Star (steroidogenic acute regulatory protein) - Rat Genome Database

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Gene: Star (steroidogenic acute regulatory protein) Rattus norvegicus
Analyze
Symbol: Star
Name: steroidogenic acute regulatory protein
RGD ID: 3770
Description: Predicted to enable cholesterol binding activity. Involved in several processes, including cellular response to organonitrogen compound; response to glucocorticoid; and steroid biosynthetic process. Located in several cellular components, including cytosol; mitochondrial envelope; and neuronal cell body. Biomarker of hypogonadism; hypothyroidism; nephrosis; polycystic ovary syndrome; and type 2 diabetes mellitus. Human ortholog(s) of this gene implicated in congenital adrenal hyperplasia. Orthologous to human STAR (steroidogenic acute regulatory protein); PARTICIPATES IN aldosterone biosynthetic pathway; cortisol biosynthetic pathway; estradiol biosynthetic pathway; INTERACTS WITH (+)-pilocarpine; (-)-citrinin; (25R)-cholest-5-ene-3beta,26-diol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: stARD1; START domain-containing protein 1; steroidogenic acute regulatory protein, mitochondrial
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21666,267,094 - 66,274,368 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1666,264,807 - 66,271,672 (-)Ensembl
Rnor_6.01671,036,204 - 71,040,847 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1671,036,204 - 71,040,847 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01670,700,880 - 70,705,523 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41670,642,580 - 70,647,203 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11670,640,558 - 70,647,408 (-)NCBI
Celera1664,176,969 - 64,181,592 (-)NCBICelera
RH 3.4 Map16622.1RGD
Cytogenetic Map16q12.4NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-dexrazoxane  (ISO)
(+)-pilocarpine  (EXP)
(-)-anisomycin  (ISO)
(-)-citrinin  (EXP)
(25R)-cholest-5-ene-3beta,26-diol  (EXP,ISO)
(6aR,11aS,11bR)-10-acetyl-11-hydroxy-7,7-dimethyl-2,6,6a,7,11a,11b-hexahydro-9H-pyrrolo[1',2':2,3]isoindolo[4,5,6-cd]indol-9-one  (EXP)
(E)-thiamethoxam  (EXP)
(R)-carnitine  (EXP)
(R)-lipoic acid  (EXP)
(R,R,R)-alpha-tocopherol  (EXP)
(S)-nicotine  (EXP,ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP)
1,2-dichloroethane  (ISO)
1,3-dichloropropan-2-ol  (EXP)
1,3-dinitrobenzene  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
17beta-hydroxy-5alpha-androstan-3-one  (EXP,ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3-bis(4-hydroxyphenyl)propionitrile  (ISO)
2,4,6-tribromophenol  (ISO)
2,4,6-trichlorophenol  (ISO)
2,4-dibromophenol  (ISO)
2,6-dibromophenol  (ISO)
2-(3,4-dimethoxyphenyl)-5-\{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino\}-2-(propan-2-yl)pentanenitrile  (ISO)
2-bromophenol  (ISO)
2-butoxyethanol  (ISO)
2-methoxyethanol  (EXP)
2-tert-butylhydroquinone  (EXP)
22-Hydroxycholesterol  (ISO)
25-hydroxycholesterol  (ISO)
26-hydroxycholesterol  (EXP,ISO)
3',5'-cyclic AMP  (ISO)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3,3',5-triiodo-L-thyronine  (ISO)
3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,10-heptadecafluoro-1-decanol  (ISO)
3,4-dichloroaniline  (ISO)
3-\{1-[3-(dimethylamino)propyl]-1H-indol-3-yl\}-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione  (EXP,ISO)
3-chloropropane-1,2-diol  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (EXP,ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-nonylphenol  (ISO)
4-tert-Octylphenol  (ISO)
4-vinylcyclohexene dioxide  (EXP)
5-formyltetrahydrofolic acid  (EXP)
6-propyl-2-thiouracil  (EXP,ISO)
8-Br-cAMP  (EXP,ISO)
acetaldehyde  (ISO)
acetamiprid  (EXP,ISO)
acrylamide  (EXP)
aflatoxin B1  (EXP)
all-trans-retinoic acid  (EXP,ISO)
allethrin  (EXP)
alpha-hexachlorocyclohexane  (ISO)
aminoglutethimide  (ISO)
ammonium chloride  (EXP)
androgen antagonist  (EXP)
antalarmin  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (EXP,ISO)
antimycin A  (ISO)
apocynin  (EXP)
arachidonic acid  (EXP)
aristolochic acid  (ISO)
Aroclor 1254  (EXP)
arsenous acid  (ISO)
astressin  (ISO)
atorvastatin calcium  (EXP)
atrazine  (EXP,ISO)
benzo[a]pyrene  (EXP,ISO)
benzofurans  (ISO)
Benzylphosphonic acid  (ISO)
bifenthrin  (EXP,ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
Bisphenol A diglycidyl ether  (ISO)
Bisphenol B  (EXP)
bisphenol F  (ISO)
bromocriptine  (EXP)
bucladesine  (EXP,ISO)
budesonide  (ISO)
Butylbenzyl phthalate  (EXP,ISO)
Butylparaben  (EXP)
cadmium atom  (EXP,ISO)
cadmium dichloride  (EXP,ISO)
caffeine  (EXP,ISO)
calcium atom  (ISO)
calcium(0)  (ISO)
carbaryl  (ISO)
carbendazim  (EXP)
celecoxib  (EXP)
cetrorelix  (ISO)
chlormequat chloride  (EXP)
chlorogenic acid  (EXP)
chlorohydrocarbon  (ISO)
chloroquine  (EXP)
chlorpyrifos  (EXP,ISO)
cholesterol  (EXP,ISO)
cholesterol sulfate  (ISO)
Chorionic gonadotropin  (EXP)
chromium atom  (EXP)
chromium(6+)  (EXP)
chrysin  (EXP)
ciglitazone  (ISO)
ciguatoxin CTX1B  (ISO)
cisplatin  (EXP,ISO)
clobetasol  (ISO)
clofibrate  (EXP)
colforsin daropate hydrochloride  (EXP,ISO)
copper(II) sulfate  (ISO)
cortisol  (ISO)
cyclosporin A  (ISO)
cyhalothrin  (EXP)
cypermethrin  (EXP,ISO)
cyproconazole  (EXP)
D-aspartic acid  (EXP)
daidzein  (EXP)
daidzein 7-O-beta-D-glucoside  (EXP)
dantrolene  (ISO)
DDE  (EXP)
decabromodiphenyl ether  (EXP,ISO)
delta-hexachlorocyclohexane  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (EXP,ISO)
Di-n-hexyl phthalate  (EXP)
diarsenic trioxide  (ISO)
diazinon  (EXP)
dibutyl phthalate  (EXP,ISO)
dibutylstannane  (EXP)
Dicyclohexyl phthalate  (EXP)
diethyl phthalate  (EXP,ISO)
diethylstilbestrol  (EXP,ISO)
diheptyl phthalate  (EXP)
diisobutyl phthalate  (EXP,ISO)
Diisodecyl phthalate  (EXP)
diisononyl phthalate  (EXP,ISO)
diltiazem  (ISO)
dimethoate  (EXP,ISO)
Dimethyl phthalate  (EXP)
dioxygen  (EXP)
dipentyl phthalate  (EXP)
disodium selenite  (ISO)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
ellagic acid  (ISO)
endosulfan  (EXP,ISO)
enilconazole  (ISO)
enniatin  (ISO)
entinostat  (ISO)
epoxiconazole  (EXP)
ethanol  (EXP,ISO)
ethylene glycol bis(2-aminoethyl)tetraacetic acid  (EXP,ISO)
etoxazole  (ISO)
fenvalerate  (EXP,ISO)
ferulic acid  (ISO)
fluconazole  (ISO)
flufenoxuron  (ISO)
fluoxetine  (EXP)
flutamide  (EXP,ISO)
fulvestrant  (EXP,ISO)
furan  (EXP)
fursultiamine  (EXP)
gamma-hexachlorocyclohexane  (EXP,ISO)
Geniposidic acid  (EXP)
genistein  (EXP,ISO)
genistein 7-O-beta-D-glucoside  (EXP)
glycidol  (ISO)
glycitein  (EXP)
glycitin  (EXP)
glyphosate  (ISO)
GW 3965  (ISO)
hexane  (EXP)
hydrogen peroxide  (EXP)
imidacloprid  (ISO)
indometacin  (ISO)
iodoacetic acid  (ISO)
isoliquiritigenin  (ISO)
Isradipine  (ISO)
ketoconazole  (ISO)
L-ascorbic acid  (EXP)
lamivudine  (ISO)
lead diacetate  (EXP,ISO)
lead(0)  (EXP)
lead(2+)  (EXP)
levetiracetam  (ISO)
linuron  (EXP)
lipoic acid  (EXP)
lipopolysaccharide  (ISO)
luteolin  (EXP)
lycopene  (EXP)
malathion  (ISO)
manganese atom  (EXP)
manganese(0)  (EXP)
manganese(II) chloride  (EXP,ISO)
Matrine  (EXP)
mercury dichloride  (EXP)
metformin  (EXP)
methotrexate  (EXP)
methoxychlor  (EXP,ISO)
midazolam  (ISO)
mifepristone  (ISO)
Mitotane  (ISO)
mono(2-ethylhexyl) phthalate  (EXP,ISO)
monobenzyl phthalate  (ISO)
Monobutylphthalate  (ISO)
monoethyl phthalate  (ISO)
morin  (EXP)
myricetin  (ISO)
N(gamma)-nitro-L-arginine methyl ester  (EXP)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (ISO)
N-[2-(methylamino)ethyl]isoquinoline-5-sulfonamide  (ISO)
N-acetyl-L-cysteine  (EXP,ISO)
N-nitrosodiethylamine  (EXP)
nickel sulfate  (EXP)
nicotine  (EXP,ISO)
nicotinic acid  (EXP)
nifedipine  (EXP,ISO)
nigericin  (ISO)
nimodipine  (ISO)
Nonylphenol  (EXP)
octreotide  (EXP,ISO)
p-tert-Amylphenol  (ISO)
paracetamol  (EXP,ISO)
pasireotide  (EXP,ISO)
pentachlorophenol  (ISO)
perflubron  (ISO)
perfluorododecanoic acid  (EXP,ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
perfluoroundecanoic acid  (EXP)
permethrin  (EXP,ISO)
phenylarsine oxide  (ISO)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
Piperophos  (EXP)
pirinixic acid  (EXP,ISO)
potassium dichromate  (EXP)
probucol  (ISO)
prochloraz  (EXP,ISO)
profenofos  (EXP)
progesterone  (EXP,ISO)
propylparaben  (ISO)
prostaglandin E2  (ISO)
quercetin  (EXP,ISO)
quinalphos  (ISO)
resveratrol  (EXP,ISO)
rolipram  (EXP,ISO)
rotenone  (ISO)
rutin  (EXP)
ryanodine  (ISO)
SB 203580  (EXP,ISO)
SB 431542  (EXP,ISO)
sertraline  (EXP)
sildenafil citrate  (EXP)
silver atom  (EXP)
silver(0)  (EXP)
simvastatin  (EXP)
sodium arsenate  (ISO)
sodium arsenite  (EXP,ISO)
sodium fluoride  (ISO)
sulfasalazine  (EXP)
sulfur dioxide  (ISO)
sulpiride  (EXP)
T-2 toxin  (EXP,ISO)
tangeretin  (EXP)
taurine  (EXP)
TEMPO  (EXP)
terbutylazine  (ISO)
testosterone  (EXP,ISO)
testosterone enanthate  (EXP,ISO)
tetrachloromethane  (EXP)
thiamethoxam  (EXP)
titanium dioxide  (EXP,ISO)
torcetrapib  (ISO)
triadimefon  (EXP)
tributylstannane  (EXP,ISO)
trichlorfon  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
triclosan  (EXP)
trimethyltin  (EXP)
triphenyl phosphate  (ISO)
triphenylstannane  (EXP,ISO)
Triptolide  (EXP)
tris(2-chloroethyl) phosphate  (ISO)
tyrphostin AG 1478  (ISO)
uranium atom  (EXP)
valproic acid  (ISO)
vecuronium bromide  (ISO)
verapamil  (ISO)
vinclozolin  (EXP)
vitamin E  (EXP)
wortmannin  (EXP)
zearalenone  (EXP,ISO)
zidovudine  (ISO)
ziram  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
bile acid biosynthetic process  (IDA)
biphenyl metabolic process  (IEP)
brain development  (IEP)
cellular lipid metabolic process  (ISO)
cellular response to alkaloid  (IEP)
cellular response to antibiotic  (IEP)
cellular response to cadmium ion  (IEP)
cellular response to cAMP  (IEP)
cellular response to dexamethasone stimulus  (IEP)
cellular response to epinephrine stimulus  (IEP)
cellular response to fibroblast growth factor stimulus  (IEP)
cellular response to follicle-stimulating hormone stimulus  (IEP)
cellular response to glucose stimulus  (IEP)
cellular response to gonadotropin stimulus  (IEP)
cellular response to growth hormone stimulus  (IEP)
cellular response to insulin stimulus  (IEP)
cellular response to interferon-alpha  (IMP)
cellular response to interferon-gamma  (IEP)
cellular response to lipopolysaccharide  (IEP)
cellular response to luteinizing hormone stimulus  (IEP)
cellular response to metal ion  (IEP)
cellular response to organic cyclic compound  (IEP)
cellular response to transforming growth factor beta stimulus  (IEP)
cholesterol metabolic process  (IEA)
circadian rhythm  (IEP)
circadian sleep/wake cycle, REM sleep  (IEP)
dibenzo-p-dioxin metabolic process  (IEP)
diterpenoid metabolic process  (IEP)
estrogen biosynthetic process  (IMP)
glucocorticoid metabolic process  (ISO)
insecticide metabolic process  (IEP)
intermembrane lipid transfer  (IEA)
intracellular cholesterol transport  (IBA,IEP)
male gonad development  (IEP)
negative regulation of neuron apoptotic process  (IMP)
organic acid metabolic process  (IEP)
phenol-containing compound metabolic process  (IEP)
phthalate metabolic process  (IEP)
positive regulation of bile acid biosynthetic process  (ISO)
positive regulation of gene expression  (IMP)
positive regulation of neurogenesis  (IMP)
regulation of neuronal synaptic plasticity  (IMP)
regulation of steroid biosynthetic process  (IBA,ISO)
response to activity  (IEP)
response to antibiotic  (IEP)
response to corticosterone  (IEP)
response to estrogen  (IEP)
response to ethanol  (IEP)
response to fungicide  (IEP)
response to gonadotropin  (IEP)
response to herbicide  (IEP)
response to hydrogen peroxide  (IEP)
response to insecticide  (IEP)
response to ionizing radiation  (IEP)
response to lead ion  (IEP)
response to leptin  (IEP)
response to nicotine  (IEP)
response to nutrient  (IEP)
response to nutrient levels  (IEP)
response to organic cyclic compound  (IEP)
response to organic substance  (IEP)
response to peptide hormone  (IEP)
response to steroid hormone  (IEP)
response to toxic substance  (IEP)
response to xenobiotic stimulus  (IEP)
steroid biosynthetic process  (IBA,TAS)
testosterone biosynthetic process  (IEP)

Cellular Component

Molecular Function

References

References - curated
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78. Thompson CJ, etal., Endocrinology. 2004 Mar;145(3):1227-37. Epub 2003 Nov 14.
79. Tsai SC, etal., J Cell Biochem. 2003 Dec 15;90(6):1276-86.
80. Vaithinathan S, etal., Arch Toxicol. 2008 Nov;82(11):833-9. Epub 2008 Apr 10.
81. Wu JJ, etal., Toxicology. 2010 Jan 31;268(1-2):1-7. Epub 2009 Oct 31.
82. Wu XY, etal., Zhonghua Nan Ke Xue. 2008 Apr;14(4):371-6.
83. Xiao YC, etal., Growth Factors. 2010 Feb;28(1):1-9.
84. Xiao YC, etal., J Androl. 2010 Jul-Aug;31(4):365-71. Epub 2010 Jan 14.
85. Yu PL, etal., J Cell Biochem. 2009 Oct 1;108(2):469-75.
86. Zachow R and Uzumcu M, Reprod Toxicol. 2006 Nov;22(4):659-65. Epub 2006 Jun 5.
87. Zhang W and Jia H, Toxicology. 2007 Oct 8;239(3):204-12. Epub 2007 Jul 13.
88. Zhao P, etal., Endocrinology. 2008 Jun;149(6):2782-9. Epub 2008 Feb 21.
89. Zhou W, etal., Mol Cell Endocrinol. 2008 Feb 13;283(1-2):12-8. Epub 2007 Oct 25.
90. Zurvarra FM, etal., Reprod Fertil Dev. 2009;21(7):827-39.
Additional References at PubMed
PMID:7626524   PMID:7961770   PMID:9015355   PMID:9328229   PMID:9516465   PMID:12477932   PMID:12530640   PMID:12697693   PMID:12958217   PMID:12959973   PMID:14651853   PMID:14694755  
PMID:15342684   PMID:15358680   PMID:15489334   PMID:15713539   PMID:16039847   PMID:16175571   PMID:16239298   PMID:16682116   PMID:17242178   PMID:17526944   PMID:17702849   PMID:17927664  
PMID:18004794   PMID:18403318   PMID:18425351   PMID:18614015   PMID:18800309   PMID:18990246   PMID:20039971   PMID:20568448   PMID:20609383   PMID:20924043   PMID:21076439   PMID:21153110  
PMID:21153282   PMID:21608230   PMID:22226148   PMID:22425774   PMID:22674924   PMID:22960446   PMID:23332974   PMID:23831818   PMID:24713504   PMID:24728861   PMID:24877623   PMID:27511375  
PMID:29859221   PMID:30884106   PMID:31028793   PMID:33526603   PMID:33670702  


Genomics

Comparative Map Data
Star
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21666,267,094 - 66,274,368 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1666,264,807 - 66,271,672 (-)Ensembl
Rnor_6.01671,036,204 - 71,040,847 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1671,036,204 - 71,040,847 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01670,700,880 - 70,705,523 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41670,642,580 - 70,647,203 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11670,640,558 - 70,647,408 (-)NCBI
Celera1664,176,969 - 64,181,592 (-)NCBICelera
RH 3.4 Map16622.1RGD
Cytogenetic Map16q12.4NCBI
STAR
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl838,142,700 - 38,150,992 (-)EnsemblGRCh38hg38GRCh38
GRCh38838,142,700 - 38,150,952 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37838,000,218 - 38,008,470 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36838,119,375 - 38,127,757 (-)NCBINCBI36hg18NCBI36
Build 34838,119,374 - 38,127,757NCBI
Celera836,952,763 - 36,961,143 (-)NCBI
Cytogenetic Map8p11.23NCBI
HuRef836,535,200 - 36,543,580 (-)NCBIHuRef
CHM1_1838,201,783 - 38,210,163 (-)NCBICHM1_1
Star
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39826,298,502 - 26,306,010 (+)NCBIGRCm39mm39
GRCm39 Ensembl826,296,583 - 26,306,010 (+)Ensembl
GRCm38825,808,474 - 25,815,982 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl825,806,555 - 25,815,982 (+)EnsemblGRCm38mm10GRCm38
MGSCv37826,918,985 - 26,926,454 (+)NCBIGRCm37mm9NCBIm37
MGSCv36827,274,058 - 27,281,527 (+)NCBImm8
Celera827,276,742 - 27,284,211 (+)NCBICelera
Cytogenetic Map8A2NCBI
cM Map814.17NCBI
Star
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495546313,760,089 - 13,765,244 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495546313,760,089 - 13,765,245 (-)NCBIChiLan1.0ChiLan1.0
STAR
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1834,622,577 - 34,629,912 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl834,623,201 - 34,629,544 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0837,446,334 - 37,454,102 (-)NCBIMhudiblu_PPA_v0panPan3
STAR
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11627,326,355 - 27,331,025 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1627,326,355 - 27,331,025 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1627,843,664 - 27,848,334 (+)NCBI
ROS_Cfam_1.01629,225,542 - 29,230,211 (+)NCBI
ROS_Cfam_1.0 Ensembl1629,225,488 - 29,230,211 (+)Ensembl
UMICH_Zoey_3.11627,447,844 - 27,452,510 (+)NCBI
UNSW_CanFamBas_1.01628,025,113 - 28,029,783 (+)NCBI
UU_Cfam_GSD_1.01628,064,539 - 28,069,208 (+)NCBI
Star
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494349,930,968 - 49,937,924 (+)NCBI
SpeTri2.0NW_0049367101,523,289 - 1,530,181 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
STAR
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1548,347,864 - 48,385,464 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11548,377,597 - 48,385,398 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21555,502,030 - 55,509,987 (+)NCBISscrofa10.2Sscrofa10.2susScr3
STAR
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1836,164,891 - 36,174,424 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl836,167,694 - 36,174,583 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660525,817,058 - 5,826,880 (+)NCBIVero_WHO_p1.0
Star
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247805,494,430 - 5,501,063 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH143429  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21666,269,932 - 66,270,083 (+)MAPPERmRatBN7.2
Rnor_6.01671,039,043 - 71,039,193NCBIRnor6.0
Rnor_5.01670,703,719 - 70,703,869UniSTSRnor5.0
RGSC_v3.41670,645,419 - 70,645,569UniSTSRGSC3.4
Celera1664,179,808 - 64,179,958UniSTS
RH 3.4 Map16623.6UniSTS
Cytogenetic Map16q12.4UniSTS
RH128847  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21666,267,090 - 66,267,281 (+)MAPPERmRatBN7.2
Rnor_6.01671,036,201 - 71,036,391NCBIRnor6.0
Rnor_5.01670,700,877 - 70,701,067UniSTSRnor5.0
RGSC_v3.41670,642,577 - 70,642,767UniSTSRGSC3.4
Celera1664,176,966 - 64,177,156UniSTS
RH 3.4 Map16624.3UniSTS
Cytogenetic Map16q12.4UniSTS
RH142227  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21666,271,657 - 66,271,812 (+)MAPPERmRatBN7.2
Rnor_6.01671,040,788 - 71,040,942NCBIRnor6.0
Rnor_5.01670,705,464 - 70,705,618UniSTSRnor5.0
RGSC_v3.41670,647,144 - 70,647,298UniSTSRGSC3.4
Celera1664,181,533 - 64,181,687UniSTS
RH 3.4 Map16622.1UniSTS
Cytogenetic Map16q12.4UniSTS
RH140293  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21666,265,087 - 66,265,296 (+)MAPPERmRatBN7.2
Rnor_6.01671,034,198 - 71,034,406NCBIRnor6.0
Rnor_5.01670,698,874 - 70,699,082UniSTSRnor5.0
RGSC_v3.41670,640,574 - 70,640,782UniSTSRGSC3.4
Celera1664,174,963 - 64,175,171UniSTS
RH 3.4 Map16623.6UniSTS
Cytogenetic Map16q12.4UniSTS
MARC_35058-35059:1074713892:4  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21666,268,238 - 66,268,885 (+)MAPPERmRatBN7.2
Rnor_6.01671,037,349 - 71,037,995NCBIRnor6.0
Rnor_5.01670,702,025 - 70,702,671UniSTSRnor5.0
RGSC_v3.41670,643,725 - 70,644,371UniSTSRGSC3.4
Celera1664,178,114 - 64,178,760UniSTS
Cytogenetic Map16q12.4UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)161900443575226532Rat
2302057Pia29Pristane induced arthritis QTL 293.60.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)162173597566735975Rat
8694453Bw172Body weight QTL 1728.330.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)162432551369325513Rat
6903294Stl30Serum triglyceride level QTL 302.60.0013blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)162515279370152793Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)163528887080288870Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)163775215682752156Rat
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)163775215682752156Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164239634584729064Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165272646484729064Rat
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165272646484729064Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165272646484729064Rat
631525Pia14Pristane induced arthritis QTL 144.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)165571108783402471Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:462
Count of miRNA genes:244
Interacting mature miRNAs:300
Transcripts:ENSRNOT00000020606
Prediction methods:Microtar, Miranda, 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 14 2
Medium 7 1 16 1 1 1 28 8 1
Low 3 39 34 32 3 32 7 10 74 35 11 3 7
Below cutoff 4 8 8 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000020606   ⟹   ENSRNOP00000020606
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1666,264,807 - 66,271,672 (-)Ensembl
Rnor_6.0 Ensembl1671,036,204 - 71,040,847 (-)Ensembl
RefSeq Acc Id: NM_031558   ⟹   NP_113746
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21666,267,094 - 66,271,717 (-)NCBI
Rnor_6.01671,036,204 - 71,040,847 (-)NCBI
Rnor_5.01670,700,880 - 70,705,523 (-)NCBI
RGSC_v3.41670,642,580 - 70,647,203 (-)RGD
Celera1664,176,969 - 64,181,592 (-)RGD
Sequence:
RefSeq Acc Id: XR_005494534
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21666,267,332 - 66,274,368 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_113746   ⟸   NM_031558
- Peptide Label: precursor
- UniProtKB: P97826 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000020606   ⟸   ENSRNOT00000020606
Protein Domains
START

Transcriptome

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

Promoters
RGD ID:13700165
Promoter ID:EPDNEW_R10689
Type:single initiation site
Name:Star_1
Description:steroidogenic acute regulatory protein
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01671,040,810 - 71,040,870EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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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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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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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
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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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: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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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
SHR/OlalpcvMcwi (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
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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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
SS/JrHsdMcwi (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
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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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
WAG/RijCrl (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: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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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
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
16 70701116 70701117 C G snv FHH/EurMcwi (MCW), SBH/Ygl (MCW), FHL/EurMcwi (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
16 70642816 70642817 C G snv FHL/EurMcwi (MCW), FHH/EurMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3770 AgrOrtholog
Ensembl Genes ENSRNOG00000015052 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000020606 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000020606 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.30.530.20 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7311249 IMAGE-MGC_LOAD
InterPro StAR UniProtKB/Swiss-Prot
  StAR-like UniProtKB/Swiss-Prot
  START-like_dom_sf UniProtKB/Swiss-Prot
  START_lipid-bd_dom UniProtKB/Swiss-Prot
KEGG Report