Cav1 (caveolin 1) - Rat Genome Database

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Gene: Cav1 (caveolin 1) Rattus norvegicus
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Symbol: Cav1
Name: caveolin 1
RGD ID: 2280
Description: Enables several functions, including enzyme binding activity; syntaxin binding activity; and transmembrane transporter binding activity. Involved in several processes, including positive regulation of cellular component organization; regulation of endothelial cell proliferation; and regulation of signal transduction. Located in several cellular components, including basal plasma membrane; focal adhesion; and lipid droplet. Part of protein-containing complex. Biomarker of several diseases, including artery disease (multiple); bone disease (multiple); brain ischemia (multiple); obesity; and sciatic neuropathy. Human ortholog(s) of this gene implicated in several diseases, including breast cancer (multiple); lipodystrophy (multiple); primary open angle glaucoma; primary pulmonary hypertension; and systemic scleroderma (multiple). Orthologous to human CAV1 (caveolin 1); PARTICIPATES IN insulin signaling pathway; platelet-derived growth factor signaling pathway; reverse cholesterol transport pathway; INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2-ethoxyethanol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: Cav; caveolin; caveolin 1, caveolae protein; Caveolin caveolae protein 22 kDa; caveolin, caveolae protein 1; Caveolin, caveolae protein, 22 kDa; caveolin-1; caveolin-like; LOC100362870; MGC187299
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Is Marker For: Strains:   BB/OK  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2445,640,624 - 45,673,708 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl445,634,918 - 45,673,705 (+)Ensembl
Rnor_6.0444,597,123 - 44,630,206 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl444,597,123 - 44,630,200 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0445,203,494 - 45,236,461 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4442,956,102 - 42,989,057 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1443,098,177 - 43,130,873 (+)NCBI
Celera440,918,628 - 40,949,677 (+)NCBICelera
Cytogenetic Map4q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
abdominal aortic aneurysm  (ISO)
acoustic neuroma  (ISO)
Acute Lung Injury  (IEP)
Alcoholic Liver Diseases  (IEP)
Alzheimer's disease  (ISS)
atherosclerosis  (IEP)
atrial fibrillation  (ISO)
brain ischemia  (IEP)
breast cancer  (ISO,ISS)
breast carcinoma  (ISO)
Breast Neoplasms  (ISO)
Carcinogenesis  (ISO)
Cardiomegaly  (IEP,ISO)
congenital generalized lipodystrophy type 3  (ISO)
Dermal Fibrosis  (ISO)
diabetes mellitus  (ISO)
diabetic neuropathy  (ISO)
diffuse scleroderma  (ISO)
exfoliation syndrome  (ISO)
Experimental Autoimmune Myocarditis  (IEP)
Experimental Autoimmune Neuritis  (IEP)
Experimental Diabetes Mellitus  (IEP,ISO)
Experimental Liver Cirrhosis  (ISO)
familial partial lipodystrophy  (ISO)
genetic disease  (ISO)
Hemorrhage  (IEP)
high grade glioma  (IEP)
Hyperplasia  (ISO)
hypertension  (IEP,ISO)
hypertrophic cardiomyopathy  (ISS)
hypothyroidism  (IEP)
invasive ductal carcinoma  (ISO)
leiomyoma  (ISO)
limited scleroderma  (ISO)
Lipodystrophy with Congenital Cataracts and Neurodegeneration  (ISO)
low tension glaucoma  (ISO)
Lung Neoplasms  (ISO)
Lymphatic Metastasis  (ISO)
Mammary Neoplasms, Experimental  (ISO)
melanoma  (ISO)
multiple sclerosis  (ISO)
Neoplasm Metastasis  (ISO)
Nephrogenic Fibrosing Dermopathy  (ISO)
obesity  (IEP)
open-angle glaucoma  (ISO)
osteoarthritis  (IEP)
ovarian carcinoma  (ISO)
Ovarian Neoplasms  (ISO)
pleomorphic xanthoastrocytoma  (ISO)
primary open angle glaucoma  (ISO)
primary pulmonary hypertension  (ISO)
Primary Pulmonary Hypertension, 3  (ISO)
prostate cancer  (ISO)
Prostatic Neoplasms  (ISO)
psoriasis  (ISO)
Pulmonary Arterial Hypertension  (ISO)
pulmonary fibrosis  (ISO)
pulmonary hypertension  (IEP,ISO)
renal cell carcinoma  (ISO)
Reperfusion Injury  (IEP)
Sarcopenia  (ISO)
sciatic neuropathy  (IEP)
Spinal Cord Injuries  (IEP)
squamous cell carcinoma  (ISO)
Stevens-Johnson syndrome  (ISO)
Stomach Neoplasms  (ISO)
systemic scleroderma  (ISO)
transient cerebral ischemia  (IEP,ISO)
transitional cell carcinoma  (ISO)
urinary bladder cancer  (ISO)
Weight Gain  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-anisomycin  (ISO)
(R,R,R)-alpha-tocopherol  (ISO)
1,1-bis(2-aminoethyl)-2-hydroxy-3-oxotriazane  (ISO)
1,2-dimethylhydrazine  (ISO)
13-HPODE  (ISO)
17beta-estradiol  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-ethoxyethanol  (EXP)
2-methoxyethanol  (EXP)
22-Hydroxycholesterol  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP,ISO)
3,3',4,4'-tetrachlorobiphenyl  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
4,4'-sulfonyldiphenol  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
acetylcholine  (ISO)
acetylsalicylic acid  (EXP)
acrolein  (ISO)
actinomycin D  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
aminoguanidine  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
amphibole asbestos  (EXP)
antirheumatic drug  (ISO)
Aroclor 1254  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (ISO)
beta-carotene  (ISO)
beta-naphthoflavone  (EXP)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
Bisphenol A diglycidyl ether  (ISO)
bisphenol F  (ISO)
bleomycin A2  (EXP)
butan-1-ol  (ISO)
butyric acid  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
cadmium nitrate  (ISO)
caffeine  (ISO)
calcitriol  (ISO)
calcium atom  (ISO)
calcium(0)  (ISO)
camptothecin  (ISO)
captan  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
carboxy-PTIO  (ISO)
celecoxib  (ISO)
chlorohydrocarbon  (EXP)
chloropicrin  (ISO)
cholesterol  (EXP,ISO)
chromium atom  (EXP)
chrysene  (ISO)
ciprofloxacin  (ISO)
cisplatin  (EXP,ISO)
clofibrate  (ISO)
cobalt dichloride  (ISO)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
cumene  (ISO)
cycloheximide  (ISO)
cyclosporin A  (ISO)
cylindrospermopsin  (ISO)
cyproconazole  (ISO)
D-glucose  (ISO)
depsipeptide  (ISO)
desferrioxamine B  (ISO)
dexamethasone  (ISO)
diallyl disulfide  (ISO)
diallyl trisulfide  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
diethylstilbestrol  (EXP)
dioxygen  (EXP,ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
equol  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
fenofibrate  (ISO)
folic acid  (ISO)
folpet  (ISO)
formaldehyde  (ISO)
fulvestrant  (EXP,ISO)
furan  (EXP)
gefitinib  (ISO)
genistein  (ISO)
geranylgeraniol  (ISO)
glucose  (ISO)
hexadecanoic acid  (ISO)
hydrogen peroxide  (ISO)
iron atom  (EXP)
iron(0)  (EXP)
iron(2+) sulfate (anhydrous)  (EXP)
isoprenaline  (ISO)
ivermectin  (ISO)
lead diacetate  (EXP)
lipopolysaccharide  (EXP,ISO)
lithocholic acid  (ISO)
lysophosphatidylcholine  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
mercury dibromide  (ISO)
methamphetamine  (EXP)
methotrexate  (ISO)
methoxychlor  (EXP)
methyl beta-cyclodextrin  (EXP,ISO)
methyl methanesulfonate  (ISO)
methylisothiazolinone  (ISO)
methylmercury chloride  (EXP)
mifepristone  (ISO)
miquelianin  (ISO)
monocrotaline  (EXP)
N-[3-(aminomethyl)benzyl]acetamidine  (ISO)
N-acetyl-L-cysteine  (ISO)
N-acetylsphingosine  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
N-nitrosodimethylamine  (EXP)
nicotinic acid  (EXP)
nimesulide  (ISO)
nitric oxide  (ISO)
nitrofen  (EXP)
nitroprusside  (ISO)
NS-398  (ISO)
nystatin  (ISO)
octanoic acid  (ISO)
ouabain  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
p-menthan-3-ol  (ISO)
paclitaxel  (ISO)
paracetamol  (ISO)
paraquat  (EXP)
phenethyl isothiocyanate  (ISO)
phenobarbital  (ISO)
phenylephrine  (ISO)
phenylmercury acetate  (ISO)
pioglitazone  (ISO)
pirinixic acid  (ISO)
piroxicam  (ISO)
poly(I:C)  (EXP)
potassium chloride  (ISO)
progesterone  (ISO)
quercetin  (EXP,ISO)
raloxifene  (EXP,ISO)
reactive oxygen species  (ISO)
rebaudioside A  (ISO)
resveratrol  (EXP,ISO)
rimonabant  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
saracatinib  (EXP)
SB 203580  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
simvastatin  (EXP,ISO)
sodium arsenite  (EXP,ISO)
Soman  (EXP)
streptozocin  (EXP)
sulfasalazine  (ISO)
tamoxifen  (ISO)
taurocholic acid  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (ISO)
tetrachloromethane  (ISO)
tetraphene  (ISO)
theophylline  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
tolfenamic acid  (ISO)
toluene 2,4-diisocyanate  (ISO)
topotecan  (EXP)
tremolite asbestos  (ISO)
triadimefon  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
trimellitic anhydride  (ISO)
Triptolide  (EXP)
troglitazone  (EXP)
tyrphostin AG 1478  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vitamin E  (ISO)
vorinostat  (ISO)
wogonin  (ISO)
wortmannin  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
angiogenesis  (IEA,ISO)
angiotensin-activated signaling pathway involved in heart process  (IEA,ISO)
animal organ regeneration  (IEP)
apoptotic signaling pathway  (IEA,ISO)
basement membrane organization  (IEA,ISO)
calcium ion homeostasis  (ISO)
calcium ion transport  (IEA,ISO)
caveola assembly  (IBA,IEA,ISO)
caveolin-mediated endocytosis  (IEA,ISO)
cell differentiation  (IBA)
cellular calcium ion homeostasis  (IMP,ISO)
cellular response to exogenous dsRNA  (IEA,ISO)
cellular response to hyperoxia  (IEA,ISO)
cellular response to mechanical stimulus  (IDA)
cellular response to peptide hormone stimulus  (ISO)
cellular response to starvation  (ISO)
cellular response to transforming growth factor beta stimulus  (IEA,ISO)
cellular senescence  (IMP)
cholesterol efflux  (IMP)
cholesterol homeostasis  (IEA,ISO)
insulin receptor internalization  (IEA,ISO)
lactation  (IEA,ISO)
lipid storage  (IEA,ISO)
maintenance of protein location in cell  (IMP)
mammary gland development  (ISO)
mammary gland involution  (IEA,ISO)
membrane depolarization  (IEA,ISO)
microtubule polymerization  (IMP)
negative regulation of anoikis  (IEA,ISO)
negative regulation of BMP signaling pathway  (ISO)
negative regulation of canonical Wnt signaling pathway  (IEA,ISO,ISS)
negative regulation of cation channel activity  (IDA)
negative regulation of cell population proliferation  (ISO)
negative regulation of cytokine-mediated signaling pathway  (IEA,ISO)
negative regulation of endothelial cell proliferation  (IBA,IEA,IMP,ISO)
negative regulation of epithelial cell differentiation  (IEA,ISO)
negative regulation of ERK1 and ERK2 cascade  (IDA)
negative regulation of inward rectifier potassium channel activity  (IEA,ISO)
negative regulation of MAP kinase activity  (IEA,ISO)
negative regulation of MAPK cascade  (ISO)
negative regulation of muscle cell apoptotic process  (IMP)
negative regulation of necroptotic process  (IEA,ISO)
negative regulation of neuron differentiation  (IMP)
negative regulation of nitric oxide biosynthetic process  (IEA,ISO)
negative regulation of nitric-oxide synthase activity  (IEA,ISO)
negative regulation of peptidyl-serine phosphorylation  (IEA,ISO)
negative regulation of peptidyl-tyrosine autophosphorylation  (IEA,ISO)
negative regulation of pinocytosis  (IEA,ISO)
negative regulation of potassium ion transmembrane transport  (ISO)
negative regulation of protein binding  (IEA,ISO)
negative regulation of protein tyrosine kinase activity  (IBA,IEA,ISO)
negative regulation of protein ubiquitination  (IEA,ISO)
negative regulation of receptor signaling pathway via JAK-STAT  (ISO)
negative regulation of signal transduction  (ISO)
negative regulation of smooth muscle cell proliferation  (IMP)
negative regulation of transcription by RNA polymerase II  (IEA,ISO,ISS)
negative regulation of transforming growth factor beta receptor signaling pathway  (IEA,ISO,ISS)
negative regulation of tyrosine phosphorylation of STAT protein  (IEA,ISO)
nitric oxide homeostasis  (IEA,ISO)
positive regulation of calcium ion transport into cytosol  (IEA,ISO)
positive regulation of canonical Wnt signaling pathway  (IEA,ISO)
positive regulation of catalytic activity  (ISO)
positive regulation of cell adhesion molecule production  (IEA,ISO)
positive regulation of cell migration  (IEA,ISO)
positive regulation of cholesterol efflux  (IEA,ISO)
positive regulation of cold-induced thermogenesis  (ISO,ISS)
positive regulation of endocytosis  (IMP)
positive regulation of endothelial cell proliferation  (IMP)
positive regulation of ER-associated ubiquitin-dependent protein catabolic process  (IEA,ISO)
positive regulation of extrinsic apoptotic signaling pathway  (IEA,ISO)
positive regulation of gap junction assembly  (IEA,ISO)
positive regulation of gene expression  (IEA,ISO)
positive regulation of intrinsic apoptotic signaling pathway  (IEA,ISO)
positive regulation of microtubule polymerization  (IMP)
positive regulation of NF-kappaB transcription factor activity  (IEA,ISO)
positive regulation of peptidase activity  (IEA)
positive regulation of peptidyl-serine phosphorylation  (IEA,ISO)
positive regulation of protein binding  (IEA,ISO)
positive regulation of protein ubiquitination  (IEA,ISO)
positive regulation of signal transduction  (IMP)
positive regulation of toll-like receptor 3 signaling pathway  (IEA,ISO)
positive regulation of vasoconstriction  (IEA,IMP,ISO)
posttranscriptional regulation of gene expression  (IEA,ISO)
protein localization  (ISO)
protein localization to basolateral plasma membrane  (ISO)
protein localization to plasma membrane raft  (ISO)
protein transport  (IEA,ISO)
receptor internalization  (ISO,ISS)
receptor internalization involved in canonical Wnt signaling pathway  (IEA,ISO)
receptor-mediated endocytosis of virus by host cell  (IEA,ISO)
regulation of blood coagulation  (IEA,ISO)
regulation of cell communication by electrical coupling involved in cardiac conduction  (IEA,ISO)
regulation of cytosolic calcium ion concentration  (IBA,ISO)
regulation of entry of bacterium into host cell  (IEA,ISO)
regulation of fatty acid metabolic process  (IEA,ISO)
regulation of heart rate by cardiac conduction  (IEA,ISO)
regulation of membrane repolarization during action potential  (IEA,ISO)
regulation of peptidase activity  (ISO)
regulation of ruffle assembly  (IEA,ISO)
regulation of smooth muscle contraction  (IEA,ISO)
regulation of the force of heart contraction  (ISO)
regulation of the force of heart contraction by chemical signal  (IEA,ISO)
regulation of ventricular cardiac muscle cell action potential  (IEA,ISO)
response to bacterium  (IEA,ISO)
response to calcium ion  (IEA,ISO)
response to estrogen  (IEA,ISO)
response to gamma radiation  (IEP)
response to glucocorticoid  (IEP)
response to hypoxia  (IEA,ISO)
response to ischemia  (IEA,ISO)
response to mechanical stimulus  (IMP)
response to nutrient  (IEP)
response to progesterone  (IEA,ISO)
response to xenobiotic stimulus  (IEP)
skeletal muscle tissue development  (IEA,ISO)
T cell costimulation  (IEA,ISO,ISS)
triglyceride metabolic process  (IEA,ISO)
vasculogenesis  (IEA,ISO)
vasoconstriction  (IEA,ISO)
vesicle organization  (ISO)
wound healing  (IMP)

Cellular Component

References

References - curated
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Additional References at PubMed
PMID:7568142   PMID:8385608   PMID:8552590   PMID:9008709   PMID:9148942   PMID:9361015   PMID:10197531   PMID:10460238   PMID:10631317   PMID:10787428   PMID:10816572   PMID:11294831  
PMID:11316799   PMID:11707266   PMID:11784086   PMID:11865038   PMID:11884617   PMID:12091389   PMID:12138167   PMID:12177436   PMID:12388077   PMID:12388596   PMID:12388746   PMID:12477932  
PMID:12562842   PMID:12633858   PMID:12651616   PMID:12743374   PMID:12759260   PMID:12832401   PMID:12852865   PMID:12927782   PMID:14559243   PMID:14581507   PMID:14600260   PMID:14681230  
PMID:14705150   PMID:14991836   PMID:15007081   PMID:15072971   PMID:15140193   PMID:15164767   PMID:15184077   PMID:15219810   PMID:15219854   PMID:15226268   PMID:15511630   PMID:15640522  
PMID:15657086   PMID:15703204   PMID:15829407   PMID:15863835   PMID:15968633   PMID:16332692   PMID:16380094   PMID:16405917   PMID:16513830   PMID:16565301   PMID:16601228   PMID:16603689  
PMID:16645331   PMID:16672766   PMID:16676355   PMID:16731532   PMID:16733664   PMID:16782699   PMID:16890161   PMID:17010968   PMID:17069850   PMID:17098833   PMID:17200204   PMID:17202321  
PMID:17287217   PMID:17326770   PMID:17349656   PMID:17375463   PMID:17416589   PMID:17431219   PMID:17464513   PMID:17482312   PMID:17684756   PMID:17687559   PMID:17848177   PMID:17982011  
PMID:18079116   PMID:18081315   PMID:18364076   PMID:18485890   PMID:18504258   PMID:18511851   PMID:18657009   PMID:18757837   PMID:18794328   PMID:18951881   PMID:19013132   PMID:19052258  
PMID:19067793   PMID:19275878   PMID:19369293   PMID:19457127   PMID:19508446   PMID:19525939   PMID:19657060   PMID:19713536   PMID:19965594   PMID:20025630   PMID:20044047   PMID:20101198  
PMID:20122998   PMID:20299334   PMID:20407877   PMID:20444327   PMID:20501440   PMID:20553910   PMID:20584649   PMID:20605793   PMID:20682791   PMID:20724702   PMID:21036148   PMID:21047970  
PMID:21092464   PMID:21109942   PMID:21169230   PMID:21172357   PMID:21372166   PMID:21382479   PMID:21423176   PMID:21721581   PMID:21745415   PMID:21822278   PMID:21829547   PMID:21861133  
PMID:21900688   PMID:21918362   PMID:21938483   PMID:21978755   PMID:22173826   PMID:22215724   PMID:22230296   PMID:22277751   PMID:22377966   PMID:22378877   PMID:22513464   PMID:22669893  
PMID:22683596   PMID:22792322   PMID:22871113   PMID:23007290   PMID:23049990   PMID:23225242   PMID:23262137   PMID:23269647   PMID:23319823   PMID:23576582   PMID:23583380   PMID:23665238  
PMID:23987506   PMID:24013648   PMID:24089527   PMID:24419512   PMID:24576892   PMID:24608114   PMID:24625804   PMID:24755228   PMID:24755854   PMID:24953158   PMID:25006397   PMID:25017399  
PMID:25204428   PMID:25204797   PMID:25322824   PMID:25419974   PMID:25450954   PMID:25527780   PMID:25556234   PMID:25618412   PMID:25661386   PMID:25674202   PMID:25748795   PMID:25893292  
PMID:26020612   PMID:26357463   PMID:26543049   PMID:26813466   PMID:26839631   PMID:26847875   PMID:26847917   PMID:27009876   PMID:27110488   PMID:27138644   PMID:27311393   PMID:27383193  
PMID:27470556   PMID:27708218   PMID:27747480   PMID:27771236   PMID:27886057   PMID:27956030   PMID:28729092   PMID:28751541   PMID:28957875   PMID:29039595   PMID:29069575   PMID:29199336  
PMID:29462885   PMID:29471582   PMID:29760379   PMID:30563532   PMID:30840346   PMID:30943774   PMID:31318049   PMID:31391685   PMID:31505169   PMID:31565882   PMID:31728004   PMID:31889352  
PMID:31911435   PMID:32311453   PMID:32554851   PMID:32810492   PMID:33000233   PMID:33148419   PMID:33423964   PMID:34360984  


Genomics

Comparative Map Data
Cav1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2445,640,624 - 45,673,708 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl445,634,918 - 45,673,705 (+)Ensembl
Rnor_6.0444,597,123 - 44,630,206 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl444,597,123 - 44,630,200 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0445,203,494 - 45,236,461 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4442,956,102 - 42,989,057 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1443,098,177 - 43,130,873 (+)NCBI
Celera440,918,628 - 40,949,677 (+)NCBICelera
Cytogenetic Map4q21NCBI
CAV1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl7116,524,994 - 116,561,179 (+)EnsemblGRCh38hg38GRCh38
GRCh387116,525,009 - 116,561,185 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh377116,165,063 - 116,201,239 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 367115,952,075 - 115,988,466 (+)NCBINCBI36hg18NCBI36
Build 347115,758,789 - 115,795,181NCBI
Celera7110,972,249 - 111,008,654 (+)NCBI
Cytogenetic Map7q31.2NCBI
HuRef7110,530,835 - 110,566,784 (+)NCBIHuRef
CHM1_17116,098,482 - 116,134,827 (+)NCBICHM1_1
CRA_TCAGchr7v27115,560,275 - 115,596,679 (+)NCBI
Cav1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39617,306,287 - 17,341,327 (+)NCBIGRCm39mm39
GRCm39 Ensembl617,306,334 - 17,341,451 (+)Ensembl
GRCm38617,306,335 - 17,341,328 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl617,306,335 - 17,341,452 (+)EnsemblGRCm38mm10GRCm38
MGSCv37617,256,370 - 17,291,324 (+)NCBIGRCm37mm9NCBIm37
MGSCv36617,256,370 - 17,291,324 (+)NCBImm8
Celera617,378,835 - 17,414,670 (+)NCBICelera
Cytogenetic Map6A2NCBI
Cav1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543222,258,250 - 22,292,403 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543222,258,262 - 22,292,403 (+)NCBIChiLan1.0ChiLan1.0
CAV1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.17121,193,678 - 121,229,655 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl7121,193,424 - 121,229,655 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v07108,497,125 - 108,533,090 (+)NCBIMhudiblu_PPA_v0panPan3
CAV1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11455,458,934 - 55,494,563 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1455,461,048 - 55,492,935 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1454,856,462 - 54,888,069 (+)NCBI
ROS_Cfam_1.01455,500,946 - 55,536,541 (+)NCBI
UMICH_Zoey_3.11455,530,973 - 55,562,566 (+)NCBI
UNSW_CanFamBas_1.01455,219,411 - 55,251,015 (+)NCBI
UU_Cfam_GSD_1.01455,590,528 - 55,622,125 (+)NCBI
Cav1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511844,152,891 - 44,185,619 (+)NCBI
SpeTri2.0NW_0049365892,504,235 - 2,536,778 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CAV1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1829,649,992 - 29,682,465 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11829,648,120 - 29,682,451 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21831,745,664 - 31,778,987 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CAV1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12185,222,724 - 85,258,562 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2185,222,879 - 85,258,627 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604218,474,866 - 18,510,943 (-)NCBIVero_WHO_p1.0
Cav1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248272,844,855 - 2,878,367 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH142797  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2445,672,046 - 45,672,280 (+)MAPPERmRatBN7.2
Rnor_6.0444,628,545 - 44,628,778NCBIRnor6.0
Rnor_5.0445,234,800 - 45,235,033UniSTSRnor5.0
RGSC_v3.4442,987,400 - 42,987,633UniSTSRGSC3.4
Celera440,948,019 - 40,948,252UniSTS
RH 3.4 Map4284.1UniSTS
Cytogenetic Map4q21UniSTS
AA946480  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2445,673,157 - 45,673,362 (+)MAPPERmRatBN7.2
Rnor_6.0444,629,656 - 44,629,860NCBIRnor6.0
Rnor_5.0445,235,911 - 45,236,115UniSTSRnor5.0
Celera440,949,130 - 40,949,334UniSTS
RH 3.4 Map4282.8UniSTS
Cytogenetic Map4q21UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4521460278882945Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
2302371Stl22Serum triglyceride level QTL 225.15blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829457114705Rat
1358203Stl19Serum triglyceride level QTL 192.80.002blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829465958103Rat
631642Stl2Serum triglyceride level QTL 23.3blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521917856647776Rat
6478724Anxrr35Anxiety related response QTL 350.00449defecation behavior trait (VT:0010462)defecation measurement (CMO:0000997)41008408955084089Rat
6478766Anxrr47Anxiety related response QTL 470.09637locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)41008408955084089Rat
6478769Anxrr48Anxiety related response QTL 480.02514locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)41008408955084089Rat
8694374Bw155Body weight QTL 1553.390.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)41008408955084089Rat
9590304Scort17Serum corticosterone level QTL 174.960.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)41008408955084089Rat
8552906Pigfal3Plasma insulin-like growth factor 1 level QTL 3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)41008408955084089Rat
631261Tcas3Tongue tumor susceptibility QTL 36.88tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)41081417091360527Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
2303585Bw86Body weight QTL 864body mass (VT:0001259)body weight (CMO:0000012)41467806559678065Rat
2313401Anxrr27Anxiety related response QTL 27aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)41793350862933508Rat
61412Pia2Pristane induced arthritis QTL 23.9joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)42133334362278020Rat
6909122Insul22Insulin level QTL 224.63blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)42690728575585128Rat
6909128Pancm4Pancreatic morphology QTL 411.35pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)42690728575585128Rat
8655906Rf60Renal function QTL 603.8blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)42949419581006281Rat
12798520Anxrr55Anxiety related response QTL 554.450.01locomotor behavior trait (VT:0001392)number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)432583980114627242Rat
11530004Niddm71Non-insulin dependent diabetes mellitus QTL 710.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)43258419952754138Rat
8552782Vie1Viral induced encephalitis QTL 126.4brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43443048482490359Rat
8552801Bw143Body weight QTL 1437.3body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)43443048482490359Rat
8552809Vie5Viral induced encephalitis QTL 525.3brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43443048482490359Rat
8655961Kidm43Kidney mass QTL 4318kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)436303261103194984Rat
1358352Srcrt3Stress Responsive Cort QTL 32.29blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)438465774146803430Rat
61475Aia2Adjuvant induced arthritis QTL 25.8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)43950527573892441Rat
1331807Rf31Renal function QTL 312.988urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)43952426474726312Rat
1300139Hrtrt6Heart rate QTL 62.85heart pumping trait (VT:2000009)heart rate (CMO:0000002)439524264116179656Rat
61445Strs3Sensitivity to stroke QTL 33cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)44043338885433388Rat
8694439Bw168Body weight QTL 1689.570.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)44043341485433414Rat
6893678Bw108Body weight QTL 1082.60.006body mass (VT:0001259)body weight (CMO:0000012)44345797688457976Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)444463720155883716Rat
1354612Foco1Food consumption QTL 18.87eating behavior trait (VT:0001431)food intake rate (CMO:0000427)444463908148090542Rat
1354660Salc1Saline consumption QTL 111.26drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)444463908148090542Rat
2312567Glom19Glomerulus QTL 191.90.006kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)445456990146803430Rat


Related Rat Strains
The following Strains have been annotated to Cav1

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:179
Count of miRNA genes:135
Interacting mature miRNAs:153
Transcripts:ENSRNOT00000009253
Prediction methods:Miranda
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 3
Medium 3 43 28 12 19 12 8 11 64 35 37 8 8
Low 29 29 29 10 4
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_031556 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_133651 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006236130 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006236131 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC087102 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC110102 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF439778 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF439779 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF489529 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC078744 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC104689 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC128717 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC161826 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB698936 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473959 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CK364516 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DP000027 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FM039194 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224228 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000141 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  Z46614 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000078250   ⟹   ENSRNOP00000073712
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl445,640,546 - 45,673,705 (+)Ensembl
Rnor_6.0 Ensembl444,597,123 - 44,630,200 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000105620   ⟹   ENSRNOP00000087572
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl445,634,918 - 45,673,700 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000111645   ⟹   ENSRNOP00000097222
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl445,641,877 - 45,673,700 (+)Ensembl
RefSeq Acc Id: NM_031556   ⟹   NP_113744
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2445,640,624 - 45,673,705 (+)NCBI
Rnor_6.0444,597,123 - 44,630,203 (+)NCBI
Rnor_5.0445,203,494 - 45,236,461 (+)NCBI
RGSC_v3.4442,956,102 - 42,989,057 (+)RGD
Celera440,918,628 - 40,949,677 (+)NCBI
Sequence:
RefSeq Acc Id: NM_133651   ⟹   NP_598412
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2445,642,058 - 45,673,705 (+)NCBI
Rnor_6.0444,598,557 - 44,630,203 (+)NCBI
Rnor_5.0445,203,494 - 45,236,461 (+)NCBI
RGSC_v3.4442,956,102 - 42,989,057 (+)RGD
Celera440,920,068 - 40,949,677 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006236130   ⟹   XP_006236192
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2445,641,347 - 45,673,708 (+)NCBI
Rnor_6.0444,597,846 - 44,630,206 (+)NCBI
Rnor_5.0445,203,494 - 45,236,461 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006236131   ⟹   XP_006236193
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2445,640,913 - 45,673,708 (+)NCBI
Rnor_6.0444,597,412 - 44,630,206 (+)NCBI
Rnor_5.0445,203,494 - 45,236,461 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_113744   ⟸   NM_031556
- Peptide Label: isoform alpha
- UniProtKB: Q2IBC6 (UniProtKB/TrEMBL),   Q3MHT6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_598412   ⟸   NM_133651
- Peptide Label: isoform beta
- UniProtKB: B1WBN8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006236193   ⟸   XM_006236131
- Peptide Label: isoform X1
- UniProtKB: B1WBN8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006236192   ⟸   XM_006236130
- Peptide Label: isoform X1
- UniProtKB: B1WBN8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000073712   ⟸   ENSRNOT00000078250
RefSeq Acc Id: ENSRNOP00000087572   ⟸   ENSRNOT00000105620
RefSeq Acc Id: ENSRNOP00000097222   ⟸   ENSRNOT00000111645

Transcriptome

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

Promoters
RGD ID:13692892
Promoter ID:EPDNEW_R3416
Type:initiation region
Name:Cav1_1
Description:caveolin 1
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_6.0444,597,216 - 44,597,276EPDNEW

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)
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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)
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)
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)
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
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