Ryr2 (ryanodine receptor 2) - Rat Genome Database
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Gene: Ryr2 (ryanodine receptor 2) Rattus norvegicus
Analyze
Symbol: Ryr2
Name: ryanodine receptor 2
RGD ID: 620314
Description: Exhibits calcium-induced calcium release activity; ryanodine-sensitive calcium-release channel activity; and scaffold protein binding activity. Involved in several processes, including metal ion transport; negative regulation of cytosolic calcium ion concentration; and response to magnesium ion. Localizes to several cellular components, including extrinsic component of cytoplasmic side of plasma membrane; sarcolemma; and sarcomere. Used to study congestive heart failure. Human ortholog(s) of this gene implicated in arrhythmogenic right ventricular cardiomyopathy; arrhythmogenic right ventricular dysplasia 2; and catecholaminergic polymorphic ventricular tachycardia 1. Orthologous to human RYR2 (ryanodine receptor 2); PARTICIPATES IN acebutolol pharmacodynamics pathway; adrenergic beta receptor agonist and beta-blocker pharmacodynamics pathway; amiodarone pharmacodynamics pathway; INTERACTS WITH (S)-nicotine; 1-[(2,3,4-trimethoxyphenyl)methyl]piperazine; 17beta-estradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: cardiac muscle ryanodine receptor; cardiac muscle ryanodine receptor-calcium release channel; cardiac-type ryaodine receptor; LOC689560; ryanodine receptor 2, cardiac; ryanodine receptor type II; RyR; RYR-2; similar to ryanodine receptor 2, cardiac; type 2 ryanodine receptor
Orthologs:
Homo sapiens (human) : RYR2 (ryanodine receptor 2)  HGNC  Alliance
Mus musculus (house mouse) : Ryr2 (ryanodine receptor 2, cardiac)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Ryr2 (ryanodine receptor 2)
Pan paniscus (bonobo/pygmy chimpanzee) : RYR2 (ryanodine receptor 2)
Canis lupus familiaris (dog) : RYR2 (ryanodine receptor 2)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Ryr2 (ryanodine receptor 2)
Sus scrofa (pig) : RYR2 (ryanodine receptor 2)
Chlorocebus sabaeus (African green monkey) : RYR2 (ryanodine receptor 2)
Heterocephalus glaber (naked mole-rat) : Ryr2 (ryanodine receptor 2)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
NCBI Annotation Information: Annotation category: partial on reference assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01765,533,998 - 65,955,606 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1765,535,403 - 65,955,606 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01767,285,205 - 67,704,766 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41768,959,042 - 69,544,816 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11769,519,966 - 69,552,036 (+)NCBI
Celera1761,573,393 - 61,976,022 (-)NCBICelera
Cytogenetic Map17q12.1NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
arrhythmogenic right ventricular cardiomyopathy  (ISO)
arrhythmogenic right ventricular dysplasia 1  (ISO)
arrhythmogenic right ventricular dysplasia 2  (ISO)
arrhythmogenic right ventricular dysplasia 9  (ISO)
autism spectrum disorder  (ISO)
Brugada syndrome  (ISO)
cardiac arrest  (ISO)
Cardiac Arrhythmias  (ISO)
Cardiac Complexes, Premature  (ISO)
cardiomyopathy  (ISO)
catecholaminergic polymorphic ventricular tachycardia  (ISO)
catecholaminergic polymorphic ventricular tachycardia 1  (ISO)
catecholaminergic polymorphic ventricular tachycardia 2  (ISO)
Childhood Schizophrenia  (ISO)
congestive heart failure  (IDA,ISO)
Developmental Disabilities  (ISO)
Diabetic Cardiomyopathies  (ISO)
Diastolic Dysfunction  (ISO)
dilated cardiomyopathy  (ISO)
dilated cardiomyopathy 1AA  (ISO)
Dilated Cardiomyopathy with Left Ventricular Noncompaction  (ISO)
Experimental Diabetes Mellitus  (IDA)
familial hypertrophic cardiomyopathy  (ISO)
Familial Sudden Death  (ISO)
Familial Ventricular Tachycardia  (ISO)
genetic disease  (ISO)
Heart Block  (ISO)
heart disease  (ISO)
hemolytic anemia  (ISO)
Hereditary Leiomyomatosis and Renal Cell Cancer  (ISO)
hypertrophic cardiomyopathy  (ISO)
hypertrophic cardiomyopathy 4  (ISO)
hypochromic anemia  (ISO)
Infant Death  (ISO)
left ventricular noncompaction  (ISO)
Liver Failure  (ISO)
long QT syndrome  (ISO)
long QT syndrome 1  (ISO)
malignant mesothelioma  (ISO)
microcytic anemia  (ISO)
Myocardial Ischemia  (ISO)
Sudden Cardiac Death  (ISO)
Sudden Death  (ISO)
Syncope  (ISO)
Tachycardia  (ISO)
Ventricular Fibrillation  (ISO)
Ventricular Fibrillation, Paroxysmal Familial, 1  (ISO)
Ventricular Tachycardia  (ISO)
Wolff-Parkinson-White syndrome  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-nicotine  (EXP,ISO)
1,2-dimethylhydrazine  (ISO)
1-[(2,3,4-trimethoxyphenyl)methyl]piperazine  (EXP)
17beta-estradiol  (EXP)
2,2',3,3',6,6'-hexachlorobiphenyl  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP)
2,3-bis(4-hydroxyphenyl)propionitrile  (EXP)
4,4'-sulfonyldiphenol  (EXP,ISO)
6-propyl-2-thiouracil  (EXP)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
Aroclor 1254  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
atenolol  (ISO)
baclofen  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
bicuculline  (EXP)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
caffeine  (EXP)
calcium atom  (EXP,ISO)
calcium(0)  (EXP,ISO)
candesartan  (EXP)
carvedilol  (EXP,ISO)
choline  (ISO)
cocaine  (EXP,ISO)
cyclic ADP-ribose  (EXP)
dantrolene  (EXP)
daunorubicin  (EXP,ISO)
dioxygen  (EXP,ISO)
doxorubicin  (EXP,ISO)
etoposide  (ISO)
fenvalerate  (EXP)
flutamide  (ISO)
folic acid  (ISO)
fonofos  (ISO)
gentamycin  (EXP)
isoprenaline  (EXP,ISO)
L-methionine  (ISO)
linsidomine  (EXP)
maraviroc  (ISO)
mercury dichloride  (EXP)
methapyrilene  (ISO)
methylmercury chloride  (ISO)
metoprolol  (ISO)
mifepristone  (ISO)
mitoxantrone  (ISO)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (EXP)
nicotine  (EXP,ISO)
O-methyleugenol  (ISO)
ouabain  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
parathion  (ISO)
perindopril  (EXP)
phenytoin  (EXP)
picrotoxin  (EXP)
progesterone  (EXP,ISO)
propofol  (EXP)
razoxane  (EXP)
resveratrol  (EXP,ISO)
rotenone  (ISO)
ryanodine  (EXP,ISO)
SCH 23390  (ISO)
simvastatin  (EXP)
sodium arsenite  (ISO)
streptozocin  (EXP,ISO)
sulforaphane  (ISO)
terbufos  (ISO)
thalidomide  (ISO)
titanium dioxide  (ISO)
trichloroethene  (EXP)
triclosan  (ISO)
valproic acid  (EXP,ISO)
vinclozolin  (EXP)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
calcium ion transmembrane transport  (IMP,ISO)
calcium ion transport  (ISO,ISS)
calcium ion transport into cytosol  (ISO)
calcium-mediated signaling  (ISO,ISS)
calcium-mediated signaling using intracellular calcium source  (IEA,ISO)
cardiac muscle contraction  (ISO)
cardiac muscle hypertrophy  (IEA,ISO)
cellular calcium ion homeostasis  (ISO,ISS)
cellular response to caffeine  (IEA,ISO,ISS)
cellular response to epinephrine stimulus  (IEA,ISO)
cytosolic calcium ion transport  (ISO)
detection of calcium ion  (IEA,ISO)
embryonic heart tube morphogenesis  (IEA,ISO,ISS)
establishment of protein localization to endoplasmic reticulum  (IEA,ISO)
ion transmembrane transport  (IMP)
left ventricular cardiac muscle tissue morphogenesis  (IEA,ISO)
manganese ion transmembrane transport  (IMP)
negative regulation of cytosolic calcium ion concentration  (IDA)
positive regulation of ATPase-coupled calcium transmembrane transporter activity  (IEA,ISO)
positive regulation of heart rate  (IEA,ISO)
positive regulation of sequestering of calcium ion  (IEA,ISO)
positive regulation of the force of heart contraction  (IEA,ISO)
Purkinje myocyte to ventricular cardiac muscle cell signaling  (IEA,ISO)
regulation of atrial cardiac muscle cell action potential  (IEA,ISO)
regulation of AV node cell action potential  (IEA,ISO)
regulation of cardiac muscle contraction  (ISO)
regulation of cardiac muscle contraction by calcium ion signaling  (ISO)
regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion  (IEA,ISO)
regulation of cytosolic calcium ion concentration  (IMP)
regulation of heart rate  (ISO)
regulation of SA node cell action potential  (IEA,ISO)
regulation of ventricular cardiac muscle cell action potential  (IEA,ISO)
release of sequestered calcium ion into cytosol  (IBA,IEA,ISO)
release of sequestered calcium ion into cytosol by sarcoplasmic reticulum  (IEA,ISO)
response to caffeine  (ISO)
response to calcium ion  (IDA)
response to drug  (IEP)
response to hypoxia  (IEA,ISO)
response to magnesium ion  (IDA)
response to muscle activity  (IEA,ISO)
response to muscle stretch  (IEA,ISO)
response to nutrient  (IEP)
response to redox state  (IEA,ISO)
sarcoplasmic reticulum calcium ion transport  (IMP)
type B pancreatic cell apoptotic process  (IEA,ISO)
ventricular cardiac muscle cell action potential  (IEA,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
acebutolol pharmacodynamics pathway  (ISO)
adrenergic beta receptor agonist and beta-blocker pharmacodynamics pathway  (ISO)
amiodarone pharmacodynamics pathway  (ISO)
amlodipine pharmacodynamics pathway  (ISO)
arrhythmogenic right ventricular cardiomyopathy pathway  (IEA)
atenolol pharmacodynamics pathway  (ISO)
betaxolol pharmacodynamics pathway  (ISO)
bisoprolol pharmacodynamics pathway  (ISO)
bupranolol drug pathway  (ISO)
bupranolol pharmacodynamics pathway  (ISO)
calcium transport pathway  (ISO)
calcium/calcium-mediated signaling pathway  (IEA,ISO)
calcium/calmodulin dependent kinase 2 signaling pathway  (ISO)
carvedilol pharmacodynamics pathway  (ISO)
dilated cardiomyopathy pathway  (IEA)
diltiazem pharmacodynamics pathway  (ISO)
disopyramide pharmacodynamics pathway  (ISO)
dobutamine pharmacodynamics pathway  (ISO)
esmolol pharmacodynamics pathway  (ISO)
flecainde pharmacodynamics pathway  (ISO)
fosphenytoin pharmacodynamics pathway  (ISO)
hypertrophic cardiomyopathy pathway  (IEA)
ibutilide pharmacodynamics pathway  (ISO)
isoprenaline pharmacodynamics pathway  (ISO)
isradipine pharmacodynamics pathway  (ISO)
levobunolol pharmacodynamics pathway  (ISO)
lidocaine pharmacodynamics pathway  (ISO)
metoprolol pharmacodynamics pathway  (ISO)
mexiletine pharmacodynamics pathway  (ISO)
nadolol pharmacodynamics pathway  (ISO)
nebivolol pharmacodynamics pathway  (ISO)
nifedipine pharmacodynamics pathway  (ISO)
nimodipine pharmacodynamics pathway  (ISO)
nisoldipine pharmacodynamics pathway  (ISO)
nitrendipine pharmacodynamics pathway  (ISO)
penbutolol pharmacodynamics pathway  (ISO)
phenytoin pharmacodynamics pathway  (ISO)
pindolol pharmacodynamics pathway  (ISO)
procainamide pharmacodynamics pathway  (ISO)
propranolol pharmacodynamics pathway  (ISO)
quinidine pharmacodynamics pathway  (ISO)
sotalol pharmacodynamics pathway  (ISO)
timolol pharmacodynamics pathway  (ISO)
verapamil pharmacodynamics pathway  (ISO)

References

References - curated
1. Bidasee KR, etal., Mol Pharmacol 2001 Dec;60(6):1356-64.
2. Bull R, etal., J Neurosci. 2008 Sep 17;28(38):9463-72.
3. Cavallaro S, etal., Proc Natl Acad Sci U S A 1997 Sep 2;94(18):9669-73.
4. Chugun A, etal., Am J Physiol Cell Physiol. 2007 Jan;292(1):C535-44. Epub 2006 Sep 13.
5. Clark JH, etal., J Biol Chem. 2010 Apr 30;285(18):13542-9. doi: 10.1074/jbc.M110.101485. Epub 2010 Feb 21.
6. Fritz N, etal., J Cell Sci. 2005 May 15;118(Pt 10):2261-70. Epub 2005 May 3.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. Ho HT, etal., J Physiol. 2011 Oct 1;589(Pt 19):4697-708. Epub 2011 Aug 1.
9. Kapiloff MS, etal., J Cell Sci. 2001 Sep;114(Pt 17):3167-76.
10. Kraner SD, etal., Am J Physiol Regul Integr Comp Physiol. 2011 Jun;300(6):R1384-91. Epub 2011 Apr 6.
11. Lanner JT, etal., Cold Spring Harb Perspect Biol. 2010 Nov;2(11):a003996. doi: 10.1101/cshperspect.a003996. Epub 2010 Oct 20.
12. Lukyanenko V, etal., J Physiol. 2007 Aug 15;583(Pt 1):251-69. Epub 2007 Jul 12.
13. NCBI rat LocusLink and RefSeq merged data July 26, 2002
14. Oda T, etal., Circ Res. 2013 Feb 1;112(3):487-97. doi: 10.1161/CIRCRESAHA.111.300290. Epub 2012 Dec 11.
15. OMIM Disease Annotation Pipeline
16. Pare GC, etal., J Cell Sci. 2005 Dec 1;118(Pt 23):5637-46.
17. Pipeline to import KEGG annotations from KEGG into RGD
18. Pipeline to import SMPDB annotations from SMPDB into RGD
19. RGD automated data pipeline
20. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
21. RGD automated import pipeline for gene-chemical interactions
22. Rokita AG and Anderson ME, Circulation. 2012 Oct 23;126(17):2125-39. doi: 10.1161/CIRCULATIONAHA.112.124990.
23. Rosker C, etal., J Biol Chem. 2009 Feb 20;284(8):5186-94. doi: 10.1074/jbc.M805587200. Epub 2008 Dec 30.
24. Scriven DR, etal., Biophys J. 2000 Nov;79(5):2682-91.
25. Scriven DR, etal., Biophys J. 2005 Sep;89(3):1893-901. Epub 2005 Jun 24.
26. Seeber S, etal., J Biol Chem. 2004 May 14;279(20):21062-8. Epub 2004 Mar 9.
27. Shao CH, etal., J Mol Cell Cardiol. 2007 Jan;42(1):234-46. Epub 2006 Oct 6.
28. Tiso N, etal., Hum Mol Genet. 2001 Feb 1;10(3):189-94.
29. Vizotto VA, etal., Braz J Med Biol Res. 2007 Jan;40(1):27-31.
30. Xiao B, etal., Biochem J. 2006 May 15;396(1):7-16.
31. Zheng X and Hu SJ, Acta Pharmacol Sin. 2005 Jun;26(6):696-704.
32. Zissimopoulos S, etal., J Cell Sci. 2006 Jun 1;119(Pt 11):2386-97.
Additional References at PubMed
PMID:9287354   PMID:9628868   PMID:10444400   PMID:10473538   PMID:10830164   PMID:11576544   PMID:11934703   PMID:12089338   PMID:12324472   PMID:12401811   PMID:12443530   PMID:12477932  
PMID:12606683   PMID:12676814   PMID:12829653   PMID:12837242   PMID:12919952   PMID:14592808   PMID:14593104   PMID:15041652   PMID:15044459   PMID:15105296   PMID:15197150   PMID:15626694  
PMID:15731460   PMID:16204356   PMID:16213210   PMID:16249429   PMID:16481613   PMID:16931553   PMID:17234969   PMID:17237229   PMID:17267548   PMID:17313373   PMID:17360443   PMID:17431507  
PMID:17516033   PMID:17569730   PMID:17630346   PMID:17652368   PMID:17693412   PMID:17823125   PMID:17872467   PMID:17875969   PMID:17921453   PMID:18468998   PMID:18718444   PMID:18755143  
PMID:18979913   PMID:19120137   PMID:19131648   PMID:19220289   PMID:19226252   PMID:19284993   PMID:19383796   PMID:20008518   PMID:20018773   PMID:20080623   PMID:20226167   PMID:20336285  
PMID:20427316   PMID:20431056   PMID:20445169   PMID:20471962   PMID:21156134   PMID:21282625   PMID:21372126   PMID:21421556   PMID:21612318   PMID:21649588   PMID:21673970   PMID:21788490  
PMID:22067155   PMID:22073362   PMID:22363773   PMID:22404946   PMID:22406107   PMID:22867515   PMID:22890710   PMID:22962011   PMID:23040497   PMID:23177664   PMID:23354458   PMID:23376485  
PMID:23454728   PMID:23499836   PMID:23943510   PMID:24186966   PMID:24417961   PMID:24631538   PMID:24693334   PMID:24786399   PMID:25263335   PMID:26046640   PMID:26071359   PMID:26092277  
PMID:26164367   PMID:26316108   PMID:26963898   PMID:27013634   PMID:27422983   PMID:27516456   PMID:28630041   PMID:29162778   PMID:29357673   PMID:30123252   PMID:30885011  


Genomics

Candidate Gene Status
Ryr2 is a candidate Gene for QTL Cm15
Comparative Map Data
Ryr2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01765,533,998 - 65,955,606 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1765,535,403 - 65,955,606 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01767,285,205 - 67,704,766 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41768,959,042 - 69,544,816 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11769,519,966 - 69,552,036 (+)NCBI
Celera1761,573,393 - 61,976,022 (-)NCBICelera
Cytogenetic Map17q12.1NCBI
RYR2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1237,042,184 - 237,833,988 (+)EnsemblGRCh38hg38GRCh38
GRCh381237,042,184 - 237,833,988 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371237,205,510 - 237,997,288 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361235,272,325 - 236,063,911 (+)NCBINCBI36hg18NCBI36
Build 341233,531,742 - 234,322,694NCBI
Celera1210,455,038 - 211,246,790 (+)NCBI
Cytogenetic Map1q43NCBI
HuRef1207,662,133 - 208,453,675 (+)NCBIHuRef
CHM1_11238,478,098 - 239,269,604 (+)NCBICHM1_1
Ryr2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391311,567,985 - 12,121,831 (-)NCBI
GRCm381311,553,099 - 12,106,945 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1311,553,102 - 12,106,945 (-)EnsemblGRCm38mm10GRCm38
MGSCv371311,645,370 - 12,199,212 (-)NCBIGRCm37mm9NCBIm37
MGSCv361311,608,677 - 12,160,499 (-)NCBImm8
Celera1311,467,020 - 12,025,871 (-)NCBICelera
Cytogenetic Map13A1NCBI
cM Map134.38NCBI
Ryr2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554922,648,956 - 3,076,509 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554922,647,597 - 3,275,512 (-)NCBIChiLan1.0ChiLan1.0
RYR2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11217,598,069 - 218,384,849 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1217,815,676 - 218,383,509 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01212,600,198 - 213,387,312 (+)NCBIMhudiblu_PPA_v0panPan3
RYR2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl42,373,114 - 2,907,875 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.142,371,868 - 2,908,132 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Ryr2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493648415,402,488 - 15,825,410 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RYR2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1453,652,245 - 54,406,355 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11453,652,140 - 54,406,691 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21457,571,491 - 58,014,914 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap14q22-q23NCBI
RYR2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl2574,389,122 - 74,953,451 (+)Ensembl
ChlSab1.12574,169,024 - 74,951,371 (+)NCBI
Ryr2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462477512,954,653 - 13,650,449 (-)NCBI

Position Markers
D17Rat123  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01765,739,231 - 65,739,401NCBIRnor6.0
Rnor_5.01767,489,835 - 67,490,005UniSTSRnor5.0
RGSC_v3.41769,337,501 - 69,337,672RGDRGSC3.4
RGSC_v3.41769,337,502 - 69,337,672UniSTSRGSC3.4
RGSC_v3.11769,348,334 - 69,348,505RGD
Celera1761,772,098 - 61,772,268UniSTS
Cytogenetic Map17q12.1UniSTS
SHRSP x BN Map1732.6999RGD
SHRSP x BN Map1732.6999UniSTS
D17Arb5  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01765,830,897 - 65,831,023NCBIRnor6.0
Rnor_5.01767,580,807 - 67,580,933UniSTSRnor5.0
RGSC_v3.41769,257,315 - 69,257,442RGDRGSC3.4
RGSC_v3.41769,257,316 - 69,257,442UniSTSRGSC3.4
RGSC_v3.11769,268,149 - 69,268,275RGD
Celera1761,848,039 - 61,848,165UniSTS
Cytogenetic Map17q12.1UniSTS
RH 3.4 Map17617.3UniSTS
RH 3.4 Map17617.3RGD
SHRSP x BN Map1732.6999UniSTS
SHRSP x BN Map1732.6999RGD
FHH x ACI Map1742.1599RGD
D17Rat68  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01765,888,732 - 65,888,902NCBIRnor6.0
Rnor_5.01767,638,898 - 67,639,068UniSTSRnor5.0
RGSC_v3.41769,196,750 - 69,196,921RGDRGSC3.4
RGSC_v3.41769,196,751 - 69,196,921UniSTSRGSC3.4
Celera1761,906,744 - 61,906,915UniSTS
Cytogenetic Map17q12.1UniSTS
FHH x ACI Map1742.19RGD
FHH x ACI Map1742.19UniSTS
D17Got79  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01765,691,658 - 65,691,765NCBIRnor6.0
Rnor_5.01767,442,262 - 67,442,369UniSTSRnor5.0
RGSC_v3.41769,384,960 - 69,385,068RGDRGSC3.4
RGSC_v3.41769,384,961 - 69,385,068UniSTSRGSC3.4
RGSC_v3.11769,395,794 - 69,395,901RGD
Celera1761,725,590 - 61,725,697UniSTS
Cytogenetic Map17q12.1UniSTS
RH 3.4 Map17619.1UniSTS
RH 3.4 Map17619.1RGD
RH 2.0 Map17479.8RGD
D17Got77  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01765,977,518 - 65,977,625NCBIRnor6.0
Rnor_5.01767,726,678 - 67,726,785UniSTSRnor5.0
RGSC_v3.41769,105,678 - 69,105,786RGDRGSC3.4
RGSC_v3.41769,105,679 - 69,105,786UniSTSRGSC3.4
RGSC_v3.11769,116,512 - 69,116,619RGD
Celera1761,997,939 - 61,998,046UniSTS
Cytogenetic Map17q12.1UniSTS
RH 3.4 Map17614.8UniSTS
RH 3.4 Map17614.8RGD
RH 2.0 Map17488.8RGD
RH131486  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01765,534,089 - 65,534,305NCBIRnor6.0
Rnor_5.01767,285,296 - 67,285,512UniSTSRnor5.0
RGSC_v3.41769,545,842 - 69,546,058UniSTSRGSC3.4
Celera1761,573,484 - 61,573,700UniSTS
Cytogenetic Map17q12.1UniSTS
RH 3.4 Map17615.9UniSTS
AU049096  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01088,096,096 - 88,097,217NCBIRnor6.0
Rnor_5.01087,888,771 - 87,889,892UniSTSRnor5.0
RGSC_v3.41769,029,828 - 69,030,313UniSTSRGSC3.4
RGSC_v3.41089,121,733 - 89,122,854UniSTSRGSC3.4
Celera1762,083,834 - 62,084,319UniSTS
Celera1083,835,564 - 83,836,678UniSTS
Cytogenetic Map17q12.1UniSTS
Cytogenetic Map10q32.1UniSTS
AU049552  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01765,739,170 - 65,739,417NCBIRnor6.0
Rnor_5.01767,489,774 - 67,490,021UniSTSRnor5.0
RGSC_v3.41769,337,486 - 69,337,733UniSTSRGSC3.4
Celera1761,772,037 - 61,772,284UniSTS
Cytogenetic Map17q12.1UniSTS
PMC21940P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01765,534,270 - 65,534,515NCBIRnor6.0
Rnor_5.01767,285,477 - 67,285,722UniSTSRnor5.0
RGSC_v3.41769,545,632 - 69,545,877UniSTSRGSC3.4
Celera1761,573,665 - 61,573,910UniSTS
Cytogenetic Map17q12.1UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17173413148Rat
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17173413148Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)17333697273413148Rat
1354651Lmblg2Limb length QTL 26tibia length (VT:0004357)tibia length (CMO:0000450)17333697273413148Rat
1354630Cm34Cardiac mass QTL 348.7heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)17333697273413148Rat
1559055Bp278Blood pressure QTL 2780.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172149095066490950Rat
12903978Cm118Cardiac mass QTL 1180.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)172149095066490950Rat
12903979Cm119Cardiac mass QTL 1190.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)172149095066490950Rat
12903980Cm120Cardiac mass QTL 1200.002heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)172149095066490950Rat
12903981Am17Aortic mass QTL 170.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)172149095066490950Rat
12903982Kidm70Kidney mass QTL 700.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)172149095074823273Rat
1354619Bp242Blood pressure QTL 2426.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172841314873413148Rat
9590107Sffal7Serum free fatty acids level QTL 74.810.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)173097522875975228Rat
8552928Pigfal9Plasma insulin-like growth factor 1 level QTL 99blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)173097522875975228Rat
2324621Coatc5Coat color QTL 5coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)173205588277922655Rat
724549Niddm56Non-insulin dependent diabetes mellitus QTL 560.03blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)173330362778303627Rat
1354663Bvd5Brain ventricular dilatation QTL 53.510.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)173330362785321557Rat
1300148Bp192Blood pressure QTL 1923.47arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)173628324577922655Rat
724528Uae4Urinary albumin excretion QTL 44.90.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)173779030673413148Rat
2317054Aia12Adjuvant induced arthritis QTL 124.24joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)174117605786176057Rat
2317060Aia26Adjuvant induced arthritis QTL 263.22joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)174117605786176057Rat
2301412Kidm40Kidney mass QTL 400.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)174173108086731080Rat
1598871Memor5Memory QTL 55.3exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)174254187285446768Rat
1358295Aocep1Aortic cell protein QTL 16.10.00000071thoracic aorta cellular protein amount (VT:0010598)aortic cell percentage174435615789356157Rat
1354635Bp245Blood pressure QTL 2456arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)174866025273413148Rat
1354635Bp245Blood pressure QTL 2456arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)174866025273413148Rat
7411575Bw140Body weight QTL 14030.20.001body mass (VT:0001259)body weight gain (CMO:0000420)175241095790843779Rat
8694181Bw151Body weight QTL 1514.360.001body mass (VT:0001259)body weight gain (CMO:0000420)175241095790843779Rat
4889894Eae33Experimental allergic encephalomyelitis QTL 335.20.0001nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)175347518090690466Rat
2317038Ginf3Gastrointestinal inflammation QTL 32.890.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)175387148890843779Rat
2303580Gluco49Glucose level QTL 492blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)175399194790843779Rat
1354588Bvd4Brain ventricular dilatation QTL 45.310.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)175622429686731080Rat
7394837Memor18Memory QTL 18exploratory behavior trait (VT:0010471)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)176135530067004384Rat
70210Cm15Cardiac mass QTL 156.5heart right ventricle mass (VT:0007033)heart right ventricle wet weight (CMO:0000072)176219570373981731Rat
1600398Edcs5Endometrial carcinoma susceptibility QTL 52.2uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)176219570374702206Rat
2302365Gluco40Glucose level QTL 404.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)176219582286194199Rat
2317045Aia11Adjuvant induced arthritis QTL 114.06joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)176367597570261772Rat
7488963Bp369Blood pressure QTL 3690.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)176549735982019219Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:14
Count of miRNA genes:5
Interacting mature miRNAs:6
Transcripts:ENSRNOT00000023601, ENSRNOT00000067949
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 43 39 8
Low 24 8 16 8 8 10 25 16 30 3 8
Below cutoff 3 11 11 2 11 10 19 11

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001191043 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_032078 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AABR07028327 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07028328 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07028329 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07028330 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07028331 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07028332 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07028333 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07028334 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07028335 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07028336 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01092223 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01092224 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01092225 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01092226 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01092227 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01092228 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01092229 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01092230 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01092231 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01092232 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01092233 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01092234 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01092235 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01092236 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01092237 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01092238 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01092239 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01092240 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01092241 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01092242 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01092243 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01092244 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01092245 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01092246 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01092247 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01092248 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01092249 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01092250 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01092251 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01092252 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01092253 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01092254 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01092255 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB204523 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB204524 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB204525 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB204526 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB204527 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB204529 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB204530 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB204531 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF011789 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF112257 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF130880 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF363960 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC167757 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU346200 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U95147 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U95157 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000023601   ⟹   ENSRNOP00000023601
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1765,535,403 - 65,955,606 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000067949   ⟹   ENSRNOP00000059019
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1765,535,403 - 65,955,606 (-)Ensembl
RefSeq Acc Id: NM_001191043   ⟹   NP_001177972
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01765,533,998 - 65,955,606 (-)NCBI
Rnor_5.01767,285,205 - 67,704,766 (-)NCBI
Celera1761,573,393 - 61,976,022 (-)NCBI
Sequence:
RefSeq Acc Id: NM_032078   ⟹   NP_114467
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01765,535,403 - 65,955,606 (-)NCBI
Rnor_5.01767,285,205 - 67,704,766 (-)NCBI
RGSC_v3.41768,959,042 - 69,544,816 (+)RGD
Celera1761,574,873 - 61,976,022 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_114467   ⟸   NM_032078
- Peptide Label: isoform 1
- UniProtKB: B0LPN4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001177972   ⟸   NM_001191043
- Peptide Label: isoform 2
- UniProtKB: B0LPN4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000023601   ⟸   ENSRNOT00000023601
RefSeq Acc Id: ENSRNOP00000059019   ⟸   ENSRNOT00000067949
Protein Domains
B30.2/SPRY   EF-hand   Ion_trans   MIR

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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