Gclc (glutamate-cysteine ligase, catalytic subunit) - Rat Genome Database

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Gene: Gclc (glutamate-cysteine ligase, catalytic subunit) Rattus norvegicus
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Symbol: Gclc
Name: glutamate-cysteine ligase, catalytic subunit
RGD ID: 619868
Description: Enables glutamate-cysteine ligase activity. Involved in several processes, including cellular response to growth factor stimulus; cellular response to hormone stimulus; and cellular response to mechanical stimulus. Part of glutamate-cysteine ligase complex. Used to study liver cirrhosis and pulmonary emphysema. Human ortholog(s) of this gene implicated in cystic fibrosis; glutamate-cysteine ligase deficiency; hemolytic anemia; and myocardial infarction. Orthologous to human GCLC (glutamate-cysteine ligase catalytic subunit); PARTICIPATES IN glutathione metabolic pathway; 2-hydroxyglutaric aciduria pathway; cysteine metabolic pathway; INTERACTS WITH (+)-schisandrin B; (R)-lipoic acid; 1,1'-azobis(N,N-dimethylformamide).
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: gamma-ECS; gamma-glutamylcysteine synthetase; GCS heavy chain; Glclc; glutamate--cysteine ligase catalytic subunit; glutamate-cysteine ligase catalytic subunit; Glutamylcysteine gamma synthetase light chain; MGC93096
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
mRatBN7.2878,629,899 - 78,668,547 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl878,630,127 - 78,668,544 (+)Ensembl
Rnor_6.0885,059,051 - 85,097,471 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl885,059,051 - 85,097,468 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0884,627,768 - 84,666,188 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4882,724,429 - 82,762,848 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1882,743,482 - 82,781,899 (+)NCBI
Celera878,379,669 - 78,418,088 (+)NCBICelera
Cytogenetic Map8q31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(-)-epigallocatechin 3-gallate  (ISO)
(2,4,5-trichlorophenoxy)acetic acid  (ISO)
(E)-cinnamyl alcohol  (ISO)
(R)-lipoic acid  (EXP,ISO)
(R,R,R)-alpha-tocopherol  (ISO)
(RS)-coclaurine  (ISO)
(RS)-norcoclaurine  (ISO)
(S)-coclaurine  (ISO)
(S)-naringenin  (ISO)
(S)-nicotine  (ISO)
1,1'-azobis(N,N-dimethylformamide)  (EXP)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1,3-benzothiazole-2-thiol  (ISO)
1,3-dichloropropan-2-ol  (EXP)
1-bromopropane  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
1-fluoro-2,4-dinitrobenzene  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
1-naphthyl isothiocyanate  (EXP)
15-deoxy-Delta(12,14)-prostaglandin J2  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
1H-pyrazole  (ISO)
2',4'-dihydroxy-6'-methoxy-3',5'-dimethylchalcone  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (ISO)
2,4,6-trinitrobenzenesulfonic acid  (EXP)
2,4-dinitrotoluene  (EXP)
2,6-di-tert-butyl-4-methylphenol  (ISO)
2,6-dinitrotoluene  (EXP)
2-(chloromethyl)pyridine  (ISO)
2-acetamidofluorene  (EXP,ISO)
2-amino-2-deoxy-D-glucopyranose  (ISO)
2-butoxyethanol  (ISO)
2-chloroethanol  (EXP)
2-hydroxyethyl methacrylate  (ISO)
2-hydroxypropanoic acid  (ISO)
2-nitrofluorene  (EXP)
2-tert-butylhydroquinone  (EXP,ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP,ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3,4-methylenedioxymethamphetamine  (EXP)
3-chloropropane-1,2-diol  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-nitropropanoic acid  (EXP)
3-O-Caffeoyl-1-O-methylquinic acid  (ISO)
3-phenylprop-2-enal  (ISO)
3H-1,2-dithiole-3-thione  (EXP,ISO)
4,4'-methylene-bis-(2-chloroaniline)  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (EXP)
4-amino-2,6-dinitrotoluene  (EXP)
4-Hydroxy-TEMPO  (EXP)
4-hydroxynon-2-enal  (EXP,ISO)
4-hydroxyphenyl retinamide  (ISO)
4-nitro-1,2-phenylenediamine  (ISO)
4-phenyl-3-furoxancarbonitrile  (ISO)
5-bromo-2'-deoxyuridine  (ISO)
7,8-dihydroxycoumarin  (ISO)
[6]-Shogaol  (ISO)
acetaldehyde  (EXP)
acetylcholine  (ISO)
acrolein  (EXP,ISO)
acrylamide  (ISO)
actinomycin D  (EXP,ISO)
aflatoxin B1  (EXP,ISO)
alachlor  (EXP)
alcohol  (ISO)
aldehydo-D-glucosamine  (ISO)
aldosterone  (EXP)
all-trans-retinal  (ISO)
all-trans-retinoic acid  (EXP)
alloxan  (EXP)
allyl isothiocyanate  (ISO)
alpha,alpha-trehalose  (EXP)
alpha-D-galactose  (EXP)
alpha-hexylcinnamaldehyde  (ISO)
alpha-linolenic acid  (ISO)
amlexanox  (ISO)
ampicillin  (ISO)
andrographolide  (EXP,ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
antimonite  (ISO)
antimony(0)  (ISO)
apigenin  (EXP,ISO)
arachidonic acid  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
artesunate  (ISO)
astilbin  (ISO)
azathioprine  (ISO)
Bandrowski's base  (ISO)
Bardoxolone methyl  (ISO)
benzalkonium chloride  (ISO)
benzene  (EXP)
benzidine  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzoic acid  (ISO)
benzoquinones  (ISO)
beta-D-glucosamine  (ISO)
beta-naphthoflavone  (ISO)
bisphenol A  (EXP,ISO)
bleomycin A2  (ISO)
bleomycin A5  (ISO)
boric acid  (ISO)
bosentan  (ISO)
Brodifacoum  (EXP)
bromobenzene  (ISO)
Brusatol  (ISO)
buspirone  (EXP)
buta-1,3-diene  (ISO)
butanal  (ISO)
butane-2,3-dione  (EXP)
butylated hydroxyanisole  (ISO)
cadmium atom  (EXP,ISO)
cadmium dichloride  (EXP,ISO)
cadmium sulfate  (ISO)
cadmium sulfide  (ISO)
cafestol  (EXP)
caffeine  (ISO)
calcitriol  (EXP)
calcium atom  (EXP)
calcium(0)  (EXP)
captan  (ISO)
carbamazepine  (ISO)
carbon disulfide  (EXP)
carbon monoxide  (EXP)
carbon nanotube  (ISO)
carmustine  (EXP)
carnosic acid  (EXP,ISO)
Carnosol  (ISO)
celastrol  (EXP)
ceric oxide  (EXP)
cerium trichloride  (ISO)
chenodeoxycholic acid  (ISO)
chlorambucil  (ISO)
chloroacetaldehyde  (ISO)
chlorogenic acid  (ISO)
chlorohydrocarbon  (ISO)
chloroprene  (EXP,ISO)
chlorpromazine  (EXP)
chlorpyrifos  (ISO)
cholesterol  (ISO)
choline  (ISO)
chromium atom  (ISO)
chromium trinitrate  (ISO)
chromium(6+)  (EXP,ISO)
chrysin  (EXP)
cidofovir anhydrous  (ISO)
cinnamyl alcohol  (ISO)
ciprofibrate  (EXP)
cisplatin  (ISO)
citraconic acid  (EXP,ISO)
Clivoline  (ISO)
clobetasol  (ISO)
clodronic acid  (ISO)
cobalt dichloride  (EXP,ISO)
cocaine  (ISO)
coniferyl aldehyde  (ISO)
conjugated linoleic acid  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) chloride  (ISO)
copper(II) sulfate  (ISO)
cortisol  (EXP)
coumarin  (EXP)
crocidolite asbestos  (ISO)
cumene hydroperoxide  (ISO)
curcumin  (EXP,ISO)
cycloheximide  (EXP,ISO)
cyclophosphamide  (ISO)
cyclosporin A  (EXP,ISO)
cylindrospermopsin  (ISO)
cysteamine  (ISO)
DDE  (ISO)
DDT  (EXP,ISO)
deguelin  (ISO)
deoxycholic acid  (ISO)
Deoxycorticosterone acetate  (EXP)
dexamethasone  (EXP,ISO)
dextran sulfate  (ISO)
diallyl disulfide  (EXP)
Diallyl sulfide  (EXP)
diarsenic trioxide  (ISO)
diazinon  (ISO)
dibenzoylmethane  (ISO)
dibutyl phthalate  (EXP)
dichloromethane  (ISO)
diclofenac  (EXP,ISO)
diethyl malate  (ISO)
diethyl maleate  (EXP,ISO)
diethyl sulfate  (ISO)
diethylstilbestrol  (EXP,ISO)
dihydrogen  (ISO)
dimethyl fumarate  (EXP,ISO)
dimethylarsinic acid  (ISO)
dinoseb  (ISO)
dioxygen  (EXP,ISO)
dipotassium bis[mu-tartrato(4-)]diantimonate(2-) trihydrate  (ISO)
diprotium  (ISO)
diprotium oxide  (ISO)
diquat  (EXP,ISO)
disodium selenite  (ISO)
disulfiram  (ISO)
diuron  (EXP)
domoic acid  (ISO)
dopamine  (ISO)
doramapimod  (ISO)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
elemental selenium  (EXP)
endosulfan  (EXP)
enzyme inhibitor  (ISO)
erastin  (EXP)
erdosteine  (ISO)
etacrynic acid  (ISO)
ethanol  (EXP,ISO)
Ethyl acrylate  (ISO)
etoposide  (ISO)
eugenol  (ISO)
farnesal  (ISO)
farrerol  (ISO)
fenofibrate  (EXP)
fipronil  (EXP)
flutamide  (EXP,ISO)
folic acid  (ISO)
folpet  (ISO)
formaldehyde  (ISO)
fulvestrant  (EXP)
furan  (EXP,ISO)
galactose  (EXP)
gamma-hexachlorocyclohexane  (ISO)
gamma-linolenic acid  (ISO)
gefitinib  (ISO)
genistein  (EXP,ISO)
ginsenoside Rg1  (ISO)
Ginsenoside Rh4  (EXP,ISO)
gliclazide  (EXP)
glutathione  (EXP,ISO)
glycerol 2-phosphate  (EXP)
guggulsterone  (ISO)
hemin  (ISO)
Hexachloro-1,3-butadiene  (EXP)
hexadecanoic acid  (EXP)
hexane  (ISO)
hydrogen chloride  (ISO)
hydrogen peroxide  (EXP,ISO)
hydroquinone  (ISO)
hypochlorous acid  (ISO)
ibuprofen  (ISO)
ifosfamide  (ISO)
indometacin  (ISO)
iron atom  (EXP,ISO)
iron trichloride  (ISO)
iron(0)  (EXP,ISO)
iron(2+) sulfate (anhydrous)  (ISO)
iron(III) nitrilotriacetate  (ISO)
isoeugenol  (ISO)
isoniazide  (EXP,ISO)
isoprenaline  (ISO)
isorhamnetin  (EXP,ISO)
isothiocyanate  (ISO)
ivermectin  (ISO)
kaempferol  (ISO)
kahweol  (EXP)
ketamine  (EXP)
ketoprofen  (ISO)
L-ascorbic acid  (EXP)
L-cysteine  (EXP)
L-gamma-glutamyl-L-cysteine  (EXP)
L-methionine  (ISO)
lead diacetate  (ISO)
lead(II) chloride  (ISO)
leflunomide  (EXP)
levofloxacin  (EXP)
linalool  (ISO)
lipoic acid  (EXP,ISO)
liquiritigenin  (EXP)
liquiritin  (EXP)
lithocholic acid  (ISO)
luteolin  (EXP)
LY294002  (EXP,ISO)
maneb  (EXP,ISO)
melatonin  (ISO)
meloxicam  (ISO)
menadione  (ISO)
mercury atom  (ISO)
mercury dibromide  (ISO)
mercury dichloride  (ISO)
mercury(0)  (ISO)
mesalamine  (ISO)
metformin  (EXP)
methapyrilene  (EXP)
methimazole  (ISO)
methotrexate  (ISO)
methoxychlor  (EXP)
methyl non-2-ynoate  (ISO)
methyl salicylate  (ISO)
methylene blue  (ISO)
methylisothiazolinone  (ISO)
methylmercury chloride  (EXP,ISO)
Methysticin  (ISO)
microcystin  (EXP)
microcystin-LR  (ISO)
mifepristone  (ISO)
miquelianin  (EXP)
MK 571  (ISO)
monocrotaline  (EXP)
N,N-diethyl-m-toluamide  (EXP)
N-[3,5-bis(trifluoromethyl)phenyl]-5-chloro-2-hydroxybenzamide  (ISO)
N-acetyl-L-cysteine  (EXP,ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-methyl-4-phenylpyridinium  (EXP,ISO)
N-methylformamide  (ISO)
N-methylnicotinate  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP,ISO)
N-tosyl-L-phenylalanyl chloromethyl ketone  (ISO)
naphthalene  (EXP,ISO)
naphthalene-1,2-diol  (ISO)
naproxen  (ISO)
naringin  (EXP)
nefazodone  (EXP)
neoastilbin  (ISO)
nickel dichloride  (EXP,ISO)
nickel sulfate  (ISO)
nicotinamide  (EXP)
nicotine  (ISO)
nimesulide  (EXP)
nimustine  (ISO)
nitisinone  (ISO)
nitric oxide  (EXP)
nitrofurantoin  (ISO)
Nodularin  (ISO)
Nonidet P-40  (ISO)
notoginsenoside R1  (EXP)
ochratoxin A  (EXP,ISO)
oleanolic acid  (EXP,ISO)
oxaliplatin  (EXP)
oxidopamine  (EXP,ISO)
ozone  (ISO)
p-chloromercuribenzoic acid  (ISO)
para-Cresidine  (ISO)
paracetamol  (EXP,ISO)
paraquat  (EXP,ISO)
perfluorohexanesulfonic acid  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
permethrin  (EXP)
phenethyl caffeate  (ISO)
phenethyl isothiocyanate  (ISO)
phenobarbital  (EXP,ISO)
phenol  (ISO)
phenylmercury acetate  (ISO)
phlorizin  (ISO)
phloroglucinol  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
phosgene  (ISO)
piperonyl butoxide  (EXP)
pirinixic acid  (EXP,ISO)
Polpunonic acid  (ISO)
potassium chloride  (EXP)
potassium chromate  (ISO)
potassium dichromate  (ISO)
pravastatin  (EXP,ISO)
prazosin  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP,ISO)
progesterone  (ISO)
propacetamol  (ISO)
propan-2-ol  (ISO)
propanal  (ISO)
prostaglandin J2  (EXP)
puerarin  (EXP,ISO)
pyocyanine  (ISO)
pyrazines  (ISO)
Pyridostigmine bromide  (EXP)
pyrroloquinoline quinone  (EXP)
quercetin  (EXP,ISO)
rac-lactic acid  (ISO)
reactive oxygen species  (EXP,ISO)
resorcinol  (ISO)
resveratrol  (EXP,ISO)
rosuvastatin calcium  (ISO)
rotenone  (EXP,ISO)
rottlerin  (EXP,ISO)
S-adenosyl-L-methioninate  (ISO)
S-adenosyl-L-methionine  (ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (EXP,ISO)
SB 203580  (ISO)
SB 431542  (ISO)
selenium atom  (EXP)
selenocystine  (ISO)
selenomethionine  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
silver(1+) nitrate  (ISO)
SL-327  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (EXP,ISO)
sodium cholate  (ISO)
sodium dichromate  (EXP,ISO)
sodium dodecyl sulfate  (ISO)
sodium fluoride  (ISO)
spironolactone  (EXP)
staurosporine  (ISO)
stavudine  (EXP)
streptozocin  (EXP,ISO)
styrene  (ISO)
succimer  (ISO)
sulforaphane  (EXP,ISO)
sulindac  (ISO)
sunitinib  (ISO)
suprofen  (ISO)
T-2 toxin  (ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (EXP,ISO)
tetrachloromethane  (EXP,ISO)
tetramethylpyrazine  (ISO)
thiabendazole  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
trans-isoeugenol  (ISO)
triacsin C  (ISO)
tributylstannane  (ISO)
trichostatin A  (ISO)
trimethyltin  (ISO)
triphenyl phosphate  (EXP)
Triptolide  (EXP,ISO)
troglitazone  (ISO)
trovafloxacin  (EXP,ISO)
tunicamycin  (ISO)
tyrphostin AG 1478  (EXP)
urethane  (ISO)
ursodeoxycholic acid  (ISO)
usnic acid  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
vanillin  (ISO)
vincristine  (ISO)
vitamin E  (EXP,ISO)
water  (ISO)
yohimbine  (ISO)
zinc atom  (EXP,ISO)
zinc dichloride  (ISO)
zinc oxide  (ISO)
zinc(0)  (EXP,ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
aging  (IEP)
blood vessel diameter maintenance  (ISO,ISS)
cell redox homeostasis  (ISO,ISS)
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 hepatocyte growth factor stimulus  (IEP)
cellular response to insulin stimulus  (IEP)
cellular response to mechanical stimulus  (IEP)
cellular response to thyroxine stimulus  (IEP)
cysteine metabolic process  (ISO,ISS)
glutamate metabolic process  (ISO,ISS)
glutathione biosynthetic process  (IBA,IEA,IMP,ISO,ISS)
glutathione metabolic process  (ISO)
L-ascorbic acid metabolic process  (ISO)
negative regulation of apoptotic process  (ISO,ISS)
negative regulation of extrinsic apoptotic signaling pathway  (ISO)
negative regulation of hepatic stellate cell activation  (IMP)
negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway  (ISO)
negative regulation of neuron apoptotic process  (IMP)
negative regulation of protein ubiquitination  (ISO)
negative regulation of transcription, DNA-templated  (ISO,ISS)
positive regulation of proteasomal ubiquitin-dependent protein catabolic process  (ISO)
regulation of mitochondrial depolarization  (ISO)
response to activity  (IEP)
response to arsenic-containing substance  (ISO)
response to auditory stimulus  (ISO)
response to cadmium ion  (IEP)
response to heat  (ISO,ISS)
response to hormone  (ISO,ISS)
response to human chorionic gonadotropin  (IEP)
response to interleukin-1  (IEP)
response to nitrosative stress  (IMP)
response to nutrient  (IEP)
response to oxidative stress  (IMP,ISO,ISS)
response to xenobiotic stimulus  (ISO)

Cellular Component

Molecular Function

References

References - curated
1. Akai S, etal., J Biol Chem. 2007 Aug 17;282(33):23996-4003. Epub 2007 Jun 15.
2. Beutler E, etal., Blood 1990 Jan 1;75(1):271-3.
3. Beutler E, etal., Blood 1999 Oct 15;94(8):2890-4.
4. Chen CN, etal., J Gerontol A Biol Sci Med Sci. 2010 Feb;65(2):129-37. doi: 10.1093/gerona/glp194. Epub 2009 Dec 16.
5. Dasgupta A, etal., Free Radic Biol Med. 2007 Mar 1;42(5):617-26. Epub 2006 Dec 15.
6. Diaz-Hernandez JI, etal., J Biol Chem. 2005 Nov 25;280(47):38992-9001. Epub 2005 Sep 23.
7. Fernandes CJ, etal., Toxicol Lett. 2002 Dec 15;136(2):107-20.
8. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
9. GOA data from the GO Consortium
10. Gualtieri AF, etal., Int J Androl. 2009 Jun;32(3):218-25. Epub 2007 Nov 27.
11. Hui L, etal., Free Radic Biol Med. 2010 Aug 1;49(3):467-73. doi: 10.1016/j.freeradbiomed.2010.05.002. Epub 2010 May 11.
12. Jang HI, etal., Nutr Res Pract. 2014 Jun;8(3):272-7. doi: 10.4162/nrp.2014.8.3.272. Epub 2014 May 15.
13. KEGG
14. Kim SK, etal., J Pharmacol Exp Ther. 2004 Oct;311(1):99-108. Epub 2004 May 28.
15. Koide S, etal., J Am Coll Cardiol 2003 Feb 19;41(4):539-45.
16. Kuo MT, etal., Cancer Res. 1996 Aug 15;56(16):3642-4.
17. Lee JI, etal., Biochem J. 2006 Jan 1;393(Pt 1):181-90.
18. Marson FA, etal., BMC Med Genet. 2014 Mar 4;15:27. doi: 10.1186/1471-2350-15-27.
19. McKone EF, etal., Am J Respir Crit Care Med. 2006 Aug 15;174(4):415-9. Epub 2006 May 11.
20. MGD data from the GO Consortium
21. NCBI rat LocusLink and RefSeq merged data July 26, 2002
22. OMIM Disease Annotation Pipeline
23. Pipeline to import KEGG annotations from KEGG into RGD
24. Pipeline to import SMPDB annotations from SMPDB into RGD
25. Ramani K, etal., J Biol Chem. 2012 Oct 19;287(43):36341-55. doi: 10.1074/jbc.M112.370775. Epub 2012 Aug 31.
26. RGD automated data pipeline
27. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
28. RGD automated import pipeline for gene-chemical interactions
29. Ristoff E, etal., Blood. 2000 Apr 1;95(7):2193-6.
30. Shukla GS, etal., Toxicol Appl Pharmacol. 2000 Mar 15;163(3):249-59.
31. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
32. Tran PO, etal., J Biol Chem. 2004 Dec 24;279(52):53988-93. Epub 2004 Oct 12.
33. Tsai-Turton M and Luderer U, Am J Physiol Endocrinol Metab. 2005 Sep;289(3):E391-402. Epub 2005 Apr 5.
34. Tsuchiya K, etal., Genomics 1995 Dec 10;30(3):630-2.
35. Tygstrup N, etal., Biochem Biophys Res Commun 2002 Jan 11;290(1):518-25.
36. Yan N and Meister A, J Biol Chem 1990 Jan 25;265(3):1588-93.
37. Yang H, etal., J Biol Chem 2002 Sep 20;277(38):35232-9.
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Additional References at PubMed
PMID:24639   PMID:8104187   PMID:9675072   PMID:9841880   PMID:10395918   PMID:10439045   PMID:10805773   PMID:10966520   PMID:11118286   PMID:11972604   PMID:12384496   PMID:12663448  
PMID:12784246   PMID:12967637   PMID:15288121   PMID:15489334   PMID:15988009   PMID:16081425   PMID:16198230   PMID:16758951   PMID:17045015   PMID:17189825   PMID:17681938   PMID:17721935  
PMID:19459163   PMID:19540342   PMID:20732396   PMID:20732852   PMID:21984568   PMID:23682816   PMID:25016074   PMID:27998794  


Genomics

Comparative Map Data
Gclc
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2878,629,899 - 78,668,547 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl878,630,127 - 78,668,544 (+)Ensembl
Rnor_6.0885,059,051 - 85,097,471 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl885,059,051 - 85,097,468 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0884,627,768 - 84,666,188 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4882,724,429 - 82,762,848 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1882,743,482 - 82,781,899 (+)NCBI
Celera878,379,669 - 78,418,088 (+)NCBICelera
Cytogenetic Map8q31NCBI
GCLC
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl653,497,341 - 53,616,970 (-)EnsemblGRCh38hg38GRCh38
GRCh38653,497,341 - 53,545,101 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37653,362,139 - 53,409,899 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36653,470,098 - 53,517,790 (-)NCBINCBI36hg18NCBI36
Build 34653,470,097 - 53,517,790NCBI
Celera655,024,301 - 55,071,990 (-)NCBI
Cytogenetic Map6p12.1NCBI
HuRef653,193,712 - 53,241,391 (-)NCBIHuRef
CHM1_1653,363,932 - 53,411,726 (-)NCBICHM1_1
Gclc
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39977,661,817 - 77,701,771 (+)NCBIGRCm39mm39
GRCm39 Ensembl977,661,817 - 77,701,767 (+)Ensembl
GRCm38977,754,535 - 77,794,489 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl977,754,535 - 77,794,485 (+)EnsemblGRCm38mm10GRCm38
MGSCv37977,602,617 - 77,641,458 (+)NCBIGRCm37mm9NCBIm37
MGSCv36977,540,494 - 77,579,335 (+)NCBImm8
Celera974,927,826 - 74,966,687 (+)NCBICelera
Cytogenetic Map9E1NCBI
cM Map943.36NCBI
Gclc
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554112,593,541 - 2,616,539 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554112,593,523 - 2,617,553 (+)NCBIChiLan1.0ChiLan1.0
GCLC
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1654,687,315 - 54,738,111 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl654,687,315 - 54,734,994 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0653,052,145 - 53,102,794 (-)NCBIMhudiblu_PPA_v0panPan3
GCLC
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11220,999,815 - 21,047,779 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1221,000,792 - 21,047,779 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1220,898,243 - 20,947,109 (-)NCBI
ROS_Cfam_1.01221,495,557 - 21,544,499 (-)NCBI
UMICH_Zoey_3.11220,996,643 - 21,045,520 (-)NCBI
UNSW_CanFamBas_1.01221,104,936 - 21,153,860 (-)NCBI
UU_Cfam_GSD_1.01221,243,198 - 21,292,135 (-)NCBI
Gclc
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494656,541,439 - 56,588,950 (-)NCBI
SpeTri2.0NW_0049364767,371,270 - 7,418,756 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GCLC
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl727,209,564 - 27,253,535 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1727,209,565 - 27,253,535 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2731,702,759 - 31,747,437 (+)NCBISscrofa10.2Sscrofa10.2susScr3
GCLC
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11719,012,994 - 19,060,617 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1719,013,026 - 19,060,659 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604453,368,286 - 53,415,900 (-)NCBIVero_WHO_p1.0
Gclc
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624850749,046 - 793,654 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH128816  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2878,668,270 - 78,668,474 (+)MAPPERmRatBN7.2
Rnor_6.0885,097,195 - 85,097,398NCBIRnor6.0
Rnor_5.0884,665,912 - 84,666,115UniSTSRnor5.0
RGSC_v3.4882,762,572 - 82,762,775UniSTSRGSC3.4
Celera878,417,812 - 78,418,015UniSTS
RH 3.4 Map8923.9UniSTS
Cytogenetic Map8q31UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
631271Lecl1Lens clarity QTL 10.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)81898416884531599Rat
731182Uae24Urinary albumin excretion QTL 246.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)81933115293965294Rat
1358892Kidm26Kidney mass QTL 263.69kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)82720571599103503Rat
1358896Bp262Blood pressure QTL 2622.89arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)82720571599103503Rat
1358907Cm40Cardiac mass QTL 401.89heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)82720571599103503Rat
8662823Vetf5Vascular elastic tissue fragility QTL 51.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)82824291299525068Rat
1549908Neudeg1Neurodegradation QTL 15.50nervous system integrity trait (VT:0010566)logarithm of the ratio of the lesioned side motor neuron count to contralateral side motor neuron count (CMO:0001986)83018886794457446Rat
2313046Bss78Bone structure and strength QTL 783.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)83084815482460899Rat
2313057Bss76Bone structure and strength QTL 7630.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)83084815482460899Rat
2313067Bss77Bone structure and strength QTL 773.10.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)83084815482460899Rat
2313088Bss75Bone structure and strength QTL 753.10.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)83084815482460899Rat
1578755Pur5Proteinuria QTL 53.30.0001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)830848154101699754Rat
1578765Klgr1Kidney lesion grade QTL 13.30.0001kidney morphology trait (VT:0002135)organ lesion measurement (CMO:0000677)830848154101699754Rat
1578769Uae31Urinary albumin excretion QTL 313.30.001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)830848154101699754Rat
2316950Scl66Serum cholesterol level QTL 664.1blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)830848259105647037Rat
61358Bp39Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83555193880551938Rat
61464Niddm11Non-insulin dependent diabetes mellitus QTL 113.10.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)83558203280582032Rat
1331838Niddm61Non-insulin dependent diabetes mellitus QTL 613.530.0004blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)83646953599083736Rat
737824Hcar10Hepatocarcinoma resistance QTL 102.9liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)84071306682925667Rat
1358906Bp253Blood pressure QTL 25340.0004arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)84071306693965294Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
1298079Activ2Activity QTL 29.50.000001voluntary movement trait (VT:0003491)rearing measurement (CMO:0001515)84186687686866876Rat
70161Bp62Blood pressure QTL 622.90.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)84269268490165460Rat
12879882Am8Aortic mass QTL 80.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)84329616998968765Rat
12879878Bw183Body weight QTL 1830.001body mass (VT:0001259)body weight (CMO:0000012)84329616998968765Rat
12879879Cm99Cardiac mass QTL 990.001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)84329616998968765Rat
12879880Cm100Cardiac mass QTL 1000.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)84329616998968765Rat
12879881Cm101Cardiac mass QTL 1010.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)84329616998968765Rat
12879883Kidm65Kidney mass QTL 650.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)84329616998968765Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)846531639119088624Rat
1331837Bw23Body weight QTL 234.190.00007body mass (VT:0001259)body weight (CMO:0000012)84653172299083736Rat
2303570Gluco48Glucose level QTL 482blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)84980583194805831Rat
2313086Bss60Bone structure and strength QTL 604.10.0001tibia length (VT:0004357)tibia length (CMO:0000450)85009524982460899Rat
4889938Bss89Bone structure and strength QTL 893.8tibia size trait (VT:0100001)tibia cortical bone volume (CMO:0001725)85009524982460899Rat
5684973Bss100Bone structure and strength QTL 1004.7tibia area (VT:1000281)tibia area measurement (CMO:0001382)85009524982460899Rat
1358912Bw51Body weight QTL 512.95body mass (VT:0001259)body weight (CMO:0000012)851351728107062046Rat
10402857Bp380Blood pressure QTL 3800.95arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)85396876598968765Rat
2301402Bp316Blood pressure QTL 3160.005arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)85396876598968765Rat
2293697Bmd39Bone mineral density QTL 39femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)85404374498968765Rat
1582243Bw66Body weight QTL 663.40.0048body mass (VT:0001259)body weight (CMO:0000012)85423764485365202Rat
1582254Kidm31Kidney mass QTL 313kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)85423764485365202Rat
631664Hcar3Hepatocarcinoma resistance QTL 32.90.0005liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)85423764499103503Rat
1300177Cm2Cardiac mass QTL 23.65heart mass (VT:0007028)heart weight (CMO:0000017)854259986100382532Rat
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)861290298119084929Rat
631653Bp125Blood pressure QTL 1253.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)866142385111142385Rat
631210Bw3Body weight QTL35.9mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight to body weight ratio (CMO:0000654)869349194112783834Rat
1300171Bp184Blood pressure QTL 1843.66arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)870513503118219066Rat
8694446Bw170Body weight QTL 17012.070.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)871888757116888757Rat
9590292Uminl3Urine mineral level QTL 33.620.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)871888757116888757Rat
8694200Abfw4Abdominal fat weight QTL 49.070.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)871888757116888757Rat
8694392Bw161Body weight QTL 1618.060.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)871888757116888757Rat
1549909Stresp11Stress response QTL 116.830.0019stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)873473045118473045Rat
10450865Bw175Body weight QTL 1754.1total fat pad mass (VT:0015008)adipose tissue molecular composition measurement (CMO:0000484)87531177784531599Rat
634332Pia18Pristane induced arthritis QTL 184joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)87531193882925521Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)876468691121468691Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:452
Count of miRNA genes:236
Interacting mature miRNAs:290
Transcripts:ENSRNOT00000033196
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 12
Medium 3 28 57 41 19 41 74 23 36 11
Low 15 8 11 5 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000033196   ⟹   ENSRNOP00000035540
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl878,630,127 - 78,668,544 (+)Ensembl
Rnor_6.0 Ensembl885,059,051 - 85,097,468 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000119398   ⟹   ENSRNOP00000081649
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl878,630,127 - 78,668,544 (+)Ensembl
RefSeq Acc Id: NM_012815   ⟹   NP_036947
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2878,630,127 - 78,668,547 (+)NCBI
Rnor_6.0885,059,051 - 85,097,471 (+)NCBI
Rnor_5.0884,627,768 - 84,666,188 (+)NCBI
RGSC_v3.4882,724,429 - 82,762,848 (+)RGD
Celera878,379,669 - 78,418,088 (+)RGD
Sequence:
RefSeq Acc Id: XM_039080870   ⟹   XP_038936798
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2878,629,899 - 78,661,120 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_036947   ⟸   NM_012815
- UniProtKB: P19468 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000035540   ⟸   ENSRNOT00000033196
RefSeq Acc Id: XP_038936798   ⟸   XM_039080870
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000081649   ⟸   ENSRNOT00000119398

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