Cyp2c6v1 (cytochrome P450, family 2, subfamily C, polypeptide 6, variant 1) - Rat Genome Database

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Gene: Cyp2c6v1 (cytochrome P450, family 2, subfamily C, polypeptide 6, variant 1) Rattus norvegicus
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Symbol: Cyp2c6v1
Name: cytochrome P450, family 2, subfamily C, polypeptide 6, variant 1
RGD ID: 619934
Description: Predicted to enable enzyme binding activity; heme binding activity; and monooxygenase activity. Involved in response to drug. Predicted to be located in endoplasmic reticulum membrane. Predicted to be active in cytoplasm and intracellular membrane-bounded organelle. Biomarker of type 2 diabetes mellitus. Human ortholog(s) of this gene implicated in several diseases, including Plasmodium falciparum malaria; eosinophilic esophagitis; invasive aspergillosis; multiple chemical sensitivity; and sickle cell anemia. Orthologous to human CYP2C19 (cytochrome P450 family 2 subfamily C member 19); PARTICIPATES IN axitinib pharmacokinetics pathway; carbamazepine pharmacokinetics pathway; citalopram pharmacodynamics pathway; INTERACTS WITH (+)-schisandrin B; 1,2-dichloroethene; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Cyp2c6; CYPIIC6; cytochrome P450 2C6; cytochrome P450 PB1; cytochrome P450, family 2, subfamily c, polypeptide 6; cytochrome P450, family 2, subfamily C, polypeptide 6-like; cytochrome P450, subfamily IIC6; cytochrome P450-like; LOC246070; LOC293989; MGC109053; PB1; PTF2
RGD Orthologs
Human
Mouse
Bonobo
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21237,938,521 - 237,976,238 (+)NCBImRatBN7.2
Rnor_6.0 Ensembl1147,713,892 - 147,888,007 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01147,713,879 - 147,814,410 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01153,451,394 - 153,454,476 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01154,005,928 - 154,103,310 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41243,859,015 - 243,896,003 (+)ENTREZGENERGSC3.4rn4RGSC3.4
Celera1137,119,477 - 137,156,491 (+)NCBICelera
Cytogenetic Map1q31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-artemisinin  (ISO)
(+)-schisandrin B  (EXP)
(3-phenoxyphenyl)methanol  (ISO)
(E)-thiamethoxam  (ISO)
(E,E)-germacrone  (ISO)
(R)-lipoic acid  (ISO)
(S)-naringenin  (ISO)
1,1,1-Trichloro-2-(4-hydroxyphenyl)-2-(4-methoxyphenyl)ethane  (ISO)
1,2-dichloroethane  (ISO)
1,2-dichloroethene  (EXP)
1,4-naphthoquinone  (ISO)
1-(1,3-benzodioxol-5-yl)-4,4-dimethyl-1-penten-3-ol  (ISO)
1-[3-(dimethylamino)propyl]-1-(4-fluorophenyl)-1,3-dihydro-2-benzofuran-5-carbonitrile  (ISO)
1-naphthol  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
1H-pyrazole  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (EXP)
2,6-di-tert-butyl-4-methylphenol  (EXP)
2-[cyclohexyl(oxo)methyl]-3,6,7,11b-tetrahydro-1H-pyrazino[2,1-a]isoquinolin-4-one  (ISO)
2-nitroanisole  (EXP,ISO)
2-tert-butylhydroquinone  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3,5,6-trichloro-2-pyridinol  (ISO)
3,5,6-trichloropyridine-2-one  (ISO)
3,5-xylenol  (ISO)
4-(methylsulfinyl)phenol  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (ISO)
4-bromo-2-chlorophenol  (ISO)
4-hydroxychalcone  (EXP)
4-hydroxycyclophosphamide  (ISO)
4-hydroxytolbutamide  (ISO)
4-Ipomeanol  (ISO)
4-nitrophenol  (ISO)
4-tert-Octylphenol  (ISO)
5-hydroxydiclofenac  (ISO)
5-Hydroxythalidomide  (ISO)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (ISO)
5-methoxy-N,N-diisopropyltryptamine  (ISO)
7,12-dimethyltetraphene  (ISO)
7-hydroxyflavone  (ISO)
acenocoumarol  (ISO)
acetamide  (EXP)
aconitine  (ISO)
acrolein  (ISO)
adinazolam  (ISO)
ADP  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (EXP,ISO)
almotriptan  (ISO)
alpha-hexachlorocyclohexane  (EXP)
alpha-linolenic acid  (ISO)
alpha-methyltryptamine  (ISO)
amiodarone  (ISO)
amitriptyline  (ISO)
amitriptylinoxide  (ISO)
ammonium chloride  (EXP)
amodiaquine  (ISO)
amphetamine  (ISO)
arachidonic acid  (ISO)
aristolochic acid  (EXP)
Aroclor 1254  (EXP,ISO)
Asiaticoside  (ISO)
atrazine  (ISO)
azoxystrobin  (ISO)
baicalein  (ISO)
barnidipine  (ISO)
benfuracarb  (ISO)
benidipine  (ISO)
benzbromarone  (ISO)
benzo[a]pyrene  (ISO)
benzylideneacetone  (EXP)
beta-hexachlorocyclohexane  (ISO)
beta-naphthoflavone  (EXP,ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bortezomib  (ISO)
bromfenac  (ISO)
Bufuralol  (EXP,ISO)
bupropion  (ISO)
cadmium dichloride  (ISO)
calcitriol  (ISO)
cannabidiol  (ISO)
capsaicin  (ISO)
captan  (ISO)
carbamazepine  (ISO)
carbendazim  (ISO)
carbofuran  (ISO)
carisoprodol  (ISO)
chalcone  (EXP)
chelidonine  (ISO)
chloramphenicol  (ISO)
chlorohydrocarbon  (EXP)
chlorpromazine  (ISO)
chlorpyrifos  (ISO)
chlorzoxazone  (EXP)
choline  (ISO)
chrysosplenetin  (ISO)
citalopram  (ISO)
Citreorosein  (ISO)
clopidogrel  (ISO)
clotrimazole  (EXP)
clozapine  (ISO)
Clozapine N-oxide  (ISO)
copper(II) chloride  (ISO)
cumene hydroperoxide  (ISO)
cyclophosphamide  (EXP,ISO)
cyclosporin A  (ISO)
cypermethrin  (ISO)
cyproconazole  (EXP,ISO)
cyprodinil  (ISO)
dapsone  (ISO)
decabromodiphenyl ether  (EXP)
dehydroepiandrosterone sulfate  (EXP)
delavirdine  (ISO)
deoxycholic acid  (EXP)
desipramine  (ISO)
dexamethasone  (EXP)
dextran sulfate  (ISO)
dextromethorphan  (ISO)
diarylheptanoid  (ISO)
diazepam  (EXP,ISO)
diazinon  (ISO)
dibenzo[a,l]pyrene  (ISO)
dichloroacetic acid  (ISO)
diclofenac  (EXP,ISO)
diethylcarbamazine  (ISO)
diethyldithiocarbamic acid  (ISO)
difenoconazole  (ISO)
dihydroartemisinin  (ISO)
dihydrocapsaicin  (ISO)
dimemorfan  (ISO)
dimethomorph  (ISO)
dimethyl sulfoxide  (EXP)
diniconazole  (ISO)
diosmetin  (ISO)
dronedarone  (ISO)
efavirenz  (ISO)
Elemicin  (ISO)
ellipticine  (ISO)
emodin  (ISO)
endosulfan  (EXP)
enfuvirtide  (ISO)
enilconazole  (ISO)
epoxiconazole  (EXP,ISO)
ethambutol  (ISO)
ethanol  (EXP,ISO)
ethoprophos  (ISO)
eupatorin  (ISO)
famotidine  (ISO)
fenhexamid  (ISO)
fenofibrate  (ISO)
fenpyroximate  (ISO)
fenvalerate  (ISO)
fipronil  (ISO)
fluconazole  (ISO)
fludioxonil  (ISO)
flunitrazepam  (ISO)
fluorescein (lactone form)  (ISO)
fluoxetine  (EXP,ISO)
fluphenazine  (ISO)
flusilazole  (ISO)
flutamide  (ISO)
fluxapyroxad  (ISO)
folic acid  (ISO)
Furafylline  (EXP,ISO)
furan  (EXP)
genistein  (EXP,ISO)
gingerol  (ISO)
glutathione  (ISO)
glyoxal  (ISO)
herbicide  (ISO)
hesperetin  (ISO)
hexobarbital  (ISO)
Hydroxymephenytoin  (ISO)
Hypaconitine  (ISO)
ifosfamide  (ISO)
imipramine  (ISO)
imipramine oxide  (ISO)
imiquimod  (ISO)
indole-3-methanol  (EXP)
iprodione  (ISO)
isocarbophos  (ISO)
isoliquiritigenin  (ISO)
ketoconazole  (EXP,ISO)
L-methionine  (ISO)
lamotrigine  (EXP)
lansoprazole  (EXP,ISO)
lefetamine  (ISO)
Licochalcone A  (ISO)
linoleic acid  (ISO)
lipoic acid  (ISO)
liquiritigenin  (ISO)
lithocholic acid  (EXP)
luteolin  (ISO)
madecassoside  (ISO)
maneb  (ISO)
mangiferin  (EXP)
mefenamic acid  (ISO)
Melarsoprol  (ISO)
melatonin  (ISO)
mephenytoin  (ISO)
mephobarbital  (ISO)
Meprobamate  (ISO)
mercury dichloride  (ISO)
metalaxyl  (ISO)
methiocarb  (ISO)
methiocarb-sulfoxide  (ISO)
methoxsalen  (EXP)
methoxychlor  (ISO)
methylmercury chloride  (EXP)
Methysticin  (EXP)
metolachlor  (ISO)
miconazole  (ISO)
Miltirone  (ISO)
Mitragynine  (ISO)
moclobemide  (ISO)
mono(2-ethyl-5-hydroxyhexyl) phthalate  (EXP,ISO)
mono(2-ethyl-5-oxohexyl) phthalate  (EXP,ISO)
mono(2-ethylhexyl) phthalate  (EXP,ISO)
monocrotaline  (ISO)
myricetin  (ISO)
N,N-diethyl-m-toluamide  (ISO)
N,N-diisopropyltryptamine  (ISO)
N,N-dimethyltryptamine  (ISO)
N-acetyl-L-cysteine  (ISO)
N-desmethylclozapine  (ISO)
N-hydroxy-PhIP  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
NADP zwitterion  (ISO)
NADP(+)  (ISO)
naphthalene  (ISO)
Nicardipine  (ISO)
nimesulide  (ISO)
norflurazon  (ISO)
norgestimate  (ISO)
Notopterol  (ISO)
O-methyleugenol  (ISO)
okanin  (ISO)
omeprazole  (ISO)
organophosphorus compound  (ISO)
orotic acid  (EXP)
oxymetazoline  (ISO)
p-tert-Amylphenol  (ISO)
pantoprazole  (ISO)
paracetamol  (ISO)
paraquat  (EXP)
parathion  (ISO)
PCB138  (ISO)
pedalitin  (ISO)
pentamidine  (ISO)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
perfluorooctanoic acid  (EXP,ISO)
permethrin  (ISO)
phenacetin  (EXP)
phencyclidine  (ISO)
phenobarbital  (EXP,ISO)
phenytoin  (EXP,ISO)
PhIP  (ISO)
phthalic acid  (EXP)
physcion  (ISO)
picoxystrobin  (ISO)
pirinixic acid  (EXP,ISO)
poly(I:C)  (EXP)
pomalidomide  (ISO)
prednisolone  (EXP)
pregnenolone 16alpha-carbonitrile  (ISO)
prochloraz  (ISO)
profenofos  (ISO)
progesterone  (ISO)
proguanil  (ISO)
propiconazole  (ISO)
propranolol  (ISO)
pterostilbene  (ISO)
pyrene  (EXP)
pyrrolidines  (ISO)
quercetin  (ISO)
quinidine  (EXP,ISO)
quinine  (EXP,ISO)
rabeprazole  (ISO)
resveratrol  (ISO)
Retrorsine  (ISO)
rifampicin  (ISO)
ritonavir  (ISO)
sertraline  (ISO)
sibutramine  (ISO)
sodium arsenite  (ISO)
sophoranone  (ISO)
Sudan I  (ISO)
sulfaphenazole  (EXP,ISO)
sulfasalazine  (ISO)
suramin  (ISO)
tacrolimus hydrate  (ISO)
tamoxifen  (ISO)
Tanshinone I  (ISO)
tert-butyl ethyl ether  (EXP)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
tetraconazole  (ISO)
tetracycline  (ISO)
thalidomide  (ISO)
thiacloprid  (ISO)
thiamethoxam  (ISO)
thioacetamide  (EXP)
thioridazine  (ISO)
thiram  (ISO)
ticlopidine  (ISO)
titanium dioxide  (ISO)
tofacitinib  (ISO)
tolbutamide  (ISO)
toluene  (EXP)
trans-1,2-dichloroethene  (EXP)
trans-chalcone  (EXP)
trans-cinnamic acid  (ISO)
tranylcypromine  (ISO)
triclosan  (ISO)
triflumuron  (ISO)
troglitazone  (ISO)
tryptamines  (ISO)
ursodeoxycholic acid  (EXP)
ursolic acid  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
vanoxerine dihydrochloride  (ISO)
veliparib  (ISO)
venlafaxine hydrochloride  (ISO)
voriconazole  (ISO)
warfarin  (ISO)
zafirlukast  (ISO)

References

References - curated
1. Babalola CP, etal., J Clin Pharm Ther. 2010 Aug;35(4):471-7. doi: 10.1111/j.1365-2710.2009.01122.x.
2. Caccamo D, etal., Oxid Med Cell Longev. 2013;2013:831969. doi: 10.1155/2013/831969. Epub 2013 Jul 7.
3. Chau TK, etal., Life Sci. 2000 Aug 25;67(14):1719-24. doi: 10.1016/s0024-3205(00)00757-8.
4. Chuwongwattana S, etal., Drug Metab Pharmacokinet. 2016 Apr;31(2):117-22. doi: 10.1016/j.dmpk.2015.12.005. Epub 2016 Jan 12.
5. Espinoza N, etal., Sci Rep. 2019 Jun 20;9(1):8863. doi: 10.1038/s41598-019-45345-2.
6. Furuta T, etal., Ann Intern Med. 1998 Dec 15;129(12):1027-30. doi: 10.7326/0003-4819-129-12-199812150-00006.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. Gonzalez FJ, etal., J Biol Chem 1986 Aug 15;261(23):10667-72.
9. Jainan W and Vilaichone RK, Asian Pac J Cancer Prev. 2014;15(24):10957-60. doi: 10.7314/apjcp.2014.15.24.10957.
10. Kaneko A, etal., Pharmacogenetics. 1999 Jun;9(3):317-26.
11. Kim SH, etal., Eur J Clin Pharmacol. 2011 Feb;67(2):121-7. doi: 10.1007/s00228-010-0912-4. Epub 2010 Oct 13.
12. Li Y, etal., Haematologica. 2007 Sep;92(9):1246-9. Epub 2007 Aug 1.
13. Lim JS, etal., Br J Clin Pharmacol. 2016 Jun;81(6):1142-52. doi: 10.1111/bcp.12886. Epub 2016 Mar 8.
14. Manuyakorn W, etal., Pediatr Allergy Immunol. 2013 May;24(3):299-303. doi: 10.1111/pai.12058. Epub 2013 Apr 3.
15. Melanson SE, etal., Am J Hematol. 2010 Dec;85(12):967-71. doi: 10.1002/ajh.21889.
16. Molina-Infante J, etal., Am J Gastroenterol. 2015 Nov;110(11):1567-75. doi: 10.1038/ajg.2015.314. Epub 2015 Sep 29.
17. Musumba CO, etal., Clin Pharmacol Ther. 2013 Feb;93(2):195-203. doi: 10.1038/clpt.2012.215. Epub 2012 Oct 26.
18. Nabinger DD, etal., Genet Mol Res. 2016 Sep 16;15(3). pii: gmr8734. doi: 10.4238/gmr.15038734.
19. NCBI rat LocusLink and RefSeq merged data July 26, 2002
20. Neyshaburinezhad N, etal., Iran J Basic Med Sci. 2020 May;23(5):629-635. doi: 10.22038/ijbms.2020.40836.9642.
21. OMIM Disease Annotation Pipeline
22. Pipeline to import SMPDB annotations from SMPDB into RGD
23. RGD automated data pipeline
24. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
25. RGD automated import pipeline for gene-chemical interactions
26. RGD comprehensive gene curation
27. Sheu BS, etal., Aliment Pharmacol Ther. 2005 Feb 1;21(3):283-8. doi: 10.1111/j.1365-2036.2005.02281.x.
28. Sheweita SA Toxicology 2003 Sep 30;191(2-3):133-42.
29. Vangsted AJ, etal., BMC Cancer. 2010 Aug 4;10:404. doi: 10.1186/1471-2407-10-404.
30. Wang T, etal., Int J Antimicrob Agents. 2014 Nov;44(5):436-42. doi: 10.1016/j.ijantimicag.2014.07.013. Epub 2014 Aug 30.
31. Xavier AS, etal., Fundam Clin Pharmacol. 2016 Dec;30(6):607-615. doi: 10.1111/fcp.12218. Epub 2016 Jul 26.
32. Zandvliet AS, etal., Clin Cancer Res. 2007 May 15;13(10):2970-6.
33. Zhou B, etal., Biomed Rep. 2016 Feb;4(2):251-255. doi: 10.3892/br.2015.563. Epub 2015 Dec 31.
Additional References at PubMed
PMID:2914909   PMID:3335521   PMID:3399405   PMID:3801454   PMID:12477932   PMID:15680923   PMID:16401082   PMID:18356043   PMID:19029318   PMID:19219744   PMID:19651758   PMID:22885143  
PMID:23118231  


Genomics

Comparative Map Data
Cyp2c6v1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21237,938,521 - 237,976,238 (+)NCBImRatBN7.2
Rnor_6.0 Ensembl1147,713,892 - 147,888,007 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01147,713,879 - 147,814,410 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01153,451,394 - 153,454,476 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01154,005,928 - 154,103,310 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41243,859,015 - 243,896,003 (+)ENTREZGENERGSC3.4rn4RGSC3.4
Celera1137,119,477 - 137,156,491 (+)NCBICelera
Cytogenetic Map1q31NCBI
CYP2C19
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1094,762,681 - 94,855,547 (+)EnsemblGRCh38hg38GRCh38
GRCh381094,762,681 - 94,855,547 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371096,522,438 - 96,615,304 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361096,512,453 - 96,602,661 (+)NCBINCBI36hg18NCBI36
Build 341096,512,452 - 96,602,661NCBI
Celera1090,262,555 - 90,352,777 (+)NCBI
Cytogenetic Map10q23.33NCBI
HuRef1090,149,122 - 90,239,340 (+)NCBIHuRef
CHM1_11096,804,212 - 96,894,435 (+)NCBICHM1_1
Cyp2c38
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391939,378,000 - 39,451,547 (-)NCBIGRCm39mm39
GRCm39 Ensembl1939,378,000 - 39,451,519 (-)Ensembl
GRCm381939,389,556 - 39,463,103 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1939,389,556 - 39,463,075 (-)EnsemblGRCm38mm10GRCm38
MGSCv371939,464,046 - 39,537,565 (-)NCBIGRCm37mm9NCBIm37
MGSCv361939,442,867 - 39,516,386 (-)NCBImm8
MGSCv361939,107,245 - 39,170,091 (-)NCBImm8
Celera1940,194,429 - 40,266,552 (-)NCBICelera
Cytogenetic Map19C3NCBI
CYP2C19
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11094,883,037 - 94,972,353 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1094,884,472 - 94,970,065 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01091,375,255 - 91,465,215 (+)NCBIMhudiblu_PPA_v0panPan3
CYP2C49
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.114106,571,803 - 106,612,082 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.214116,191,543 - 116,244,868 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CYP2C19
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1987,981,300 - 88,025,007 (+)NCBI
Vero_WHO_p1.0NW_02366604848,761,705 - 48,797,570 (+)NCBI

Position Markers
D1Wox24  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21237,976,134 - 237,976,247 (+)MAPPERmRatBN7.2
Rnor_6.01147,814,307 - 147,814,419NCBIRnor6.0
Rnor_5.01154,103,207 - 154,103,319UniSTSRnor5.0
RGSC_v3.41243,895,915 - 243,896,027UniSTSRGSC3.4
RGSC_v3.41243,898,025 - 243,898,152RGDRGSC3.4
RGSC_v3.41243,895,914 - 243,896,027RGDRGSC3.4
RGSC_v3.41243,898,026 - 243,898,152UniSTSRGSC3.4
RGSC_v3.11243,994,584 - 243,994,711RGD
RH 3.4 Map11617.4UniSTS
RH 3.4 Map11617.4RGD
RH 2.0 Map11221.3RGD
Cytogenetic Map1q53UniSTS
D1Got233  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.01154,098,589 - 154,098,780NCBIRnor5.0
RGSC_v3.41244,294,363 - 244,294,596UniSTSRGSC3.4
RGSC_v3.41243,889,774 - 243,889,999UniSTSRGSC3.4
Celera1137,151,906 - 137,152,139UniSTS
RH 3.4 Map11587.31UniSTS
RH 3.4 Map11587.31RGD
RH 2.0 Map11224.1RGD
Cytogenetic Map1q52UniSTS
Cytogenetic Map1q53UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2292216Bw80Body weight QTL 803.230.0019body mass (VT:0001259)body weight (CMO:0000012)1213533809243914901Rat
70211Niddm24Non-insulin dependent diabetes mellitus QTL 243.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1214647894259647894Rat
631215Stl8Serum triglyceride level QTL 89.270.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1225126575260522016Rat
2302040Pia35Pristane induced arthritis QTL 353.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)1216255568260522016Rat
2302375Bw83Body weight QTL 834.870.0002body mass (VT:0001259)body weight (CMO:0000012)1197697768242697768Rat
2302378Insul11Insulin level QTL 113.25blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1144267353251128347Rat
61455Niddm7Non-insulin dependent diabetes mellitus QTL 75.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1214537555238757011Rat
724531Uae5Urinary albumin excretion QTL 54urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)1150700142252085212Rat
724533Rf51Renal function QTL 515.30.0002kidney plasma flow trait (VT:0005524)renal plasma flow (CMO:0001914)1218753816256448513Rat
724538Kidm1Kidney mass QTL 13.2kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1213707201252085212Rat
724552Glom2Glomerulus QTL 23.30.0001kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)1222363780260522016Rat
734767Niddm57Non-insulin dependent diabetes mellitus QTL 57body mass (VT:0001259)body weight (CMO:0000012)1224054293260122809Rat
734768Niddm59Non-insulin dependent diabetes mellitus QTL 59body mass (VT:0001259)body weight (CMO:0000012)1213843987258843987Rat
734769Niddm58Non-insulin dependent diabetes mellitus QTL 58body mass (VT:0001259)body weight (CMO:0000012)1224569538260122809Rat
1298084Thym4Thymus enlargement QTL 410.68thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)1197814409242814409Rat
631658Cm7Cardiac mass QTL 75.320.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)1196248093241248093Rat
631669Iddm9Insulin dependent diabetes mellitus QTL 92.80.039blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1233190394258625266Rat
631690Scl5Serum cholesterol level QTL 52.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1236125214260522016Rat
1354580Scort1Serum corticosterone level QTL 13.4blood corticosterone amount (VT:0005345)blood corticosterone level (CMO:0001172)1156677124256448636Rat
1581544Rf52Renal function QTL 520.05total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)1232156370259647894Rat
731175Uae20Urinary albumin excretion QTL 203.50.0018urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1221264111259647894Rat
738032Hcas5Hepatocarcinoma susceptibility QTL 53.12liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1176426412257976495Rat
631536Lnnr2Liver neoplastic nodule remodeling QTL 22.90.0005liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)1233948574260522016Rat
1641926Teswt2Testicular weight QTL 22.82testis mass (VT:1000644)both testes wet weight (CMO:0000175)1197697768238755659Rat
1598821Rf55Renal function QTL 556.3renal blood flow trait (VT:2000006)ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)1218748008257976495Rat
2300175Bmd40Bone mineral density QTL 4015.40.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)1201554356246554356Rat
2293655Bss36Bone structure and strength QTL 3610.660.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)1201554356246554356Rat
2293674Bss39Bone structure and strength QTL 397.10.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)1201554356246554356Rat
2293694Bss38Bone structure and strength QTL 387.050.0001femur strength trait (VT:0010010)femur stiffness (CMO:0001674)1201554356246554356Rat
2293700Bmd27Bone mineral density QTL 276.60.0001femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1224054293243747962Rat
2293701Bmd34Bone mineral density QTL 348.30.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)1224054293243747962Rat
631836Stl31Serum triglyceride level QTL 314.640.00000487blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)1237147813260522016Rat
631843Bw116Body weight QTL 1164.10.016abdominal adipose amount (VT:1000220)abdominal fat pad weight (CMO:0000088)1224054293260122809Rat
634313Niddm43Non-insulin dependent diabetes mellitus QTL 43blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1199050459259647894Rat
634321Hc1Hypercalciuria QTL 12.91urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1178810256240830002Rat
1357335Bw39Body weight QTL 393.3body mass (VT:0001259)body weight (CMO:0000012)1197814409242814409Rat
1357399Bw45Body weight QTL 453.05body mass (VT:0001259)body mass index (BMI) (CMO:0000105)1206329708251329708Rat
1357404Bw42Body weight QTL 424.490.0001body mass (VT:0001259)body weight (CMO:0000012)1206329708251329708Rat
1600363Hc6Hypercalciuria QTL 62.7urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1203995416244113296Rat
1600374Mcs17Mammary carcinoma susceptibility QTL 173mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1197670404242670404Rat
1600388Niddm67Non-insulin dependent diabetes mellitus QTL 675.840.000004blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1195804352257091168Rat
1600392Bw123Body weight QTL 1230.001body mass (VT:0001259)body weight (CMO:0000012)1223201027260522016Rat
1600395Niddm69Non-insulin dependent diabetes mellitus QTL 694.140.0002blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1195804352257091168Rat
1600396Niddm68Non-insulin dependent diabetes mellitus QTL 684.970.0003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1195804352257091168Rat
1600397Edcs4Endometrial carcinoma susceptibility QTL 42.2uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)1206081677251081677Rat
1578759Uae30Urinary albumin excretion QTL 303.30.003urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1150700247252085048Rat
1578763Kidm29Kidney mass QTL 293.30.0001kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1179567751260522016Rat
1578778Pur4Proteinuria QTL 43.30.003total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1150700247252085048Rat
1300108Rf8Renal function QTL 83.75renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1228581588259647894Rat
1354610Bw34Body weight QTL 344.1body mass (VT:0001259)body weight (CMO:0000012)1151162512256448636Rat
1354624Cm35Cardiac mass QTL355.7heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1177227632256448636Rat
1354646Kidm18Kidney mass QTL 185.7kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1151162512256448636Rat
1354652Kidm20Kidney mass QTL 204.3kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1177227632256448636Rat
1354661Bw33Body weight QTL 335.2body mass (VT:0001259)body weight (CMO:0000012)1151162512256448636Rat
1549910Bw54Body weight QTL 540.05body mass (VT:0001259)body weight (CMO:0000012)1214647894259647894Rat
2316896Gluco57Glucose level QTL 577.2blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1228985440245907899Rat
1549837Hcar15Hepatocarcinoma resistance QTL 150.05liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1153136852260522016Rat
1358191Ept10Estrogen-induced pituitary tumorigenesis QTL 103.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)1192825253243914732Rat
2292220Bp306Blood pressure QTL 3063.470.00087arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1164310393243914901Rat
1358890Bp259Blood pressure QTL 2593.06arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1210702053260522016Rat
1358898Bp255Blood pressure QTL 2553.6arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1191019702246062233Rat
1358916Kidm22Kidney mass QTL 223.32kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1210702053240947965Rat
1358292Cm37Cardiac mass QTL 376.20.00000081heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)1196248093241248093Rat
61327Eae7Experimental allergic encephalomyelitis QTL 75.6body mass (VT:0001259)change in body weight (CMO:0002045)1216255568260522016Rat
61376Bp42Blood pressure QTL 4223.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1197814409242814409Rat
61400Niddm1Non-insulin dependent diabetes mellitus QTL 111blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1218753689245907899Rat
8655655Arrd2Age-related retinal degeneration QTL 27.79retinal layer morphology trait (VT:0003727)percentage of study population developing retinopathy during a period of time (CMO:0002453)1183970203243914901Rat
7794788Mcs32Mammary carcinoma susceptibility QTL 322.61mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)1115540693238914717Rat
7421630Bp362Blood pressure QTL 3620.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1118608292241799120Rat
8552891Epfw5Epididymal fat weight QTL 54.4epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1193113876238113876Rat
7394701Uae46Urinary albumin excretion QTL 463.60.0056urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1201554356246554356Rat
8655855Arrd3Age-related retinal degeneration QTL 33.07lens clarity trait (VT:0001304)cataract incidence/prevalence measurement (CMO:0001585)1183970203243914901Rat
10053715Scort24Serum corticosterone level QTL 242.130.0088blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1221414816260522016Rat
10059587Bw173Body weight QTL 1733.230.025body mass (VT:0001259)body weight (CMO:0000012)1202069611247069611Rat


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 6 6
Medium 15 15 15 1
Low 2 7 18 2 18 2 8 8 10 9 10 9 8
Below cutoff 1 4 2 2 1 2 2 23 12 18 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001013904 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008759613 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008759614 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008759615 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108989 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108994 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109003 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109009 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109012 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AH002220 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC089886 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC100092 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210718 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210770 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218109 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218861 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219350 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000050 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  K03501 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M13711 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000054742   ⟹   ENSRNOP00000051625
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1147,713,892 - 147,814,395 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000074103   ⟹   ENSRNOP00000066819
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1147,713,898 - 147,888,007 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092772
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1147,884,177 - 147,887,326 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092785
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1147,713,974 - 147,723,145 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092842   ⟹   ENSRNOP00000076057
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1147,713,944 - 147,725,654 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092928   ⟹   ENSRNOP00000076032
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1147,723,534 - 147,885,897 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092985   ⟹   ENSRNOP00000075936
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1147,713,892 - 147,814,389 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092999   ⟹   ENSRNOP00000075960
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1147,713,938 - 147,808,383 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093050
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1147,723,355 - 147,884,130 (+)Ensembl
RefSeq Acc Id: NM_001013904   ⟹   NP_001013926
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21237,938,521 - 237,976,223 (+)NCBI
Rnor_6.01147,713,901 - 147,814,395 (+)NCBI
Rnor_5.01154,005,928 - 154,103,310 (+)NCBI
Celera1137,119,477 - 137,156,491 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039108989   ⟹   XP_038964917
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21237,938,582 - 237,976,238 (+)NCBI
RefSeq Acc Id: XM_039108994   ⟹   XP_038964922
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21237,938,524 - 237,976,100 (+)NCBI
RefSeq Acc Id: XM_039109003   ⟹   XP_038964931
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21237,938,524 - 237,976,094 (+)NCBI
RefSeq Acc Id: XM_039109009   ⟹   XP_038964937
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21237,938,524 - 237,976,094 (+)NCBI
RefSeq Acc Id: XM_039109012   ⟹   XP_038964940
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21237,938,561 - 237,976,238 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001013926   ⟸   NM_001013904
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: ENSRNOP00000076057   ⟸   ENSRNOT00000092842
RefSeq Acc Id: ENSRNOP00000075960   ⟸   ENSRNOT00000092999
RefSeq Acc Id: ENSRNOP00000075936   ⟸   ENSRNOT00000092985
RefSeq Acc Id: ENSRNOP00000076032   ⟸   ENSRNOT00000092928
RefSeq Acc Id: ENSRNOP00000051625   ⟸   ENSRNOT00000054742
RefSeq Acc Id: ENSRNOP00000066819   ⟸   ENSRNOT00000074103
RefSeq Acc Id: XP_038964922   ⟸   XM_039108994
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038964937   ⟸   XM_039109009
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038964931   ⟸   XM_039109003
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038964940   ⟸   XM_039109012
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038964917   ⟸   XM_039108989
- Peptide Label: isoform X1

Transcriptome

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

Promoters
RGD ID:13690173
Promoter ID:EPDNEW_R697
Type:initiation region
Name:Cyp2c6v1_1
Description:cytochrome P450, family 2, subfamily C, polypeptide 6, variant1
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_6.01147,713,890 - 147,713,950EPDNEW

Strain Variation

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:619934 AgrOrtholog
Ensembl Genes ENSRNOG00000024016 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000051625 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000066819 UniProtKB/TrEMBL
  ENSRNOP00000075936 UniProtKB/TrEMBL
  ENSRNOP00000075960 UniProtKB/TrEMBL
  ENSRNOP00000076032 UniProtKB/TrEMBL
  ENSRNOP00000076057 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000054742 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000074103 UniProtKB/TrEMBL
  ENSRNOT00000092842 UniProtKB/TrEMBL
  ENSRNOT00000092928 UniProtKB/TrEMBL
  ENSRNOT00000092985 UniProtKB/TrEMBL
  ENSRNOT00000092999 UniProtKB/TrEMBL
Gene3D-CATH 1.10.630.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7370532 IMAGE-MGC_LOAD
  IMAGE:7372330 IMAGE-MGC_LOAD
InterPro Cyt_P450 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cyt_P450_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cyt_P450_E_grp-I UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cyt_P450_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:293989 UniProtKB/TrEMBL
MGC_CLONE MGC:109053 IMAGE-MGC_LOAD
  MGC:112798 IMAGE-MGC_LOAD
NCBI Gene Cyp2c6v1 ENTREZGENE
Pfam p450 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB CYP2C19 RGD
PhenoGen Cyp2c6v1 PhenoGen
PRINTS EP450I UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P450 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CYTOCHROME_P450 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48264 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A1B0GWL1_RAT UniProtKB/TrEMBL
  A0A1B0GWN4_RAT UniProtKB/TrEMBL
  A0A1B0GWV3_RAT UniProtKB/TrEMBL
  A0A1B0GWX5_RAT UniProtKB/TrEMBL
  CP2C6_RAT UniProtKB/Swiss-Prot
  F1LR47_RAT UniProtKB/TrEMBL
  M0RB90_RAT UniProtKB/TrEMBL
  P05178 ENTREZGENE
  Q5EB99_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-09-24 Cyp2c6v1  cytochrome P450, family 2, subfamily C, polypeptide 6, variant 1  LOC246070  cytochrome P450, family 2, subfamily C, polypeptide 6-like  Data Merged 737654 APPROVED
2011-11-18 Cyp2c6  cytochrome P450, family 2, subfamily c, polypeptide 6  Cyp2c6v1  cytochrome P450, family 2, subfamily C, polypeptide 6, variant 1  Data Merged 737654 APPROVED
2011-11-18 Cyp2c6v1  cytochrome P450, family 2, subfamily C, polypeptide 6, variant 1  LOC293989  cytochrome P450-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-11-18 Cyp2c6v1  cytochrome P450, family 2, subfamily C, polypeptide 6, variant 1  Cyp2c6  cytochrome P450, family 2, subfamily c, polypeptide 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-04-19 Cyp2c6  cytochrome P450, family 2, subfamily c, polypeptide 6  Cyp2c6  cytochrome P450, subfamily IIC6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Cyp2c6  cytochrome P450, subfamily IIC6   Cyp2c6_predicted  cytochrome P450, subfamily IIC6 (predicted)  'predicted' is removed 2292626 APPROVED
2007-09-27 Cyp2c6_predicted  cytochrome P450, subfamily IIC6 (predicted)  Cyp2c6  cytochrome P450, subfamily IIC6  Symbol and Name updated 1299863 APPROVED
2006-11-20 LOC293989  cytochrome P450-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2002-08-07 Cyp2c6        Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_drugs expression in liver is induced after single dose treatment with heroin but may be reduced in response to repeated heroin doses 728216