Cd36 (CD36 molecule) - Rat Genome Database

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Gene: Cd36 (CD36 molecule) Rattus norvegicus
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Symbol: Cd36
Name: CD36 molecule
RGD ID: 2301
Description: Enables several functions, including oleic acid binding activity; scavenger receptor activity; and thrombospondin receptor activity. Involved in several processes, including fatty acid metabolic process; positive regulation of macromolecule metabolic process; and response to peptide hormone. Located in several cellular components, including brush border membrane; caveola; and sarcolemma. Part of protein-containing complex. Used to study interstitial lung disease (multiple); macular degeneration; myocardial infarction; obesity; and polycystic ovary syndrome. Biomarker of artery disease (multiple); hypertrophic cardiomyopathy; nephrosis; obesity; and type 2 diabetes mellitus. Human ortholog(s) of this gene implicated in several diseases, including blood platelet disease (multiple); hemolytic-uremic syndrome; osteoarthritis; pulmonary tuberculosis; and type 2 diabetes mellitus. Orthologous to human CD36 (CD36 molecule); PARTICIPATES IN retinol metabolic pathway; cell-extracellular matrix signaling pathway; eicosanoid signaling pathway via peroxisome proliferator-activated receptor gamma; INTERACTS WITH (R,R,R)-alpha-tocopherol; 1,2-dimethylhydrazine; 1-naphthyl isothiocyanate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: adipocyte membrane protein; CD36 antigen; CD36 antigen (collagen type I receptor, thrombospondin receptor); Cd36 antigen-like; CD36 molecule (thrombospondin receptor); collagen type I receptor thrombospondin receptor; Fat; fatty acid translocase; fatty acid transport protein; glycoprotein IIIb; GPIIIB; GPIV; LOC499984; MGC108510; MGC91634; PAS IV; PAS-4; platelet glycoprotein 4; platelet glycoprotein IV; RGD1562323; similar to fatty acid translocase/CD36
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Is Marker For: Strains:   BN   SHR   WKY   BN.SHR-(Il6-Cd36)/Cub   SHR-Tg(Ef1a-Cd36)10Ipcv   SHR-Tg(Ef1a-Cd36)19Ipcv   SHR-Tg(Ef1a-Cd36)93Ipcv   SHR-Tg(Ef1a-Cd36)106Ipcv   SHR/4Dmcr   SHRSP/3Dmcr   SHR/2Dmcr   SHR/3Dmcr   SHRSP/4Dmcr   SHRSP/5Dmcr   SHRSP/2Dmcr  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2417,317,343 - 17,410,084 (+)NCBImRatBN7.2
Rnor_6.0414,150,309 - 14,191,498 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl414,001,761 - 14,249,749 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0414,125,297 - 14,166,434 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4413,534,582 - 13,554,416 (+)NCBIRGSC3.4rn4RGSC3.4
Celera412,880,238 - 12,941,086 (+)NCBICelera
Cytogenetic Map4q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
Acute Lung Injury  (ISO)
Alcoholic Fatty Liver  (ISO)
allergic contact dermatitis  (ISO)
Alzheimer's disease  (ISO)
arteriosclerosis  (ISO)
atherosclerosis  (IEP,ISO)
atrial fibrillation  (ISO)
blood platelet disease  (ISO)
brain ischemia  (ISO)
Cardiac Arrhythmias  (IMP)
Cardiomegaly  (ISO)
cardiomyopathy  (ISO)
celiac disease  (ISO)
Cerebral Hemorrhage  (ISO)
cerebral infarction  (ISO)
cerebral malaria  (ISO)
chronic myeloid leukemia  (ISO)
colitis  (ISO)
corneal neovascularization  (ISO)
Coronary Disease  (ISO)
dermatomyositis  (ISO)
diabetes mellitus  (ISO)
Diabetic Nephropathies  (IEP)
dilated cardiomyopathy  (ISO)
endometriosis  (ISO)
epilepsy  (ISO)
essential thrombocythemia  (ISO)
Experimental Diabetes Mellitus  (IEP)
Experimental Liver Cirrhosis  (ISO)
fatty liver disease  (ISO)
glucose intolerance  (ISO)
granulomatosis with polyangiitis  (ISO)
Hematoma  (ISO)
hemolytic-uremic syndrome  (ISO)
Hypercholesterolemia  (ISO)
hypertension  (IEP,ISO)
hypertrophic cardiomyopathy  (IEP)
inclusion body myositis  (ISO)
Inflammation  (ISO)
Insulin Resistance  (IMP,ISO)
Knee Osteoarthritis  (IEP,ISO)
liver cirrhosis  (ISO)
macular degeneration  (IAGP)
malaria  (ISO)
Metabolic Syndrome  (IAGP,ISO)
middle cerebral artery infarction  (ISO)
Mycobacterium Infections  (ISO)
myeloid neoplasm  (ISO)
myocardial infarction  (IMP)
Myocardial Ischemia  (ISO)
nephrosis  (IEP)
non-alcoholic fatty liver disease  (ISO)
obesity  (IEP,IMP,ISO)
osteoarthritis  (ISO)
pemphigus  (ISO)
platelet-type bleeding disorder 10  (ISO)
pleomorphic xanthoastrocytoma  (ISO)
polycystic ovary syndrome  (IDA)
polycythemia vera  (ISO)
primary immunodeficiency disease  (ISO)
pulmonary fibrosis  (IMP,ISO)
pulmonary tuberculosis  (ISO)
relapsing-remitting multiple sclerosis  (ISO)
Reperfusion Injury  (ISO)
Retroperitoneal Fibrosis  (ISO)
rheumatic heart disease  (ISO)
Sepsis  (ISO)
sickle cell anemia  (ISO)
silicosis  (IMP)
Staphylococcal Infections  (ISO)
Tachycardia  (IEP)
thrombotic thrombocytopenic purpura  (ISO)
type 1 diabetes mellitus  (ISO)
type 2 diabetes mellitus  (IEP,ISO)
visual epilepsy  (ISO)
Weight Gain  (ISO)
Wounds, Penetrating  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(24S)-24-hydroxycholesterol  (ISO)
(25R)-cholest-5-ene-3beta,26-diol  (ISO)
(R)-lipoic acid  (ISO)
(R,R,R)-alpha-tocopherol  (EXP)
(RS)-coclaurine  (ISO)
(RS)-norcoclaurine  (ISO)
(S)-coclaurine  (ISO)
(Z)-ligustilide  (ISO)
1,2-dimethylhydrazine  (EXP,ISO)
1,3-dichloropropan-2-ol  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
2,4-dinitrotoluene  (EXP,ISO)
2-arachidonoylglycerol  (ISO)
2-butoxyethanol  (ISO)
26-hydroxycholesterol  (ISO)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (EXP,ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP,ISO)
3,3',4,4'-tetrachlorobiphenyl  (ISO)
3-aminobenzamide  (EXP)
3-chloropropane-1,2-diol  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (EXP,ISO)
4,4'-sulfonyldiphenol  (ISO)
4-(ethoxymethylene)-2-phenyloxazol-5-one  (ISO)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-phenylbutyric acid  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-methyl-4-oxido-2-pyrazin-4-iumcarboxylic acid  (ISO)
6-(4-chlorophenyl)imidazo[2,1-b][1,3]thiazole-5-carbaldehyde O-(3,4-dichlorobenzyl)oxime  (ISO)
6-propyl-2-thiouracil  (EXP)
7alpha-hydroxycholesterol  (ISO)
9-cis-retinoic acid  (ISO)
9E,11E-octadecadienoic acid  (ISO)
acetamide  (EXP)
acetylsalicylic acid  (EXP,ISO)
acrylamide  (EXP)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
AICA ribonucleotide  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
allopurinol  (EXP,ISO)
alpha-hexachlorocyclohexane  (EXP)
aluminium oxide  (ISO)
amiodarone  (ISO)
ammonium chloride  (EXP)
anandamide  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
apocynin  (ISO)
aristolochic acid  (ISO)
Aroclor 1254  (EXP,ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
atorvastatin calcium  (EXP,ISO)
azathioprine  (EXP)
benazepril  (EXP)
benzbromarone  (ISO)
benzene  (EXP)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
Benzo[k]fluoranthene  (ISO)
benzylpenicillin  (ISO)
berberine  (ISO)
beta-naphthoflavone  (ISO)
bexarotene  (EXP)
bezafibrate  (EXP,ISO)
bifenthrin  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisdemethoxycurcumin  (ISO)
bisphenol A  (EXP,ISO)
Bisphenol A diglycidyl ether  (EXP)
Bisphenol B  (ISO)
bisphenol F  (ISO)
bleomycin A2  (ISO)
buta-1,3-diene  (ISO)
cadmium atom  (EXP,ISO)
cadmium dichloride  (EXP,ISO)
caffeine  (ISO)
candesartan  (EXP,ISO)
captan  (ISO)
carbamazepine  (EXP)
carbon nanotube  (ISO)
chlorpyrifos  (EXP,ISO)
cholesterol  (ISO)
choline  (ISO)
chromium(6+)  (ISO)
ciprofibrate  (ISO)
clofibrate  (EXP,ISO)
cobalt dichloride  (EXP,ISO)
conjugated linoleic acid  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) sulfate  (ISO)
corticosterone  (EXP)
crocidolite asbestos  (ISO)
cucurbitacin B  (ISO)
cucurbitacin I  (ISO)
curcumin  (ISO)
cyclosporin A  (ISO)
cyproconazole  (EXP,ISO)
D-glucose  (ISO)
dapagliflozin  (EXP)
DDE  (ISO)
demethoxycurcumin  (ISO)
desferrioxamine B  (ISO)
dexamethasone  (EXP,ISO)
Diallyl sulfide  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP,ISO)
dichloroacetic acid  (ISO)
diethylstilbestrol  (ISO)
dimethylarsinic acid  (ISO)
Diosbulbin B  (ISO)
dioxygen  (ISO)
disulfiram  (ISO)
diuron  (EXP)
dorsomorphin  (EXP)
doxorubicin  (ISO)
duvoglustat  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
epoxiconazole  (EXP,ISO)
erythromycin A  (ISO)
ethanol  (EXP,ISO)
eugenol  (ISO)
fenofibrate  (EXP,ISO)
fenvalerate  (ISO)
fipronil  (EXP)
flutamide  (EXP)
folic acid  (EXP,ISO)
formaldehyde  (ISO)
fructose  (EXP,ISO)
fulvestrant  (ISO)
genistein  (ISO)
gentamycin  (EXP)
glucose  (ISO)
glutathione  (ISO)
GW 4064  (ISO)
GW 7647  (ISO)
hexachlorobenzene  (EXP)
hexadecanoic acid  (ISO)
ibuprofen  (ISO)
imidacloprid  (ISO)
indinavir  (ISO)
indometacin  (ISO)
irinotecan  (EXP)
iron atom  (EXP)
iron(0)  (EXP)
isoprenaline  (EXP)
ivermectin  (ISO)
L-methionine  (ISO)
lamivudine  (ISO)
lead diacetate  (ISO)
linoleic acid  (EXP)
lipoic acid  (ISO)
lipopolysaccharide  (ISO)
losartan  (ISO)
LY294002  (ISO)
malathion  (ISO)
malonaldehyde  (ISO)
mangiferin  (EXP)
melatonin  (ISO)
menadione  (ISO)
methapyrilene  (EXP,ISO)
methotrexate  (ISO)
methyllycaconitine  (ISO)
methylmercury chloride  (ISO)
mifepristone  (ISO)
miquelianin  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
myxothiazol  (ISO)
N-acetyl-L-cysteine  (EXP,ISO)
N-ethyl-N-nitrosourea  (ISO)
N-methylnicotinate  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
N-nitrosodimethylamine  (EXP)
nevirapine  (EXP)
nickel atom  (ISO)
nickel sulfate  (ISO)
nicotinic acid  (EXP,ISO)
oleic acid  (EXP,ISO)
orphenadrine  (EXP)
oxaliplatin  (EXP)
ozone  (EXP,ISO)
paclitaxel  (EXP)
paracetamol  (ISO)
pentane-2,3-dione  (EXP)
perfluorobutanesulfonic acid  (ISO)
perfluorododecanoic acid  (EXP)
perfluorohexanesulfonic acid  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
perfluorooctanoic acid  (EXP,ISO)
perfluoroundecanoic acid  (ISO)
permethrin  (EXP,ISO)
Phenelzine  (ISO)
phenobarbital  (EXP,ISO)
Phenylamil  (ISO)
phorbol 13-acetate 12-myristate  (EXP,ISO)
picolinic acid  (ISO)
pioglitazone  (EXP,ISO)
piperonyl butoxide  (EXP)
pirinixic acid  (EXP,ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
prochloraz  (EXP)
progesterone  (EXP)
propiconazole  (ISO)
PX-866  (ISO)
quercetin  (ISO)
reactive oxygen species  (ISO)
Rebamipide  (EXP)
resveratrol  (EXP,ISO)
retinyl acetate  (ISO)
rifampicin  (ISO)
rifaximin  (ISO)
rimonabant  (ISO)
ritodrine  (ISO)
rotenone  (ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (ISO)
saquinavir  (ISO)
saroglitazar  (ISO)
serpentine asbestos  (ISO)
silicon dioxide  (ISO)
sirolimus  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP,ISO)
sodium fluoride  (ISO)
Sodium oleate  (ISO)
streptozocin  (ISO)
succimer  (ISO)
sunitinib  (ISO)
tamibarotene  (ISO)
tamoxifen  (ISO)
Tanshinone I  (ISO)
tebuconazole  (EXP,ISO)
telmisartan  (ISO)
Tesaglitazar  (EXP)
testosterone  (EXP)
tetrachloroethene  (ISO)
tetrachloromethane  (EXP,ISO)
tetracycline  (ISO)
theophylline  (ISO)
thiacloprid  (ISO)
thioacetamide  (EXP)
thiophanate-methyl  (ISO)
titanium dioxide  (ISO)
tolcapone  (ISO)
toluene 2,4-diisocyanate  (ISO)
topotecan  (EXP)
tributylstannane  (ISO)
trichloroethene  (EXP,ISO)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
triphenyl phosphate  (ISO)
Triptolide  (EXP)
troglitazone  (EXP,ISO)
trovafloxacin  (EXP)
urethane  (ISO)
valproic acid  (EXP,ISO)
vanadium atom  (ISO)
vanadium(0)  (ISO)
varenicline  (ISO)
vinclozolin  (EXP)
vincristine  (EXP)
wortmannin  (ISO)
yohimbine  (ISO)
zearalenone  (EXP,ISO)
zidovudine  (ISO)
zinc atom  (EXP,ISO)
zinc oxide  (ISO)
zinc sulfate  (EXP,ISO)
zinc(0)  (EXP,ISO)
ziram  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
amyloid fibril formation  (ISO,ISS)
amyloid-beta clearance by cellular catabolic process  (IBA,IMP,ISO)
apoptotic cell clearance  (ISO)
cell adhesion  (IEA)
cell surface receptor signaling pathway  (IEA,ISO)
cell-cell adhesion via plasma-membrane adhesion molecules  (IEP)
cellular response to amyloid-beta  (ISO)
cellular response to bacterial lipopeptide  (ISO)
cellular response to diacyl bacterial lipopeptide  (ISO,ISS)
cellular response to hydroperoxide  (ISO)
cellular response to insulin stimulus  (IEP)
cellular response to lipopolysaccharide  (ISO)
cellular response to lipoteichoic acid  (ISO)
cellular response to low-density lipoprotein particle stimulus  (ISO,ISS)
cellular response to oxidised low-density lipoprotein particle stimulus  (ISO)
cGMP-mediated signaling  (ISO)
cholesterol import  (ISO,ISS)
cholesterol transport  (ISO)
defense response to Gram-positive bacterium  (ISO)
digestive tract development  (IEP)
eating behavior  (IMP)
energy homeostasis  (IMP,ISO)
fatty acid metabolic process  (IDA,IMP)
fatty acid oxidation  (IMP)
fatty acid transport  (IDA,IEP,IMP)
glucose homeostasis  (IMP)
immune response  (IEA)
intestinal absorption  (ISO,ISS)
intestinal cholesterol absorption  (ISO,ISS)
lipid storage  (IBA,ISO)
lipid transport across blood-brain barrier  (ISO)
lipoprotein transport  (IBA,ISO)
long-chain fatty acid import across plasma membrane  (ISO)
long-chain fatty acid import into cell  (IBA,ISO,ISS)
long-chain fatty acid metabolic process  (IMP)
long-chain fatty acid transport  (IMP,ISO)
low-density lipoprotein particle clearance  (IBA,ISO)
low-density lipoprotein particle mediated signaling  (ISO)
maternal placenta development  (IEP)
negative regulation of angiogenesis  (IMP)
negative regulation of gene expression  (ISO)
negative regulation of protein import into nucleus  (ISO)
negative regulation of systemic arterial blood pressure  (IMP)
negative regulation of transcription by RNA polymerase II  (ISO)
nitric oxide mediated signal transduction  (ISO)
oxidised low-density lipoprotein particle clearance  (ISO)
phagocytosis, recognition  (ISO)
plasma lipoprotein particle clearance  (ISO)
positive regulation of blood coagulation  (ISO)
positive regulation of blood microparticle formation  (ISO)
positive regulation of cell death  (ISO)
positive regulation of cell-matrix adhesion  (ISO)
positive regulation of cholesterol storage  (ISO)
positive regulation of cold-induced thermogenesis  (ISO,ISS)
positive regulation of cytokine production  (IMP)
positive regulation of cytosolic calcium ion concentration  (ISO,ISS)
positive regulation of ERK1 and ERK2 cascade  (ISO)
positive regulation of gene expression  (ISO)
positive regulation of glycogen biosynthetic process  (IDA)
positive regulation of I-kappaB kinase/NF-kappaB signaling  (ISO)
positive regulation of interleukin-1 beta production  (ISO,ISS)
positive regulation of interleukin-12 production  (ISO)
positive regulation of interleukin-6 production  (ISO)
positive regulation of macrophage cytokine production  (ISO)
positive regulation of macrophage derived foam cell differentiation  (ISO)
positive regulation of MAPK cascade  (ISO)
positive regulation of NF-kappaB transcription factor activity  (ISO)
positive regulation of nitric oxide biosynthetic process  (ISO)
positive regulation of NLRP3 inflammasome complex assembly  (ISO,ISS)
positive regulation of peptidyl-tyrosine phosphorylation  (ISO)
positive regulation of phagocytosis  (IMP)
positive regulation of phagocytosis, engulfment  (ISO)
positive regulation of reactive oxygen species biosynthetic process  (ISO)
positive regulation of reactive oxygen species metabolic process  (ISO)
positive regulation of triglyceride metabolic process  (IDA)
positive regulation of tumor necrosis factor production  (ISO)
receptor internalization  (ISO,ISS)
receptor-mediated endocytosis  (IBA,IMP,ISO)
regulation of action potential  (ISO)
regulation of protein-containing complex assembly  (ISO)
regulation of removal of superoxide radicals  (ISO)
regulation of toll-like receptor signaling pathway  (ISO)
response to activity  (IEP)
response to bacterium  (ISO)
response to estradiol  (IEP)
response to fatty acid  (IDA,IMP,ISO)
response to growth hormone  (IEP)
response to linoleic acid  (ISO,ISS)
response to lipid  (IMP,ISO)
response to mechanical stimulus  (IMP)
response to nutrient  (IEP)
response to stilbenoid  (ISO)
response to xenobiotic stimulus  (IEP)
sensory perception of taste  (ISO,ISS)
short-chain fatty acid transport  (ISO)
triglyceride metabolic process  (IMP)
triglyceride transport  (ISO,ISS)

Cellular Component

References

References - curated
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Additional References at PubMed
PMID:7504047   PMID:9568716   PMID:10772654   PMID:12376530   PMID:14729860   PMID:15166001   PMID:15220187   PMID:15280390   PMID:15496455   PMID:15647754   PMID:15690042   PMID:15752738  
PMID:15915335   PMID:16061696   PMID:16276419   PMID:16484294   PMID:16502470   PMID:16718359   PMID:16880211   PMID:16939881   PMID:17086191   PMID:17416590   PMID:17507371   PMID:17639306  
PMID:18162488   PMID:18167317   PMID:18650314   PMID:18722097   PMID:19041881   PMID:19066404   PMID:19380575   PMID:19513812   PMID:19596004   PMID:19878707   PMID:20023206   PMID:20398376  
PMID:20582536   PMID:20926122   PMID:20978343   PMID:21297178   PMID:21395585   PMID:21418266   PMID:21510957   PMID:21545834   PMID:21625957   PMID:21773965   PMID:22022213   PMID:22184632  
PMID:22292032   PMID:22473311   PMID:22662869   PMID:22693206   PMID:22780108   PMID:22915197   PMID:23012479   PMID:23395392   PMID:23444136   PMID:23812099   PMID:23940308   PMID:24040150  
PMID:24154509   PMID:24895286   PMID:25172177   PMID:25197426   PMID:25211142   PMID:26449856   PMID:26590355   PMID:26707062   PMID:26739391   PMID:27133433   PMID:27607416   PMID:27806984  
PMID:27827305   PMID:28302572   PMID:28374891   PMID:28419197   PMID:28445772   PMID:28500736   PMID:28653652   PMID:29111364   PMID:29518356   PMID:29619884   PMID:29916179   PMID:30506990  
PMID:31838198   PMID:32965022  


Genomics

Comparative Map Data
Cd36
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2417,317,343 - 17,410,084 (+)NCBImRatBN7.2
Rnor_6.0414,150,309 - 14,191,498 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl414,001,761 - 14,249,749 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0414,125,297 - 14,166,434 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4413,534,582 - 13,554,416 (+)NCBIRGSC3.4rn4RGSC3.4
Celera412,880,238 - 12,941,086 (+)NCBICelera
Cytogenetic Map4q11NCBI
CD36
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl780,369,575 - 80,679,277 (+)EnsemblGRCh38hg38GRCh38
GRCh38780,602,207 - 80,679,277 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37780,231,523 - 80,308,593 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36780,069,459 - 80,144,262 (+)NCBINCBI36hg18NCBI36
Build 34779,912,607 - 79,950,974NCBI
Celera774,932,098 - 75,009,206 (+)NCBI
Cytogenetic Map7q21.11NCBI
HuRef774,834,319 - 74,911,371 (+)NCBIHuRef
CHM1_1780,162,020 - 80,239,042 (+)NCBICHM1_1
CRA_TCAGchr7v2779,562,929 - 79,640,010 (+)NCBI
Cd36
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39517,986,688 - 18,093,957 (-)NCBIGRCm39mm39
GRCm39 Ensembl517,986,688 - 18,093,799 (-)Ensembl
GRCm38517,781,690 - 17,888,959 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl517,781,690 - 17,888,801 (-)EnsemblGRCm38mm10GRCm38
MGSCv37517,287,508 - 17,394,777 (-)NCBIGRCm37mm9NCBIm37
MGSCv36517,293,840 - 17,347,520 (-)NCBImm8
Celera514,757,802 - 14,864,361 (-)NCBICelera
Cytogenetic Map5A3NCBI
cM Map58.11NCBI
Cd36
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554105,003,668 - 5,075,313 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554105,003,720 - 5,120,903 (-)NCBIChiLan1.0ChiLan1.0
CD36
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1786,228,856 - 86,305,865 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl786,265,114 - 86,305,865 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0772,566,478 - 72,643,517 (+)NCBIMhudiblu_PPA_v0panPan3
CD36
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11820,299,808 - 20,375,856 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1820,339,050 - 20,372,639 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1820,015,595 - 20,045,069 (+)NCBI
ROS_Cfam_1.01820,745,564 - 20,821,666 (+)NCBI
UMICH_Zoey_3.11820,418,233 - 20,447,673 (+)NCBI
UNSW_CanFamBas_1.01819,970,682 - 20,000,166 (+)NCBI
UU_Cfam_GSD_1.01820,626,442 - 20,655,919 (+)NCBI
Cd36
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511862,188,852 - 62,269,004 (+)NCBI
SpeTri2.0NW_004936810791,823 - 838,303 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CD36
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl999,605,181 - 99,782,105 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1999,685,748 - 99,782,296 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.29110,037,583 - 110,106,975 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CD36
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12168,214,875 - 68,309,336 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2168,216,201 - 68,268,669 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604235,654,688 - 35,734,209 (+)NCBIVero_WHO_p1.0
Cd36
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473929,341,620 - 29,441,232 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH132455  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map4q11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61351Bp33Blood pressure QTL 330.0018arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4127716890Rat
61408Scl23Serum cholesterol level QTL 230.0005blood HDL phospholipid amount (VT:0010504)serum high density lipoprotein phospholipid level (CMO:0001567)4127716890Rat
724557Plsm1Polydactyly-luxate syndrome (PLS) morphotypes QTL 10.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)4127716890Rat
1641905Colcr1Colorectal carcinoma resistance QTL 14.30.0003intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)4129494328Rat
61333Gluco16Glucose level QTL 164.30.00001adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)4130372989Rat
9589097Slep11Serum leptin concentration QTL 115.090.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)4131934116Rat
8552903Pigfal2Plasma insulin-like growth factor 1 level QTL 27.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)4131934116Rat
9589046Scfw2Subcutaneous fat weight QTL 25.540.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)4131934116Rat
9590100Sffal4Serum free fatty acids level QTL 47.360.05blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)4131934116Rat
738021Hcar13Hepatocarcinoma resistance QTL 134.3liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)4132584199Rat
1357341Gluco5Glucose level QTL 56.4adipocyte free fatty acid secretion trait (VT:0010465)absolute change in adipocyte free fatty acid secretion per unit volume (CMO:0001446)4133250345Rat
1357343Gluco4Glucose level QTL 40.00002adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake to basal glucose uptake ratio (CMO:0000874)4133250345Rat
61415Eae11Experimental allergic encephalomyelitis QTL 112.9nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)4139505420Rat
634323Hc2Hypercalciuria QTL 22.15urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)421079645210796Rat
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
1358201Gluco12Glucose level QTL121.6adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake (CMO:0000870)4521839229593287Rat
631642Stl2Serum triglyceride level QTL 23.3blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521917856647776Rat
631209Bw2Body weight QTL24.2retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)4994088544463908Rat
1300141Bp178Blood pressure QTL 178arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)41002490139524530Rat
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



miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:556
Count of miRNA genes:234
Interacting mature miRNAs:270
Transcripts:ENSRNOT00000008319, ENSRNOT00000061687
Prediction methods:Microtar, 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
Medium 31 25 14 15 14 8 9 2 10 8
Low 3 12 31 26 4 26 2 9 35 38 1
Below cutoff 1 1 1 61 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_031561 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107190 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107191 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107192 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107193 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107194 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107195 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107196 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB188503 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB188504 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB188505 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF317787 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC072543 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EF116601 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EF116602 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EF116603 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216627 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000141 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: NM_031561   ⟹   NP_113749
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2417,354,525 - 17,410,084 (+)NCBI
Rnor_6.0414,150,309 - 14,191,498 (+)NCBI
Rnor_5.0414,125,297 - 14,166,434 (+)NCBI
RGSC_v3.4413,471,878 - 13,525,620 (+)RGD
Celera412,880,238 - 12,941,086 (+)RGD
Sequence:
RefSeq Acc Id: XM_039107190   ⟹   XP_038963118
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2417,317,452 - 17,410,084 (+)NCBI
RefSeq Acc Id: XM_039107191   ⟹   XP_038963119
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2417,354,485 - 17,410,084 (+)NCBI
RefSeq Acc Id: XM_039107192   ⟹   XP_038963120
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2417,318,764 - 17,410,084 (+)NCBI
RefSeq Acc Id: XM_039107193   ⟹   XP_038963121
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2417,355,196 - 17,410,084 (+)NCBI
RefSeq Acc Id: XM_039107194   ⟹   XP_038963122
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2417,317,406 - 17,410,084 (+)NCBI
RefSeq Acc Id: XM_039107195   ⟹   XP_038963123
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2417,355,196 - 17,410,084 (+)NCBI
RefSeq Acc Id: XM_039107196   ⟹   XP_038963124
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2417,317,343 - 17,410,084 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_113749   ⟸   NM_031561
- UniProtKB: Q6IMX5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_038963124   ⟸   XM_039107196
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038963122   ⟸   XM_039107194
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038963118   ⟸   XM_039107190
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038963120   ⟸   XM_039107192
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038963119   ⟸   XM_039107191
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038963121   ⟸   XM_039107193
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038963123   ⟸   XM_039107195
- Peptide Label: isoform X1

Transcriptome

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

Promoters
RGD ID:13692830
Promoter ID:EPDNEW_R3344
Type:initiation region
Name:Cd36_3
Description:CD36 molecule
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R3343  EPDNEW_R3342  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0414,151,345 - 14,151,405EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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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
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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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
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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