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; mental depression; middle cerebral artery infarction; and pulmonary hypertension. 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-aminopyridine.
Type: protein-coding
RefSeq Status: PROVISIONAL
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21087,152,978 - 87,187,921 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1087,152,978 - 87,188,235 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1092,182,699 - 92,217,573 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01091,654,605 - 91,689,512 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01087,047,923 - 87,082,826 (-)NCBIRnor_WKY
Rnor_6.01090,140,183 - 90,169,853 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1090,140,183 - 90,151,042 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01089,927,486 - 89,956,390 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41091,266,512 - 91,277,705 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11091,290,701 - 91,292,062 (-)NCBI
Celera1085,868,901 - 85,904,236 (-)NCBICelera
Cytogenetic Map10q32.1NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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-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)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
aristolochic acid  (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)
C60 fullerene  (EXP)
cadmium dichloride  (EXP)
carbon nanotube  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
cocaine  (ISO)
dexamethasone  (EXP,ISO)
dibutyl phthalate  (EXP,ISO)
dioxygen  (EXP,ISO)
dorsomorphin  (ISO)
doxorubicin  (EXP)
endosulfan  (EXP)
ethanol  (EXP,ISO)
fluoxetine  (ISO)
folic acid  (ISO)
fonofos  (ISO)
fructose  (EXP)
gentamycin  (EXP)
Goe 6976  (ISO)
hypochlorous acid  (ISO)
imipramine  (ISO)
KN-93  (ISO)
monosodium L-glutamate  (ISO)
nickel atom  (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  (ISO)
pterostilbene  (ISO)
resveratrol  (ISO)
rifampicin  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
streptozocin  (EXP)
sulforaphane  (ISO)
sunitinib  (ISO)
tauroursodeoxycholic acid  (EXP)
terbufos  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
thapsigargin  (ISO)
thioacetamide  (EXP)
trichloroethene  (EXP)
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

Biological Process

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. 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.
14. 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.
15. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
16. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
17. 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.
18. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
19. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
20. Comprehensive gene review and curation RGD comprehensive gene curation
21. 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.
22. 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.
23. 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.
24. 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.
25. 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:28230854   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  


Genomics

Comparative Map Data
Hdac5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21087,152,978 - 87,187,921 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1087,152,978 - 87,188,235 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1092,182,699 - 92,217,573 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01091,654,605 - 91,689,512 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01087,047,923 - 87,082,826 (-)NCBIRnor_WKY
Rnor_6.01090,140,183 - 90,169,853 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1090,140,183 - 90,151,042 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01089,927,486 - 89,956,390 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41091,266,512 - 91,277,705 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11091,290,701 - 91,292,062 (-)NCBI
Celera1085,868,901 - 85,904,236 (-)NCBICelera
Cytogenetic Map10q32.1NCBI
HDAC5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381744,076,753 - 44,123,641 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1744,076,746 - 44,123,702 (-)EnsemblGRCh38hg38GRCh38
GRCh371742,154,121 - 42,201,009 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361739,509,647 - 39,556,540 (-)NCBINCBI36Build 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
GRCm3911102,086,573 - 102,120,998 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl11102,085,258 - 102,120,992 (-)EnsemblGRCm39 Ensembl
GRCm3811102,195,747 - 102,230,172 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11102,194,432 - 102,230,166 (-)EnsemblGRCm38mm10GRCm38
MGSCv3711102,057,061 - 102,091,486 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3611102,011,837 - 102,040,929 (-)NCBIMGSCv36mm8
Celera11113,901,623 - 113,936,685 (-)NCBICelera
Cytogenetic Map11DNCBI
Hdac5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545117,223,287 - 17,244,051 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495545117,223,217 - 17,246,451 (-)NCBIChiLan1.0ChiLan1.0
HDAC5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11713,464,171 - 13,480,763 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1713,446,836 - 13,479,140 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01713,273,052 - 13,319,695 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
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 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha918,651,855 - 18,687,786 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0919,957,058 - 19,992,997 (+)NCBIROS_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_1.0
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
SpeTri2.0NW_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 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624795814,134 - 838,031 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Position Markers
RH130527  
Rat AssemblyChrPosition (strand)SourceJBrowse
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


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)101981604299406971Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102242750090627625Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102652195798003205Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102652195798952741Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
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)1040035094102359817Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042045676104670812Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)14232313287323132Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)104232313287323132Rat
9589030Epfw9Epididymal fat weight QTL 919.240.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)104444169989441699Rat
7411614Foco18Food consumption QTL 180.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)104444169989441699Rat
8694173Bw149Body weight QTL 1494.380.001body mass (VT:0001259)body weight gain (CMO:0000420)104444169989441699Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104502965095600334Rat
631547Bp87Blood pressure QTL 874.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104736947092369470Rat
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105057470795574707Rat
70364Bp72Blood pressure QTL 72arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)105112110096121100Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1051770177107211142Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1051770177107211142Rat
1359017Hrtrt21Heart rate QTL 212.4heart pumping trait (VT:2000009)heart rate (CMO:0000002)105177294096772940Rat
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)105177461295600334Rat
631535Cm51Cardiac mass QTL 513heart mass (VT:0007028)calculated heart weight (CMO:0000073)105178628291669536Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1053797385107211142Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)105379749498952626Rat
1354608Cm33Cardiac mass QTL 332.8heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)105480929299809292Rat
2312662Slep8Serum leptin concentration QTL 80.05blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1057134272102134272Rat
2312668Scl65Serum cholesterol level QTL 650.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1057134272102134272Rat
2312672Insul15Insulin level QTL 150.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1057134272102134272Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1057576521102576521Rat
2293698Bss43Bone structure and strength QTL 435.330.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1059209888104209888Rat
2306970Anxrr22Anxiety related response QTL 225.95fear/anxiety-related behavior trait (VT:1000241)number of periods of voluntary immobility (CMO:0001045)106134527698211570Rat
6893336Cm75Cardiac mass QTL 750.10.87heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)106134527699703528Rat
1558643Cm44Cardiac mass QTL 444.80.0000368heart mass (VT:0007028)heart wet weight (CMO:0000069)106134527699703528Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1062057807107057807Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1062057807107057807Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1063221094107211142Rat
1357344Bp249Blood pressure QTL 2490.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)106674365598003205Rat
2317029Aia19Adjuvant induced arthritis QTL 192.98joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1066978955107211142Rat
2317039Aia6Adjuvant induced arthritis QTL 64.31joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)1066978955107211142Rat
10450498Bp384Blood pressure QTL 3840.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1067750049107211142Rat
1642980Bp300Blood pressure QTL 300arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068383129107211142Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068420376107211142Rat
2300172Bmd57Bone mineral density QTL 579.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1069738412107211142Rat
2293646Bss25Bone structure and strength QTL 2510.960.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1069738412107211142Rat
2293663Bss33Bone structure and strength QTL 339.340.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1069738412107211142Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1070199100107211142Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1072224939107211142Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1072224939107211142Rat
2306793Ean5Experimental allergic neuritis QTL 54.7nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)107255241693995749Rat
1358188Ept9Estrogen-induced pituitary tumorigenesis QTL 93.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107345313696120911Rat
2292617Ept18Estrogen-induced pituitary tumorigenesis QTL 183.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107345313696120911Rat
1579919Bp281Blood pressure QTL 2810.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107437208494965338Rat
10450495Bp383Blood pressure QTL 3830.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107624608594965338Rat
2292438Bp311Blood pressure QTL 311arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1076246085107211142Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1076452683107211142Rat
4889492Pancm2Pancreatic morphology QTL 23.2pancreatic beta cell morphology trait (VT:0005217)ratio of insulin-positive cell area to total area of splenic region of pancreas (CMO:0001814)1076748906107211142Rat
1300107Rf18Renal function QTL 183.41urine output (VT:0003620)timed urine volume (CMO:0000260)107877551698279596Rat
1358915Stresp7Stress response QTL 73.52blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)107889965587307728Rat
631555Bp134Blood pressure QTL 1340.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)108051528791230079Rat
6893357Bw102Body weight QTL 1020.50.36body mass (VT:0001259)body weight (CMO:0000012)1080515287101325465Rat
2303589Bw87Body weight QTL 872body mass (VT:0001259)body weight (CMO:0000012)1081285008107211142Rat
4889948Bss91Bone structure and strength QTL 914tibia area (VT:1000281)tibia midshaft total cross-sectional area (CMO:0001715)108256485692369470Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)1082685200107211142Rat
12880055Am11Aortic mass QTL 110.004aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)108400727295933025Rat
2301398Kidm38Kidney mass QTL 380.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)108400727295933025Rat
2306792Ean4Experimental allergic neuritis QTL 44nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)108402232193995963Rat
1600367Mcs15Mammary carcinoma susceptibility QTL 154.5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1085565469103884409Rat
631538Oia5Oil induced arthritis QTL 5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1087055121107211142Rat

miRNA Target Status

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.


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 appendage
High
Medium 3 43 55 41 17 41 8 11 74 35 36 11 8
Low 2 2 5
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000055187   ⟹   ENSRNOP00000052059
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1087,152,978 - 87,164,053 (-)Ensembl
Rnor_6.0 Ensembl1090,140,183 - 90,151,042 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000101600   ⟹   ENSRNOP00000080604
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1087,152,978 - 87,188,235 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000105575   ⟹   ENSRNOP00000077322
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1087,152,978 - 87,188,235 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000107360   ⟹   ENSRNOP00000088847
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1087,152,978 - 87,188,235 (-)Ensembl
RefSeq Acc Id: NM_053450   ⟹   NP_445902
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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_039086983   ⟹   XP_038942911
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21087,153,189 - 87,176,407 (-)NCBI
RefSeq Acc Id: XM_039086984   ⟹   XP_038942912
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21087,153,065 - 87,187,921 (-)NCBI
RefSeq Acc Id: XM_039086985   ⟹   XP_038942913
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21087,153,065 - 87,176,465 (-)NCBI
RefSeq Acc Id: XM_039086986   ⟹   XP_038942914
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21087,153,065 - 87,176,406 (-)NCBI
RefSeq Acc Id: XM_039086987   ⟹   XP_038942915
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21087,153,065 - 87,187,921 (-)NCBI
RefSeq Acc Id: XM_039086988   ⟹   XP_038942916
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21087,153,065 - 87,187,920 (-)NCBI
RefSeq Acc Id: XM_039086989   ⟹   XP_038942917
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21087,153,065 - 87,169,622 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_445902   ⟸   NM_053450
- Sequence:
RefSeq Acc Id: ENSRNOP00000052059   ⟸   ENSRNOT00000055187
RefSeq Acc Id: XP_038942915   ⟸   XM_039086987
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038942912   ⟸   XM_039086984
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038942916   ⟸   XM_039086988
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038942913   ⟸   XM_039086985
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038942914   ⟸   XM_039086986
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038942917   ⟸   XM_039086989
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038942911   ⟸   XM_039086983
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000088847   ⟸   ENSRNOT00000107360
RefSeq Acc Id: ENSRNOP00000080604   ⟸   ENSRNOT00000101600
RefSeq Acc Id: ENSRNOP00000077322   ⟸   ENSRNOT00000105575
Protein Domains
HDAC4_Gln   Hist_deacetyl

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


Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program

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 Protein ENSRNOP00000052059 ENTREZGENE
  ENSRNOP00000052059.5 UniProtKB/TrEMBL
  ENSRNOP00000077322 ENTREZGENE
  ENSRNOP00000077322.1 UniProtKB/TrEMBL
  ENSRNOP00000080604 ENTREZGENE
  ENSRNOP00000080604.1 UniProtKB/TrEMBL
  ENSRNOP00000088847.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000055187 ENTREZGENE
  ENSRNOT00000055187.5 UniProtKB/TrEMBL
  ENSRNOT00000101600 ENTREZGENE
  ENSRNOT00000101600.1 UniProtKB/TrEMBL
  ENSRNOT00000105575 ENTREZGENE
  ENSRNOT00000105575.1 UniProtKB/TrEMBL
  ENSRNOT00000107360.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.800.20 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7301599 IMAGE-MGC_LOAD
InterPro His_deacetylse UniProtKB/TrEMBL
  His_deacetylse_dom UniProtKB/TrEMBL
  His_deacetylse_dom_sf UniProtKB/TrEMBL
  Hist_deacetylase_Gln_rich_N UniProtKB/TrEMBL
  Histone_deAcase_II_euk UniProtKB/TrEMBL
  Histone_deacetylase_5 UniProtKB/TrEMBL
  Ureohydrolase_domain UniProtKB/TrEMBL
MGC_CLONE MGC:105937 IMAGE-MGC_LOAD
NCBI Gene 84580 ENTREZGENE
PANTHER PTHR45364 UniProtKB/TrEMBL
  PTHR45364:SF2 UniProtKB/TrEMBL
Pfam HDAC4_Gln UniProtKB/TrEMBL
  Hist_deacetyl UniProtKB/TrEMBL
PhenoGen Hdac5 PhenoGen
PIRSF HDAC_II_euk UniProtKB/TrEMBL
PRINTS HDASUPER UniProtKB/TrEMBL
Superfamily-SCOP SSF52768 UniProtKB/TrEMBL
UniProt A0A8I5XW09_RAT UniProtKB/TrEMBL
  A0A8I6AAJ0_RAT UniProtKB/TrEMBL
  A0A8I6G4R8_RAT 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