Sirt1 (sirtuin 1) - Rat Genome Database

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Gene: Sirt1 (sirtuin 1) Rattus norvegicus
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Symbol: Sirt1
Name: sirtuin 1
RGD ID: 1308542
Description: Exhibits NAD-dependent histone deacetylase activity and protein kinase B binding activity. Involved in several processes, including cellular response to ketone; negative regulation of apoptotic process; and regulation of peptide hormone secretion. Localizes to cytosol; growth cone; and nucleus. Predicted to colocalize with ESC/E(Z) complex. Used to study middle cerebral artery infarction; obesity; osteoporosis; and type 2 diabetes mellitus. Biomarker of several diseases, including acute kidney failure; artery disease (multiple); impotence; non-alcoholic fatty liver disease; and obesity. Human ortholog(s) of this gene implicated in Huntington's disease and prostate cancer. Orthologous to human SIRT1 (sirtuin 1); PARTICIPATES IN histone modification pathway; hypoxia inducible factor pathway; p53 signaling pathway; INTERACTS WITH (+)-pilocarpine; (+)-taxifolin; (-)-epigallocatechin 3-gallate.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: NAD-dependent deacetylase sirtuin-1; NAD-dependent protein deacetylase sirtuin-1; NAD-dependent protein deacylase sirtuin-1; Sir2; Sir2alpha; sirtuin (silent mating type information regulation 2 homolog) 1 (S. cerevisiae); sirtuin 1 ((silent mating type information regulation 2, homolog) 1; sirtuin 1 ((silent mating type information regulation 2, homolog) 1 (S. cerevisiae)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22025,307,143 - 25,329,260 (+)NCBI
Rnor_6.0 Ensembl2026,833,357 - 26,852,199 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02026,831,971 - 26,851,587 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0208,139,854 - 8,159,830 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42025,675,302 - 25,686,494 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12025,681,998 - 25,700,388 (-)NCBI
Celera2026,607,505 - 26,627,344 (+)NCBICelera
Cytogenetic Map20p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
acute kidney failure  (IEP,ISO)
Alzheimer's disease  (ISO)
amyotrophic lateral sclerosis  (ISO)
atherosclerosis  (IEP,ISO)
atrial fibrillation  (ISO)
autoimmune disease  (ISO)
Binge Drinking  (IEP)
brain infarction  (ISO)
Brain Injuries  (IEP)
Brain Neoplasms  (ISO)
Breast Neoplasms  (ISO)
Cardiomegaly  (IEP)
Carotid Atherosclerosis  (ISO)
colitis  (ISO)
congestive heart failure  (ISO)
demyelinating disease  (ISO)
diabetes mellitus  (ISO)
diabetic retinopathy  (ISO)
epilepsy  (IEP)
Experimental Autoimmune Encephalomyelitis  (ISO)
Experimental Autoimmune Myocarditis  (IEP)
Experimental Diabetes Mellitus  (IEP,ISO)
Experimental Liver Cirrhosis  (ISO)
fatty liver disease  (ISO)
Fibrosis  (ISO)
Genomic Instability  (ISO)
glucose intolerance  (ISO)
heart disease  (ISO)
Hemorrhagic Shock  (IEP,IMP)
human immunodeficiency virus infectious disease  (ISO)
Huntington's disease  (ISO)
Hypertrophy  (ISO)
impotence  (IEP)
Insulin Resistance  (IDA,ISO)
Kidney Reperfusion Injury  (IEP)
Left Ventricular Hypertrophy  (IEP)
Liver Injury  (IEP)
Liver Reperfusion Injury  (IEP)
Lung Injury  (ISO)
macular degeneration  (ISO)
Metabolic Syndrome  (IDA,IEP,ISO)
middle cerebral artery infarction  (IMP,ISO)
myocardial infarction  (IEP)
Myocardial Reperfusion Injury  (ISO)
Neoplasm Metastasis  (ISO)
nephrogenic diabetes insipidus  (ISS)
Nerve Degeneration  (ISO)
neurodegenerative disease  (ISO)
neuronal ceroid lipofuscinosis 1  (ISO)
non-alcoholic fatty liver disease  (IEP,ISO)
obesity  (IEP,IMP,ISO)
osteoporosis  (IDA,IMP)
osteosarcoma  (ISO)
Paralysis  (ISO)
Pneumococcal Pneumonia  (ISO)
pneumonia  (ISO)
prostate cancer  (ISO)
Prostatic Neoplasms  (ISO)
retinal disease  (ISO)
senile cataract  (ISO)
systemic scleroderma  (ISO)
thrombosis  (ISO)
type 2 diabetes mellitus  (IMP,ISO)
Wallerian Degeneration  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-epicatechin-3-O-gallate  (ISO)
(+)-pilocarpine  (EXP)
(+)-taxifolin  (EXP)
(-)-epigallocatechin 3-gallate  (EXP,ISO)
(20S)-ginsenoside Rg3  (EXP)
(R)-lipoic acid  (EXP)
(S)-nicotine  (ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4,6-trinitrobenzenesulfonic acid  (EXP)
2,4-dinitrotoluene  (EXP)
2-acetamidofluorene  (EXP)
2-butoxyethanol  (ISO)
2-methylcholine  (ISO)
3,3',5-triiodo-L-thyronine  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
3-hydroxybutyric acid  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-nitropropanoic acid  (EXP,ISO)
4-hydroxynon-2-enal  (ISO)
4-phenylbutyric acid  (EXP)
5-(2-chloroethyl)-4-methylthiazole  (ISO)
6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxamide  (EXP,ISO)
6alpha-methylprednisolone  (ISO)
8-Br-cAMP  (ISO)
acadesine  (ISO)
acetylcholine  (EXP)
acetylsalicylic acid  (ISO)
actinomycin D  (ISO)
aflatoxin B1  (EXP,ISO)
aflatoxin M1  (ISO)
AICA ribonucleotide  (EXP,ISO)
aldehydo-D-glucose  (EXP,ISO)
allethrin  (EXP)
alpha-D-galactose  (EXP,ISO)
amino acid  (ISO)
aminoguanidine  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (EXP,ISO)
antimony trichloride  (ISO)
apocynin  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (EXP,ISO)
aspartame  (ISO)
ATP  (EXP)
atrazine  (EXP,ISO)
bafilomycin A1  (EXP)
benzamide  (ISO)
benzophenanthridine  (ISO)
berberine  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bleomycin A2  (ISO)
buta-1,3-diene  (ISO)
butein  (ISO)
Butylbenzyl phthalate  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
caffeine  (EXP,ISO)
Calcimycin  (EXP)
camptothecin  (ISO)
carbon nanotube  (ISO)
carnosic acid  (ISO)
CDP-choline  (EXP)
CGS-21680  (ISO)
Chikusetsusaponin-V  (ISO)
chlorpyrifos  (ISO)
cholesterol  (EXP)
chromium(6+)  (EXP)
cilostazol  (ISO)
cisplatin  (EXP,ISO)
clofibrate  (ISO)
cobalt atom  (ISO)
cobalt dichloride  (EXP,ISO)
colforsin daropate hydrochloride  (EXP,ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
cortisol  (ISO)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
cudraflavone B  (ISO)
curcumin  (EXP,ISO)
cycloheximide  (ISO)
cyclosporin A  (EXP,ISO)
cyhalothrin  (EXP)
cypermethrin  (EXP)
D-glucose  (EXP,ISO)
dehydroepiandrosterone  (ISO)
dehydroepiandrosterone sulfate  (EXP)
desferrioxamine B  (ISO)
dexamethasone  (EXP,ISO)
dextran sulfate  (ISO)
Di-n-hexyl phthalate  (EXP)
diarsenic trioxide  (EXP,ISO)
dibutyl phthalate  (EXP)
dihydrogen  (ISO)
diisononyl phthalate  (ISO)
dioxygen  (EXP,ISO)
diprotium  (ISO)
disulfiram  (ISO)
dorsomorphin  (EXP,ISO)
doxorubicin  (EXP,ISO)
elemental selenium  (ISO)
enzyme inhibitor  (ISO)
ergosterol  (EXP)
Erythropoietin  (ISO)
ethanol  (EXP,ISO)
everolimus  (ISO)
excitatory amino acid agonist  (EXP)
fenvalerate  (EXP)
fisetin  (ISO)
folic acid  (ISO)
fructose  (EXP,ISO)
fulvestrant  (ISO)
galactose  (EXP,ISO)
gallic acid  (ISO)
gallocatechin  (ISO)
Genipin  (ISO)
genistein  (ISO)
geraniol  (ISO)
ginsenoside Rg1  (ISO)
glucose  (EXP,ISO)
glutathione  (ISO)
glycyrrhizinic acid  (EXP)
Goe 6976  (ISO)
GW 501516  (ISO)
hesperidin  (EXP)
hexadecanoic acid  (EXP,ISO)
hydrogen peroxide  (EXP,ISO)
hydroquinone  (ISO)
icariin  (EXP,ISO)
imidacloprid  (ISO)
ionomycin  (EXP)
isoniazide  (ISO)
isonicotinamide  (ISO)
isoquinoline-1,5-diol  (ISO)
kainic acid  (EXP,ISO)
KT 5720  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
Licarin A  (ISO)
linagliptin  (ISO)
lipoic acid  (EXP)
lipopolysaccharide  (EXP,ISO)
lithocholic acid  (ISO)
luzindole  (ISO)
lycopene  (ISO)
Magnolol  (EXP)
malonaldehyde  (ISO)
mancozeb  (ISO)
maneb  (ISO)
medroxyprogesterone acetate  (ISO)
melatonin  (EXP,ISO)
metformin  (EXP,ISO)
methylglyoxal  (EXP)
metiram  (ISO)
mithramycin  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
monooxygen  (ISO)
monosodium L-glutamate  (ISO)
myricetin  (ISO)
N,N-dimethylglycine  (ISO)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (ISO)
N-acetyl-L-cysteine  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-methyl-4-phenylpyridinium  (EXP,ISO)
N-methyl-D-aspartic acid  (ISO)
N-methylformamide  (ISO)
N-nitrosodiethylamine  (ISO)
NAD zwitterion  (EXP,ISO)
NAD(+)  (EXP,ISO)
naringin  (EXP)
nickel dichloride  (ISO)
nicotinamide  (EXP,ISO)
nicotine  (ISO)
nimesulide  (ISO)
nitric oxide  (ISO)
nitrites  (EXP)
nitroprusside  (ISO)
nitroxoline  (ISO)
oleic acid  (EXP,ISO)
organoselenium compound  (EXP)
oxaloacetic acid  (ISO)
oxidopamine  (ISO)
P(1),P(5)-bis(5'-adenosyl) pentaphosphate  (EXP)
paclitaxel  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
pentachlorophenol  (EXP)
perfluorododecanoic acid  (EXP)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
perfluorooctanoic acid  (ISO)
phenformin  (ISO)
phenobarbital  (ISO)
phenol  (ISO)
potassium atom  (EXP)
potassium dichromate  (EXP)
pregnenolone 16alpha-carbonitrile  (ISO)
propionic acid  (ISO)
prostaglandin E2  (ISO)
prostaglandin F2alpha  (ISO)
pterostilbene  (ISO)
pyruvic acid  (ISO)
quercetin  (EXP,ISO)
quercetin 3-O-beta-D-galactopyranoside  (ISO)
ramipril  (EXP)
reactive oxygen species  (EXP,ISO)
rebaudioside A  (ISO)
resveratrol  (EXP,ISO)
rotenone  (EXP,ISO)
rutin  (EXP)
S-nitroso-L-cysteine  (ISO)
salicylic acid  (EXP)
Salidroside  (ISO)
Salvianolic acid A  (ISO)
salvianolic acid B  (EXP,ISO)
SB 203580  (ISO)
selenium atom  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sirolimus  (EXP,ISO)
sirtinol  (EXP,ISO)
sodium arsenite  (ISO)
sodium fluoride  (EXP,ISO)
splitomicin  (EXP,ISO)
staurosporine  (ISO)
steviol  (ISO)
stevioside  (ISO)
streptozocin  (EXP,ISO)
sulindac  (ISO)
sunitinib  (ISO)
superoxide  (EXP)
suramin  (ISO)
taurine  (ISO)
tert-butanol  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP,ISO)
thimerosal  (ISO)
thymoquinone  (ISO)
thyroxine  (ISO)
triphenylstannane  (EXP,ISO)
Triptolide  (EXP,ISO)
triptonide  (ISO)
tris(2-chloroethyl) phosphate  (ISO)
Tungsten carbide  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vitamin E  (ISO)
wortmannin  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)
ziram  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
angiogenesis  (IEA,ISO)
behavioral response to starvation  (ISO)
cell aging  (IEP)
cellular glucose homeostasis  (ISO)
cellular response to amyloid-beta  (IEP,IMP)
cellular response to antibiotic  (IEP)
cellular response to curcumin  (IEP)
cellular response to DNA damage stimulus  (ISO)
cellular response to hydrogen peroxide  (IEA,IEP,ISO)
cellular response to hypoxia  (IEA,ISO)
cellular response to ionizing radiation  (ISO)
cellular response to leukemia inhibitory factor  (ISO)
cellular response to organic cyclic compound  (IEP)
cellular response to rotenone  (IEP)
cellular response to starvation  (ISO)
cellular response to tumor necrosis factor  (IEA,ISO)
cellular response to vitamin B3  (IEP)
cellular triglyceride homeostasis  (ISO)
cholesterol homeostasis  (ISO)
chromatin organization  (ISO)
circadian regulation of gene expression  (IEA,ISO)
circadian rhythm  (ISO)
DNA synthesis involved in DNA repair  (ISO)
energy homeostasis  (IMP)
fatty acid homeostasis  (ISO)
heterochromatin assembly  (ISO)
heterochromatin maintenance  (IEA,ISO)
histone deacetylation  (ISO)
histone H3 deacetylation  (IBA,IMP,ISO)
histone H3-K9 deacetylation  (IEA)
histone H3-K9 modification  (IEA)
intrinsic apoptotic signaling pathway  (ISO)
intrinsic apoptotic signaling pathway in response to DNA damage  (ISO)
intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator  (IEA,ISO)
leptin-mediated signaling pathway  (ISO)
macrophage differentiation  (ISO)
mitochondrion organization  (ISO)
muscle organ development  (IEA)
negative regulation of adipose tissue development  (ISO)
negative regulation of androgen receptor signaling pathway  (IEA,ISO)
negative regulation of apoptotic process  (ISO)
negative regulation of cAMP-dependent protein kinase activity  (IEA,ISO)
negative regulation of cardiac muscle cell apoptotic process  (IMP)
negative regulation of cell death  (IMP)
negative regulation of cell growth  (IEA,ISO)
negative regulation of cellular response to testosterone stimulus  (IEA,ISO)
negative regulation of cellular senescence  (IEA,ISO)
negative regulation of DNA binding  (IMP)
negative regulation of DNA damage response, signal transduction by p53 class mediator  (IEA,ISO)
negative regulation of DNA-binding transcription factor activity  (ISO)
negative regulation of fat cell differentiation  (ISO)
negative regulation of fibroblast apoptotic process  (IMP)
negative regulation of gene expression  (ISO)
negative regulation of growth hormone secretion  (IMP)
negative regulation of helicase activity  (IEA,ISO)
negative regulation of histone H3-K14 acetylation  (IEA,ISO)
negative regulation of histone H3-K9 trimethylation  (ISO)
negative regulation of histone H4-K16 acetylation  (IEA,ISO)
negative regulation of I-kappaB kinase/NF-kappaB signaling  (IEA,ISO)
negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator  (ISO)
negative regulation of neuron apoptotic process  (IMP)
negative regulation of neuron death  (ISO)
negative regulation of NF-kappaB transcription factor activity  (IEA,ISO)
negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway  (IEA,ISO)
negative regulation of peptidyl-lysine acetylation  (ISO)
negative regulation of phosphorylation  (ISO)
negative regulation of prostaglandin biosynthetic process  (ISO)
negative regulation of protein acetylation  (IMP,ISO)
negative regulation of protein kinase B signaling  (IEA,ISO)
negative regulation of protein localization to nucleus  (IMP)
negative regulation of reactive oxygen species biosynthetic process  (IMP)
negative regulation of TOR signaling  (IEA,ISO)
negative regulation of transcription by RNA polymerase II  (IEA,ISO)
negative regulation of transcription, DNA-templated  (IBA,ISO)
negative regulation of transforming growth factor beta receptor signaling pathway  (ISO)
negative regulation of tumor necrosis factor production  (IMP)
ovulation from ovarian follicle  (ISO)
peptidyl-lysine acetylation  (IEA,ISO)
peptidyl-lysine deacetylation  (IEA,ISO)
positive regulation of adaptive immune response  (IEA,ISO)
positive regulation of adipose tissue development  (ISO)
positive regulation of angiogenesis  (IEA,ISO)
positive regulation of apoptotic process  (IEA,ISO)
positive regulation of ATP biosynthetic process  (ISO)
positive regulation of blood vessel endothelial cell migration  (IEA,ISO)
positive regulation of cAMP-dependent protein kinase activity  (IEA,ISO)
positive regulation of cell growth involved in cardiac muscle cell development  (IMP)
positive regulation of cell population proliferation  (ISO)
positive regulation of cellular senescence  (IEA,ISO)
positive regulation of cholesterol efflux  (ISO)
positive regulation of cysteine-type endopeptidase activity involved in apoptotic process  (IEA,ISO)
positive regulation of DNA repair  (IEA,ISO)
positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway  (ISO)
positive regulation of endothelial cell proliferation  (IEA,ISO)
positive regulation of gene expression  (ISO)
positive regulation of gluconeogenesis  (IEA,IMP,ISO)
positive regulation of granulosa cell apoptotic process  (ISO)
positive regulation of heart rate  (IMP)
positive regulation of histone H3-K9 methylation  (IEA,ISO)
positive regulation of insulin receptor signaling pathway  (IEA,ISO)
positive regulation of insulin secretion involved in cellular response to glucose stimulus  (IMP)
positive regulation of macroautophagy  (IEA,ISO)
positive regulation of macrophage apoptotic process  (ISO)
positive regulation of macrophage cytokine production  (ISO)
positive regulation of MHC class II biosynthetic process  (IEA,ISO)
positive regulation of mitochondrial membrane potential  (ISO)
positive regulation of neuron projection development  (IMP)
positive regulation of phosphatidylinositol 3-kinase signaling  (ISO)
positive regulation of protein deacetylation  (IMP)
positive regulation of protein phosphorylation  (ISO)
positive regulation of skeletal muscle cell proliferation  (IMP)
positive regulation of smooth muscle cell differentiation  (ISO)
positive regulation of thyroid-stimulating hormone secretion  (IMP)
positive regulation of transcription by RNA polymerase II  (IEA,ISO)
positive regulation of triglyceride catabolic process  (ISO)
proteasome-mediated ubiquitin-dependent protein catabolic process  (IEA,ISO)
protein deacetylation  (IDA,ISO)
protein depropionylation  (ISO,ISS)
protein destabilization  (IEA,ISO)
protein ubiquitination  (IEA,ISO)
pyrimidine dimer repair by nucleotide-excision repair  (IEA,ISO)
rDNA heterochromatin assembly  (IEA,ISO)
regulation of apoptotic process  (ISO)
regulation of bile acid biosynthetic process  (ISO)
regulation of brown fat cell differentiation  (ISO)
regulation of cell population proliferation  (ISO)
regulation of centrosome duplication  (IEA,ISO,ISS)
regulation of endodeoxyribonuclease activity  (IEA,ISO)
regulation of glucose metabolic process  (ISO)
regulation of lipid storage  (ISO)
regulation of mitotic cell cycle  (IEA,ISO)
regulation of peroxisome proliferator activated receptor signaling pathway  (ISO)
regulation of protein serine/threonine kinase activity  (ISO)
regulation of smooth muscle cell apoptotic process  (ISO)
response to ethanol  (IDA)
response to fluoride  (IEP)
response to hydrogen peroxide  (ISO)
response to insulin  (ISO)
response to kainic acid  (IEP)
response to leptin  (ISO)
response to mycotoxin  (IEP)
response to nutrient levels  (IEP)
response to oxidative stress  (ISO)
response to resveratrol  (IEP)
single strand break repair  (IEA,ISO)
spermatogenesis  (ISO)
stress-induced premature senescence  (IEA,ISO)
transforming growth factor beta receptor signaling pathway  (IEA,ISO)
triglyceride mobilization  (ISO)
UV-damage excision repair  (IEA,ISO)
vasodilation  (IMP)
white fat cell differentiation  (ISO)

Cellular Component
axon  (IDA)
chromatin  (ISO)
chromatin silencing complex  (IEA,ISO)
cytoplasm  (ISO)
cytosol  (IDA,IEA,ISO)
ESC/E(Z) complex  (IEA,ISO)
euchromatin  (IEA,ISO)
fibrillar center  (IEA,ISO)
growth cone  (IDA)
heterochromatin  (ISO)
mitochondrion  (IEA,ISO)
nuclear envelope  (ISO)
nuclear inner membrane  (IBA,ISO)
nucleolus  (ISO)
nucleoplasm  (IBA,ISO)
nucleus  (IBA,IDA,ISO)
PML body  (IEA,ISO)
protein-containing complex  (ISO)
rDNA heterochromatin  (IBA,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
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Additional References at PubMed
PMID:10693811   PMID:11250901   PMID:11672522   PMID:11672523   PMID:12006491   PMID:12482959   PMID:12535671   PMID:12837246   PMID:14976264   PMID:15152190   PMID:15175761   PMID:15220471  
PMID:15381699   PMID:15469825   PMID:15604409   PMID:15684044   PMID:15692560   PMID:15716268   PMID:15744310   PMID:16079181   PMID:16183991   PMID:16269335   PMID:16687393   PMID:16790548  
PMID:16813520   PMID:16892051   PMID:16959573   PMID:17041012   PMID:17098745   PMID:17172643   PMID:17197703   PMID:17317627   PMID:17347648   PMID:17505061   PMID:17521387   PMID:17612497  
PMID:17680780   PMID:17785417   PMID:17884810   PMID:17901049   PMID:17916362   PMID:17936707   PMID:18004385   PMID:18069916   PMID:18203716   PMID:18239056   PMID:18296641   PMID:18342626  
PMID:18404539   PMID:18414679   PMID:18420994   PMID:18424637   PMID:18485871   PMID:18555842   PMID:18590691   PMID:18662546   PMID:18687677   PMID:18931029   PMID:19039676   PMID:19047049  
PMID:19237425   PMID:19265035   PMID:19299583   PMID:19415680   PMID:19479941   PMID:19549533   PMID:19578370   PMID:19797682   PMID:19876588   PMID:19913571   PMID:19934257   PMID:20020036  
PMID:20027304   PMID:20042607   PMID:20074560   PMID:20097625   PMID:20100829   PMID:20167603   PMID:20169165   PMID:20203304   PMID:20225204   PMID:20375098   PMID:20424141   PMID:20439489  
PMID:20467811   PMID:20620956   PMID:20620997   PMID:20651844   PMID:20668205   PMID:20670893   PMID:20673376   PMID:20801633   PMID:20813124   PMID:20955178   PMID:20972425   PMID:21149440  
PMID:21149730   PMID:21165789   PMID:21189328   PMID:21196578   PMID:21216258   PMID:21241768   PMID:21295052   PMID:21504832   PMID:21541336   PMID:21543634   PMID:21719763   PMID:21722091  
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PMID:23880291   PMID:23891692   PMID:23951196   PMID:23960241   PMID:23973301   PMID:23973402   PMID:23994215   PMID:24043310   PMID:24048733   PMID:24052229   PMID:24058702   PMID:24089055  
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PMID:25782776   PMID:25843933   PMID:25849131   PMID:25863291   PMID:25965594   PMID:25966629   PMID:26086862   PMID:26185373   PMID:26203862   PMID:26252661   PMID:26261574   PMID:26273643  
PMID:26329673   PMID:26339397   PMID:26379395   PMID:26384348   PMID:26489513   PMID:26522222   PMID:26720481   PMID:26755731   PMID:26767982   PMID:26845416   PMID:26872534   PMID:26891083  
PMID:26968221   PMID:27035562   PMID:27076782   PMID:27133433   PMID:27174562   PMID:27212443   PMID:27270300   PMID:27294899   PMID:27339462   PMID:27357961   PMID:27363270   PMID:27387128  
PMID:27526155   PMID:27547294   PMID:27573670   PMID:27581932   PMID:27600292   PMID:27631411   PMID:27735947   PMID:27749604   PMID:27878231   PMID:27916733   PMID:27980322   PMID:27989594  
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Genomics

Comparative Map Data
Sirt1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22025,307,143 - 25,329,260 (+)NCBI
Rnor_6.0 Ensembl2026,833,357 - 26,852,199 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02026,831,971 - 26,851,587 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0208,139,854 - 8,159,830 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42025,675,302 - 25,686,494 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12025,681,998 - 25,700,388 (-)NCBI
Celera2026,607,505 - 26,627,344 (+)NCBICelera
Cytogenetic Map20p11NCBI
SIRT1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1067,884,656 - 67,918,390 (+)EnsemblGRCh38hg38GRCh38
GRCh381067,884,656 - 67,918,390 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371069,644,414 - 69,678,147 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361069,314,433 - 69,348,149 (+)NCBINCBI36hg18NCBI36
Build 341069,314,432 - 69,348,147NCBI
Celera1062,919,307 - 62,953,016 (+)NCBI
Cytogenetic Map10q21.3NCBI
HuRef1063,643,871 - 63,677,731 (+)NCBIHuRef
CHM1_11069,926,404 - 69,960,153 (+)NCBICHM1_1
Sirt1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391063,154,784 - 63,174,814 (-)NCBIGRCm39mm39
GRCm39 Ensembl1063,154,784 - 63,217,483 (-)Ensembl
GRCm381063,319,005 - 63,339,035 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1063,319,005 - 63,381,704 (-)EnsemblGRCm38mm10GRCm38
MGSCv371062,781,753 - 62,801,783 (-)NCBIGRCm37mm9NCBIm37
MGSCv361062,714,418 - 62,734,374 (-)NCBImm8
Celera1064,419,012 - 64,437,105 (-)NCBICelera
Cytogenetic Map10B4NCBI
Sirt1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542520,279,963 - 20,307,663 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542520,280,725 - 20,307,663 (+)NCBIChiLan1.0ChiLan1.0
SIRT1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11066,681,983 - 66,714,065 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1066,681,598 - 66,715,069 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01064,368,878 - 64,401,684 (+)NCBIMhudiblu_PPA_v0panPan3
SIRT1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1419,188,616 - 19,220,031 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl419,188,675 - 19,218,279 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha419,317,273 - 19,349,181 (+)NCBI
ROS_Cfam_1.0419,454,692 - 19,486,553 (+)NCBI
UMICH_Zoey_3.1419,337,295 - 19,369,150 (+)NCBI
UNSW_CanFamBas_1.0419,559,257 - 19,591,114 (+)NCBI
UU_Cfam_GSD_1.0419,901,939 - 19,934,337 (+)NCBI
Sirt1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721361,803,376 - 61,829,477 (-)NCBI
SpeTri2.0NW_00493652110,296,097 - 10,316,673 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SIRT1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1471,091,157 - 71,123,299 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11471,091,167 - 71,126,351 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21477,182,651 - 77,184,716 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Sscrofa10.21477,053,991 - 77,079,850 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SIRT1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1963,463,059 - 63,497,893 (-)NCBI
ChlSab1.1 Ensembl963,462,389 - 63,497,867 (-)Ensembl
Sirt1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247542,304,476 - 2,332,705 (+)NCBI

Position Markers
RH140601  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02026,832,814 - 26,833,001NCBIRnor6.0
Rnor_5.0208,140,697 - 8,140,884UniSTSRnor5.0
RGSC_v3.42025,667,457 - 25,667,644UniSTSRGSC3.4
Celera2026,626,314 - 26,626,501UniSTS
RH 3.4 Map1909.3UniSTS
Cytogenetic Map20p11UniSTS
RH124528  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02026,833,546 - 26,833,794NCBIRnor6.0
Rnor_5.0208,141,429 - 8,141,677UniSTSRnor5.0
RGSC_v3.42025,668,189 - 25,668,437UniSTSRGSC3.4
Celera2026,625,521 - 26,625,769UniSTS
Cytogenetic Map20p11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20127357423Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20128375393Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20128375393Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20128375393Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20128375393Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20128375393Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20133300419Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20137550487Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20137550487Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20201865447018654Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20299970747999707Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20340211127968216Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)20410895649108956Rat
4889870Pur30Proteinuria QTL 30190.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20865434130991290Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201383430956205956Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201383430956205956Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201782709656205956Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201887215049108956Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)202085847056205956Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202660884356205956Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202660884356205956Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202660884356205956Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202671232356205956Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:138
Count of miRNA genes:84
Interacting mature miRNAs:91
Transcripts:ENSRNOT00000000427, ENSRNOT00000057829
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 31 40 24 19 24 6 6 72 35 39 11 6
Low 12 17 17 17 2 5 2 2 2
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000078739   ⟹   ENSRNOP00000070943
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2026,833,357 - 26,852,199 (-)Ensembl
RefSeq Acc Id: NM_001372090   ⟹   NP_001359019
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22025,315,088 - 25,329,260 (+)NCBI
RefSeq Acc Id: XM_008772947   ⟹   XP_008771169
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02026,831,971 - 26,846,080 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008774950   ⟹   XP_008773172
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2026,618,412 - 26,627,344 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017588053   ⟹   XP_017443542
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2026,613,077 - 26,627,344 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017588054   ⟹   XP_017443543
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2026,607,505 - 26,624,749 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601788   ⟹   XP_017457277
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02026,831,971 - 26,846,232 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017601789   ⟹   XP_017457278
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02026,834,566 - 26,851,587 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039098755   ⟹   XP_038954683
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22025,307,143 - 25,329,260 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001359019 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954683 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein A0A0G2JZ79 (Get FASTA)   NCBI Sequence Viewer  
  EDL97350 (Get FASTA)   NCBI Sequence Viewer  
  EDL97351 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_008773172   ⟸   XM_008774950
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008771169   ⟸   XM_008772947
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017443543   ⟸   XM_017588054
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017443542   ⟸   XM_017588053
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017457277   ⟸   XM_017601788
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017457278   ⟸   XM_017601789
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000070943   ⟸   ENSRNOT00000078739
RefSeq Acc Id: XP_038954683   ⟸   XM_039098755
- Peptide Label: isoform X1
RefSeq Acc Id: NP_001359019   ⟸   NM_001372090
Protein Domains
Deacetylase sirtuin-type

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)
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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/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 (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)
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
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)
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)
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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/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
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 (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
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
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
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
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
MHS/Gib (RGD)
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Platform: