Lep (leptin) - Rat Genome Database

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Gene: Lep (leptin) Rattus norvegicus
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Symbol: Lep
Name: leptin
RGD ID: 3000
Description: Exhibits hormone activity and peptide hormone receptor binding activity. Involved in several processes, including positive regulation of cell communication; regulation of apoptotic process; and response to vitamin. Localizes to cytosol and extracellular space. Used to study several diseases, including alcohol dependence; glucose metabolism disease (multiple); liver disease (multiple); neurodegenerative disease (multiple); and short bowel syndrome. Biomarker of several diseases, including Huntington's disease; acute pancreatitis; alcohol dependence; fatty liver disease (multiple); and lipid metabolism disorder (multiple). Human ortholog(s) of this gene implicated in several diseases, including alcohol dependence; congenital leptin deficiency; fatty liver disease (multiple); liver disease (multiple); and lung disease (multiple). Orthologous to human LEP (leptin); PARTICIPATES IN energy homeostasis pathway; leptin system pathway; hypoxia inducible factor pathway; INTERACTS WITH (+)-catechin; (R)-lipoic acid; (S)-nicotine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: OB; obese; obesity (murine homolog leptin); obesity factor
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Lepem5Mcwi   Lepm1Kyo   Lepem1Sage   Lepem1  
Genetic Models: SD-Lepem1 SD-Lepem1Sage+/- SD-Lepem1Sage-/- W.F344-Lepm1Kyo F344-Lepm1Kyo SS-Lepem5Mcwi
Is Marker For: Strains:   F344-Lepm1Kyo   SD-Lepem1Narl  
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2457,661,127 - 57,675,262 (+)NCBI
Rnor_6.0 Ensembl456,337,695 - 56,351,818 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0456,337,695 - 56,351,818 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0456,085,079 - 56,099,209 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4455,943,837 - 55,945,938 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1456,185,364 - 56,197,221 (+)NCBI
Celera452,770,132 - 52,784,148 (+)NCBICelera
RH 3.4 Map4309.5RGD
Cytogenetic Map4q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
abdominal obesity-metabolic syndrome  (ISS)
abdominal obesity-metabolic syndrome 1  (ISS)
acute pancreatitis  (IEP)
adult respiratory distress syndrome  (ISO)
alcohol dependence  (IDA,IEP)
alcoholic liver cirrhosis  (IDA)
Alzheimer's disease  (IDA,ISO)
asthma  (ISO)
autistic disorder  (ISO)
autoimmune hepatitis  (ISO)
bacterial pneumonia  (ISO)
Body Weight Changes  (IMP)
Brain Injuries  (IEP)
breast cancer  (ISO)
Breast Neoplasms  (ISO)
Choroidal Neovascularization  (IEP)
Chronic Hepatitis C  (IEP)
chronic obstructive pulmonary disease  (ISO)
Colonic Neoplasms  (ISO)
congenital leptin deficiency  (ISO)
congestive heart failure  (ISO)
Crohn's disease  (ISO)
cystic fibrosis  (ISO)
diabetes mellitus  (ISO)
Diabetic Nephropathies  (ISO)
Dyslipidemias  (IEP)
End Stage Liver Disease  (IEP)
end stage renal disease  (ISO)
Experimental Arthritis  (ISO)
Experimental Diabetes Mellitus  (IDA,IMP,ISO)
Experimental Liver Cirrhosis  (IMP,ISO)
familial hyperlipidemia  (IEP)
fatty liver disease  (IEP,ISO)
Female Infertility  (ISO)
Femoral Fractures  (IEP)
Fetal Growth Retardation  (IDA)
gastric ulcer  (ISO)
gestational diabetes  (ISO)
glucose intolerance  (IMP,ISO)
hepatocellular carcinoma  (IAGP,IEP)
hepatocellular clear cell carcinoma  (ISO)
Hepatomegaly  (ISO)
heroin dependence  (ISO)
Huntington's disease  (IEP)
Hypercapnia  (ISO)
Hypercholesterolemia  (IMP,ISO)
hyperglycemia  (ISO)
hyperinsulinism  (IMP,ISO)
Hyperphagia  (ISO)
Hyperplasia  (ISO)
hypertension  (IDA,ISO)
Hypertriglyceridemia  (IMP)
hypogonadism  (IDA,ISO)
Hypoventilation  (ISO)
Inflammation  (ISO)
Insulin Resistance  (IEP,IMP,ISO)
Kidney Reperfusion Injury  (IDA)
Knee Osteoarthritis  (ISO)
lipid metabolism disorder  (IEP)
lung disease  (ISO)
lung non-small cell carcinoma  (ISO)
Mammary Neoplasms, Experimental  (IEP)
Metabolic Syndrome  (IEP,ISO)
morbid obesity  (ISO)
Myocardial Reperfusion Injury  (IEP)
Nerve Degeneration  (ISO)
non-alcoholic fatty liver disease  (IEP,ISO)
obesity  (IDA,IEP,IMP,ISO)
obstructive sleep apnea  (ISO)
Oral Ulcer  (ISO)
osteoarthritis  (ISO)
osteoporosis  (IDA,IEP,ISO)
Parkinson's disease  (IDA)
pleomorphic xanthoastrocytoma  (ISO)
Pneumococcal Pneumonia  (ISO)
polycystic ovary syndrome  (ISO)
Polydipsia  (ISO)
Polyuria  (ISO)
pre-eclampsia  (IEP)
primary biliary cholangitis  (ISO)
Prostatic Neoplasms  (ISO)
proteinuria  (ISO)
renal cell carcinoma  (ISO)
Reperfusion Injury  (IDA)
rhinitis  (ISO)
Sepsis  (IEP)
short bowel syndrome  (IDA)
Spinal Cord Injuries  (IEP)
Tachycardia  (ISO)
type 2 diabetes mellitus  (IMP,ISO)
visual epilepsy  (ISO)
Weight Gain  (ISO)
Weight Loss  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (EXP,ISO)
(+)-epicatechin-3-O-gallate  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
(R)-lipoic acid  (EXP,ISO)
(R)-mevalonic acid  (ISO)
(S)-nicotine  (EXP)
1,8-cineole  (ISO)
1-(3-chlorophenyl)piperazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
15-deoxy-Delta(12,14)-prostaglandin J2  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP,ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrophenol  (ISO)
2,6-di-tert-butyl-4-methylphenol  (ISO)
2-acetamidofluorene  (EXP)
2-amino-2-deoxy-D-galactopyranose  (ISO)
2-amino-2-deoxy-D-glucopyranose 6-phosphate  (ISO)
2-aminopurine  (ISO)
2-arachidonoylglycerol  (ISO)
2-deoxy-D-glucose  (EXP)
2-hydroxypropanoic acid  (ISO)
2-methyl-4-chlorophenoxybutyric acid  (EXP)
2-trans,6-trans,10-trans-geranylgeranyl diphosphate  (ISO)
24,25-Dihydroxyvitamin D  (ISO)
3',5'-cyclic AMP  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3,4-methylenedioxymethamphetamine  (EXP)
3,5-diethoxycarbonyl-1,4-dihydrocollidine  (ISO)
3-aminobenzamide  (EXP)
3-chloropropane-1,2-diol  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxy-17beta-estradiol  (ISO)
4-hydroxybenzoic acid  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-nonylphenol  (EXP)
5-aza-2'-deoxycytidine  (ISO)
8-Br-cAMP  (ISO)
9-cis-retinoic acid  (EXP)
AACOCF3  (ISO)
acarbose  (EXP)
acetaldehyde  (ISO)
acetylsalicylic acid  (EXP)
actinomycin D  (EXP)
aflatoxin B1  (ISO)
AH23848  (ISO)
aldehydo-D-glucosamine 6-phosphate  (ISO)
aldehydo-D-glucose  (EXP,ISO)
all-trans-retinol  (EXP)
allopurinol  (EXP)
AM-251  (ISO)
amlodipine  (ISO)
ammonium chloride  (EXP)
anandamide  (ISO)
androst-4-ene-3,17-dione  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
apigenin  (ISO)
apocynin  (ISO)
arachidonic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
aspartame  (EXP,ISO)
atorvastatin calcium  (EXP)
ATP  (EXP)
Aurothioglucose  (ISO)
azoxystrobin  (ISO)
benzo[a]pyrene  (ISO)
Benzyl parahydroxybenzoate  (ISO)
beta-D-glucosamine 6-sulfate  (ISO)
beta-naphthoflavone  (ISO)
bezafibrate  (EXP,ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
Bisphenol A diglycidyl ether  (ISO)
Bisphenol B  (ISO)
bisphenol F  (ISO)
bleomycin A2  (ISO)
boric acid  (ISO)
BQ 123  (ISO)
bromodichloromethane  (ISO)
bucladesine  (ISO)
Butylparaben  (ISO)
butyric acid  (ISO)
cadmium dichloride  (ISO)
caffeine  (EXP,ISO)
calcitriol  (ISO)
calcium atom  (EXP,ISO)
calcium(0)  (EXP,ISO)
candesartan  (EXP,ISO)
capsaicin  (EXP,ISO)
capsazepine  (ISO)
carbon nanotube  (ISO)
carvacrol  (EXP)
CCCP  (ISO)
cerulenin  (ISO)
CGS-21680  (ISO)
chlorohydrocarbon  (ISO)
chloroquine  (ISO)
chlorpromazine  (EXP)
chlorpyrifos  (ISO)
choline  (ISO)
chromium atom  (EXP,ISO)
cisplatin  (EXP)
clofibrate  (EXP,ISO)
clozapine  (EXP,ISO)
cobalt dichloride  (EXP,ISO)
colforsin daropate hydrochloride  (ISO)
conjugated linoleic acid  (ISO)
corticosterone  (ISO)
crocidolite asbestos  (ISO)
cycloheximide  (ISO)
cyclosporin A  (EXP)
cyhalothrin  (EXP)
cyromazine  (EXP)
D-glucose  (EXP,ISO)
dantrolene  (EXP)
DDE  (ISO)
DDT  (ISO)
dehydroepiandrosterone  (EXP)
deoxycholic acid  (ISO)
desferrioxamine B  (EXP,ISO)
dexamethasone  (EXP,ISO)
dextran sulfate  (ISO)
diazoxide  (EXP)
dibenziodolium  (ISO)
dibutylstannane  (ISO)
diethylstilbestrol  (ISO)
diiodine  (EXP)
dioxygen  (ISO)
dipyridamole  (EXP)
disodium selenite  (ISO)
dobutamine  (ISO)
DPCPX  (EXP)
edelfosine  (ISO)
efavirenz  (ISO)
elemental selenium  (ISO)
enalapril  (ISO)
ethambutol  (EXP)
ethanol  (EXP,ISO)
ethionamide  (EXP)
Ethyl icosapentate  (ISO)
ethylparaben  (ISO)
fenofibrate  (EXP)
fenoterol  (ISO)
fenvalerate  (EXP)
ferroheme b  (ISO)
flufenamic acid  (ISO)
flutamide  (EXP)
fonofos  (ISO)
fructose  (EXP)
furan  (EXP)
gallocatechin  (ISO)
gamma-hexachlorocyclohexane  (EXP)
Ganoderic acid A  (ISO)
gemcitabine  (ISO)
gemfibrozil  (EXP)
genistein  (ISO)
gingerol  (ISO)
glucagon  (ISO)
glucose  (EXP,ISO)
glycine  (ISO)
heme b  (ISO)
hesperidin  (EXP)
hydrogen peroxide  (ISO)
imidacloprid  (ISO)
indinavir  (ISO)
indometacin  (EXP,ISO)
inulin  (EXP)
iodide salt  (EXP)
iron(2+) sulfate (anhydrous)  (ISO)
isoflavones  (EXP)
isoprenaline  (EXP,ISO)
isotretinoin  (EXP)
kainic acid  (ISO)
L-ascorbic acid  (EXP)
L-methionine  (ISO)
lamivudine  (ISO)
lanthanum atom  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
Licarin A  (ISO)
lipoic acid  (EXP,ISO)
lipopolysaccharide  (EXP,ISO)
loganin  (ISO)
lopinavir  (ISO)
LY294002  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
melatonin  (EXP,ISO)
menadione  (ISO)
mercury dichloride  (EXP,ISO)
metformin  (ISO)
methacholine chloride  (ISO)
methadone  (ISO)
methapyrilene  (EXP)
methotrexate  (ISO)
methylmercury chloride  (ISO)
methylparaben  (ISO)
MK-2206  (ISO)
monocrotaline  (EXP,ISO)
monosodium L-glutamate  (EXP,ISO)
morin  (EXP)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-methyl-N-nitrosourea  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP)
naproxen  (EXP)
naringin  (EXP,ISO)
nelfinavir  (ISO)
nevirapine  (ISO)
nickel atom  (ISO)
nickel dichloride  (EXP,ISO)
nickel sulfate  (ISO)
nicotine  (EXP)
nicotinic acid  (ISO)
nitric oxide  (ISO)
Nonylphenol  (ISO)
NS-398  (ISO)
olanzapine  (ISO)
oleanolic acid  (ISO)
oleic acid  (EXP,ISO)
orlistat  (EXP,ISO)
ozone  (EXP,ISO)
paracetamol  (ISO)
paraquat  (EXP)
parathion  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perindopril  (EXP)
permethrin  (ISO)
phencyclidine  (ISO)
phenethyl caffeate  (ISO)
phenobarbital  (EXP)
phosphatidylcholine  (ISO)
phosphoramidon  (EXP)
pioglitazone  (EXP)
piperine  (EXP)
pirimicarb  (EXP)
pirinixic acid  (ISO)
pitavastatin  (ISO)
pitavastatin(1-)  (ISO)
pluronic P-123  (EXP)
Poloxamer  (EXP)
potassium dichromate  (ISO)
pravastatin  (ISO)
prochloraz  (ISO)
progesterone  (ISO)
propranolol  (EXP,ISO)
propylparaben  (ISO)
prostaglandin E2  (EXP)
Ptaquiloside  (ISO)
Pyridostigmine bromide  (ISO)
pyruvic acid  (EXP)
quercetin  (EXP,ISO)
rac-lactic acid  (ISO)
ramipril  (ISO)
reactive oxygen species  (ISO)
rebaudioside A  (ISO)
reserpine  (ISO)
resveratrol  (EXP,ISO)
rifampicin  (EXP)
rimonabant  (ISO)
ritonavir  (ISO)
rotenone  (ISO)
roxarsone  (ISO)
ruthenium red  (ISO)
rutin  (EXP)
S-adenosyl-L-methioninate  (ISO)
S-adenosyl-L-methionine  (ISO)
saquinavir  (ISO)
SB 203580  (ISO)
selenium atom  (ISO)
serpentine asbestos  (ISO)
silicon dioxide  (ISO)
simvastatin  (EXP,ISO)
SKF-96365 hydrochloride  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium perchlorate  (EXP)
stavudine  (ISO)
steviol  (ISO)
stevioside  (ISO)
streptozocin  (EXP,ISO)
sumatriptan  (EXP)
superoxide  (ISO)
terbufos  (ISO)
terbutaline  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP,ISO)
thiram  (EXP)
titanium dioxide  (ISO)
tributylstannane  (EXP,ISO)
trichloroethene  (ISO)
trichostatin A  (ISO)
triflumizole  (ISO)
triphenyl phosphate  (ISO)
triptonide  (ISO)
troglitazone  (EXP,ISO)
U-73122  (ISO)
ursolic acid  (ISO)
vanadium atom  (EXP)
vanadium(0)  (EXP)
vinclozolin  (EXP)
vitamin E  (EXP)
wortmannin  (ISO)
xanthone  (EXP)
zidovudine  (ISO)
zinc atom  (EXP,ISO)
zinc dichloride  (ISO)
zinc molecular entity  (EXP)
zinc sulfate  (EXP)
zinc(0)  (EXP,ISO)
ziram  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of protein kinase C activity  (IBA,ISO,ISS)
adipose tissue development  (ISO)
adult feeding behavior  (ISO,ISS)
angiogenesis  (ISO)
aorta development  (ISO)
bile acid metabolic process  (ISO)
bone growth  (ISO,ISS)
bone mineralization involved in bone maturation  (IDA)
cAMP-mediated signaling  (TAS)
cardiac muscle hypertrophy  (IDA)
cellular response to insulin stimulus  (ISO)
cellular response to L-ascorbic acid  (IEP)
cellular response to leptin stimulus  (ISO)
cellular response to retinoic acid  (IEP)
central nervous system neuron development  (ISO)
cholesterol metabolic process  (ISO)
circadian rhythm  (IEP)
determination of adult lifespan  (ISO)
eating behavior  (ISO)
elastin metabolic process  (ISO)
energy reserve metabolic process  (IBA,IDA)
fatty acid beta-oxidation  (ISO)
fatty acid catabolic process  (IDA)
female pregnancy  (IEP)
glucose homeostasis  (ISO)
glucose metabolic process  (ISO)
glycerol biosynthetic process  (IDA)
hormone metabolic process  (ISO)
insulin secretion  (ISO)
intestinal absorption  (ISO,ISS)
intracellular signal transduction  (IDA,TAS)
leptin-mediated signaling pathway  (IDA,ISO)
leukocyte tethering or rolling  (IDA)
lipid metabolic process  (IBA,IEP,ISO)
negative regulation of apoptotic process  (IDA)
negative regulation of appetite  (ISO,ISS)
negative regulation of appetite by leptin-mediated signaling pathway  (IBA,IDA)
negative regulation of autophagy  (ISO,ISS)
negative regulation of cartilage development  (IDA)
negative regulation of glucagon secretion  (ISO)
negative regulation of glucose import  (ISO,ISS)
negative regulation of glutamine transport  (IMP)
negative regulation of lipid storage  (IDA)
negative regulation of metabolic process  (IDA)
negative regulation of transcription by RNA polymerase II  (ISO)
negative regulation of vasoconstriction  (IDA)
ovulation from ovarian follicle  (IDA)
phagocytosis  (IDA,ISO,ISS)
placenta development  (ISO)
positive regulation of cell population proliferation  (IDA)
positive regulation of cold-induced thermogenesis  (ISO,ISS)
positive regulation of cytokine production  (IEP)
positive regulation of developmental growth  (ISO)
positive regulation of fat cell apoptotic process  (IDA)
positive regulation of follicle-stimulating hormone secretion  (IEP)
positive regulation of hepatic stellate cell activation  (IDA)
positive regulation of insulin receptor signaling pathway  (IDA)
positive regulation of interleukin-12 production  (ISO,ISS)
positive regulation of interleukin-6 production  (ISO,ISS)
positive regulation of interleukin-8 production  (ISO,ISS)
positive regulation of ion transport  (IDA)
positive regulation of luteinizing hormone secretion  (IEP)
positive regulation of MAPK cascade  (IDA,ISO)
positive regulation of myeloid cell differentiation  (ISO)
positive regulation of p38MAPK cascade  (IBA,ISO,ISS)
positive regulation of peroxisome proliferator activated receptor signaling pathway  (IDA)
positive regulation of phosphatidylinositol 3-kinase signaling  (IBA,IDA,ISO)
positive regulation of protein import into nucleus  (ISO)
positive regulation of protein kinase B signaling  (ISO,ISS)
positive regulation of protein phosphorylation  (ISO)
positive regulation of reactive oxygen species metabolic process  (IDA)
positive regulation of receptor signaling pathway via JAK-STAT  (IBA,IMP,ISO,ISS)
positive regulation of T cell proliferation  (ISO,ISS)
positive regulation of TOR signaling  (IBA,ISO,ISS)
positive regulation of tumor necrosis factor production  (ISO,ISS)
positive regulation of tyrosine phosphorylation of STAT protein  (IMP)
prostaglandin secretion  (ISO,ISS)
receptor signaling pathway via JAK-STAT  (TAS)
regulation of angiogenesis  (ISO,ISS)
regulation of blood pressure  (IDA)
regulation of bone remodeling  (ISO,ISS)
regulation of brown fat cell differentiation  (ISO,ISS)
regulation of catalytic activity  (ISO)
regulation of cell cycle  (ISO,ISS)
regulation of cytokine production involved in inflammatory response  (ISO,ISS)
regulation of endothelial cell proliferation  (ISO,ISS)
regulation of fat cell differentiation  (ISO)
regulation of gluconeogenesis  (ISO)
regulation of insulin secretion  (ISO)
regulation of intestinal cholesterol absorption  (ISO)
regulation of lipid biosynthetic process  (ISO)
regulation of lipoprotein lipid oxidation  (IDA)
regulation of metabolic process  (ISO)
regulation of natural killer cell activation  (ISO,ISS)
regulation of natural killer cell mediated cytotoxicity  (ISO,ISS)
regulation of natural killer cell proliferation  (ISO,ISS)
regulation of nitric-oxide synthase activity  (ISO,ISS)
regulation of protein localization to nucleus  (ISO)
regulation of protein phosphorylation  (ISO)
regulation of steroid biosynthetic process  (ISO)
response to activity  (IEP)
response to dietary excess  (IMP,ISO)
response to estradiol  (IEP)
response to ethanol  (IEP)
response to hypoxia  (IEP)
response to insulin  (IBA,ISO)
response to nutrient  (IEP)
response to nutrient levels  (IEP)
response to vitamin E  (IEP)
sexual reproduction  (ISO)
T cell differentiation  (ISO,ISS)
tyrosine phosphorylation of STAT protein  (IBA,ISO)

Cellular Component
cytoplasm  (ISO)
cytosol  (IDA)
extracellular space  (IBA,IDA,ISO)

Molecular Function

References

References - curated
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Genomics

Comparative Map Data
Lep
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2457,661,127 - 57,675,262 (+)NCBI
Rnor_6.0 Ensembl456,337,695 - 56,351,818 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0456,337,695 - 56,351,818 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0456,085,079 - 56,099,209 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4455,943,837 - 55,945,938 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1456,185,364 - 56,197,221 (+)NCBI
Celera452,770,132 - 52,784,148 (+)NCBICelera
RH 3.4 Map4309.5RGD
Cytogenetic Map4q22NCBI
LEP
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl7128,241,278 - 128,257,629 (+)EnsemblGRCh38hg38GRCh38
GRCh387128,241,201 - 128,257,629 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh377127,881,331 - 127,897,682 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 367127,668,567 - 127,684,917 (+)NCBINCBI36hg18NCBI36
Build 347127,475,281 - 127,491,632NCBI
Celera7122,684,619 - 122,700,967 (+)NCBI
Cytogenetic Map7q32.1NCBI
HuRef7122,242,298 - 122,258,647 (+)NCBIHuRef
CHM1_17127,814,632 - 127,830,980 (+)NCBICHM1_1
CRA_TCAGchr7v27127,264,455 - 127,280,803 (+)NCBI
Lep
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39629,060,220 - 29,073,875 (+)NCBIGRCm39mm39
GRCm39 Ensembl629,060,219 - 29,073,876 (+)Ensembl
GRCm38629,060,221 - 29,073,876 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl629,060,220 - 29,073,877 (+)EnsemblGRCm38mm10GRCm38
MGSCv37629,010,221 - 29,023,876 (+)NCBIGRCm37mm9NCBIm37
MGSCv36629,010,231 - 29,023,886 (+)NCBImm8
Celera629,063,769 - 29,077,429 (+)NCBICelera
Cytogenetic Map6A3.3NCBI
cM Map612.3NCBI
Lep
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554799,274,516 - 9,279,472 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554799,266,604 - 9,276,568 (+)NCBIChiLan1.0ChiLan1.0
LEP
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.17132,884,994 - 132,901,519 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl7132,885,011 - 132,901,519 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v07120,230,896 - 120,248,602 (+)NCBIMhudiblu_PPA_v0panPan3
LEP
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1148,115,396 - 8,130,946 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl148,116,122 - 8,131,395 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha147,802,696 - 7,807,108 (-)NCBI
ROS_Cfam_1.0147,880,580 - 7,897,895 (-)NCBI
UMICH_Zoey_3.1148,087,574 - 8,091,986 (-)NCBI
UNSW_CanFamBas_1.0147,828,397 - 7,832,809 (-)NCBI
UU_Cfam_GSD_1.0147,975,126 - 7,979,538 (-)NCBI
LOC101968976
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511854,282,689 - 54,287,494 (+)NCBI
SpeTri2.0NW_00493647915,394,966 - 15,411,334 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LEP
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1820,106,868 - 20,123,447 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11820,106,867 - 20,124,071 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21821,200,988 - 21,231,275 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LOC103226854
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12197,056,913 - 97,071,161 (+)NCBI
ChlSab1.1 Ensembl2197,057,529 - 97,071,220 (+)Ensembl
Vero_WHO_p1.0NW_0236660426,335,426 - 6,349,076 (-)NCBI
Lep
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247837,708,820 - 7,721,610 (-)NCBI

Position Markers
PMC21729P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2457,672,228 - 57,672,419 (+)MAPPER
Rnor_6.0456,348,785 - 56,348,975NCBIRnor6.0
Rnor_5.0456,096,176 - 56,096,366UniSTSRnor5.0
RGSC_v3.4455,945,637 - 55,945,827UniSTSRGSC3.4
Celera452,781,115 - 52,781,305UniSTS
Cytogenetic Map4q22UniSTS
RH94808  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2457,672,559 - 57,672,658 (+)MAPPER
Rnor_6.0456,349,116 - 56,349,214NCBIRnor6.0
Rnor_5.0456,096,507 - 56,096,605UniSTSRnor5.0
RGSC_v3.4455,945,968 - 55,946,066UniSTSRGSC3.4
Celera452,781,446 - 52,781,544UniSTS
RH 3.4 Map4309.5UniSTS
Cytogenetic Map4q22UniSTS
Lep  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2846,479,601 - 46,480,909 (+)MAPPER
Rnor_6.0850,477,430 - 50,478,737NCBIRnor6.0
Rnor_5.0849,103,749 - 49,105,056UniSTSRnor5.0
Celera846,061,659 - 46,062,966UniSTS
Cytogenetic Map4q22UniSTS
LEP-3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2457,670,569 - 57,672,217 (+)MAPPER
Rnor_6.0456,347,126 - 56,348,773NCBIRnor6.0
Rnor_5.0456,094,517 - 56,096,164UniSTSRnor5.0
RGSC_v3.4455,943,978 - 55,945,625UniSTSRGSC3.4
Celera452,779,456 - 52,781,103UniSTS
Cytogenetic Map4q22UniSTS


QTLs in Region (Rnor_6.0)
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)4304323179575658Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)43043231145254791Rat
1358203Stl19Serum triglyceride level QTL 192.80.002blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4304401764915903Rat
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)4734240492484039Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)47850904182171018Rat
2303585Bw86Body weight QTL 864body mass (VT:0001259)body weight (CMO:0000012)41263897457638974Rat
7387227Uae40Urinary albumin excretion QTL 402.90.0052urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)41614994161149941Rat
61412Pia2Pristane induced arthritis QTL 23.9joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)41822218761039065Rat
10755501Bp390Blood pressure QTL 3902.5arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)423850384169318094Rat
6909122Insul22Insulin level QTL 224.63blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)42399172176238799Rat
6909128Pancm4Pancreatic morphology QTL 411.35pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)42399172176238799Rat
1578655Bmd11Bone mineral density QTL 1111femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)42463187469631874Rat
8655906Rf60Renal function QTL 603.8blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)42665474981874227Rat
12798520Anxrr55Anxiety related response QTL 554.450.01locomotor behavior trait (VT:0001392)number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)429549895112807890Rat
8552782Vie1Viral induced encephalitis QTL 126.4brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43182556083531021Rat
8552801Bw143Body weight QTL 1437.3body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)43182556083531021Rat
8552809Vie5Viral induced encephalitis QTL 525.3brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43182556083531021Rat
2313401Anxrr27Anxiety related response QTL 27aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)43363780361708341Rat
8655961Kidm43Kidney mass QTL 4318kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)43427793299067150Rat
1358352Srcrt3Stress Responsive Cort QTL 32.29blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)436615599145611886Rat
61475Aia2Adjuvant induced arthritis QTL 25.8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)43768517573066691Rat
1331807Rf31Renal function QTL 312.988urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)43770327275345433Rat
1300139Hrtrt6Heart rate QTL 62.85heart pumping trait (VT:2000009)heart rate (CMO:0000002)437703272115372927Rat
61445Strs3Sensitivity to stroke QTL 33cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)43920822284208222Rat
8694439Bw168Body weight QTL 1689.570.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)43920824784208247Rat
6893678Bw108Body weight QTL 1082.60.006body mass (VT:0001259)body weight (CMO:0000012)44241577787415777Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)443414605155469929Rat
1354660Salc1Saline consumption QTL 111.26drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)443414792146942075Rat
1354612Foco1Food consumption QTL 18.87eating behavior trait (VT:0001431)food intake rate (CMO:0000427)443414792146942075Rat
1298082Stresp4Stress response QTL 4blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)446898276145611886Rat
2312567Glom19Glomerulus QTL 191.90.006kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)449906054145611886Rat
4889969Bss96Bone structure and strength QTL 964.9tibia size trait (VT:0100001)tibia cortical bone volume (CMO:0001725)45532485779575658Rat
4889972Bss97Bone structure and strength QTL 975.6tibia size trait (VT:0100001)tibia total bone volume (CMO:0001724)45532485779575658Rat
5685009Bmd86Bone mineral density QTL 863.7tibia mineral mass (VT:1000283)bone mineral density (CMO:0001226)45532485779575658Rat
5685012Bmd87Bone mineral density QTL 875.1tibia mineral mass (VT:1000283)bone mineral content (CMO:0001554)45532485779575658Rat
70200Alc18Alcohol consumption QTL 189.2drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)455324953148360954Rat
1641833Alc21Alcohol consumption QTL 218.60.0001drinking behavior trait (VT:0001422)ethanol drink intake rate (CMO:0001407)455375865125671711Rat
634311Sach7Saccharin preference QTL 7taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)45579156482134846Rat
631546Bp86Blood pressure QTL 863.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)45579156492484312Rat
61336Bp21Blood pressure QTL 214.6arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)45579183479557856Rat
1578657Bss12Bone structure and strength QTL 128.9femur morphology trait (VT:0000559)femoral neck cross-sectional area (CMO:0001697)456092756101092756Rat
1578658Bss13Bone structure and strength QTL 138femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)456092756101092756Rat


Related Rat Strains
The following Strains have been annotated to Lep


Genetic Models
This gene Lep is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:471
Count of miRNA genes:263
Interacting mature miRNAs:330
Transcripts:ENSRNOT00000071926
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 7 3 2
Low 2 6 7 5 8 8 12 7 9 8
Below cutoff 1 13 7 5 8 5 3 8 12 5 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000071926   ⟹   ENSRNOP00000066184
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl456,337,695 - 56,351,818 (+)Ensembl
RefSeq Acc Id: NM_013076   ⟹   NP_037208
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2457,661,131 - 57,675,262 (+)NCBI
Rnor_6.0456,337,695 - 56,351,818 (+)NCBI
Rnor_5.0456,085,079 - 56,099,209 (+)NCBI
RGSC_v3.4455,943,837 - 55,945,938 (+)RGD
Celera452,770,132 - 52,784,148 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008762762   ⟹   XP_008760984
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0456,345,623 - 56,351,818 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039107126   ⟹   XP_038963054
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2457,661,127 - 57,675,262 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_037208   ⟸   NM_013076
- Peptide Label: precursor
- UniProtKB: P50596 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008760984   ⟸   XM_008762762
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000066184   ⟸   ENSRNOT00000071926
RefSeq Acc Id: XP_038963054   ⟸   XM_039107126
- Peptide Label: isoform X1

Transcriptome

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


Strain Variation

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