 33,606,357 (+)NCBI
Hdac3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624774845,970 - 864,080 (-)NCBI

Position Markers
HSC11A022  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh375141,000,527 - 141,000,727UniSTSGRCh37
Build 365140,980,711 - 140,980,911RGDNCBI36
Celera5137,077,255 - 137,077,455RGD
Cytogenetic Map5q31UniSTS
HuRef5136,145,167 - 136,145,367UniSTS
GeneMap99-GB4 RH Map5531.12UniSTS
Whitehead-RH Map5440.3UniSTS
NCBI RH Map5889.1UniSTS
SGC30748  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh375141,016,104 - 141,016,323UniSTSGRCh37
Build 365140,996,288 - 140,996,507RGDNCBI36
Celera5137,092,832 - 137,093,051RGD
Cytogenetic Map5q31.3UniSTS
Cytogenetic Map5q31UniSTS
HuRef5136,160,611 - 136,160,830UniSTS
GeneMap99-GB4 RH Map5531.42UniSTS
Whitehead-RH Map5441.9UniSTS
NCBI RH Map5889.1UniSTS
HDAC3_1724  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh375141,000,249 - 141,001,093UniSTSGRCh37
Build 365140,980,433 - 140,981,277RGDNCBI36
Celera5137,076,977 - 137,077,821RGD
HuRef5136,144,889 - 136,145,733UniSTS
SGC33638  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh375141,006,859 - 141,006,996UniSTSGRCh37
Build 365140,987,043 - 140,987,180RGDNCBI36
Celera5137,083,587 - 137,083,724RGD
Cytogenetic Map5q31UniSTS
HuRef5136,151,366 - 136,151,503UniSTS
GeneMap99-GB4 RH Map5531.22UniSTS
Whitehead-RH Map5440.4UniSTS
NCBI RH Map5889.1UniSTS
A007C33  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh375141,000,447 - 141,000,699UniSTSGRCh37
Build 365140,980,631 - 140,980,883RGDNCBI36
Celera5137,077,175 - 137,077,427RGD
Cytogenetic Map5q31UniSTS
HuRef5136,145,087 - 136,145,339UniSTS
GeneMap99-GB4 RH Map5529.2UniSTS
NCBI RH Map5889.1UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:3530
Count of miRNA genes:1105
Interacting mature miRNAs:1383
Transcripts:ENST00000305264, ENST00000459727, ENST00000467533, ENST00000469207, ENST00000469550, ENST00000471968, ENST00000475549, ENST00000476739, ENST00000486618, ENST00000490808, ENST00000491581, ENST00000492407, ENST00000492506, ENST00000495485, ENST00000519474, ENST00000523088
Prediction methods:Microtar, 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.


Expression


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 sensory system visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 2435 2872 1692 592 1921 434 4357 2115 3423 398 1442 1610 173 1 1204 2788 5
Low 4 119 34 32 30 31 82 311 21 18 3 2 1 2
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NG_029678 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001355039 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001355040 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001355041 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_003883 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_149164 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_149165 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_149166 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_149167 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_149168 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_149169 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB457579 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC008781 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF005482 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF039703 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF059650 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AH005964 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY429537 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY429538 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC000614 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BM461585 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471062 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DB456387 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KC877130 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KF458019 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U66914 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U75696 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U75697 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000305264   ⟹   ENSP00000302967
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl5141,620,881 - 141,636,849 (-)Ensembl
RefSeq Acc Id: ENST00000459727
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl5141,621,485 - 141,628,562 (-)Ensembl
RefSeq Acc Id: ENST00000467533
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl5141,625,701 - 141,629,972 (-)Ensembl
RefSeq Acc Id: ENST00000469207
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl5141,620,925 - 141,626,070 (-)Ensembl
RefSeq Acc Id: ENST00000469550
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl5141,620,876 - 141,635,164 (-)Ensembl
RefSeq Acc Id: ENST00000471968
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl5141,629,266 - 141,634,856 (-)Ensembl
RefSeq Acc Id: ENST00000475549
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl5141,626,026 - 141,626,444 (-)Ensembl
RefSeq Acc Id: ENST00000476739
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl5141,627,899 - 141,629,224 (-)Ensembl
RefSeq Acc Id: ENST00000486618
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl5141,625,208 - 141,626,485 (-)Ensembl
RefSeq Acc Id: ENST00000490808
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl5141,628,605 - 141,629,742 (-)Ensembl
RefSeq Acc Id: ENST00000491581
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl5141,624,862 - 141,627,936 (-)Ensembl
RefSeq Acc Id: ENST00000492407
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl5141,625,750 - 141,629,258 (-)Ensembl
RefSeq Acc Id: ENST00000492506
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl5141,635,909 - 141,636,843 (-)Ensembl
RefSeq Acc Id: ENST00000495485
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl5141,628,559 - 141,636,825 (-)Ensembl
RefSeq Acc Id: ENST00000519474   ⟹   ENSP00000430782
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl5141,627,892 - 141,636,838 (-)Ensembl
RefSeq Acc Id: ENST00000523088   ⟹   ENSP00000429099
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl5141,626,233 - 141,636,833 (-)Ensembl
RefSeq Acc Id: NM_001355039   ⟹   NP_001341968
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385141,624,862 - 141,636,849 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001355040   ⟹   NP_001341969
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385141,620,881 - 141,636,849 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001355041   ⟹   NP_001341970
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385141,620,881 - 141,636,849 (-)NCBI
Sequence:
RefSeq Acc Id: NM_003883   ⟹   NP_003874
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385141,620,881 - 141,636,849 (-)NCBI
GRCh375141,000,443 - 141,016,423 (-)ENTREZGENE
Build 365140,980,627 - 140,996,607 (-)NCBI Archive
HuRef5136,145,083 - 136,160,930 (-)ENTREZGENE
CHM1_15140,433,725 - 140,449,704 (-)NCBI
Sequence:
RefSeq Acc Id: NR_149164
RefSeq Status: REVIEWED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385141,620,881 - 141,636,849 (-)NCBI
Sequence:
RefSeq Acc Id: NR_149165
RefSeq Status: REVIEWED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385141,620,881 - 141,636,849 (-)NCBI
Sequence:
RefSeq Acc Id: NR_149166
RefSeq Status: REVIEWED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385141,620,881 - 141,636,849 (-)NCBI
Sequence:
RefSeq Acc Id: NR_149167
RefSeq Status: REVIEWED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385141,624,862 - 141,636,849 (-)NCBI
Sequence:
RefSeq Acc Id: NR_149168
RefSeq Status: REVIEWED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385141,620,881 - 141,636,849 (-)NCBI
Sequence:
RefSeq Acc Id: NR_149169
RefSeq Status: REVIEWED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385141,620,881 - 141,636,849 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_003874   ⟸   NM_003883
- Peptide Label: isoform 2
- UniProtKB: O15379 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001341969   ⟸   NM_001355040
- Peptide Label: isoform 3
- Sequence:
RefSeq Acc Id: NP_001341970   ⟸   NM_001355041
- Peptide Label: isoform 4
- Sequence:
RefSeq Acc Id: NP_001341968   ⟸   NM_001355039
- Peptide Label: isoform 1
- Sequence:
RefSeq Acc Id: ENSP00000430782   ⟸   ENST00000519474
RefSeq Acc Id: ENSP00000429099   ⟸   ENST00000523088
RefSeq Acc Id: ENSP00000302967   ⟸   ENST00000305264
Protein Domains
Hist_deacetyl

Promoters
RGD ID:6803503
Promoter ID:HG_KWN:51374
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   CD4+TCell_2Hour,   HeLa_S3,   K562,   Lymphoblastoid,   NB4
Transcripts:NM_001130029,   OTTHUMT00000251807,   OTTHUMT00000251824,   OTTHUMT00000318598,   OTTHUMT00000318599,   UC003LLG.1,   UC010JGD.1,   UC010JGE.1,   UC010JGF.1
Position:
Human AssemblyChrPosition (strand)Source
Build 365140,995,921 - 140,998,192 (+)MPROMDB
RGD ID:6871042
Promoter ID:EPDNEW_H8685
Type:initiation region
Name:HDAC3_1
Description:histone deacetylase 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh385141,636,849 - 141,636,909EPDNEW

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 5q23.3-33.2(chr5:130860928-155321811)x3 copy number gain See cases [RCV000051193] Chr5:130860928..155321811 [GRCh38]
Chr5:130196621..154701371 [GRCh37]
Chr5:130224520..154681564 [NCBI36]
Chr5:5q23.3-33.2
pathogenic
GRCh38/hg38 5q31.2-32(chr5:138871137-145812309)x1 copy number loss See cases [RCV000052142] Chr5:138871137..145812309 [GRCh38]
Chr5:138206826..145191872 [GRCh37]
Chr5:138234725..145172065 [NCBI36]
Chr5:5q31.2-32
pathogenic
GRCh38/hg38 5q21.3-33.2(chr5:106619588-156124387)x1 copy number loss See cases [RCV000053524] Chr5:106619588..156124387 [GRCh38]
Chr5:105955289..155551397 [GRCh37]
Chr5:105983188..155483975 [NCBI36]
Chr5:5q21.3-33.2
pathogenic
GRCh38/hg38 5q31.3(chr5:140963199-142322798)x1 copy number loss See cases [RCV000136949] Chr5:140963199..142322798 [GRCh38]
Chr5:140453735..141702363 [GRCh37]
Chr5:140322968..141682547 [NCBI36]
Chr5:5q31.3
uncertain significance
GRCh38/hg38 5q23.3-33.2(chr5:129847794-153353546)x3 copy number gain See cases [RCV000138808] Chr5:129847794..153353546 [GRCh38]
Chr5:129183487..152733106 [GRCh37]
Chr5:129211386..152713299 [NCBI36]
Chr5:5q23.3-33.2
pathogenic
GRCh38/hg38 5q31.3-32(chr5:141089988-149530678)x3 copy number gain See cases [RCV000139504] Chr5:141089988..149530678 [GRCh38]
Chr5:140469572..148910241 [GRCh37]
Chr5:140449756..148890434 [NCBI36]
Chr5:5q31.3-32
pathogenic
GRCh38/hg38 5q31.2-31.3(chr5:138942857-144605017)x3 copy number gain See cases [RCV000142806] Chr5:138942857..144605017 [GRCh38]
Chr5:138278546..143984580 [GRCh37]
Chr5:138306445..143964773 [NCBI36]
Chr5:5q31.2-31.3
uncertain significance
GRCh37/hg19 5q15-35.3(chr5:94844077-178830410)x3 copy number gain not provided [RCV000487658] Chr5:94844077..178830410 [GRCh37]
Chr5:5q15-35.3
likely benign
NM_003883.4(HDAC3):c.902G>A (p.Arg301Gln) single nucleotide variant Inborn genetic diseases [RCV000624003] Chr5:141626212 [GRCh38]
Chr5:141005779 [GRCh37]
Chr5:5q31.3
likely pathogenic
GRCh37/hg19 5q23.3-33.3(chr5:130125085-157574910)x3 copy number gain See cases [RCV000449349] Chr5:130125085..157574910 [GRCh37]
Chr5:5q23.3-33.3
pathogenic
GRCh37/hg19 5p15.33-q35.3(chr5:113577-180719789) copy number gain See cases [RCV000510723] Chr5:113577..180719789 [GRCh37]
Chr5:5p15.33-q35.3
pathogenic
GRCh37/hg19 5q21.3-35.3(chr5:106716357-180687338)x3 copy number gain See cases [RCV000448245] Chr5:106716357..180687338 [GRCh37]
Chr5:5q21.3-35.3
pathogenic
NC_000005.9:g.(?_86400000)_(154000000_?)del deletion Hereditary cancer-predisposing syndrome [RCV000554476] Chr5:86400000..154000000 [GRCh37]
Chr5:5q14.3-33.2
pathogenic
GRCh37/hg19 5p15.1-q35.2(chr5:17628741-176575720)x1 copy number loss See cases [RCV000511978] Chr5:17628741..176575720 [GRCh37]
Chr5:5p15.1-q35.2
pathogenic
GRCh37/hg19 5p15.33-q35.3(chr5:113577-180719789)x3 copy number gain See cases [RCV000512039] Chr5:113577..180719789 [GRCh37]
Chr5:5p15.33-q35.3
pathogenic
NM_003883.4(HDAC3):c.50_55+5del deletion Ependymoma [RCV000577862] Chr5:141636731..141636741 [GRCh38]
Chr5:141016298..141016308 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_003883.4(HDAC3):c.893A>G (p.Tyr298Cys) single nucleotide variant Inborn genetic diseases [RCV000623424] Chr5:141626221 [GRCh38]
Chr5:141005788 [GRCh37]
Chr5:5q31.3
likely pathogenic
GRCh37/hg19 5q31.2-31.3(chr5:139147238-141540491)x1 copy number loss not provided [RCV000682600] Chr5:139147238..141540491 [GRCh37]
Chr5:5q31.2-31.3
pathogenic
GRCh37/hg19 5p15.33-q35.3(chr5:25328-180693344)x3 copy number gain not provided [RCV000744323] Chr5:25328..180693344 [GRCh37]
Chr5:5p15.33-q35.3
pathogenic
GRCh37/hg19 5p15.33-q35.3(chr5:13648-180905029)x3 copy number gain not provided [RCV000744317] Chr5:13648..180905029 [GRCh37]
Chr5:5p15.33-q35.3
pathogenic
NM_003883.4(HDAC3):c.1217G>A (p.Arg406Lys) single nucleotide variant not provided [RCV000998448] Chr5:141625208 [GRCh38]
Chr5:141004775 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_003883.4(HDAC3):c.950A>G (p.Glu317Gly) single nucleotide variant not provided [RCV000998449] Chr5:141626042 [GRCh38]
Chr5:141005609 [GRCh37]
Chr5:5q31.3
uncertain significance
Single allele deletion Neurodevelopmental disorder [RCV000787436] Chr5:14685137..149511942 [GRCh37]
Chr5:5p15.2-q32
uncertain significance
GRCh37/hg19 5q31.3-32(chr5:140424333-148985999)x3 copy number gain not provided [RCV000848228] Chr5:140424333..148985999 [GRCh37]
Chr5:5q31.3-32
uncertain significance
NM_003883.4(HDAC3):c.966G>A (p.Glu322=) single nucleotide variant not provided [RCV000963849] Chr5:141626026 [GRCh38]
Chr5:141005593 [GRCh37]
Chr5:5q31.3
benign
NM_003883.4(HDAC3):c.1232A>G (p.Asn411Ser) single nucleotide variant not provided [RCV000975084] Chr5:141621523 [GRCh38]
Chr5:141001090 [GRCh37]
Chr5:5q31.3
benign

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:4854 AgrOrtholog
COSMIC HDAC3 COSMIC
Ensembl Genes ENSG00000171720 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSP00000302967 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000429099 UniProtKB/TrEMBL
  ENSP00000430782 UniProtKB/TrEMBL
Ensembl Transcript ENST00000305264 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000519474 UniProtKB/TrEMBL
  ENST00000523088 UniProtKB/TrEMBL
Gene3D-CATH 3.40.800.20 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000171720 GTEx
HGNC ID HGNC:4854 ENTREZGENE
Human Proteome Map HDAC3 Human Proteome Map
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 hsa:8841 UniProtKB/Swiss-Prot
NCBI Gene 8841 ENTREZGENE
OMIM 605166 OMIM
Pfam Hist_deacetyl UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA29228 PharmGKB
PIRSF His_deacetylse_1 UniProtKB/Swiss-Prot
PRINTS HDASUPER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HISDACETLASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF52768 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt B5MGH4_HUMAN UniProtKB/TrEMBL
  E7ESJ6_HUMAN UniProtKB/TrEMBL
  E7EW19_HUMAN UniProtKB/TrEMBL
  HDAC3_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary D3DQE1 UniProtKB/Swiss-Prot
  O43268 UniProtKB/Swiss-Prot
  Q9UEI5 UniProtKB/Swiss-Prot
  Q9UEV0 UniProtKB/Swiss-Prot