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: Enables 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. Located in several cellular components, including A band; sarcolemma; and sarcoplasmic reticulum membrane. Is extrinsic component of cytoplasmic side of plasma membrane. Part of protein-containing complex. Colocalizes with Z disc. 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: VALIDATED
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
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
mRatBN7.21758,389,925 - 58,975,641 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1758,389,925 - 58,975,142 (+)Ensembl
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)
cardiomyopathy  (ISO)
catecholaminergic polymorphic ventricular tachycardia  (ISO)
catecholaminergic polymorphic ventricular tachycardia 1  (ISO)
catecholaminergic polymorphic ventricular tachycardia 2  (ISO)
Childhood Schizophrenia  (ISO)
congenital heart disease  (ISO)
congestive heart failure  (IDA,ISO)
Diabetic Cardiomyopathies  (ISO)
Diastolic Dysfunction  (ISO)
dilated cardiomyopathy  (ISO)
dilated cardiomyopathy 1AA  (ISO)
dilated cardiomyopathy 1B  (ISO)
Dilated Cardiomyopathy with Left Ventricular Noncompaction  (ISO)
Experimental Diabetes Mellitus  (IDA)
familial hypertrophic cardiomyopathy  (ISO)
Familial Sudden Death  (ISO)
Familial Ventricular Tachycardia  (ISO)
gastrointestinal stromal tumor  (ISO)
genetic disease  (ISO)
Heart Block  (ISO)
heart disease  (ISO,ISS)
Hereditary Leiomyomatosis and Renal Cell Cancer  (ISO)
hypertrophic cardiomyopathy  (ISO)
hypertrophic cardiomyopathy 4  (ISO)
Infant Death  (ISO)
left ventricular noncompaction  (ISO)
long QT syndrome  (ISO)
long QT syndrome 1  (ISO)
malignant mesothelioma  (ISO)
Myocardial Ischemia  (ISO)
parathyroid carcinoma  (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)
cadmium dichloride  (EXP)
caffeine  (EXP)
calcium atom  (EXP,ISO)
calcium(0)  (EXP,ISO)
candesartan  (EXP)
carvedilol  (EXP,ISO)
chlorpyrifos  (ISO)
choline  (ISO)
cocaine  (EXP,ISO)
Cuprizon  (EXP)
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)
triptonide  (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 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)
response to xenobiotic stimulus  (IEP)
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   PMID:31505169  
PMID:31916935  


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
mRatBN7.21758,389,925 - 58,975,641 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1758,389,925 - 58,975,142 (+)Ensembl
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
GRCh371237,205,484 - 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 (-)NCBIGRCm39mm39
GRCm39 Ensembl1311,567,988 - 12,121,831 (-)Ensembl
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
CanFam3.142,371,868 - 2,908,132 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl42,373,114 - 2,907,875 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha42,419,733 - 3,146,551 (-)NCBI
ROS_Cfam_1.042,390,864 - 3,118,926 (-)NCBI
UMICH_Zoey_3.142,386,589 - 3,119,270 (-)NCBI
UNSW_CanFamBas_1.042,522,518 - 3,249,453 (-)NCBI
UU_Cfam_GSD_1.042,743,722 - 3,470,663 (-)NCBI
Ryr2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934439,237,258 - 39,734,210 (-)NCBI
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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12574,169,024 - 74,951,371 (+)NCBI
ChlSab1.1 Ensembl2574,389,122 - 74,953,451 (+)Ensembl
Vero_WHO_p1.0NW_02366605576,267,928 - 77,050,853 (+)NCBI
Ryr2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462477512,954,653 - 13,650,449 (-)NCBI

Position Markers
D17Rat123  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21758,768,794 - 58,768,965 (-)MAPPERmRatBN7.2
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
SHRSP x BN Map1732.6999RGD
SHRSP x BN Map1732.6999UniSTS
Cytogenetic Map17q12.1UniSTS
D17Arb5  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21758,691,835 - 58,691,962 (-)MAPPERmRatBN7.2
Rnor_6.01765,830,897 - 65,831,023NCBIRnor6.0
Rnor_5.01767,580,807 - 67,580,933UniSTSRnor5.0
RGSC_v3.41769,257,316 - 69,257,442UniSTSRGSC3.4
RGSC_v3.41769,257,315 - 69,257,442RGDRGSC3.4
RGSC_v3.11769,268,149 - 69,268,275RGD
Celera1761,848,039 - 61,848,165UniSTS
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
Cytogenetic Map17q12.1UniSTS
D17Rat68  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21758,632,929 - 58,633,100 (-)MAPPERmRatBN7.2
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
FHH x ACI Map1742.19UniSTS
FHH x ACI Map1742.19RGD
Cytogenetic Map17q12.1UniSTS
D17Got79  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21758,816,258 - 58,816,366 (-)MAPPERmRatBN7.2
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
RH 3.4 Map17619.1UniSTS
RH 3.4 Map17619.1RGD
RH 2.0 Map17479.8RGD
Cytogenetic Map17q12.1UniSTS
D17Got77  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21758,541,482 - 58,541,590 (-)MAPPERmRatBN7.2
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
RH 3.4 Map17614.8UniSTS
RH 3.4 Map17614.8RGD
RH 2.0 Map17488.8RGD
Cytogenetic Map17q12.1UniSTS
RH131486  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21758,975,330 - 58,975,547 (-)MAPPERmRatBN7.2
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
RH 3.4 Map17615.9UniSTS
Cytogenetic Map17q12.1UniSTS
AU049096  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21085,116,089 - 85,117,213 (+)MAPPERmRatBN7.2
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
mRatBN7.21758,768,778 - 58,769,026 (-)MAPPERmRatBN7.2
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
mRatBN7.21758,975,120 - 58,975,366 (-)MAPPERmRatBN7.2
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17160781592Rat
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17169599340Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17169599340Rat
1354596Bw32Body weight QTL 324.5body mass (VT:0001259)body weight (CMO:0000012)17429913060781592Rat
1354630Cm34Cardiac mass QTL 348.7heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)17429913069599340Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)17429913069599340Rat
1354651Lmblg2Limb length QTL 26tibia length (VT:0004357)tibia length (CMO:0000450)17429913069599340Rat
1354640Scl32Serum cholesterol level QTL 325.4blood HDL cholesterol amount (VT:0000184)blood high density lipoprotein cholesterol level (CMO:0000052)171578159260781592Rat
1354659Scl68Serum cholesterol level QTL 683.9blood VLDL cholesterol amount (VT:0005144)blood very low density lipoprotein cholesterol level (CMO:0000648)171578159260781592Rat
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)171864018263640182Rat
1354628Stl13Serum triglyceride level QTL 133.8blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)172129303960781592Rat
61394Bp8Blood pressure QTL 82.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172308056759555013Rat
12903978Cm118Cardiac mass QTL 1180.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)172365318468653184Rat
12903979Cm119Cardiac mass QTL 1190.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)172365318468653184Rat
12903980Cm120Cardiac mass QTL 1200.002heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)172365318468653184Rat
12903981Am17Aortic mass QTL 170.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)172365318468653184Rat
1559055Bp278Blood pressure QTL 2780.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172365318468653184Rat
12903982Kidm70Kidney mass QTL 700.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)172365318470974005Rat
1354619Bp242Blood pressure QTL 2426.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172459934069599340Rat
4889955Bss93Bone structure and strength QTL 934.4tibia size trait (VT:0100001)tibia cortical bone volume to tibia total bone volume ratio (CMO:0001727)172702794960463643Rat
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)172840914773409147Rat
9590107Sffal7Serum free fatty acids level QTL 74.810.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)172840914773409147Rat
10450503Bp386Blood pressure QTL 3860.28arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)173136839162109574Rat
2324621Coatc5Coat color QTL 5coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)173136839173951021Rat
724549Niddm56Non-insulin dependent diabetes mellitus QTL 560.03blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)173199078476990784Rat
1354663Bvd5Brain ventricular dilatation QTL 53.510.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)173199078481292925Rat
1300148Bp192Blood pressure QTL 1923.47arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)173455084373951021Rat
724528Uae4Urinary albumin excretion QTL 44.90.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)173583708569599340Rat
2301412Kidm40Kidney mass QTL 400.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)173747984782479847Rat
2317054Aia12Adjuvant induced arthritis QTL 124.24joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)173828150983281509Rat
2317060Aia26Adjuvant induced arthritis QTL 263.22joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)173828150983281509Rat
1598871Memor5Memory QTL 55.3exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)174054004180387013Rat
1358295Aocep1Aortic cell protein QTL 16.10.00000071thoracic aorta cellular protein amount (VT:0010598)aortic cell percentage174099000585990005Rat
631497Bp98Blood pressure QTL 983.66arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)174135465160463643Rat
1354635Bp245Blood pressure QTL 2456arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)174207316069599340Rat
1354635Bp245Blood pressure QTL 2456arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)174207316069599340Rat
7411575Bw140Body weight QTL 14030.20.001body mass (VT:0001259)body weight gain (CMO:0000420)174856093586533673Rat
8694181Bw151Body weight QTL 1514.360.001body mass (VT:0001259)body weight gain (CMO:0000420)174856093586533673Rat
2317038Ginf3Gastrointestinal inflammation QTL 32.890.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)174992015486533673Rat
2303580Gluco49Glucose level QTL 492blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)175004027186533673Rat
1354629Scl31Serum cholesterol level QTL 314.1blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)175089090860781592Rat
1354654Spl7Serum phospholipid level QTL 75.5blood phospholipid amount (VT:0006084)blood phospholipid level (CMO:0001169)175089090860781592Rat
4889894Eae33Experimental allergic encephalomyelitis QTL 335.20.0001nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)175090909986022412Rat
2317053Aia25Adjuvant induced arthritis QTL 252.69joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)175090919660781426Rat
1354588Bvd4Brain ventricular dilatation QTL 45.310.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)175349882882479847Rat
61466Niddm12Non-insulin dependent diabetes mellitus QTL 123.20.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)175402992960463637Rat
70210Cm15Cardiac mass QTL 156.5heart right ventricle mass (VT:0007033)heart right ventricle wet weight (CMO:0000072)175724672370156904Rat
1600398Edcs5Endometrial carcinoma susceptibility QTL 52.2uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)175724672370852846Rat
2302365Gluco40Glucose level QTL 404.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)175724684382046127Rat

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
  XM_039096071 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039096072 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039096073 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039096074 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039096075 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039096076 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039096077 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039096078 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039096079 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039096080 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039096081 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039096082 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039096083 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039096084 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005495333 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide 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
  AB204528 (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
  JACYVU010000293 (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
mRatBN7.2 Ensembl1758,389,925 - 58,975,142 (+)Ensembl
Rnor_6.0 Ensembl1765,535,403 - 65,955,606 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000067949   ⟹   ENSRNOP00000059019
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1758,389,925 - 58,975,142 (+)Ensembl
Rnor_6.0 Ensembl1765,535,403 - 65,955,606 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000111439   ⟹   ENSRNOP00000087428
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1758,562,590 - 58,975,142 (+)Ensembl
RefSeq Acc Id: NM_001191043   ⟹   NP_001177972
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21758,390,200 - 58,975,638 (+)NCBI
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: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21758,390,292 - 58,974,204 (+)NCBI
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:
RefSeq Acc Id: XM_039096071   ⟹   XP_038951999
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21758,390,217 - 58,975,641 (+)NCBI
RefSeq Acc Id: XM_039096072   ⟹   XP_038952000
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21758,389,925 - 58,975,641 (+)NCBI
RefSeq Acc Id: XM_039096073   ⟹   XP_038952001
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21758,390,217 - 58,975,641 (+)NCBI
RefSeq Acc Id: XM_039096074   ⟹   XP_038952002
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21758,390,217 - 58,975,641 (+)NCBI
RefSeq Acc Id: XM_039096075   ⟹   XP_038952003
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21758,390,217 - 58,975,641 (+)NCBI
RefSeq Acc Id: XM_039096076   ⟹   XP_038952004
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21758,390,217 - 58,975,641 (+)NCBI
RefSeq Acc Id: XM_039096077   ⟹   XP_038952005
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21758,390,217 - 58,975,641 (+)NCBI
RefSeq Acc Id: XM_039096078   ⟹   XP_038952006
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21758,390,217 - 58,975,641 (+)NCBI
RefSeq Acc Id: XM_039096079   ⟹   XP_038952007
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21758,390,217 - 58,975,641 (+)NCBI
RefSeq Acc Id: XM_039096080   ⟹   XP_038952008
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21758,390,217 - 58,975,641 (+)NCBI
RefSeq Acc Id: XM_039096081   ⟹   XP_038952009
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21758,390,217 - 58,910,257 (+)NCBI
RefSeq Acc Id: XM_039096082   ⟹   XP_038952010
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21758,390,217 - 58,828,017 (+)NCBI
RefSeq Acc Id: XM_039096083   ⟹   XP_038952011
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21758,390,217 - 58,975,641 (+)NCBI
RefSeq Acc Id: XM_039096084   ⟹   XP_038952012
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21758,390,217 - 58,975,641 (+)NCBI
RefSeq Acc Id: XR_005495333
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21758,390,217 - 58,858,418 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001177972 (Get FASTA)   NCBI Sequence Viewer  
  NP_114467 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951999 (Get FASTA)   NCBI Sequence Viewer  
  XP_038952000 (Get FASTA)   NCBI Sequence Viewer  
  XP_038952001 (Get FASTA)   NCBI Sequence Viewer  
  XP_038952002 (Get FASTA)   NCBI Sequence Viewer  
  XP_038952003 (Get FASTA)   NCBI Sequence Viewer  
  XP_038952004 (Get FASTA)   NCBI Sequence Viewer  
  XP_038952005 (Get FASTA)   NCBI Sequence Viewer  
  XP_038952006 (Get FASTA)   NCBI Sequence Viewer  
  XP_038952007 (Get FASTA)   NCBI Sequence Viewer  
  XP_038952008 (Get FASTA)   NCBI Sequence Viewer  
  XP_038952009 (Get FASTA)   NCBI Sequence Viewer  
  XP_038952010 (Get FASTA)   NCBI Sequence Viewer  
  XP_038952011 (Get FASTA)   NCBI Sequence Viewer  
  XP_038952012 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAB65757 (Get FASTA)   NCBI Sequence Viewer  
  AAB70011 (Get FASTA)   NCBI Sequence Viewer  
  AAB70013 (Get FASTA)   NCBI Sequence Viewer  
  AAD31271 (Get FASTA)   NCBI Sequence Viewer  
  AAD48900 (Get FASTA)   NCBI Sequence Viewer  
  AAI67757 (Get FASTA)   NCBI Sequence Viewer  
  AAK37569 (Get FASTA)   NCBI Sequence Viewer  
  ABY79796 (Get FASTA)   NCBI Sequence Viewer  
  B0LPN4 (Get FASTA)   NCBI Sequence Viewer  
  BAJ10276 (Get FASTA)   NCBI Sequence Viewer  
  BAJ10277 (Get FASTA)   NCBI Sequence Viewer  
  BAJ10278 (Get FASTA)   NCBI Sequence Viewer  
  BAJ10279 (Get FASTA)   NCBI Sequence Viewer  
  BAJ10280 (Get FASTA)   NCBI Sequence Viewer  
  BAJ10281 (Get FASTA)   NCBI Sequence Viewer  
  BAJ10282 (Get FASTA)   NCBI Sequence Viewer  
  BAJ10283 (Get FASTA)   NCBI Sequence Viewer  
  BAJ10284 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_114467   ⟸   NM_032078
- Peptide Label: isoform 1
- Sequence:
RefSeq Acc Id: NP_001177972   ⟸   NM_001191043
- Peptide Label: isoform 2
- Sequence:
RefSeq Acc Id: ENSRNOP00000023601   ⟸   ENSRNOT00000023601
RefSeq Acc Id: ENSRNOP00000059019   ⟸   ENSRNOT00000067949
RefSeq Acc Id: XP_038952000   ⟸   XM_039096072
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038951999   ⟸   XM_039096071
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038952001   ⟸   XM_039096073
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038952005   ⟸   XM_039096077
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038952003   ⟸   XM_039096075
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038952007   ⟸   XM_039096079
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038952006   ⟸   XM_039096078
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038952008   ⟸   XM_039096080
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038952004   ⟸   XM_039096076
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038952011   ⟸   XM_039096083
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038952012   ⟸   XM_039096084
- Peptide Label: isoform X14
RefSeq Acc Id: XP_038952002   ⟸   XM_039096074
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038952009   ⟸   XM_039096081
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038952010   ⟸   XM_039096082
- Peptide Label: isoform X12
RefSeq Acc Id: ENSRNOP00000087428   ⟸   ENSRNOT00000111439
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 (2019)
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Sequenced By: MCW
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/EurMcwi (MCW)
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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)
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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
ACI/N (2020)
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Sequenced By: MCW
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
ACI/N (MCW)
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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)
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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
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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/SsN (MCW)
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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 (2020)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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
Buf/N (MCW)
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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)
DA/OlaHsd (2019)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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/NCrl (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