Hdac5 (histone deacetylase 5) - Rat Genome Database

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Gene: Hdac5 (histone deacetylase 5) Rattus norvegicus
Analyze
Symbol: Hdac5
Name: histone deacetylase 5
RGD ID: 619980
Description: Enables chromatin binding activity. Involved in several processes, including cellular response to lipopolysaccharide; response to activity; and response to cocaine. Located in cytoplasm and nucleus. Part of protein-containing complex. Biomarker of acute kidney failure; depressive disorder; middle cerebral artery infarction; pulmonary hypertension; and transient cerebral ischemia. Orthologous to human HDAC5 (histone deacetylase 5); PARTICIPATES IN calcium/calmodulin dependent kinase 2 signaling pathway; histone modification pathway; INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 4,4'-sulfonyldiphenol.
Type: protein-coding
RefSeq Status: PROVISIONAL
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81087,653,139 - 87,688,078 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1087,652,656 - 87,694,244 (-)EnsemblGRCr8
mRatBN7.21087,152,978 - 87,187,921 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1087,152,978 - 87,188,235 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1092,182,699 - 92,217,573 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01091,654,605 - 91,689,512 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01087,047,923 - 87,082,826 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01090,140,183 - 90,169,853 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1090,140,183 - 90,151,042 (-)Ensemblrn6Rnor6.0
Rnor_5.01089,927,486 - 89,956,390 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41091,266,512 - 91,277,705 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1085,868,901 - 85,904,236 (-)NCBICelera
RGSC_v3.11091,290,701 - 91,292,062 (-)NCBI
Cytogenetic Map10q32.1NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-butoxyethanol  (ISO)
3,3'-diindolylmethane  (ISO)
3-methylcholanthrene  (ISO)
4,4'-sulfonyldiphenol  (EXP,ISO)
4-aminopyridine  (EXP)
5-aza-2'-deoxycytidine  (ISO)
8-Br-cAMP  (ISO)
acetate ester  (EXP)
acrolein  (ISO)
acrylamide  (EXP)
AICA ribonucleotide  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
amitrole  (EXP)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
aristolochic acid A  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
aspartame  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (EXP,ISO)
berberine  (ISO)
bicuculline  (EXP)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (EXP)
C60 fullerene  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
caffeine  (ISO)
Calcimycin  (ISO)
carbon nanotube  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
cocaine  (ISO)
copper(II) chloride  (ISO)
dexamethasone  (EXP,ISO)
dibutyl phthalate  (EXP,ISO)
diethylstilbestrol  (EXP)
dioxygen  (EXP,ISO)
dorsomorphin  (ISO)
doxorubicin  (EXP)
endosulfan  (EXP)
ethanol  (EXP,ISO)
fluoxetine  (ISO)
folic acid  (ISO)
fonofos  (ISO)
FR900359  (ISO)
fructose  (EXP)
gentamycin  (EXP)
Goe 6976  (ISO)
GSK-J4  (ISO)
hypochlorous acid  (ISO)
imipramine  (ISO)
ivermectin  (ISO)
KN-93  (ISO)
L-methionine  (ISO)
lipopolysaccharide  (EXP,ISO)
methimazole  (EXP)
monosodium L-glutamate  (ISO)
morphine  (EXP)
nickel atom  (ISO)
niclosamide  (ISO)
nitrates  (ISO)
ozone  (ISO)
paracetamol  (EXP,ISO)
parathion  (ISO)
phenylephrine  (ISO)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
phosgene  (ISO)
potassium chloride  (ISO)
propiconazole  (EXP,ISO)
pterostilbene  (ISO)
resveratrol  (ISO)
rifampicin  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
SB 431542  (ISO)
semaglutide  (EXP,ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
streptozocin  (EXP)
sulfadimethoxine  (EXP)
sulforaphane  (ISO)
sunitinib  (ISO)
tartrazine  (ISO)
tauroursodeoxycholic acid  (EXP)
terbufos  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
thapsigargin  (ISO)
thioacetamide  (EXP)
thiram  (ISO)
trichloroethene  (EXP)
triphenyl phosphate  (ISO)
triptonide  (ISO)
troglitazone  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vitamin E  (ISO)
vorinostat  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Upregulation of class II histone deacetylases mRNA during neural differentiation of cultured rat hippocampal progenitor cells. Ajamian F, etal., Neurosci Lett 2003 Jul 31;346(1-2):57-60.
2. CaM kinase II selectively signals to histone deacetylase 4 during cardiomyocyte hypertrophy. Backs J, etal., J Clin Invest. 2006 Jul;116(7):1853-64. Epub 2006 Jun 8.
3. Ca(2)(+)-calmodulin-dependent protein kinase II regulation of cardiac excitation-transcription coupling. Bers DM Heart Rhythm. 2011 Jul;8(7):1101-4. doi: 10.1016/j.hrthm.2011.01.030. Epub 2011 Jan 18.
4. Histone deacetylases facilitate sodium/calcium exchanger up-regulation in adult cardiomyocytes. Chandrasekaran S, etal., FASEB J. 2009 Nov;23(11):3851-64. doi: 10.1096/fj.09-132415. Epub 2009 Jul 28.
5. A comparison of molecular alterations in environmental and genetic rat models of ADHD: a pilot study. DasBanerjee T, etal., Am J Med Genet B Neuropsychiatr Genet. 2008 Dec 5;147B(8):1554-63.
6. Cocaine induces the expression of MEF2C transcription factor in rat striatum through activation of SIK1 and phosphorylation of the histone deacetylase HDAC5. Dietrich JB, etal., Synapse. 2012 Jan;66(1):61-70. doi: 10.1002/syn.20988. Epub 2011 Nov 3.
7. 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.
8. MEF2 is regulated by CaMKIIdelta2 and a HDAC4-HDAC5 heterodimer in vascular smooth muscle cells. Ginnan R, etal., Biochem J. 2012 May 15;444(1):105-14. doi: 10.1042/BJ20120152.
9. Exercise impacts brain-derived neurotrophic factor plasticity by engaging mechanisms of epigenetic regulation. Gomez-Pinilla F, etal., Eur J Neurosci. 2011 Feb;33(3):383-90. doi: 10.1111/j.1460-9568.2010.07508.x. Epub 2010 Dec 31.
10. HDAC4/5-HMGB1 signalling mediated by NADPH oxidase activity contributes to cerebral ischaemia/reperfusion injury. He M, etal., J Cell Mol Med. 2013 Apr;17(4):531-42. doi: 10.1111/jcmm.12040. Epub 2013 Mar 11.
11. alpha2-Adrenoceptor agonist dexmedetomidine protects septic acute kidney injury through increasing BMP-7 and inhibiting HDAC2 and HDAC5. Hsing CH, etal., Am J Physiol Renal Physiol. 2012 Nov 15;303(10):F1443-53. doi: 10.1152/ajprenal.00143.2012. Epub 2012 Aug 29.
12. Isolation of a novel histone deacetylase reveals that class I and class II deacetylases promote SMRT-mediated repression. Kao HY, etal., Genes Dev 2000 Jan 1;14(1):55-66.
13. Opposite effects of HDAC5 and p300 on MRTF-A-related neuronal apoptosis during ischemia/reperfusion injury in rats. Li N, etal., Cell Death Dis. 2017 Feb 23;8(2):e2624. doi: 10.1038/cddis.2017.16.
14. Inactivation of the myocyte enhancer factor-2 repressor histone deacetylase-5 by endogenous Ca(2+) //calmodulin-dependent kinase II promotes depolarization-mediated cerebellar granule neuron survival. Linseman DA, etal., J Biol Chem 2003 Oct 17;278(42):41472-81. Epub 2003 Aug 01.
15. Histone acetylation and expression of mono-aminergic transmitters synthetases involved in CUS-induced depressive rats. Liu D, etal., Exp Biol Med (Maywood). 2014 Mar;239(3):330-6. doi: 10.1177/1535370213513987. Epub 2014 Feb 4.
16. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
17. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
18. 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.
19. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
20. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
21. Comprehensive gene review and curation RGD comprehensive gene curation
22. 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.
23. 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.
24. YY1 protects cardiac myocytes from pathologic hypertrophy by interacting with HDAC5. Sucharov CC, etal., Mol Biol Cell. 2008 Oct;19(10):4141-53. doi: 10.1091/mbc.E07-12-1217. Epub 2008 Jul 16.
25. Histone deacetylase 4 selectively contributes to podocyte injury in diabetic nephropathy. Wang X, etal., Kidney Int. 2014 Oct;86(4):712-25. doi: 10.1038/ki.2014.111. Epub 2014 Apr 9.
26. 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.
Additional References at PubMed
PMID:10748098   PMID:10869435   PMID:10983972   PMID:11081517   PMID:11641275   PMID:12007404   PMID:12242305   PMID:12477932   PMID:15367668   PMID:15601857   PMID:15990875   PMID:16221676  
PMID:16236793   PMID:16260608   PMID:17011572   PMID:17468767   PMID:17786239   PMID:17823368   PMID:17940050   PMID:17988634   PMID:18198354   PMID:18292392   PMID:18332106   PMID:18768922  
PMID:19071119   PMID:19351956   PMID:20123967   PMID:20181743   PMID:20188095   PMID:20408817   PMID:23161540   PMID:23867755   PMID:23926128   PMID:24413532   PMID:25012661   PMID:25514029  
PMID:25661252   PMID:26157139   PMID:26777998   PMID:28343149   PMID:28505206   PMID:28957664   PMID:29397902   PMID:29522762   PMID:30483749   PMID:30649921   PMID:30913399   PMID:30962285  
PMID:31696766   PMID:32485181   PMID:32646070   PMID:34716230   PMID:35704695   PMID:36579750  


Genomics

Comparative Map Data
Hdac5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81087,653,139 - 87,688,078 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1087,652,656 - 87,694,244 (-)EnsemblGRCr8
mRatBN7.21087,152,978 - 87,187,921 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1087,152,978 - 87,188,235 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1092,182,699 - 92,217,573 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01091,654,605 - 91,689,512 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01087,047,923 - 87,082,826 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01090,140,183 - 90,169,853 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1090,140,183 - 90,151,042 (-)Ensemblrn6Rnor6.0
Rnor_5.01089,927,486 - 89,956,390 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41091,266,512 - 91,277,705 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1085,868,901 - 85,904,236 (-)NCBICelera
RGSC_v3.11091,290,701 - 91,292,062 (-)NCBI
Cytogenetic Map10q32.1NCBI
HDAC5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381744,076,753 - 44,123,641 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1744,076,746 - 44,123,702 (-)Ensemblhg38GRCh38
GRCh371742,154,121 - 42,201,009 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361739,509,647 - 39,556,540 (-)NCBIBuild 36Build 36hg18NCBI36
Celera1738,862,215 - 38,909,110 (-)NCBICelera
Cytogenetic Map17q21.31NCBI
HuRef1737,918,049 - 37,965,007 (-)NCBIHuRef
CHM1_11742,389,491 - 42,436,420 (-)NCBICHM1_1
T2T-CHM13v2.01744,929,260 - 44,976,146 (-)NCBIT2T-CHM13v2.0
Hdac5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3911102,085,244 - 102,120,968 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl11102,085,258 - 102,120,992 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm3811102,195,747 - 102,230,172 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11102,194,432 - 102,230,166 (-)Ensemblmm10GRCm38
MGSCv3711102,057,061 - 102,091,486 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv3611102,011,837 - 102,040,929 (-)NCBIMGSCv36mm8
Celera11113,901,623 - 113,936,685 (-)NCBICelera
Cytogenetic Map11DNCBI
cM Map1165.82NCBI
Hdac5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545117,223,287 - 17,244,051 (-)Ensembl
ChiLan1.0NW_00495545117,223,217 - 17,246,451 (-)NCBIChiLan1.0ChiLan1.0
HDAC5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21920,783,181 - 20,828,927 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11722,748,121 - 22,794,804 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01713,273,052 - 13,319,695 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11713,464,171 - 13,480,763 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1713,446,836 - 13,479,140 (+)EnsemblpanPan2panpan1.1
HDAC5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1919,261,075 - 19,297,669 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl919,260,893 - 19,297,623 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha918,651,855 - 18,687,786 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0919,957,058 - 19,992,997 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl919,957,080 - 19,994,564 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1918,810,173 - 18,846,100 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0918,993,422 - 19,029,330 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0919,138,202 - 19,174,140 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Hdac5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560218,595,662 - 18,631,399 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936541558,414 - 599,195 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936541561,721 - 598,915 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HDAC5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1219,078,005 - 19,121,154 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11219,077,910 - 19,119,463 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21219,364,064 - 19,374,963 (-)NCBISscrofa10.2Sscrofa10.2susScr3
HDAC5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11662,267,837 - 62,314,914 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1662,274,041 - 62,315,094 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366607733,041,248 - 33,087,000 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Hdac5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624795818,154 - 837,961 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_004624795814,134 - 838,031 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Hdac5
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1961,492,692 - 61,527,424 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Hdac5
274 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:38
Count of miRNA genes:31
Interacting mature miRNAs:36
Transcripts:ENSRNOT00000055187
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105107189796071897Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102702353598502431Rat
8657410Bp374Blood pressure QTL 374heart left ventricle size trait (VT:0002753)heart left ventricle end-diastolic diameter (CMO:0000982)1067476608107713808Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1063719161107713808Rat
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)103550938391417879Rat
631555Bp134Blood pressure QTL 1340.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)108101207791729860Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042546145107713808Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1058073360103073360Rat
12903252Cm113Cardiac mass QTL 1130.047heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)1066817119107713808Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)105429633699451733Rat
4889948Bss91Bone structure and strength QTL 914tibia area (VT:1000281)tibia midshaft total cross-sectional area (CMO:0001715)108306123692869129Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1064939013107713808Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1076951790107713808Rat
1579919Bp281Blood pressure QTL 2810.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)105046480295464802Rat
1300107Rf18Renal function QTL 183.41urine output (VT:0003620)timed urine volume (CMO:0000260)1079272424102982300Rat
70168Eae12Experimental allergic encephalomyelitis QTL 120.0009nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)1073599825107713808Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104552916496099749Rat
8694173Bw149Body weight QTL 1494.380.001body mass (VT:0001259)body weight gain (CMO:0000420)104493935989939359Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1054296227107713808Rat
10450495Bp383Blood pressure QTL 3830.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107674313395464802Rat
12903269Am15Aortic mass QTL 150.042aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)1066817119107713808Rat
10450493Bp382Blood pressure QTL 3820.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)105086028895860288Rat
12903266Cm114Cardiac mass QTL 1140.02heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)1066817119107713808Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
2292617Ept18Estrogen-induced pituitary tumorigenesis QTL 183.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107395035396620293Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1062556066107556066Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)14282327487823274Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1072724423107713808Rat
12880372Am12Aortic mass QTL 120.003aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)1066817119107713808Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1062556066107556066Rat
12880375Kidm66Kidney mass QTL 660.009kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1066817119107713808Rat
1357344Bp249Blood pressure QTL 2490.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)106724133498502431Rat
9589030Epfw9Epididymal fat weight QTL 919.240.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)104493935989939359Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014991535107556066Rat
12880370Cm105Cardiac mass QTL 1050.008heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)1066817119107713808Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)104282327487823274Rat
12880371Cm106Cardiac mass QTL 1060.007heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)1066817119107713808Rat
2306970Anxrr22Anxiety related response QTL 225.95fear/anxiety-related behavior trait (VT:1000241)number of periods of voluntary immobility (CMO:0001045)106184349698710773Rat
1359017Hrtrt21Heart rate QTL 212.4heart pumping trait (VT:2000009)heart rate (CMO:0000002)107369533997272278Rat
11565453Kidm58Kidney mass QTL 580.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1066817119107713808Rat
7387312Bw125Body weight QTL 12530.0047retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight (CMO:0000356)1065390777107713808Rat
6893357Bw102Body weight QTL 1020.50.36body mass (VT:0001259)body weight (CMO:0000012)1081012077101828297Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102293137391127454Rat
2306793Ean5Experimental allergic neuritis QTL 54.7nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)107304965694495280Rat
2306792Ean4Experimental allergic neuritis QTL 44nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)104949549294495492Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1052269185107713808Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068920187107713808Rat
1358915Stresp7Stress response QTL 73.52blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)1065307813107713808Rat
70363Bp71Blood pressure QTL 710.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1061843496106843496Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)102980091091417879Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1070698731107713808Rat
631530Tls3T-lymphoma susceptibility QTL 300.0001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)102758722696099902Rat
1354608Cm33Cardiac mass QTL 332.8heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)105530797293608131Rat
1558643Cm44Cardiac mass QTL 444.80.0000368heart mass (VT:0007028)heart wet weight (CMO:0000069)1061843496100198886Rat
8552805Bw145Body weight QTL 1452.2body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)104360879388608793Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040535708107713808Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1040535708107713808Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014991535107713808Rat
7207811Bmd90Bone mineral density QTL 905.2femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)104994371094943710Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040535708107713808Rat
1581559Eae18Experimental allergic encephalomyelitis QTL 180.00002nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1066108888107555881Rat
7411614Foco18Food consumption QTL 180.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)104493935989939359Rat
6893336Cm75Cardiac mass QTL 750.10.87heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)1061843496100198886Rat
631547Bp87Blood pressure QTL 874.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104786912992869129Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10686461896620484Rat
12880055Am11Aortic mass QTL 110.004aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)108450348796432422Rat
2292438Bp311Blood pressure QTL 311arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107674313395604677Rat
2301398Kidm38Kidney mass QTL 380.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)108450348796432422Rat
2292436Bp310Blood pressure QTL 310arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)105060467795604677Rat
1600367Mcs15Mammary carcinoma susceptibility QTL 154.5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1072724423107713808Rat
6893342Cm78Cardiac mass QTL 780.10.88heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)103550938388177745Rat
631537Oia4Oil induced arthritis QTL 4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1076128947107713808Rat
1358188Ept9Estrogen-induced pituitary tumorigenesis QTL 93.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107395035396620293Rat
634354Rends3Renal damage susceptibility QTL 30.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)1061997479106997479Rat
2301405Cm69Cardiac mass QTL 690.031heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)1066817119107713808Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102702353599451848Rat

Markers in Region
RH130527  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr81087,653,185 - 87,653,456 (+)Marker Load Pipeline
mRatBN7.21087,153,024 - 87,153,295 (+)MAPPERmRatBN7.2
Rnor_6.01090,140,230 - 90,140,500NCBIRnor6.0
Rnor_5.01089,927,533 - 89,927,803UniSTSRnor5.0
RGSC_v3.41091,266,559 - 91,266,829UniSTSRGSC3.4
Celera1085,868,948 - 85,869,218UniSTS
RH 3.4 Map10883.5UniSTS
Cytogenetic Map10q32.1UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 162 91 90 59 92 59 6 356 192 11 141 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000055187   ⟹   ENSRNOP00000052059
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1087,653,139 - 87,673,539 (-)Ensembl
mRatBN7.2 Ensembl1087,152,978 - 87,164,053 (-)Ensembl
Rnor_6.0 Ensembl1090,140,183 - 90,151,042 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000101600   ⟹   ENSRNOP00000080604
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1087,653,139 - 87,694,244 (-)Ensembl
mRatBN7.2 Ensembl1087,152,978 - 87,188,235 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000105575   ⟹   ENSRNOP00000077322
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1087,652,656 - 87,688,312 (-)Ensembl
mRatBN7.2 Ensembl1087,152,978 - 87,188,235 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000107360   ⟹   ENSRNOP00000088847
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1087,653,139 - 87,694,244 (-)Ensembl
mRatBN7.2 Ensembl1087,152,978 - 87,188,235 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000168842   ⟹   ENSRNOP00000107526
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1087,653,139 - 87,675,953 (-)Ensembl
RefSeq Acc Id: NM_053450   ⟹   NP_445902
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81087,653,139 - 87,688,054 (-)NCBI
mRatBN7.21087,152,978 - 87,187,895 (-)NCBI
Rnor_6.01090,140,183 - 90,169,853 (-)NCBI
Rnor_5.01089,927,486 - 89,956,390 (-)NCBI
RGSC_v3.41091,266,512 - 91,277,705 (-)RGD
Celera1085,868,901 - 85,904,236 (-)RGD
Sequence:
RefSeq Acc Id: XM_039086984   ⟹   XP_038942912
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81087,653,144 - 87,688,078 (-)NCBI
mRatBN7.21087,153,065 - 87,187,921 (-)NCBI
RefSeq Acc Id: XM_039086985   ⟹   XP_038942913
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81087,653,144 - 87,676,625 (-)NCBI
mRatBN7.21087,153,065 - 87,176,465 (-)NCBI
RefSeq Acc Id: XM_039086987   ⟹   XP_038942915
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81087,653,144 - 87,688,078 (-)NCBI
mRatBN7.21087,153,065 - 87,187,921 (-)NCBI
RefSeq Acc Id: XM_039086988   ⟹   XP_038942916
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81087,653,144 - 87,688,078 (-)NCBI
mRatBN7.21087,153,065 - 87,187,920 (-)NCBI
RefSeq Acc Id: XM_039086989   ⟹   XP_038942917
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81087,653,144 - 87,669,776 (-)NCBI
mRatBN7.21087,153,065 - 87,169,622 (-)NCBI
RefSeq Acc Id: XM_063269997   ⟹   XP_063126067
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81087,653,144 - 87,676,569 (-)NCBI
RefSeq Acc Id: XM_063269998   ⟹   XP_063126068
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81087,653,144 - 87,669,853 (-)NCBI
RefSeq Acc Id: XM_063269999   ⟹   XP_063126069
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81087,653,144 - 87,661,703 (-)NCBI
RefSeq Acc Id: NP_445902   ⟸   NM_053450
- UniProtKB: A6HJH3 (UniProtKB/TrEMBL),   A0A8I6AAJ0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000052059   ⟸   ENSRNOT00000055187
RefSeq Acc Id: XP_038942915   ⟸   XM_039086987
- Peptide Label: isoform X5
- UniProtKB: A0A8I5XW09 (UniProtKB/TrEMBL),   A0A8I6AAJ0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038942912   ⟸   XM_039086984
- Peptide Label: isoform X2
- UniProtKB: A0A8I6G4R8 (UniProtKB/TrEMBL),   A0A8I6AAJ0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038942916   ⟸   XM_039086988
- Peptide Label: isoform X4
- UniProtKB: A0A8I6AAJ0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038942913   ⟸   XM_039086985
- Peptide Label: isoform X3
- UniProtKB: A0A8I6AAJ0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038942917   ⟸   XM_039086989
- Peptide Label: isoform X4
- UniProtKB: A0A8I6AAJ0 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000088847   ⟸   ENSRNOT00000107360
Ensembl Acc Id: ENSRNOP00000080604   ⟸   ENSRNOT00000101600
Ensembl Acc Id: ENSRNOP00000077322   ⟸   ENSRNOT00000105575
RefSeq Acc Id: XP_063126067   ⟸   XM_063269997
- Peptide Label: isoform X1
- UniProtKB: A0A8I6AAJ0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063126068   ⟸   XM_063269998
- Peptide Label: isoform X4
- UniProtKB: A0A8I6AAJ0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063126069   ⟸   XM_063269999
- Peptide Label: isoform X6
Ensembl Acc Id: ENSRNOP00000107526   ⟸   ENSRNOT00000168842
Protein Domains
Histone deacetylase   Histone deacetylase glutamine rich N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LM64-F1-model_v2 AlphaFold F1LM64 1-947 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:619980 AgrOrtholog
BioCyc Gene G2FUF-23121 BioCyc
Ensembl Genes ENSRNOG00000020905 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000055187 ENTREZGENE
  ENSRNOT00000055187.6 UniProtKB/TrEMBL
  ENSRNOT00000101600 ENTREZGENE
  ENSRNOT00000101600.2 UniProtKB/TrEMBL
  ENSRNOT00000105575 ENTREZGENE
  ENSRNOT00000105575.2 UniProtKB/TrEMBL
  ENSRNOT00000107360.2 UniProtKB/TrEMBL
  ENSRNOT00000168842.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.800.20 UniProtKB/TrEMBL
  6.10.250.1550 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7301599 IMAGE-MGC_LOAD
InterPro HDAC4/5/7/9 UniProtKB/TrEMBL
  His_deacetylse UniProtKB/TrEMBL
  His_deacetylse_dom UniProtKB/TrEMBL
  His_deacetylse_dom_sf UniProtKB/TrEMBL
  Hist_deacetylase_Gln_rich_N UniProtKB/TrEMBL
  Ureohydrolase_domain UniProtKB/TrEMBL
KEGG Report rno:84580 UniProtKB/TrEMBL
MGC_CLONE MGC:105937 IMAGE-MGC_LOAD
NCBI Gene 84580 ENTREZGENE
PANTHER HISTONE DEACETYLASE UniProtKB/TrEMBL
  HISTONE DEACETYLASE 5 UniProtKB/TrEMBL
  HISTONE DEACETYLASE HDAC1-RELATED UniProtKB/TrEMBL
  PTHR45364 UniProtKB/TrEMBL
Pfam HDAC4_Gln UniProtKB/TrEMBL
  Hist_deacetyl UniProtKB/TrEMBL
PhenoGen Hdac5 PhenoGen
PIRSF HDAC_II_euk UniProtKB/TrEMBL
PRINTS HDASUPER UniProtKB/TrEMBL
RatGTEx ENSRNOG00000020905 RatGTEx
Superfamily-SCOP SSF52768 UniProtKB/TrEMBL
UniProt A0A8I5XW09 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6AAJ0 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6G4R8 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0LYD2_RAT UniProtKB/TrEMBL
  A6HJH3 ENTREZGENE, UniProtKB/TrEMBL
  F1LM64_RAT UniProtKB/TrEMBL
  Q5RJZ2_RAT UniProtKB/TrEMBL
  Q99P98_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Hdac5  histone deacetylase 5      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Hdac5  histone deacetylase 5      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_regulation function inhibited by CamK phosphorylation of serines 1304416