Nr1h4 (nuclear receptor subfamily 1, group H, member 4) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Nr1h4 (nuclear receptor subfamily 1, group H, member 4) Rattus norvegicus
Analyze
Symbol: Nr1h4
Name: nuclear receptor subfamily 1, group H, member 4
RGD ID: 628831
Description: Enables several functions, including DNA-binding transcription factor activity, RNA polymerase II-specific; bile acid receptor activity; and chenodeoxycholic acid binding activity. Contributes to double-stranded DNA binding activity. Involved in several processes, including lipid homeostasis; liver development; and negative regulation of biosynthetic process. Located in nucleus. Part of receptor complex. Used to study extrahepatic cholestasis; intrahepatic cholestasis; and portal hypertension. Biomarker of bile duct disease (multiple); liver disease (multiple); non-alcoholic fatty liver disease (multiple); obesity; and premature menopause. Human ortholog(s) of this gene implicated in extrahepatic cholestasis; hepatocellular carcinoma; and progressive familial intrahepatic cholestasis 5. Orthologous to human NR1H4 (nuclear receptor subfamily 1 group H member 4); PARTICIPATES IN bile acid signaling pathway; bile acid signaling pathway; bile acid signaling pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: bile acid receptor; farnesoid X activated receptor; farnesoid X-activated receptor; farnesol receptor HRR-1; Fxr; MGC94878; nuclear receptor subfamily 1 group H member 4; retinoid X receptor-interacting protein 14; RXR-interacting protein 14
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
mRatBN7.2723,846,122 - 23,942,085 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl723,846,122 - 23,942,047 (-)Ensembl
Rnor_6.0730,003,429 - 30,162,095 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl730,003,429 - 30,162,056 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0730,170,397 - 30,214,796 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0730,104,960 - 30,107,142 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4726,189,759 - 26,307,061 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1726,210,029 - 26,327,332 (-)NCBI
Celera720,992,814 - 21,085,820 (-)NCBICelera
Cytogenetic Map7q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-epicatechin-3-O-gallate  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
(S)-colchicine  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP,ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (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  (ISO)
2-amino-2-deoxy-D-glucopyranose  (EXP)
22,23-dihydroavermectin B1a  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3,3',4,4'-tetrachlorobiphenyl  (ISO)
3,6-diaminoacridine  (ISO)
3-chloropropane-1,2-diol  (EXP)
3alpha-hydroxy-5beta-pregnan-20-one  (ISO)
4'-epidoxorubicin  (ISO)
4,4'-diaminodiphenylmethane  (EXP,ISO)
4,4'-sulfonyldiphenol  (ISO)
4-\{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbonyl]amino\}benzoic acid  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-(4-chlorophenyl)imidazo[2,1-b][1,3]thiazole-5-carbaldehyde O-(3,4-dichlorobenzyl)oxime  (ISO)
6-propyl-2-thiouracil  (EXP)
8-Br-cAMP  (EXP)
9-aminoacridine  (ISO)
abamectin  (ISO)
acadesine  (EXP,ISO)
acrylamide  (EXP)
actinomycin D  (ISO)
aflatoxin B1  (ISO)
AICA ribonucleotide  (EXP)
albendazole  (ISO)
albendazole S-oxide  (ISO)
aldehydo-D-glucosamine  (EXP)
all-trans-retinoic acid  (EXP,ISO)
alpha-linolenic acid  (ISO)
alvocidib  (ISO)
ammonium chloride  (EXP)
angelicin  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
apigenin  (ISO)
arachidonic acid  (ISO)
arjunolic acid  (EXP)
arotinoid acid  (ISO)
arsenite(3-)  (ISO)
atazanavir sulfate  (ISO)
benazepril  (ISO)
benidipine  (ISO)
benomyl  (ISO)
benzo[a]pyrene  (ISO)
beta-D-glucosamine  (EXP)
beta-hexachlorocyclohexane  (ISO)
beta-naphthoflavone  (EXP,ISO)
bezafibrate  (ISO)
bifenthrin  (ISO)
biochanin A  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
Boldine  (EXP)
bortezomib  (ISO)
bosentan  (ISO)
butachlor  (ISO)
butanal  (ISO)
carbendazim  (ISO)
carbon nanotube  (ISO)
chenodeoxycholic acid  (EXP,ISO)
chlorpromazine  (EXP)
cholanic acid  (ISO)
cholate  (ISO)
cholesterol  (EXP,ISO)
cholic acid  (EXP,ISO)
chrysin  (ISO)
ciclobendazole  (ISO)
cilnidipine  (ISO)
cisplatin  (ISO)
citric acid  (ISO)
clevidipine  (ISO)
clofibrate  (ISO)
clofibric acid  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
corilagin  (EXP)
Cyclopamine  (ISO)
cyclophosphamide  (EXP)
cyclosporin A  (EXP,ISO)
cyfluthrin  (ISO)
cyhalothrin  (ISO)
cypermethrin  (ISO)
daunorubicin  (ISO)
DDE  (ISO)
deoxycholic acid  (EXP,ISO)
dexamethasone  (EXP,ISO)
dextran sulfate  (ISO)
dichloroacetic acid  (ISO)
dicrotophos  (ISO)
digoxin  (ISO)
dihydroartemisinin  (EXP,ISO)
dimethyl sulfoxide  (EXP)
Diosbulbin B  (ISO)
dioscin  (EXP)
diosgenin  (EXP)
Diphenadione  (ISO)
dipyridamole  (ISO)
dobutamine  (ISO)
Doramectin  (ISO)
dorsomorphin  (EXP)
doxorubicin  (EXP,ISO)
emamectin  (ISO)
emetine  (ISO)
emodin  (ISO)
endosulfan  (EXP)
enilconazole  (ISO)
eprinomectin  (ISO)
ethacridine  (ISO)
ethanol  (EXP,ISO)
ethylestrenol  (ISO)
farnesol  (ISO)
felodipine  (ISO)
fenbendazole  (ISO)
fenofibrate  (EXP,ISO)
fenvalerate  (ISO)
Fexaramine  (ISO)
flucythrinate  (ISO)
fluoranthene  (ISO)
fluoxastrobin  (ISO)
fluvalinate  (ISO)
fulvestrant  (ISO)
furan  (EXP,ISO)
gallocatechin  (ISO)
Geniposide  (EXP)
genistein  (ISO)
Gentiopicrin  (EXP)
ginsenoside Rg1  (EXP)
glafenine  (EXP)
glyburide  (EXP)
glycochenodeoxycholic acid  (ISO)
glycocholic acid  (ISO)
glycodeoxycholic acid  (ISO)
glycyrrhetinic acid  (EXP)
griseofulvin  (ISO)
guggulsterone  (EXP,ISO)
GW 3965  (ISO)
GW 4064  (EXP,ISO)
GW 7647  (ISO)
hexadecanoic acid  (ISO)
high-density lipoprotein cholesterol  (ISO)
hydrogen peroxide  (ISO)
ibuprofen  (ISO)
idarubicin  (ISO)
imazamox  (ISO)
imazapyr  (ISO)
Imazethapyr  (ISO)
isoniazide  (EXP,ISO)
isoprenaline  (EXP)
isotretinoin  (ISO)
Isradipine  (ISO)
ivermectin  (ISO)
juvenile hormone III  (ISO)
kadethrin  (ISO)
ketoconazole  (ISO)
lacidipine  (ISO)
lercanidipine  (ISO)
lipopolysaccharide  (EXP,ISO)
lithocholic acid  (EXP,ISO)
malic acid  (ISO)
manidipine  (ISO)
mebendazole  (ISO)
menadione  (ISO)
methapyrilene  (EXP)
methotrexate  (EXP)
methoxsalen  (EXP)
methyl 2-methylpropyl 2,6-dimethyl-4-(2-nitrophenyl)-1,4-dihydropyridine-3,5-dicarboxylate  (ISO)
methylmercury chloride  (ISO)
milbemycin  (ISO)
mitomycin C  (ISO)
monascin  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
montelukast  (ISO)
N,N-diethyl-m-toluamide  (EXP)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (EXP)
N-nitrosodiethylamine  (EXP,ISO)
naphthalenes  (ISO)
nefazodone  (EXP,ISO)
nemorubicin  (ISO)
nicardipine  (ISO)
nifedipine  (ISO)
nimesulide  (EXP)
nimodipine  (ISO)
nisoldipine  (ISO)
nitrendipine  (ISO)
nitrofen  (EXP)
nocodazole  (ISO)
obeticholic acid  (EXP,ISO)
oleanolic acid  (ISO)
oleic acid  (ISO)
oxfendazole  (ISO)
ozone  (ISO)
papaverine  (ISO)
paracetamol  (ISO)
pentamidine  (ISO)
pentanal  (ISO)
perfluorohexanesulfonic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP,ISO)
permethrin  (EXP,ISO)
phenethyl caffeate  (ISO)
phenobarbital  (ISO)
phenothrin  (ISO)
picoxystrobin  (ISO)
picropodophyllotoxin  (ISO)
Pirarubicin  (ISO)
pirinixic acid  (ISO)
platycodin D  (ISO)
podophyllotoxin  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
propanal  (ISO)
psoralen  (EXP)
pyrazinecarboxamide  (EXP)
quercetin  (ISO)
quinolines  (ISO)
resveratrol  (EXP)
rifaximin  (ISO)
ritonavir  (ISO)
rosuvastatin  (EXP)
rotenone  (ISO)
Salidroside  (ISO)
Selamectin  (ISO)
senecionine  (EXP)
silibinin  (EXP)
silicon dioxide  (ISO)
simvastatin  (EXP)
sirolimus  (ISO)
sodium arsenite  (ISO)
stigmasterol  (ISO)
streptozocin  (ISO)
tamibarotene  (ISO)
tamoxifen  (EXP)
tartrazine  (ISO)
taurine  (ISO)
tauro-beta-muricholic acid  (ISO)
taurocholic acid  (ISO)
taurodeoxycholic acid  (ISO)
temozolomide  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
tetracycline  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (ISO)
triclosan  (ISO)
trifloxystrobin  (ISO)
Triptolide  (ISO)
tris(2-butoxyethyl) phosphate  (ISO)
uranium atom  (EXP)
urethane  (ISO)
ursodeoxycholic acid  (EXP,ISO)
valproic acid  (EXP,ISO)
vincaleukoblastine  (ISO)
vincristine  (ISO)
vinorelbine  (ISO)
Yangonin  (ISO)
zinc acetate  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
bile acid and bile salt transport  (IDA,IEP,IMP)
bile acid metabolic process  (IDA,IMP,ISO)
bile acid signaling pathway  (IBA,IDA,IEP,IMP,ISO)
cell differentiation  (IBA)
cell-cell junction assembly  (ISO)
cellular glucose homeostasis  (IEA,ISO)
cellular response to bile acid  (IDA,IEA,ISO)
cellular response to fatty acid  (IEA,ISO)
cellular response to lipopolysaccharide  (IEA,ISO)
cellular response to organonitrogen compound  (IEA,ISO)
cellular response to xenobiotic stimulus  (IDA,IEP)
cellular triglyceride homeostasis  (IEA,ISO)
cholesterol homeostasis  (IEA,IEP,IMP,ISO)
defense response to bacterium  (IEA,ISO)
digestive tract development  (IEP)
fatty acid homeostasis  (IEA,ISO)
glucose homeostasis  (IEP,ISO)
hepatocyte proliferation  (IEP)
histone H3-R17 methylation  (IEA,ISO)
innate immune response  (IEA)
intracellular bile acid receptor signaling pathway  (IDA,IEA,ISO)
intracellular receptor signaling pathway  (ISO)
leukocyte migration involved in inflammatory response  (IEP)
lipid localization  (IEP)
liver regeneration  (IEP)
negative regulation of apoptotic process  (IEA,ISO)
negative regulation of collagen biosynthetic process  (IMP)
negative regulation of I-kappaB kinase/NF-kappaB signaling  (IEA,ISO)
negative regulation of inflammatory response  (IBA,IEA,ISO)
negative regulation of interferon-gamma production  (IEA,ISO)
negative regulation of interleukin-1 production  (ISO)
negative regulation of interleukin-2 production  (IEA,ISO)
negative regulation of interleukin-6 production  (ISO)
negative regulation of monocyte chemotactic protein-1 production  (ISO)
negative regulation of NF-kappaB transcription factor activity  (IEA,ISO)
negative regulation of transcription by RNA polymerase II  (IBA,IEA,IMP,ISO)
negative regulation of triglyceride biosynthetic process  (IMP)
negative regulation of tumor necrosis factor production  (IEA,ISO)
negative regulation of tumor necrosis factor-mediated signaling pathway  (ISO)
negative regulation of very-low-density lipoprotein particle remodeling  (IEA,ISO)
Notch signaling pathway  (IEA,ISO)
positive regulation of adipose tissue development  (IEA,ISO)
positive regulation of ammonia assimilation cycle  (IEA,ISO)
positive regulation of gene expression  (IMP)
positive regulation of glutamate metabolic process  (ISO)
positive regulation of insulin receptor signaling pathway  (IEA,ISO)
positive regulation of insulin secretion involved in cellular response to glucose stimulus  (IEA,ISO)
positive regulation of interleukin-17 production  (IEA,ISO)
positive regulation of phosphatidic acid biosynthetic process  (IEA,ISO)
positive regulation of transcription by RNA polymerase II  (IBA,IDA,IEA,IMP,ISO)
positive regulation of transcription, DNA-templated  (ISO)
regulation of bile acid secretion  (IEP)
regulation of carbohydrate metabolic process  (IMP)
regulation of gene expression  (IEP,IMP)
regulation of insulin secretion involved in cellular response to glucose stimulus  (IEA,ISO)
regulation of lipid storage  (IEP)
regulation of low-density lipoprotein particle clearance  (IEA,ISO)
regulation of transcription by RNA polymerase II  (IDA,ISO)
regulation of transcription, DNA-templated  (ISO)
regulation of urea metabolic process  (IEA,ISO)
response to 17alpha-ethynylestradiol  (IEP)
response to cholesterol  (IEP)
response to ethanol  (IEP)
response to fenofibrate  (IEP)
response to glucose  (IEP)
response to lipopolysaccharide  (IEP)
response to norepinephrine  (IMP)
response to nutrient levels  (IEP)
response to organic cyclic compound  (IEP)
response to xenobiotic stimulus  (IEP)
toll-like receptor 4 signaling pathway  (IEA,ISO)
toll-like receptor 9 signaling pathway  (ISO)
triglyceride homeostasis  (IEP,IMP,ISO)

Cellular Component
euchromatin  (IEA,ISO)
nucleus  (IDA,IEA)
receptor complex  (IDA,IEA,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
liver fibrosis  (IDA,IMP)
References

References - curated
1. Alvarez L, etal., Hum Mol Genet. 2004 Oct 15;13(20):2451-60. Epub 2004 Aug 18.
2. Bhargava P, etal., Nat Med. 2012 Nov;18(11):1665-72. doi: 10.1038/nm.2962. Epub 2012 Oct 28.
3. Bjursell M, etal., PLoS One. 2013 May 20;8(5):e64721. doi: 10.1371/journal.pone.0064721. Print 2013.
4. Byun S, etal., Nat Commun. 2018 Jul 3;9(1):2590. doi: 10.1038/s41467-018-04697-5.
5. Chen Y, etal., Hepatology. 2013 Apr;57(4):1530-41. doi: 10.1002/hep.26187. Epub 2013 Feb 15.
6. Côté I, etal., Br J Nutr. 2014 Nov 28;112(10):1592-600. doi: 10.1017/S0007114514002517. Epub 2014 Sep 29.
7. Côté I, etal., Eur J Nutr. 2013 Aug;52(5):1523-32. doi: 10.1007/s00394-012-0459-5. Epub 2012 Nov 2.
8. Degirolamo C, etal., Hepatology. 2015 Jan;61(1):161-70. doi: 10.1002/hep.27274. Epub 2014 Oct 30.
9. Dikopoulos N, etal., Eur J Clin Invest. 2003 Jan;33(1):58-64.
10. Duran-Sandoval D, etal., Diabetes. 2004 Apr;53(4):890-8.
11. Evans MJ, etal., Am J Physiol Gastrointest Liver Physiol. 2009 Mar;296(3):G543-52. doi: 10.1152/ajpgi.90585.2008. Epub 2009 Jan 8.
12. Fiorucci S, etal., J Pharmacol Exp Ther. 2005 Aug;314(2):584-95. Epub 2005 Apr 28.
13. Fiorucci S, etal., J Pharmacol Exp Ther. 2005 May;313(2):604-12. Epub 2005 Jan 11.
14. Fiorucci S, etal., J Pharmacol Exp Ther. 2005 Oct;315(1):58-68. Epub 2005 Jun 24.
15. Forman BM, etal., Cell 1995 Jun 2;81(5):687-93.
16. Gai Z, etal., Mol Pharmacol. 2018 Aug;94(2):802-811. doi: 10.1124/mol.117.111047. Epub 2018 May 9.
17. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
18. Ghoneim RH, etal., Br J Nutr. 2015 Feb 14;113(3):507-16. doi: 10.1017/S0007114514003717. Epub 2015 Jan 23.
19. GOA data from the GO Consortium
20. Han H, etal., Cell Physiol Biochem. 2018;49(4):1304-1319. doi: 10.1159/000493409. Epub 2018 Sep 17.
21. Honda A, etal., J Lipid Res. 2005 Feb;46(2):287-96. Epub 2004 Dec 1.
22. Hu T, etal., J Biol Chem. 2006 Dec 29;281(52):39831-8. Epub 2006 Oct 25.
23. Hu YB, etal., Drug Des Devel Ther. 2018 Jul 16;12:2213-2221. doi: 10.2147/DDDT.S170518. eCollection 2018.
24. Hwang ST, etal., Gastroenterology. 2002 May;122(5):1483-92.
25. Jia WJ, etal., Mol Med Rep. 2018 Jan;17(1):1545-1554. doi: 10.3892/mmr.2017.8025. Epub 2017 Nov 10.
26. Jiao N, etal., Gut. 2018 Oct;67(10):1881-1891. doi: 10.1136/gutjnl-2017-314307. Epub 2017 Aug 3.
27. Kim I, etal., Carcinogenesis. 2007 May;28(5):940-6. doi: 10.1093/carcin/bgl249. Epub 2006 Dec 20.
28. Kukla M, etal., World J Gastroenterol. 2017 Apr 14;23(14):2613-2624. doi: 10.3748/wjg.v23.i14.2613.
29. Lee FY, etal., Mol Endocrinol. 2010 Aug;24(8):1626-36. doi: 10.1210/me.2010-0117. Epub 2010 Jun 23.
30. Li G, etal., Toxicol Appl Pharmacol. 2013 Oct 15;272(2):299-305. doi: 10.1016/j.taap.2013.06.016. Epub 2013 Jun 26.
31. Li X, etal., Arch Toxicol. 2017 Jan;91(1):481-494. doi: 10.1007/s00204-016-1697-8. Epub 2016 Apr 18.
32. Lisman T, etal., Liver Int. 2018 Nov;38(11):1988-1996. doi: 10.1111/liv.13882. Epub 2018 May 30.
33. Liu Y, etal., J Clin Invest. 2003 Dec;112(11):1678-87. Epub 2003 Nov 17.
34. Lozano E, etal., Mol Cancer Res. 2014 Jan;12(1):91-100. doi: 10.1158/1541-7786.MCR-13-0503. Epub 2013 Nov 19.
35. Ma K, etal., J Clin Invest. 2006 Apr;116(4):1102-9. Epub 2006 Mar 23.
36. Magdy YM, etal., Exp Mol Pathol. 2018 Dec;105(3):293-310. doi: 10.1016/j.yexmp.2018.10.004. Epub 2018 Oct 9.
37. Makishima M, etal., Science. 1999 May 21;284(5418):1362-5. doi: 10.1126/science.284.5418.1362.
38. MGD data from the GO Consortium
39. Mi LZ, etal., Mol Cell. 2003 Apr;11(4):1093-100.
40. Modica S, etal., Gastroenterology. 2012 Feb;142(2):355-65.e1-4. doi: 10.1053/j.gastro.2011.10.028. Epub 2011 Nov 2.
41. Ogura J, etal., J Pharm Pharm Sci. 2012;15(5):616-31. doi: 10.18433/j38c88.
42. Pipeline to import KEGG annotations from KEGG into RGD
43. Pircher PC, etal., J Biol Chem. 2003 Jul 25;278(30):27703-11. Epub 2003 May 16.
44. Qu X, etal., Biol Pharm Bull. 2018;41(8):1211-1218. doi: 10.1248/bpb.b18-00028.
45. Renga B, etal., World J Gastroenterol. 2009 May 7;15(17):2097-108. doi: 10.3748/wjg.15.2097.
46. RGD automated data pipeline
47. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
48. RGD automated import pipeline for gene-chemical interactions
49. Saliola M, etal., Gut. 1998 Sep;43(3):428-32. doi: 10.1136/gut.43.3.428.
50. Schwabl P, etal., J Hepatol. 2017 Apr;66(4):724-733. doi: 10.1016/j.jhep.2016.12.005. Epub 2016 Dec 18.
51. Song CS, etal., J Biol Chem 2001 Nov 9;276(45):42549-56.
52. Stayrook KR, etal., Endocrinology. 2005 Mar;146(3):984-91. Epub 2004 Nov 24.
53. Tian J, etal., Sci Rep. 2017 Aug 21;7(1):8938. doi: 10.1038/s41598-017-09131-2.
54. Toppo E, etal., Biomed Pharmacother. 2018 Nov;107:979-988. doi: 10.1016/j.biopha.2018.08.019. Epub 2018 Aug 23.
55. Tripodi A, etal., Hepatology. 2005 Mar;41(3):553-8. doi: 10.1002/hep.20569.
56. Tully DC, etal., J Med Chem. 2017 Dec 28;60(24):9960-9973. doi: 10.1021/acs.jmedchem.7b00907. Epub 2017 Dec 8.
57. Verbeke L, etal., Hepatology. 2014 Jun;59(6):2286-98. doi: 10.1002/hep.26939. Epub 2014 Apr 14.
58. Violi F, etal., Gastroenterology. 1995 Aug;109(2):531-9. doi: 10.1016/0016-5085(95)90342-9.
59. Wagner M, etal., Gastroenterology. 2003 Sep;125(3):825-38. doi: 10.1016/s0016-5085(03)01068-0.
60. Wu SY, etal., Acta Pharmacol Sin. 2018 Dec;39(12):1865-1873. doi: 10.1038/s41401-018-0110-y. Epub 2018 Jul 30.
61. Xu W, etal., Toxicol Appl Pharmacol. 2017 Jan 15;315:23-34. doi: 10.1016/j.taap.2016.12.001. Epub 2016 Dec 6.
62. Yamagata H, etal., J Gastroenterol Hepatol. 1995 Jan-Feb;10(1):8-13. doi: 10.1111/j.1440-1746.1995.tb01040.x.
63. Yan X, etal., BMC Endocr Disord. 2017 Sep 25;17(1):60. doi: 10.1186/s12902-017-0211-5.
64. Yang F, etal., Br J Pharmacol. 2018 Mar;175(5):810-829. doi: 10.1111/bph.14126. Epub 2018 Jan 25.
65. Yang F, etal., Cancer Res. 2007 Feb 1;67(3):863-7. doi: 10.1158/0008-5472.CAN-06-1078.
66. Zhang F, etal., Eur J Pharm Sci. 2018 Oct 15;123:404-415. doi: 10.1016/j.ejps.2018.08.005. Epub 2018 Aug 2.
67. Zhang L, etal., Hepatology. 2012 Dec;56(6):2336-43. doi: 10.1002/hep.25905.
68. Zheng L, etal., Biomed Pharmacother. 2018 Jan;97:481-488. doi: 10.1016/j.biopha.2017.10.153. Epub 2017 Nov 6.
69. Zhu L, etal., J Hepatobiliary Pancreat Sci. 2018 Mar;25(3):195-205. doi: 10.1002/jhbp.537.
70. Zollner G, etal., J Hepatol. 2003 Oct;39(4):480-8. doi: 10.1016/s0168-8278(03)00228-9.
Additional References at PubMed
PMID:7760852   PMID:12421815   PMID:12477932   PMID:12660231   PMID:12815072   PMID:12891557   PMID:12917447   PMID:14729567   PMID:14990788   PMID:15471871   PMID:15521018   PMID:15590640  
PMID:15721319   PMID:16357303   PMID:16446356   PMID:16473946   PMID:18006431   PMID:18006476   PMID:18029909   PMID:18467501   PMID:18510855   PMID:18972444   PMID:19027009   PMID:19864602  
PMID:20026603   PMID:20155456   PMID:20305288   PMID:20447400   PMID:21205480   PMID:21242261   PMID:21757002   PMID:21924881   PMID:22661717   PMID:23070085   PMID:23372731   PMID:23410061  
PMID:23767959   PMID:23835330   PMID:23861371   PMID:24211198   PMID:24266967   PMID:25446530   PMID:25771127   PMID:26392308   PMID:26782298   PMID:26888176   PMID:27050864   PMID:27190252  
PMID:27896916   PMID:29198707   PMID:32443832   PMID:33092050  


Genomics

Comparative Map Data
Nr1h4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2723,846,122 - 23,942,085 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl723,846,122 - 23,942,047 (-)Ensembl
Rnor_6.0730,003,429 - 30,162,095 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl730,003,429 - 30,162,056 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0730,170,397 - 30,214,796 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0730,104,960 - 30,107,142 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4726,189,759 - 26,307,061 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1726,210,029 - 26,327,332 (-)NCBI
Celera720,992,814 - 21,085,820 (-)NCBICelera
Cytogenetic Map7q13NCBI
NR1H4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl12100,473,708 - 100,564,414 (+)EnsemblGRCh38hg38GRCh38
GRCh3812100,473,866 - 100,564,414 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3712100,867,644 - 100,958,192 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361299,391,810 - 99,481,774 (+)NCBINCBI36hg18NCBI36
Build 341299,370,146 - 99,460,111NCBI
Celera12100,532,992 - 100,622,995 (+)NCBI
Cytogenetic Map12q23.1NCBI
HuRef1297,928,334 - 98,018,410 (+)NCBIHuRef
CHM1_112100,833,597 - 100,923,679 (+)NCBICHM1_1
Nr1h4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391089,290,096 - 89,369,484 (-)NCBIGRCm39mm39
GRCm39 Ensembl1089,290,096 - 89,369,447 (-)Ensembl
GRCm381089,454,234 - 89,533,645 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1089,454,234 - 89,533,585 (-)EnsemblGRCm38mm10GRCm38
MGSCv371088,916,979 - 88,996,367 (-)NCBIGRCm37mm9NCBIm37
MGSCv361088,884,177 - 88,936,426 (-)NCBImm8
Celera1091,441,224 - 91,574,747 (-)NCBICelera
Cytogenetic Map10C2NCBI
cM Map1044.98NCBI
Nr1h4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540536,160,049 - 36,237,751 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540536,160,360 - 36,236,258 (+)NCBIChiLan1.0ChiLan1.0
NR1H4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.112101,457,885 - 101,548,058 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl12101,457,885 - 101,548,058 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01298,052,778 - 98,144,085 (+)NCBIMhudiblu_PPA_v0panPan3
NR1H4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11539,497,313 - 39,608,120 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1539,536,290 - 39,608,116 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1539,876,387 - 39,987,365 (+)NCBI
ROS_Cfam_1.01540,161,103 - 40,272,109 (+)NCBI
UMICH_Zoey_3.11539,418,531 - 39,529,420 (+)NCBI
UNSW_CanFamBas_1.01539,525,061 - 39,636,033 (+)NCBI
UU_Cfam_GSD_1.01539,799,183 - 39,910,169 (+)NCBI
Nr1h4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494520,304,852 - 20,379,409 (-)NCBI
SpeTri2.0NW_00493649213,315,265 - 13,365,186 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NR1H4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl583,604,288 - 83,684,604 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1583,607,222 - 83,732,668 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2587,754,914 - 87,828,507 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NR1H4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11195,792,428 - 95,877,989 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1195,792,996 - 95,878,293 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666037149,156,310 - 149,247,016 (-)NCBIVero_WHO_p1.0
Nr1h4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247507,222,306 - 7,303,809 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D7Wox37  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2723,846,173 - 23,846,345 (+)MAPPERmRatBN7.2
Rnor_6.0730,003,481 - 30,003,652NCBIRnor6.0
Rnor_5.0730,105,012 - 30,105,183UniSTSRnor5.0
RGSC_v3.4726,189,811 - 26,189,982UniSTSRGSC3.4
Celera720,992,866 - 20,993,037UniSTS
Cytogenetic Map7q13UniSTS
RH129412  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2723,846,369 - 23,846,561 (+)MAPPERmRatBN7.2
Rnor_6.0730,003,677 - 30,003,868NCBIRnor6.0
Rnor_5.0730,105,208 - 30,105,399UniSTSRnor5.0
RGSC_v3.4726,190,007 - 26,190,198UniSTSRGSC3.4
Celera720,993,062 - 20,993,253UniSTS
RH 3.4 Map7108.9UniSTS
Cytogenetic Map7q13UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7127829089Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7131962314Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7131962314Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)766427026029351Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)7946224658265113Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)7986646760460686Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)71557388960573889Rat
1582260Bw72Body weight QTL 723.20.0043body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
1582261Bw69Body weight QTL 693.20.0048body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
1582262Bw75Body weight QTL 7530.0038body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
2317059Aia15Adjuvant induced arthritis QTL 152.46joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)71700459862004598Rat
10755451Coatc11Coat color QTL 110coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)71794435762944357Rat
70207Niddm31Non-insulin dependent diabetes mellitus QTL 313.9blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)71816950526029351Rat
61369Mcs2Mammary carcinoma susceptibility QTL 23.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)71903280735526300Rat
1354637Scl30Serum cholesterol level QTL 303.7blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)71965431749753746Rat
1354644Spl4Serum phospholipid level QTL 44.9blood phospholipid amount (VT:0006084)blood phospholipid level (CMO:0001169)71965431749753746Rat
1354639Spl5Serum phospholipid level QTL 53.9blood LDL phospholipid amount (VT:0010505)blood low density lipoprotein phospholipid level (CMO:0001568)71965431752888450Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)71965431784928080Rat
2290372Gluco33Glucose level QTL 332.71blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)72055570529891047Rat
7411569Bw137Body weight QTL 1370.001body mass (VT:0001259)body weight gain (CMO:0000420)72192119566921195Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:244
Count of miRNA genes:154
Interacting mature miRNAs:172
Transcripts:ENSRNOT00000009910
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 23 23 23 23
Low 24 34 18 16 18 1 1 32 10 37 9 1
Below cutoff 19 3 7 7 42 2 4 2 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009910   ⟹   ENSRNOP00000009910
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl723,846,122 - 23,942,047 (-)Ensembl
Rnor_6.0 Ensembl730,003,429 - 30,162,056 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000091227   ⟹   ENSRNOP00000073765
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl723,846,351 - 23,903,525 (-)Ensembl
Rnor_6.0 Ensembl730,003,586 - 30,105,132 (-)Ensembl
RefSeq Acc Id: NM_021745   ⟹   NP_068513
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2723,846,122 - 23,942,047 (-)NCBI
Rnor_6.0730,003,429 - 30,162,056 (-)NCBI
Rnor_5.0730,104,960 - 30,107,142 (-)NCBI
Rnor_5.0730,170,397 - 30,214,796 (-)NCBI
RGSC_v3.4726,189,759 - 26,307,061 (-)RGD
Celera720,992,814 - 21,085,820 (-)RGD
Sequence:
RefSeq Acc Id: XM_008765260   ⟹   XP_008763482
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2723,846,354 - 23,904,247 (-)NCBI
Rnor_6.0730,003,578 - 30,105,682 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008765261   ⟹   XP_008763483
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2723,846,350 - 23,904,242 (-)NCBI
Rnor_6.0730,003,594 - 30,105,681 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008765262   ⟹   XP_008763484
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2723,846,354 - 23,942,085 (-)NCBI
Rnor_6.0730,003,578 - 30,162,095 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039079832   ⟹   XP_038935760
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2723,872,295 - 23,904,238 (-)NCBI
RefSeq Acc Id: XR_005486714
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2723,872,176 - 23,904,237 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_068513   ⟸   NM_021745
- UniProtKB: Q62735 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008763484   ⟸   XM_008765262
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008763482   ⟸   XM_008765260
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008763483   ⟸   XM_008765261
- Peptide Label: isoform X2
- UniProtKB: A0A0G2K6D2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000073765   ⟸   ENSRNOT00000091227
RefSeq Acc Id: ENSRNOP00000009910   ⟸   ENSRNOT00000009910
RefSeq Acc Id: XP_038935760   ⟸   XM_039079832
- Peptide Label: isoform X4
Protein Domains
NR LBD   Nuclear receptor

Transcriptome

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

Promoters
RGD ID:13695135
Promoter ID:EPDNEW_R5660
Type:multiple initiation site
Name:Nr1h4_1
Description:nuclear receptor subfamily 1, group H, member 4
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_6.0730,162,060 - 30,162,120EPDNEW

Strain Variation

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