F5 (coagulation factor V) - Rat Genome Database

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Gene: F5 (coagulation factor V) Rattus norvegicus
Analyze
Symbol: F5
Name: coagulation factor V
RGD ID: 1589758
Description: Predicted to enable oxidoreductase activity. Involved in blood coagulation and response to vitamin K. Located in Golgi apparatus; endoplasmic reticulum; and extracellular space. Used to study membranoproliferative glomerulonephritis. Biomarker of hepatitis and portal hypertension. Human ortholog(s) of this gene implicated in several diseases, including artery disease (multiple); end stage renal disease; factor V deficiency; liver disease (multiple); and non-arteritic anterior ischemic optic neuropathy. Orthologous to human F5 (coagulation factor V); PARTICIPATES IN coagulation cascade pathway; acenocoumarol pharmacodynamics pathway; alteplase pharmacodynamics pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Ac2-120; coagulation factor 5; coagulation factor 5 (mapped); coagulation factor V (proaccelerin, labile factor); F5_mapped
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
mRatBN7.21376,513,463 - 76,583,106 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1376,513,255 - 76,582,317 (+)Ensembl
Rnor_6.01382,479,997 - 82,535,540 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1382,479,998 - 82,535,534 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01387,355,980 - 87,417,686 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41379,934,956 - 79,997,285 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1376,256,969 - 76,316,731 (+)NCBICelera
Cytogenetic Map13q23NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
1q24 Deletion Syndrome  (ISO)
Acute Liver Failure  (ISO)
Behcet's disease  (ISO)
blood coagulation disease  (ISO)
brain ischemia  (ISO)
breast cancer  (ISO)
Budd-Chiari syndrome  (ISO)
cerebral infarction  (ISO)
Colonic Neoplasms  (IEP,ISO)
colorectal adenoma  (ISO)
COVID-19  (ISO)
Dysarthria  (ISO)
Dyspnea  (ISO)
end stage renal disease  (ISO)
Endotoxemia  (IEP)
Experimental Liver Cirrhosis  (IEP)
factor V deficiency  (ISO)
familial adenomatous polyposis  (ISO)
Femur Head Necrosis  (ISO)
Fetal Death  (ISO)
gastrointestinal stromal tumor  (ISO)
Habitual Abortions  (ISO)
hemorrhagic disease  (ISO)
hepatitis  (IEP,ISO)
Hereditary Thrombophilia  (ISO)
Hirschsprung's disease  (ISO)
hypereosinophilic syndrome  (ISO)
liver cirrhosis  (ISO)
membranoproliferative glomerulonephritis  (IMP)
Mesenteric Ischemia  (ISO)
myocardial infarction  (ISO)
Myocardial Ischemia  (ISO)
non-arteritic anterior ischemic optic neuropathy  (ISO)
parathyroid carcinoma  (ISO)
Peritoneal Fibrosis  (IEP)
portal hypertension  (IEP)
pre-eclampsia  (ISO)
prostate cancer  (ISO)
pulmonary embolism  (ISO)
pulmonary fibrosis  (ISO)
pulmonary hypertension  (ISO)
retinal artery occlusion  (ISO)
retinal vein occlusion  (ISO)
sagittal sinus thrombosis  (ISO)
sensorineural hearing loss  (ISO)
Sepsis  (IMP,ISO)
Septic Peritonitis  (ISO)
Spontaneous Abortions  (ISO)
Stroke  (ISO)
thrombocytopenia  (ISO)
Thromboembolism  (ISO)
thrombophilia due to activated protein C resistance  (ISO)
thrombophilia due to thrombin defect  (ISO)
thrombosis  (ISO)
Venous Thromboembolism  (ISO)
Venous Thrombosis  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-demecolcine  (ISO)
1-naphthyl isothiocyanate  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3-dimethoxynaphthalene-1,4-dione  (ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
3,3',4,4'-tetrachlorobiphenyl  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
acenocoumarol  (EXP)
acetamide  (EXP)
acrylamide  (EXP)
aflatoxin B1  (EXP,ISO)
all-trans-retinoic acid  (ISO)
antimony(0)  (ISO)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
aspalathin  (ISO)
atorvastatin calcium  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
beta-naphthoflavone  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
buta-1,3-diene  (ISO)
butanal  (ISO)
cadmium atom  (ISO)
calcitriol  (ISO)
calcium dichloride  (ISO)
chloroprene  (EXP)
chromium atom  (ISO)
chrysene  (ISO)
clofibrate  (EXP,ISO)
clofibric acid  (EXP)
clomiphene  (ISO)
cobalt dichloride  (EXP)
cyclosporin A  (ISO)
cyproconazole  (ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
diazinon  (EXP)
dichloroacetic acid  (ISO)
dicrotophos  (ISO)
dipotassium bis[mu-tartrato(4-)]diantimonate(2-) trihydrate  (ISO)
dorsomorphin  (ISO)
entinostat  (ISO)
epoxiconazole  (ISO)
Ethyl icosapentate  (EXP)
flutamide  (EXP)
folic acid  (ISO)
furan  (EXP)
glycidol  (EXP)
ivermectin  (ISO)
lead diacetate  (EXP)
leflunomide  (EXP)
levonorgestrel  (ISO)
lithium chloride  (ISO)
mercury atom  (ISO)
mercury dibromide  (ISO)
mercury(0)  (ISO)
methapyrilene  (EXP)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (ISO)
nickel atom  (ISO)
nickel dichloride  (ISO)
nitrofen  (EXP)
ochratoxin A  (ISO)
p-chloromercuribenzoic acid  (ISO)
paracetamol  (ISO)
paraquat  (EXP)
PCB138  (EXP)
pentanal  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (ISO)
phenprocoumon  (EXP)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
potassium dichromate  (ISO)
propanal  (ISO)
propiconazole  (ISO)
quinapril hydrochloride  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
Tesaglitazar  (EXP)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
titanium dioxide  (ISO)
tolcapone  (EXP)
trichostatin A  (ISO)
Triptolide  (EXP)
valproic acid  (ISO)
vinclozolin  (EXP)
warfarin  (EXP,ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
1. Akman B, etal., Transplant Proc. 2006 Mar;38(2):413-5.
2. Amalia PM, etal., Dig Dis Sci. 2007 Oct;52(10):2616-21. Epub 2007 Apr 12.
3. Arsene S, etal., Thromb Haemost. 2005 Jul;94(1):101-6.
4. Ben-Ari Z, etal., Am J Gastroenterol. 1999 Oct;94(10):2977-82. doi: 10.1111/j.1572-0241.1999.01446.x.
5. Benfield TL, etal., J Infect Dis. 2005 Nov 15;192(10):1851-7. Epub 2005 Oct 12.
6. Cadoni G, etal., Ann Otol Rhinol Laryngol. 2006 Mar;115(3):195-200.
7. Capaccio P, etal., Laryngoscope. 2007 Mar;117(3):547-51.
8. Castoldi E and Rosing J, Curr Opin Hematol. 2004 May;11(3):176-81.
9. Coen D, etal., Croat Med J. 2001 Aug;42(4):488-92.
10. Colak Y, etal., Eur J Gastroenterol Hepatol. 2006 Aug;18(8):917-20.
11. Cornillon B, etal., Comp Biochem Physiol B. 1986;83(2):397-401.
12. Cui J, etal., Blood. 2000 Dec 15;96(13):4222-6.
13. Duga S, etal., Int J Biochem Cell Biol. 2004 Aug;36(8):1393-9.
14. Ekmekci Y, etal., Nephrol Dial Transplant. 2006 Dec;21(12):3555-8. Epub 2006 Sep 12.
15. El Sebay HM, etal., J Gastroenterol Hepatol. 2016 Jan;31(1):235-40. doi: 10.1111/jgh.13066.
16. Emiroglu O, etal., J Cardiothorac Surg. 2011 Sep 28;6:120.
17. Engelmann MG, etal., Angiology. 2004 Mar-Apr;55(2):221-5.
18. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
19. Goforth RL, etal., Kidney Int. 2006 Aug;70(4):743-50. Epub 2006 Jun 7.
20. Gorur K, etal., Otol Neurotol. 2005 Jul;26(4):599-601.
21. Gowda MS, etal., J Thromb Thrombolysis. 2000 Jan;9(1):43-5.
22. Guan ZY, etal., Eur Rev Med Pharmacol Sci. 2018 May;22(9):2742-2750. doi: 10.26355/eurrev_201805_14971.
23. Gul A, etal., Br J Rheumatol. 1996 Nov;35(11):1178-80.
24. Haller MJ, etal., Pediatr Diabetes. 2006 Aug;7(4):229-31.
25. Hefler L, etal., J Soc Gynecol Investig. 2004 Jan;11(1):42-4.
26. Irish AB, etal., Transplantation. 1997 Aug 27;64(4):604-7.
27. Ivancic MM, etal., Cancer Prev Res (Phila). 2014 Nov;7(11):1160-9. doi: 10.1158/1940-6207.CAPR-14-0056. Epub 2014 Sep 8.
28. Ivancic MM, etal., Proc Natl Acad Sci U S A. 2019 Apr 23;116(17):8471-8480. doi: 10.1073/pnas.1813212116. Epub 2019 Apr 10.
29. Juul K, etal., Ann Intern Med. 2004 Mar 2;140(5):330-7.
30. Juul K, etal., Arch Intern Med. 2005 Sep 26;165(17):2032-6.
31. Kaiser R, etal., J Rheumatol. 2012 Aug;39(8):1603-10. Epub 2012 Jun 15.
32. Kalayci D, etal., Acta Ophthalmol Scand. 1999 Dec;77(6):622-4.
33. Kerschen E, etal., J Thromb Haemost. 2015 Jun;13(6):1073-80. doi: 10.1111/jth.12876. Epub 2015 Mar 31.
34. Klai S, etal., Blood Coagul Fibrinolysis. 2012 Jul;23(5):406-10.
35. Laudes IJ, etal., Am J Pathol. 2002 May;160(5):1867-75.
36. Liu N, etal., Am J Physiol Renal Physiol. 2004 Oct;287(4):F612-20. Epub 2004 Jun 1.
37. Ludemann P, etal., Stroke. 1998 Dec;29(12):2507-10.
38. Mahmoud AE, etal., Gut. 1997 Jun;40(6):798-800. doi: 10.1136/gut.40.6.798.
39. Mazzorana M, etal., Thromb Res. 1989 Jun 15;54(6):655-75.
40. Mello G, etal., Hypertension. 2005 Dec;46(6):1270-4. Epub 2005 Oct 24.
41. Middendorf K, etal., Am Heart J. 2004 May;147(5):897-904.
42. Nagy V, etal., Acta Ophthalmol Scand. 2004 Apr;82(2):140-3.
43. Nobukata H, etal., Toxicol Lett. 1999 Jan 11;104(1-2):93-101.
44. Norris LA, Best Pract Res Clin Obstet Gynaecol. 2003 Jun;17(3):369-83.
45. OMIM Disease Annotation Pipeline
46. Owen CA Jr and Bowie EJ, Haemostasis. 1978;7(4):189-201.
47. Pereira LM, etal., Gut. 1992 Jan;33(1):98-102. doi: 10.1136/gut.33.1.98.
48. Pipeline to import KEGG annotations from KEGG into RGD
49. Pipeline to import SMPDB annotations from SMPDB into RGD
50. Plompen EP, etal., J Hepatol. 2015 Dec;63(6):1459-65. doi: 10.1016/j.jhep.2015.07.026. Epub 2015 Jul 27.
51. RGD automated data pipeline
52. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
53. RGD automated import pipeline for gene-chemical interactions
54. RGD comprehensive gene curation
55. Saito H, etal., Perit Dial Int. 2009 May-Jun;29(3):340-51.
56. Siguret V, etal., J Gerontol A Biol Sci Med Sci. 2015 Aug;70(8):977-81. doi: 10.1093/gerona/glu240. Epub 2015 Feb 9.
57. Silingardi M, etal., Arthritis Rheum. 2004 Apr 15;51(2):177-83.
58. Sinclair SB and Levy GA, Dig Dis Sci. 1991 Jun;36(6):791-800. doi: 10.1007/bf01311239.
59. Smith SA, etal., Crit Rev Biochem Mol Biol. 2015;50(4):326-36. doi: 10.3109/10409238.2015.1050550. Epub 2015 May 28.
60. Sundquist K, etal., Thromb Haemost. 2015 Nov 25;114(6):1156-64. doi: 10.1160/TH15-01-0031. Epub 2015 Aug 6.
61. Tinholt M, etal., BMC Cancer. 2014 Nov 19;14:845. doi: 10.1186/1471-2407-14-845.
62. Tripathi G, etal., Clin Appl Thromb Hemost. 2010 Apr;16(2):132-40. Epub 2009 Jun 10.
63. Valla D, etal., Hepatology. 1989 Oct;10(4):482-7.
64. van Wijk R, etal., Br J Haematol. 2001 Sep;114(4):871-4.
65. Verity DH, etal., Am J Ophthalmol. 1999 Sep;128(3):352-6.
66. Weger M, etal., Eye. 2003 Aug;17(6):731-4.
67. Weischer M, etal., Atherosclerosis. 2010 Feb;208(2):480-3. Epub 2009 May 21.
68. Wong CL, etal., Blood Coagul Fibrinolysis. 2010 Apr;21(3):201-6.
69. Xu Z, etal., Thromb Haemost. 2001 Mar;85(3):441-4.
70. Yamaguchi K, etal., Shock. 2000 Nov;14(5):535-43.
71. Zou ZS, etal., Zhonghua Shi Yan He Lin Chuang Bing Du Xue Za Zhi. 2003 Sep;17(3):274-6.
Additional References at PubMed
PMID:8900278   PMID:10669158   PMID:12816857   PMID:12855561   PMID:19946888   PMID:20664909   PMID:24769233   PMID:31904090  


Genomics

Comparative Map Data
F5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21376,513,463 - 76,583,106 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1376,513,255 - 76,582,317 (+)Ensembl
Rnor_6.01382,479,997 - 82,535,540 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1382,479,998 - 82,535,534 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01387,355,980 - 87,417,686 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41379,934,956 - 79,997,285 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1376,256,969 - 76,316,731 (+)NCBICelera
Cytogenetic Map13q23NCBI
F5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1169,511,951 - 169,586,588 (-)EnsemblGRCh38hg38GRCh38
GRCh381169,511,951 - 169,586,630 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371169,481,189 - 169,555,719 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361167,747,816 - 167,822,393 (-)NCBINCBI36hg18NCBI36
Build 341166,215,066 - 166,287,379NCBI
Celera1142,590,970 - 142,665,548 (-)NCBI
Cytogenetic Map1q24.2NCBI
HuRef1140,703,881 - 140,778,453 (-)NCBIHuRef
CHM1_11170,903,222 - 170,977,927 (-)NCBICHM1_1
F5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391163,979,404 - 164,047,846 (+)NCBIGRCm39mm39
GRCm39 Ensembl1163,979,407 - 164,047,846 (+)Ensembl
GRCm381164,151,835 - 164,220,277 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1164,151,838 - 164,220,277 (+)EnsemblGRCm38mm10GRCm38
MGSCv371166,081,990 - 166,150,405 (+)NCBIGRCm37mm9NCBIm37
MGSCv361165,988,633 - 166,056,215 (+)NCBImm8
Celera1166,589,960 - 166,658,650 (+)NCBICelera
Cytogenetic Map1H2.2NCBI
cM Map171.46NCBI
F5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554627,694,939 - 7,757,463 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554627,695,004 - 7,757,832 (+)NCBIChiLan1.0ChiLan1.0
F5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11148,718,748 - 148,791,049 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1148,718,897 - 148,790,915 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01144,996,757 - 145,070,046 (-)NCBIMhudiblu_PPA_v0panPan3
F5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1728,999,481 - 29,069,603 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl728,999,512 - 29,069,296 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha728,531,164 - 28,601,084 (+)NCBI
ROS_Cfam_1.0728,801,509 - 28,871,406 (+)NCBI
UMICH_Zoey_3.1728,649,506 - 28,719,863 (+)NCBI
UNSW_CanFamBas_1.0728,685,240 - 28,755,563 (+)NCBI
UU_Cfam_GSD_1.0728,922,027 - 28,992,360 (+)NCBI
F5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934499,267,628 - 99,332,463 (+)NCBI
SpeTri2.0NW_00493648117,114,441 - 17,178,902 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
F5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl481,403,232 - 81,485,055 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1481,403,273 - 81,484,908 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2489,027,936 - 89,109,573 (+)NCBISscrofa10.2Sscrofa10.2susScr3
F5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12559,465,610 - 59,539,022 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2559,466,378 - 59,538,872 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605561,142,905 - 61,215,886 (+)NCBIVero_WHO_p1.0
F5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248267,438,632 - 7,507,322 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
AI173222  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21376,580,791 - 76,580,882 (+)MAPPERmRatBN7.2
Rnor_6.01382,534,017 - 82,534,107NCBIRnor6.0
Rnor_5.01387,416,163 - 87,416,253UniSTSRnor5.0
RGSC_v3.41379,995,762 - 79,995,852UniSTSRGSC3.4
Celera1376,315,208 - 76,315,298UniSTS
Cytogenetic Map13q22UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131101056920Rat
1581554Pur11Proteinuria QTL 11urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13599483377046787Rat
1581573Uae36Urinary albumin excretion QTL 36urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13599483377046787Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)138897350101631289Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1320605871101339738Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1330395351101056920Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133124133193395974Rat
2303563Bw89Body weight QTL 896body mass (VT:0001259)body weight (CMO:0000012)133228447177284471Rat
61340Bp25Blood pressure QTL 254.20.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133453521879535218Rat
12879477Bp401Blood pressure QTL 401arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133726209282262092Rat
61349Bp31Blood pressure QTL 315.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)133737450982374509Rat
70220Bp55Blood pressure QTL 555.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)133737450982374509Rat
4889861Pur29Proteinuria QTL 2913.80.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)133741558480753406Rat
1331750Bp220Blood pressure QTL 2202.98arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133741558482415584Rat
1549897Stresp12Stress response QTL 123.35stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)133843340883433408Rat
619615Bp80Blood pressure QTL 800.0354arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133975454484754544Rat
12879444Bp397Blood pressure QTL 397arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134504940490049404Rat
12879471Bp398Blood pressure QTL 398arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134551471990514719Rat
12879441Bp396Blood pressure QTL 396arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134569998390699983Rat
1298066Bp159Blood pressure QTL 1590.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134608804691088046Rat
71119Thym2Thymus enlargement QTL 23.8thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)134619797684753113Rat
1641901Alcrsp6Alcohol response QTL 6response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)135236217197362171Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1356056920101056920Rat
724564Uae11Urinary albumin excretion QTL 115.7urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)135949252277046890Rat
738026Lnnr5Liver neoplastic nodule remodeling QTL 53.29liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)135987440885581182Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1361825626106807694Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1365103704106807694Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1365103704106807694Rat
8655951Rf63Renal function QTL 6312.2blood urea nitrogen amount (VT:0005265)plasma urea nitrogen level (CMO:0000586)136906051977046890Rat
8655945Rf61Renal function QTL 613.6blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)136906051986800898Rat
1331783Bp221Blood pressure QTL 2213.72886arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)136906051986800898Rat
1300166Kidm6Kidney mass QTL 63.93kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)136906051986800898Rat
11530006Niddm72Non-insulin dependent diabetes mellitus QTL 720.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)137402391880753406Rat
8655959Pur32Proteinuria QTL 328.4total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)137402391897213863Rat
738027Lnnr6Liver neoplastic nodule remodeling QTL 63.3liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)137486211785581182Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1374862117101339893Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:80
Count of miRNA genes:66
Interacting mature miRNAs:78
Transcripts:ENSRNOT00000033157
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 41 41 6 41 4 7 1
Low 2 38 16 13 1 1 59 28 27 11 1
Below cutoff 1 5 7 9 11 13 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000079872   ⟹   ENSRNOP00000070280
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1376,524,340 - 76,582,315 (+)Ensembl
Rnor_6.0 Ensembl1382,479,998 - 82,528,172 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000080759   ⟹   ENSRNOP00000072800
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1376,513,255 - 76,582,317 (+)Ensembl
Rnor_6.0 Ensembl1382,496,022 - 82,535,534 (+)Ensembl
RefSeq Acc Id: NM_001047878   ⟹   NP_001041343
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21376,524,340 - 76,582,315 (+)NCBI
Rnor_6.01382,479,997 - 82,535,540 (+)NCBI
Rnor_5.01387,355,980 - 87,417,686 (+)NCBI
RGSC_v3.41379,934,956 - 79,997,285 (+)RGD
Celera1376,256,969 - 76,316,731 (+)RGD
Sequence:
RefSeq Acc Id: XM_039090783   ⟹   XP_038946711
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21376,513,463 - 76,583,106 (+)NCBI
RefSeq Acc Id: XM_039090784   ⟹   XP_038946712
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21376,524,094 - 76,583,106 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001041343 (Get FASTA)   NCBI Sequence Viewer  
  XP_038946711 (Get FASTA)   NCBI Sequence Viewer  
  XP_038946712 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAP86265 (Get FASTA)   NCBI Sequence Viewer  
  EDM09360 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001041343   ⟸   NM_001047878
- UniProtKB: Q7TPK2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000072800   ⟸   ENSRNOT00000080759
RefSeq Acc Id: ENSRNOP00000070280   ⟸   ENSRNOT00000079872
RefSeq Acc Id: XP_038946711   ⟸   XM_039090783
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038946712   ⟸   XM_039090784
- Peptide Label: isoform X2
Protein Domains
F5/8 type C

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)
Visual CSV TAB Printer
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)
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 (2020)
Visual CSV TAB Printer
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)
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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 (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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
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
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
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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
Sequenced By: MCW
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
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/FarMcwi (2019)
Visual CSV TAB Printer
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
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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
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
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
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
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
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
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
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
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
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
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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
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 (2019)
Visual CSV TAB Printer
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
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
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
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
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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/MavRrrc (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/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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/MavRrrc (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
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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/MavRrrc (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
LN/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/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
M520/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
M520/NRrrcMcwi (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
MHS/Gib (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
MNS/Gib (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
MR/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
MR/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
MWF/Hsd (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
PVG/Seac (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (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: SBH/Ygl sequenced by MCW
SBH/Ygl (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
SBN/Ygl (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: SBN/Ygl sequenced by MCW
SBN/Ygl (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
SHR/NHsd (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
SHR/OlalpcvMcwi (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
SHRSP/A3NCrl (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
SHRSP/Gcrc (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
SR/JrHsd (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: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (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
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
WAG/Rij (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
WAG/RijCrl (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: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (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
WKY/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
WKY/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
WKY/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
WKY/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
WKY/NHsd (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
WN/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
WN/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
Damaging Variants


Assembly: Rnor_5.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
13 87378653 87378654 G A snv SS/JrHsdMcwi (MCW), HWY/Slc (KyushuU), BUF/MNa (KyushuU), SS/JrHsdMcwi (KNAW), SS/Jr (KNAW)
13 87389019 87389020 A T snv RCS/Kyo (KyushuU), DOB/Oda (KyushuU)
13 87408505 87408506 C G snv BUF/N (KNAW), SS/JrHsdMcwi (KNAW), FHL/EurMcwi (KNAW), GK/Ox (KNAW), LE/Stm (Illumina) (KNAW), LE/Stm (SOLiD) (KNAW), WKY/N (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), BUF/MNa (KyushuU), LE/Stm (KyushuU), RCS/Kyo (KyushuU), HWY/Slc (KyushuU), DOB/Oda (KyushuU), SS/Jr (KNAW), SS/JrHsdMcwi (MCW), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), FHH/EurMcwi (KNAW)


Assembly: mRatBN7.2
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
13 76542132 76542133 G A snv SS/JrHsdMcwi (2019)
13 76553184 76553185 A T snv BUF/N (2020)
13 76573134 76573135 C G snv GK/FarMcwi (2019), WKY/N (2020), LEXF4/Stm (2020), LE/Stm (2019), SS/JrHsdMcwi (2019), WKY/NCrl (2019), FHH/EurMcwi (2019), BUF/N (2020), LEXF11/Stm (2020)


Assembly: RGSC_v3.4
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
13 79953259 79953260 G A snv SS/JrHsdMcwi (ICL), SS/Jr (ICL), SS/JrHsdMcwi (MDC), SS/JrHsdMcwi (MCW)
13 79967519 79967520 A T snv BUF/N (KNAW)
13 79974922 79974923 G C snv LCR/2Mco (UMich), HCR/2Mco (UMich)
13 79988079 79988080 C G snv WKY/N (KNAW), FHH/EurMcwi (ICL), FHL/EurMcwi (ICL), GK/Ox (ICL), LE/Stm (ICL), SS/Jr (ICL), SS/JrHsdMcwi (ICL), WKY/NCrl (ICL), LE/Stm (KNAW), BUF/N (KNAW), WKY/NHsd (ICL), FHH/EurMcwi (MDC), SS/JrHsdMcwi (MCW), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), SS/JrHsdMcwi (MDC)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1589758 AgrOrtholog
Ensembl Genes ENSRNOG00000057855 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000070280 UniProtKB/TrEMBL
  ENSRNOP00000072800 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000079872 UniProtKB/TrEMBL
  ENSRNOT00000080759 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.420 UniProtKB/TrEMBL
InterPro Coagulation_fac_5/8-C_type_dom UniProtKB/TrEMBL
  Cu-oxidase_3 UniProtKB/TrEMBL
  Cupredoxin UniProtKB/TrEMBL
  Factor_5/8_like UniProtKB/TrEMBL
  Galactose-bd-like UniProtKB/TrEMBL
KEGG Report rno:304929 UniProtKB/TrEMBL
NCBI Gene 304929 ENTREZGENE
Pfam Cu-oxidase_3 UniProtKB/TrEMBL
  F5_F8_type_C UniProtKB/TrEMBL
PharmGKB F5 RGD
PhenoGen F5 PhenoGen
PIRSF Factors_V_VIII UniProtKB/TrEMBL
PROSITE FA58C_1 UniProtKB/TrEMBL
  FA58C_2 UniProtKB/TrEMBL
  FA58C_3 UniProtKB/TrEMBL
SMART FA58C UniProtKB/TrEMBL
Superfamily-SCOP Cupredoxin UniProtKB/TrEMBL
  Gal_bind_like UniProtKB/TrEMBL
UniProt A0A0G2JXI1_RAT UniProtKB/TrEMBL
  A0A0G2K3W2_RAT UniProtKB/TrEMBL
  Q7TPK2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-20 F5  coagulation factor V  F5  coagulation factor V (proaccelerin, labile factor)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-01-20 F5  coagulation factor V  F5  coagulation factor V  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-01-20 F5  coagulation factor V  F5  coagulation factor V  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-10-17 F5  coagulation factor V (proaccelerin, labile factor)  F5  coagulation factor V  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-04 F5  coagulation factor V  F5  coagulation factor 5 (mapped)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2007-04-06 F5  coagulation factor 5 (mapped)  F5_mapped  coagulation factor 5 (mapped)  Data Merged 737654 PROVISIONAL
2006-11-19 F5  coagulation factor 5 (mapped)      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-11-17 F5_mapped  coagulation factor 5 (mapped)  F5  coagulation factor 5   Symbol and Name updated 1556543 APPROVED
2003-04-09 F5  coagulation factor 5     Coagulation factor V (proaccelerin, labile factor)  Name updated 629478 APPROVED
2002-06-10 F5  Coagulation factor V (proaccelerin, labile factor)      Symbol and Name status set to approved 70586 APPROVED