F2 (coagulation factor II) - Rat Genome Database

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Gene: F2 (coagulation factor II) Rattus norvegicus
Analyze
Symbol: F2
Name: coagulation factor II
RGD ID: 61996
Description: Predicted to enable several functions, including heparin binding activity; lipopolysaccharide binding activity; and serine-type endopeptidase activity. Involved in several processes, including cellular response to mechanical stimulus; response to thyrotropin-releasing hormone; and response to thyroxine. Located in collagen-containing extracellular matrix and extracellular space. Used to study several diseases, including atherosclerosis; end stage renal disease; hyperhomocysteinemia; obesity; and thrombophilia (multiple). Biomarker of bacterial pneumonia; brain edema; calcium oxalate nephrolithiasis; and thrombosis. Human ortholog(s) of this gene implicated in several diseases, including X-linked recessive disease (multiple); appendicitis; artery disease (multiple); autoimmune disease (multiple); and thrombophilia (multiple). Orthologous to human F2 (coagulation factor II, thrombin); PARTICIPATES IN coagulation cascade pathway; acenocoumarol pharmacodynamics pathway; alteplase pharmacodynamics pathway; INTERACTS WITH (+)-schisandrin B; 1,3-dinitrobenzene; 17beta-estradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: coagulation factor 2; prothrombin; thrombin
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2377,596,196 - 77,609,486 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl377,596,198 - 77,609,486 (-)Ensembl
Rnor_6.0380,529,468 - 80,542,993 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl380,529,428 - 80,543,031 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0387,228,703 - 87,242,228 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4376,005,318 - 76,018,603 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1375,901,694 - 75,914,982 (-)NCBI
Celera376,801,000 - 76,814,280 (-)NCBICelera
Cytogenetic Map3q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
acquired angioedema  (ISO)
Acute Coronary Syndrome  (ISO)
Acute Lung Injury  (IDA)
allergic rhinitis  (ISO)
Alzheimer's disease  (ISO)
appendicitis  (ISO)
asthma  (ISO)
atherosclerosis  (IDA)
atopic dermatitis  (ISO)
autoimmune hepatitis  (ISO)
bacterial pneumonia  (IEP)
blood coagulation disease  (ISO)
brain edema  (IEP)
Brain Injuries  (ISO)
brain ischemia  (ISO)
bullous pemphigoid  (ISO)
calcium oxalate nephrolithiasis  (IEP)
carotid stenosis  (ISO)
celiac disease  (ISO)
Cerebral Hemorrhage  (ISO)
cerebral infarction  (ISO)
Chagas disease  (ISO)
chronic obstructive pulmonary disease  (ISO)
clear cell renal cell carcinoma  (ISO)
congenital disorder of glycosylation type IIc  (ISO)
Congenital Prothrombin Deficiency  (ISO)
Contusions  (IEP)
coronary artery disease  (ISO)
COVID-19  (ISO)
Crohn's disease  (ISO)
dengue disease  (ISO)
Diabetic Nephropathies  (ISO)
disseminated intravascular coagulation  (IDA,ISO)
end stage renal disease  (IDA)
Endotoxemia  (IDA,IEP,ISO)
Experimental Arthritis  (ISO)
Experimental Diabetes Mellitus  (ISO)
eye disease  (ISO)
factor VIII deficiency  (ISO)
Familial Amyloid Polyneuropathies  (ISO)
familial Mediterranean fever  (ISO)
fatty liver disease  (ISO)
Femur Head Necrosis  (ISO)
genetic disease  (ISO)
glomerulonephritis  (ISO)
hemolytic-uremic syndrome  (ISO)
hemophilia B  (ISO)
Hemorrhage  (IDA,IMP,ISO)
Hemorrhagic Shock  (IEP)
hepatitis C  (ISO)
hepatocellular carcinoma  (ISO)
hereditary angioedema  (ISO)
herpes zoster  (ISO)
high grade glioma  (IMP)
Human Viral Hepatitis  (ISO)
Huntington's disease  (ISO)
Hyperalgesia  (ISO)
hyperglycemia  (ISO)
hyperhomocysteinemia  (IDA)
Hypertrophy  (ISO)
intellectual disability  (ISO)
intracranial sinus thrombosis  (ISO)
Kidney Calculi  (ISO)
Knee Osteoarthritis  (ISO)
leptospirosis  (ISO)
liver cirrhosis  (ISO)
Liver Failure  (ISO)
Mesenteric Ischemia  (ISO)
middle cerebral artery infarction  (ISO)
myocardial infarction  (ISO)
Neoplasm Metastasis  (ISO)
nephrosis  (IMP,ISO)
Nerve Degeneration  (ISO)
non-alcoholic fatty liver disease  (ISO)
obesity  (IDA,ISO)
ovarian cancer  (ISO)
Paratuberculosis  (ISO)
Pediatric Crohn's Disease  (ISO)
portal vein thrombosis  (ISO)
pre-eclampsia  (ISO)
prostate cancer  (ISO)
prothrombin deficiency  (ISO)
pulmonary embolism  (ISO)
pulmonary fibrosis  (ISO)
Reperfusion Injury  (IMP)
retinal vein occlusion  (ISO)
rheumatoid arthritis  (ISO)
schizophrenia  (ISO)
sensorineural hearing loss  (ISO)
Sepsis  (IDA,ISO)
Septic Peritonitis  (ISO)
sickle cell anemia  (ISO)
Spinal Cord Injuries  (IEP)
Spontaneous Abortions  (ISO)
Stroke  (ISO)
systemic lupus erythematosus  (ISO)
systemic scleroderma  (ISO)
Thromboembolism  (ISO)
thrombophilia  (IDA,ISO)
thrombophilia due to thrombin defect  (ISO)
thrombosis  (IDA,IEP,ISO)
toxic shock syndrome  (ISO)
type 2 diabetes mellitus  (ISO)
ulcerative colitis  (ISO)
urinary bladder cancer  (ISO)
Urinary Calculi  (ISO)
urticaria  (ISO)
vascular skin disease  (ISO)
Venous Thromboembolism  (ISO)
Venous Thrombosis  (IMP,ISO)
Ventricular Dysfunction, Left  (ISO)
Ventricular Fibrillation  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (ISO)
(+)-schisandrin B  (EXP)
(-)-epigallocatechin 3-gallate  (ISO)
(2R,4R)-1-[(2S)-5-(diaminomethylideneamino)-2-[(3-methyl-1,2,3,4-tetrahydroquinolin-8-yl)sulfonylamino]-1-oxopentyl]-4-methyl-2-piperidinecarboxylic acid  (ISO)
(S)-colchicine  (ISO)
(S)-nicotine  (ISO)
1,3-dinitrobenzene  (EXP)
1-naphthyl isothiocyanate  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,6-dinitrotoluene  (EXP)
3,3-diphenyl-N-(1-phenylethyl)-1-propanamine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
acenocoumarol  (EXP)
acetamide  (EXP)
acetylsalicylic acid  (ISO)
ADP  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
amidotrizoic acid  (ISO)
amiodarone  (ISO)
ammonium chloride  (EXP)
amphetamine  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
apigenin  (ISO)
argatroban  (ISO)
aristolochic acid  (ISO)
arsenite(3-)  (ISO)
aspalathin  (ISO)
aspartame  (ISO)
atorvastatin calcium  (ISO)
ATP  (ISO)
atropine  (ISO)
barium(0)  (ISO)
benzo[a]pyrene  (ISO)
bexarotene  (EXP)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bivalirudin  (ISO)
buta-1,3-diene  (ISO)
butanal  (ISO)
cadmium atom  (ISO)
calcium atom  (ISO)
calcium dichloride  (ISO)
calcium(0)  (ISO)
calmidazolium  (ISO)
capsaicin  (EXP)
cerivastatin  (ISO)
chlorogenic acid  (ISO)
chlorpromazine  (ISO)
chlorpyrifos  (ISO)
clobazam  (ISO)
clopidogrel  (ISO)
clothianidin  (ISO)
cobalt atom  (ISO)
colforsin daropate hydrochloride  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) chloride  (ISO)
copper(II) sulfate  (ISO)
curcumin  (EXP)
cycloheximide  (ISO)
cyclosporin A  (EXP,ISO)
cytarabine  (ISO)
dabigatran  (ISO)
dermatan sulfate  (ISO)
dexamethasone  (EXP,ISO)
dichlorine  (EXP)
dichloroacetic acid  (ISO)
dienogest  (ISO)
Difethialone  (EXP)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
eptifibatide  (ISO)
Ethyl icosapentate  (EXP)
etonogestrel  (EXP)
fenofibrate  (ISO)
flutamide  (EXP)
furan  (EXP)
genistein  (EXP,ISO)
gestodene  (ISO)
heparin  (ISO)
hydrocortisone succinate  (ISO)
indometacin  (ISO)
ioxaglic acid  (ISO)
iron atom  (ISO)
iron(0)  (ISO)
iron(2+) sulfate (anhydrous)  (ISO)
iron(III) citrate  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
lepirudin  (ISO)
lipopolysaccharide  (ISO)
LY294002  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
medroxyprogesterone acetate  (EXP,ISO)
melagatran  (ISO)
methotrexate  (ISO)
ML-7  (EXP,ISO)
morphine  (EXP)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (EXP)
nickel atom  (ISO)
nicotine  (ISO)
nimesulide  (EXP,ISO)
nitric oxide  (ISO)
nitrofen  (EXP)
NS-398  (ISO)
ochratoxin A  (EXP)
olanzapine  (ISO)
ozone  (EXP)
paclitaxel  (ISO)
paracetamol  (EXP,ISO)
paraoxon  (ISO)
paraquat  (EXP)
PCB138  (ISO)
pentanal  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (EXP)
phenprocoumon  (EXP)
phenytoin  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
phosphatidylinositol 4-phosphate  (ISO)
phylloquinone  (ISO)
pirinixic acid  (ISO)
potassium chloride  (EXP)
potassium dichromate  (ISO)
progesterone  (ISO)
propanal  (ISO)
prostaglandin E2  (EXP,ISO)
quercetin  (ISO)
quinapril hydrochloride  (ISO)
reactive oxygen species  (EXP)
resveratrol  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
simvastatin  (ISO)
sirolimus  (EXP)
sodium arsenite  (EXP,ISO)
sodium fluoride  (ISO)
splitomicin  (ISO)
tamoxifen  (ISO)
testosterone enanthate  (ISO)
tetrachloromethane  (EXP,ISO)
thromboxane A2  (ISO)
thromboxane B2  (ISO)
titanium dioxide  (EXP,ISO)
trichloroethene  (ISO)
trimellitic anhydride  (ISO)
triptonide  (ISO)
tropan-3alpha-yl 3-hydroxy-2-phenylpropanoate  (ISO)
trovafloxacin  (ISO)
U-73122  (ISO)
valproic acid  (ISO)
venom  (ISO)
vincristine  (ISO)
vitamin E  (ISO)
vorinostat  (ISO)
warfarin  (EXP,ISO)
ximelagatran  (ISO)
Y-27632  (ISO)
zinc atom  (ISO)
zinc protoporphyrin  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
acute-phase response  (IEA)
antimicrobial humoral immune response mediated by antimicrobial peptide  (IEA,ISO)
blood coagulation  (IDA)
blood coagulation, common pathway  (ISO)
cell surface receptor signaling pathway  (IEA,ISO)
cellular response to mechanical stimulus  (IEP)
cytolysis by host of symbiont cells  (IEA,ISO)
fibrinolysis  (IEA,ISO)
negative regulation of astrocyte differentiation  (IEA,ISO)
negative regulation of catalytic activity  (IEA)
negative regulation of cytokine production involved in inflammatory response  (IEA,ISO)
negative regulation of proteolysis  (IEA,ISO)
neutrophil-mediated killing of gram-negative bacterium  (IEA,ISO)
platelet activation  (IBA,IEA,ISO)
positive regulation of blood coagulation  (IBA,IEA,IMP,ISO)
positive regulation of cell growth  (IEA,ISO)
positive regulation of cell population proliferation  (IEA,ISO)
positive regulation of collagen biosynthetic process  (IEA,ISO)
positive regulation of lipid kinase activity  (IEA,ISO)
positive regulation of phosphatidylinositol 3-kinase signaling  (IEA,ISO)
positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway  (IEA,ISO)
positive regulation of protein localization to nucleus  (IEA,ISO)
positive regulation of protein phosphorylation  (IEA,ISO)
positive regulation of reactive oxygen species metabolic process  (IEA,ISO)
positive regulation of release of sequestered calcium ion into cytosol  (IEA,ISO)
proteolysis  (IEA,ISO)
regulation of cell shape  (IEA,ISO)
regulation of cytosolic calcium ion concentration  (ISO)
regulation of gene expression  (ISO)
response to inactivity  (IEP)
response to Thyroglobulin triiodothyronine  (IEP)
response to thyrotropin-releasing hormone  (IEP)
response to thyroxine  (IEP)
response to wounding  (ISO)
zymogen activation  (ISO)

Cellular Component

Molecular Function

References

References - curated
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Additional References at PubMed
PMID:1672265   PMID:1691280   PMID:1695900   PMID:2435757   PMID:7559487   PMID:8626514   PMID:9038223   PMID:9639571   PMID:11309392   PMID:12479881   PMID:12855810   PMID:14753426  
PMID:16502470   PMID:16720835   PMID:17275676   PMID:17380206   PMID:18083763   PMID:18305483   PMID:18398001   PMID:18474218   PMID:18622025   PMID:18636965   PMID:18667434   PMID:19052258  
PMID:19103257   PMID:19383433   PMID:20150433   PMID:20164183   PMID:20421939   PMID:20806126   PMID:20819545   PMID:20926146   PMID:21209875   PMID:21736902   PMID:22015349   PMID:22516433  
PMID:23043906   PMID:23103417   PMID:23338707   PMID:23376485   PMID:23533145   PMID:24916589   PMID:28059686   PMID:28489922  


Genomics

Comparative Map Data
F2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2377,596,196 - 77,609,486 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl377,596,198 - 77,609,486 (-)Ensembl
Rnor_6.0380,529,468 - 80,542,993 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl380,529,428 - 80,543,031 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0387,228,703 - 87,242,228 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4376,005,318 - 76,018,603 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1375,901,694 - 75,914,982 (-)NCBI
Celera376,801,000 - 76,814,280 (-)NCBICelera
Cytogenetic Map3q24NCBI
F2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1146,719,196 - 46,739,506 (+)EnsemblGRCh38hg38GRCh38
GRCh381146,719,213 - 46,739,506 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371146,740,763 - 46,761,056 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361146,697,331 - 46,717,631 (+)NCBINCBI36hg18NCBI36
Build 341146,697,330 - 46,717,631NCBI
Celera1146,888,702 - 46,909,014 (+)NCBI
Cytogenetic Map11p11.2NCBI
HuRef1146,446,660 - 46,466,973 (+)NCBIHuRef
CHM1_11146,739,149 - 46,759,462 (+)NCBICHM1_1
F2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39291,442,742 - 91,466,802 (-)NCBIGRCm39mm39
GRCm39 Ensembl291,455,665 - 91,466,759 (-)Ensembl
GRCm38291,612,397 - 91,636,457 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl291,625,320 - 91,636,414 (-)EnsemblGRCm38mm10GRCm38
MGSCv37291,465,477 - 91,476,571 (-)NCBIGRCm37mm9NCBIm37
MGSCv36291,426,159 - 91,437,253 (-)NCBImm8
Celera293,014,831 - 93,025,920 (-)NCBICelera
Cytogenetic Map2E1NCBI
cM Map250.63NCBI
F2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554221,356,769 - 1,367,517 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554221,356,675 - 1,367,788 (-)NCBIChiLan1.0ChiLan1.0
F2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11147,227,891 - 47,249,157 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1147,227,891 - 47,249,157 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01146,669,925 - 46,690,391 (+)NCBIMhudiblu_PPA_v0panPan3
F2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11842,782,744 - 42,799,531 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1842,782,751 - 42,799,459 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1841,511,662 - 41,528,485 (-)NCBI
ROS_Cfam_1.01843,438,760 - 43,455,850 (-)NCBI
UMICH_Zoey_3.11842,924,063 - 42,940,888 (-)NCBI
UNSW_CanFamBas_1.01842,479,219 - 42,496,510 (-)NCBI
UU_Cfam_GSD_1.01843,208,980 - 43,225,802 (-)NCBI
F2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494720,260,330 - 20,277,033 (-)NCBI
SpeTri2.0NW_0049365622,371,725 - 2,388,617 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
F2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl215,791,451 - 15,819,138 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1215,793,257 - 15,819,151 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2217,145,002 - 17,170,975 (-)NCBISscrofa10.2Sscrofa10.2susScr3
F2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247671,876,974 - 1,887,720 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D3Chm80  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2377,604,312 - 77,604,554 (+)MAPPERmRatBN7.2
Rnor_6.0380,537,822 - 80,538,061NCBIRnor6.0
Rnor_5.0387,237,057 - 87,237,296UniSTSRnor5.0
RGSC_v3.4376,013,431 - 76,013,671RGDRGSC3.4
RGSC_v3.4376,013,432 - 76,013,671UniSTSRGSC3.4
Celera376,809,107 - 76,809,348UniSTS
Cytogenetic Map3q24UniSTS
RH140523  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2377,596,263 - 77,596,426 (+)MAPPERmRatBN7.2
Rnor_6.0380,529,536 - 80,529,698NCBIRnor6.0
Rnor_5.0387,228,771 - 87,228,933UniSTSRnor5.0
RGSC_v3.4376,005,386 - 76,005,548UniSTSRGSC3.4
Celera376,801,068 - 76,801,230UniSTS
Cytogenetic Map3q24UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31086191289878372Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)329463235118376539Rat
61419Cia11Collagen induced arthritis QTL 115.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)33035677398535386Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
1354589Bw31Body weight QTL 313.3body mass (VT:0001259)body weight (CMO:0000012)33370334778196190Rat
1354604Bw36Body weight QTL 362.9body mass (VT:0001259)body weight (CMO:0000012)333703347104104347Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)338192233133483320Rat
738019Anxrr10Anxiety related response QTL 103.9exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)33851780383517803Rat
1331777Bw24Body weight QTL 243.503body mass (VT:0001259)body weight (CMO:0000012)33945463789115240Rat
1331795Rf30Renal function QTL 303.708urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)33945463789115240Rat
1354597Kidm13Kidney mass QTL 132.9kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)341874578104104347Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
1300178Hrtrt4Heart rate QTL 43.74heart pumping trait (VT:2000009)heart rate (CMO:0000002)34382736490905114Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)343827364121056321Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
1358186Ept2Estrogen-induced pituitary tumorigenesis QTL 28.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)347233430110362260Rat
2292613Ept16Estrogen-induced pituitary tumorigenesis QTL 168.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)347233430110362260Rat
631665Bw8Body weight QTL 85.5body mass (VT:0001259)body weight (CMO:0000012)350437042119183768Rat
724523Tsu1Thymus enlargement suppressive QTL 13.84thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)350437504115638231Rat
1582218Bw74Body weight QTL 743.90.0021body mass (VT:0001259)body weight (CMO:0000012)353184593115665732Rat
1582238Bw68Body weight QTL 683.20.0064body mass (VT:0001259)body weight (CMO:0000012)353184593115665732Rat
1582239Epfw1Epididymal fat weight QTL 14.50.0006epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)353184593115665732Rat
61377Edpm3Estrogen-dependent pituitary mass QTL 37.050.038pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)35318469289878207Rat
731180Bp152Blood pressure QTL 1520.03arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)35378111291609953Rat
731180Bp152Blood pressure QTL 1520.03arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)35378111291609953Rat
731180Bp152Blood pressure QTL 1520.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)35378111291609953Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)359242096157323038Rat
1300111Rf12Renal function QTL 123.78renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)361017749121056321Rat
631200Cm25Cardiac mass QTL 254.80.0001heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)36113434889115068Rat
1582210Bw71Body weight QTL 713.30.0012body mass (VT:0001259)body weight (CMO:0000012)364655305115665732Rat
1582221Kidm30Kidney mass QTL 303.50.0008kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)364655305115665732Rat
12879848Bw181Body weght QTL 1810.015body mass (VT:0001259)body weight (CMO:0000012)370348525121056321Rat
2301414Kidm37Kidney mass QTL 370.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)370653097121056321Rat
1600376Arunc5Aerobic running capacity QTL 50.21exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)373376539118376539Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:159
Count of miRNA genes:134
Interacting mature miRNAs:144
Transcripts:ENSRNOT00000022233
Prediction methods:Microtar, 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 31 31 25
Medium 25 16 7 16 9 2 1
Low 3 5 7 10 8 10 25 26 33 10 8
Below cutoff 13 2 1 26 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000022233   ⟹   ENSRNOP00000022233
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl377,596,198 - 77,609,486 (-)Ensembl
Rnor_6.0 Ensembl380,529,428 - 80,543,031 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000095299   ⟹   ENSRNOP00000086700
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl377,596,310 - 77,609,486 (-)Ensembl
RefSeq Acc Id: NM_022924   ⟹   NP_075213
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2377,596,196 - 77,609,486 (-)NCBI
Rnor_6.0380,529,468 - 80,542,993 (-)NCBI
Rnor_5.0387,228,703 - 87,242,228 (-)NCBI
RGSC_v3.4376,005,318 - 76,018,603 (-)RGD
Celera376,801,000 - 76,814,280 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_075213 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA42240 (Get FASTA)   NCBI Sequence Viewer  
  CAA37017 (Get FASTA)   NCBI Sequence Viewer  
  EDL79531 (Get FASTA)   NCBI Sequence Viewer  
  EDL79532 (Get FASTA)   NCBI Sequence Viewer  
  P18292 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_075213   ⟸   NM_022924
- Peptide Label: precursor
- UniProtKB: G3V843 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000022233   ⟸   ENSRNOT00000022233
RefSeq Acc Id: ENSRNOP00000086700   ⟸   ENSRNOT00000095299
Protein Domains
Gla   Kringle   Peptidase S1

Transcriptome

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

Promoters
RGD ID:13692216
Promoter ID:EPDNEW_R2740
Type:multiple initiation site
Name:F2_1
Description:coagulation factor II
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0380,542,983 - 80,543,043EPDNEW

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)
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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
F344/NRrrc (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
F344/Stm (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
FHH/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
FHH/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)
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)
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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)
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)
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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
FXLE18/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (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)
GK/FarMcwi (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
GK/Ox (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
HXB10/IpcvMcwi (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
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)
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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
HXB31/IpcvMcwi (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
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)
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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
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)
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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
LEXF11/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (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
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)
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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
LH/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
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)
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
M520/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
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)
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
MNS/Gib (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
MR/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
MR/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
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)
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
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)
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
SBN/Ygl (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: SBN/Ygl sequenced by MCW
SBN/Ygl (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
SHR/NHsd (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
SHR/OlalpcvMcwi (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
SHRSP/A3NCrl (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
SHRSP/Gcrc (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
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)
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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (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
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
WAG/Rij (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
WAG/RijCrl (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: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (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
WKY/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
WKY/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
WKY/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
WKY/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
WKY/NHsd (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
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
3 87241742 87241743 G T snv BUF/N (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
3 80542507 80542508 G T snv Buf/N (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
3 76018117 76018118 G T snv BUF/N (KNAW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:61996 AgrOrtholog
Ensembl Genes ENSRNOG00000016325 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000022233 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000022233 UniProtKB/TrEMBL
Gene3D-CATH 2.40.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2.40.20.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  4.10.140.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro GLA-like_dom_SF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GLA_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kringle UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kringle-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kringle_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kringle_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peptidase_S1_PA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peptidase_S1_PA_chymotrypsin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peptidase_S1A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Prothrombin/thrombin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Thrombin_light_chain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Thrombin_light_chain_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Trypsin_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TRYPSIN_HIS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TRYPSIN_SER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29251 UniProtKB/TrEMBL
NCBI Gene 29251 ENTREZGENE
PANTHER PTHR24254:SF10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Gla UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kringle UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Thrombin_light UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Trypsin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB F2 RGD
PhenoGen F2 PhenoGen
PIRSF Thrombin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PRINTS CHYMOTRYPSIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GLABLOOD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTHROMBIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE GLA_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GLA_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  KRINGLE_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  KRINGLE_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TRYPSIN_DOM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TRYPSIN_HIS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TRYPSIN_SER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART GLA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00130 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tryp_SPc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF50494 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF57440 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF57630 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC220290
UniProt G3V843 ENTREZGENE, UniProtKB/TrEMBL
  P18292 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-09 F2  coagulation factor II (thrombin)  F2  coagulation factor II  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-28   coagulation factor II  F2  coagulation factor 2  Name updated to reflect Human and Mouse nomenclature 1299863 APPROVED
2004-12-14 F2  coagulation factor 2      Symbol and Name status set to approved 1299863 APPROVED
2002-06-10 F2  coagulation factor 2      Name updated 70585 PROVISIONAL

RGD Curation Notes
Note Type Note Reference