Abcb11 (ATP binding cassette subfamily B member 11) - Rat Genome Database

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Gene: Abcb11 (ATP binding cassette subfamily B member 11) Rattus norvegicus
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Symbol: Abcb11
Name: ATP binding cassette subfamily B member 11
RGD ID: 619930
Description: Enables ABC-type xenobiotic transporter activity; bile acid transmembrane transporter activity; and carbohydrate transmembrane transporter activity. Involved in several processes, including canalicular bile acid transport; drug export; and drug transmembrane transport. Located in Golgi membrane; intracellular canaliculus; and recycling endosome membrane. Used to study cholestasis. Biomarker of alcoholic hepatitis and cholestasis. Human ortholog(s) of this gene implicated in benign recurrent intrahepatic cholestasis 2; intrahepatic cholestasis; liver cirrhosis; and progressive familial intrahepatic cholestasis 2. Orthologous to human ABCB11 (ATP binding cassette subfamily B member 11); PARTICIPATES IN bile acid signaling pathway; statin pharmacokinetics pathway; bile acid transport pathway; INTERACTS WITH (-)-epigallocatechin 3-gallate; (S)-colchicine; 1,3,5-trinitro-1,3,5-triazinane.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: ATP-binding cassette sub-family B member 11; ATP-binding cassette, sub-family B (MDR/TAP), member 11; ATP-binding cassette, subfamily B (MDR/TAP), member 11; bile salt export pump; Bsep; sister of P-glycoprotein; Spgp
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Abcb11em1Sage  
Genetic Models: SD-Abcb11em1Sage
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2354,016,854 - 54,112,797 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl354,017,127 - 54,112,730 (-)Ensembl
Rnor_6.0355,480,024 - 55,587,946 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl355,480,024 - 55,587,946 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0362,091,490 - 62,092,502 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0362,106,821 - 62,195,528 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera353,579,155 - 53,674,029 (-)NCBICelera
Cytogenetic Map3q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
(+)-epicatechin-3-O-gallate  (ISO)
(-)-epigallocatechin 3-gallate  (EXP,ISO)
(S)-colchicine  (EXP)
1,3,5-trinitro-1,3,5-triazinane  (EXP)
1-(5-isoquinolinesulfonyl)-2-methylpiperazine  (EXP)
1-[4-(1,3-benzodioxol-5-ylmethyl)-1-piperazinyl]-2-(4-chlorophenoxy)ethanone  (ISO)
1-naphthyl isothiocyanate  (EXP,ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP)
17beta-estradiol 17-glucosiduronic acid  (EXP)
17beta-estradiol 3-glucosiduronic acid  (EXP)
2'-(4-ethoxyphenyl)-5-(4-methylpiperazin-1-yl)-2,5'-bibenzimidazole  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (EXP)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
2-butan-2-yl-4-[4-[4-[4-[[2-(2,4-dichlorophenyl)-2-(1,2,4-triazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy]phenyl]-1-piperazinyl]phenyl]-1,2,4-triazol-3-one  (ISO)
3,3',5-triiodo-L-thyronine  (ISO)
4,4-difluoro-4-bora-3a,4a-diaza-s-indacene  (ISO)
4-amino-5-chloro-N-[1-[3-(4-fluorophenoxy)propyl]-3-methoxy-4-piperidinyl]-2-methoxybenzamide  (ISO)
5-(2-methylpiperazine-1-sulfonyl)isoquinoline  (EXP)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (ISO)
7,9-dihydro-1H-purine-2,6,8(3H)-trione  (ISO)
8-(4-chlorophenylthio)-cAMP  (ISO)
8-Br-cAMP  (EXP)
8-Epidiosbulbin E acetate  (ISO)
acadesine  (EXP,ISO)
acetamide  (EXP)
aflatoxin B1  (ISO)
AICA ribonucleotide  (EXP)
allopurinol  (ISO)
alpha-linolenic acid  (ISO)
amiodarone  (EXP,ISO)
amitriptyline  (EXP)
amprenavir  (ISO)
angelicin  (EXP)
ANTIMYCIN  (ISO)
arachidonic acid  (ISO)
astemizole  (ISO)
atazanavir sulfate  (ISO)
atenolol  (ISO)
atorvastatin calcium  (ISO)
ATP  (EXP,ISO)
atropine  (ISO)
azathioprine  (EXP)
benzbromarone  (ISO)
benziodarone  (ISO)
benzo[a]pyrene  (ISO)
beta-hexachlorocyclohexane  (ISO)
bexarotene  (EXP)
bezafibrate  (ISO)
bicalutamide  (ISO)
bilirubin IXalpha  (EXP)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
Boldine  (EXP)
bosentan  (EXP,ISO)
bromfenac  (ISO)
bucladesine  (EXP)
budesonide  (ISO)
buta-1,3-diene  (ISO)
cadmium dichloride  (EXP)
calcein am  (ISO)
calcium atom  (ISO)
calcium(0)  (ISO)
cefaclor  (ISO)
cefalotin  (ISO)
celecoxib  (ISO)
cerivastatin  (ISO)
cetirizine  (ISO)
cetrorelix  (ISO)
chelerythrine  (ISO)
chenodeoxycholic acid  (EXP,ISO)
chlordiazepoxide  (ISO)
chloroform  (EXP)
chlorohydrocarbon  (ISO)
chlorpromazine  (EXP,ISO)
cholate  (ISO)
cholesterol  (ISO)
cholic acid  (EXP,ISO)
choline  (ISO)
chrysophanol  (EXP)
ciglitazone  (ISO)
cinnarizine  (ISO)
ciprofibrate  (ISO)
cisapride  (ISO)
clarithromycin  (ISO)
clofazimine  (ISO)
clofibrate  (ISO)
clofibric acid  (EXP)
clotrimazole  (ISO)
cloxacillin  (EXP,ISO)
clozapine  (ISO)
copper(II) sulfate  (ISO)
coumarin  (EXP)
cyclosporin A  (EXP,ISO)
cyproconazole  (EXP)
danazol  (ISO)
DDE  (ISO)
dehydroepiandrosterone sulfate  (ISO)
deoxycholic acid  (EXP,ISO)
dexamethasone  (EXP,ISO)
dextran sulfate  (ISO)
diclofenac  (ISO)
dicloxacillin  (ISO)
diethylstilbestrol  (ISO)
dihydroartemisinin  (EXP)
dihydroergotamine  (ISO)
dioscin  (EXP)
dioxygen  (ISO)
dipyridamole  (ISO)
disodium selenite  (ISO)
disulfiram  (ISO)
dobutamine  (ISO)
dorsomorphin  (EXP,ISO)
doxycycline  (EXP)
drospirenone  (ISO)
drotaverine  (ISO)
efavirenz  (ISO)
emodin  (EXP,ISO)
enilconazole  (ISO)
epoxiconazole  (EXP)
ergocristine  (ISO)
erythromycin A  (ISO)
erythromycin estolate  (EXP,ISO)
ethanol  (EXP)
etoricoxib  (ISO)
everolimus  (ISO)
ezetimibe  (ISO)
felodipine  (ISO)
fenofibrate  (EXP,ISO)
Fexofenadine hydrochloride  (EXP,ISO)
finasteride  (ISO)
flucloxacillin  (ISO)
flutamide  (EXP)
fluvastatin  (ISO)
fluvoxamine  (ISO)
folic acid  (ISO)
furan  (EXP,ISO)
fusidic acid  (EXP,ISO)
gallocatechin  (ISO)
gefitinib  (ISO)
ginsenoside Re  (EXP,ISO)
ginsenoside Rg1  (EXP,ISO)
glafenine  (EXP)
glimepiride  (ISO)
glipizide  (ISO)
glyburide  (EXP,ISO)
glycochenodeoxycholic acid  (ISO)
glycocholic acid  (ISO)
glycodeoxycholic acid  (ISO)
glycyrrhetinate  (ISO)
glycyrrhetinic acid  (ISO)
glycyrrhizinic acid  (ISO)
Goe 6976  (EXP)
guggulsterone  (EXP,ISO)
GW 4064  (EXP,ISO)
Heliotrine  (ISO)
ibuprofen  (ISO)
iloperidone  (ISO)
imipenem hydrate  (ISO)
indinavir  (ISO)
indocyanine green  (ISO)
indometacin  (ISO)
irbesartan  (ISO)
isoniazide  (EXP)
Isradipine  (ISO)
itraconazole  (ISO)
ketoconazole  (ISO)
kynurenic acid  (ISO)
L-methionine  (ISO)
lapatinib  (ISO)
Lasiocarpine  (ISO)
latanoprost  (ISO)
lipopolysaccharide  (EXP,ISO)
lithocholic acid  (ISO)
lopinavir  (ISO)
Loratadine  (ISO)
losartan  (ISO)
lovastatin  (ISO)
Maprotiline  (EXP)
medroxyprogesterone acetate  (ISO)
megestrol acetate  (ISO)
metformin  (EXP,ISO)
methapyrilene  (ISO)
methimazole  (ISO)
methoxsalen  (EXP)
methylisothiazolinone  (ISO)
methyltestosterone  (ISO)
Mibefradil  (ISO)
midazolam  (ISO)
Midecamycin  (EXP,ISO)
mifepristone  (ISO)
MK 571  (ISO)
morin  (ISO)
N,N-diethyl-m-toluamide  (ISO)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (EXP)
N-[2-amino-6-[(4-fluorophenyl)methylamino]-3-pyridinyl]carbamic acid ethyl ester  (ISO)
N-nitrosodiethylamine  (EXP)
naproxen  (ISO)
nefazodone  (EXP,ISO)
nelfinavir  (ISO)
neomycin  (ISO)
neratinib  (ISO)
Nicardipine  (ISO)
nifedipine  (ISO)
nitrendipine  (ISO)
nitrofen  (EXP)
nitrofurantoin  (ISO)
norethisterone  (ISO)
notoginsenoside R1  (EXP,ISO)
O-methyleugenol  (ISO)
obeticholic acid  (EXP,ISO)
ochratoxin A  (EXP)
octreotide  (ISO)
ofloxacin  (ISO)
olanzapine  (ISO)
oleanolic acid  (ISO)
oleic acid  (EXP)
olmesartan  (ISO)
Olmesartan medoxomil  (ISO)
oltipraz  (ISO)
omeprazole  (ISO)
oxybutynin  (ISO)
paclitaxel  (ISO)
paracetamol  (EXP,ISO)
pazopanib  (ISO)
PCB138  (ISO)
perfluorohexanesulfonic acid  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
perfluorooctanoic acid  (ISO)
perhexiline  (EXP)
phalloidin  (EXP)
phenobarbital  (ISO)
phosphatidylcholine  (ISO)
physcion  (EXP)
Pilsicainide hydrochloride  (ISO)
pimecrolimus  (ISO)
pioglitazone  (ISO)
pirinixic acid  (ISO)
pitavastatin  (ISO)
pitavastatin(1-)  (ISO)
posaconazole  (ISO)
potassium dichromate  (ISO)
pravastatin  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
primaquine  (ISO)
primidone  (ISO)
prochloraz  (EXP)
progesterone  (ISO)
psoralen  (EXP)
pyrazinecarboxamide  (EXP)
quercetin  (EXP)
ranolazine  (ISO)
Repaglinide  (ISO)
reserpine  (ISO)
rifabutin  (ISO)
rifampicin  (EXP,ISO)
rifamycin SV  (ISO)
rifapentine  (ISO)
ritonavir  (ISO)
rosuvastatin calcium  (EXP,ISO)
Salidroside  (ISO)
saquinavir  (ISO)
senecionine  (ISO)
Senkirkine  (ISO)
silibinin  (EXP)
simvastatin  (EXP,ISO)
simvastatin hydroxy acid  (ISO)
sodium arsenite  (ISO)
sodium chloride  (ISO)
sodium dichromate  (EXP)
sorafenib  (ISO)
soybean oil  (EXP)
spironolactone  (ISO)
staurosporine  (ISO)
stigmasterol  (ISO)
streptozocin  (EXP,ISO)
sulfamethoxazole  (ISO)
sulfinpyrazone  (ISO)
tacrolimus hydrate  (ISO)
tamoxifen  (EXP,ISO)
tasosartan  (ISO)
taurine  (EXP)
tauro-beta-muricholic acid  (EXP)
taurochenodeoxycholic acid  (EXP,ISO)
taurocholic acid  (EXP,ISO)
taurodeoxycholic acid  (EXP,ISO)
taurolithocholic acid  (EXP,ISO)
tauroursodeoxycholic acid  (EXP)
telithromycin  (ISO)
telmisartan  (ISO)
Temsirolimus  (ISO)
Terfenadine  (ISO)
tert-butyl hydroperoxide  (EXP)
tetrachloromethane  (EXP,ISO)
tetracycline  (EXP)
thioacetamide  (EXP)
ticlopidine  (EXP,ISO)
tinidazole  (ISO)
tipranavir  (ISO)
tolcapone  (ISO)
Tolvaptan  (ISO)
triphenyl phosphate  (ISO)
Triptolide  (EXP,ISO)
triptonide  (ISO)
troglitazone  (EXP,ISO)
tropan-3alpha-yl 3-hydroxy-2-phenylpropanoate  (ISO)
ursodeoxycholic acid  (EXP,ISO)
valinomycin  (ISO)
valproic acid  (EXP,ISO)
valrubicin  (ISO)
vancomycin  (ISO)
vincaleukoblastine  (ISO)
wortmannin  (EXP,ISO)
Yangonin  (ISO)
zafirlukast  (ISO)
zidovudine  (EXP)
zinc acetate  (ISO)
zinc sulfate  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Besheer T, etal., Turk J Gastroenterol. 2018 May;29(3):299-307. doi: 10.5152/tjg.2018.17570.
2. Cai SY, etal., Gastroenterology. 2009 Mar;136(3):1060-9. doi: 10.1053/j.gastro.2008.10.025. Epub 2008 Nov 1.
3. Chen R, etal., Sci Rep. 2016 Jun 13;6:27750. doi: 10.1038/srep27750.
4. Crocenzi FA, etal., Am J Physiol Gastrointest Liver Physiol. 2003 Aug;285(2):G449-59. Epub 2003 Apr 17.
5. Cusato J, etal., J Antimicrob Chemother. 2017 Oct 1;72(10):2846-2849. doi: 10.1093/jac/dkx237.
6. Fuchs CD, etal., J Hepatol. 2017 Jan;66(1):95-101. doi: 10.1016/j.jhep.2016.08.017. Epub 2016 Sep 1.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. Gerloff T, etal., Eur J Biochem 2002 Jul;269(14):3495-503.
9. Gerloff T, etal., J Biol Chem 1998 Apr 17;273(16):10046-50.
10. GOA data from the GO Consortium
11. Hayashi H and Sugiyama Y, Mol Pharmacol. 2009 Jan;75(1):143-50. doi: 10.1124/mol.108.049288. Epub 2008 Oct 1.
12. Hayashi H, etal., Biochim Biophys Acta. 2005 Dec 30;1738(1-3):54-62. doi: 10.1016/j.bbalip.2005.10.006. Epub 2005 Nov 15.
13. Hayashi H, etal., Hepatology. 2012 Jun;55(6):1889-900. doi: 10.1002/hep.25591.
14. Henkel AS, etal., Gastroenterology. 2011 Oct;141(4):1404-11, 1411.e1-2. doi: 10.1053/j.gastro.2011.06.062. Epub 2011 Jul 2.
15. Hirano M, etal., J Pharmacol Exp Ther. 2005 Aug;314(2):876-82. Epub 2005 May 18.
16. Homolya L, etal., PLoS One. 2014 Mar 18;9(3):e91921. doi: 10.1371/journal.pone.0091921. eCollection 2014.
17. Kato T, etal., Biochim Biophys Acta. 2010 Sep;1801(9):1005-12. doi: 10.1016/j.bbalip.2010.04.002. Epub 2010 Apr 14.
18. Kipp H and Arias IM, J Biol Chem. 2000 May 26;275(21):15917-25.
19. Kipp H, etal., J Biol Chem. 2001 Mar 9;276(10):7218-24. doi: 10.1074/jbc.M007794200. Epub 2000 Dec 11.
20. Kubitz R, etal., Gastroenterology. 2004 Feb;126(2):541-53.
21. Li X, etal., Arch Toxicol. 2017 Jan;91(1):481-494. doi: 10.1007/s00204-016-1697-8. Epub 2016 Apr 18.
22. Marrone J, etal., IUBMB Life. 2017 Dec;69(12):978-984. doi: 10.1002/iub.1689. Epub 2017 Oct 31.
23. Matsushima S, etal., Mol Pharmacol. 2008 May;73(5):1474-83. doi: 10.1124/mol.107.041459. Epub 2008 Feb 1.
24. MGD data from the GO Consortium
25. Mochizuki K, etal., Am J Physiol Gastrointest Liver Physiol. 2007 Mar;292(3):G818-28. doi: 10.1152/ajpgi.00415.2006. Epub 2006 Nov 2.
26. Monte MJ, etal., Clin Sci (Lond). 2005 Aug;109(2):199-207.
27. M├╝llenbach R, etal., BMC Gastroenterol. 2012 Jun 8;12:63. doi: 10.1186/1471-230X-12-63.
28. NCBI rat LocusLink and RefSeq merged data July 26, 2002
29. OMIM Disease Annotation Pipeline
30. Ortiz DF, etal., J Biol Chem 2004 Jul 30;279(31):32761-70. Epub 2004 May 24.
31. Pawlikowska L, etal., J Hepatol. 2010 Jul;53(1):170-8. doi: 10.1016/j.jhep.2010.01.034. Epub 2010 Apr 13.
32. Perez LM, etal., Toxicol Sci. 2006 May;91(1):150-8. Epub 2006 Feb 1.
33. Pipeline to import KEGG annotations from KEGG into RGD
34. RGD automated data pipeline
35. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
36. RGD automated import pipeline for gene-chemical interactions
37. Stindt J, etal., Liver Int. 2013 Nov;33(10):1527-35. doi: 10.1111/liv.12217. Epub 2013 Jun 12.
38. Strautnieks SS, etal., Nat Genet. 1998 Nov;20(3):233-8.
39. Takahashi T, etal., Hepatol Int. 2018 May;12(3):254-261. doi: 10.1007/s12072-018-9860-3. Epub 2018 Apr 12.
40. Tygstrup N, etal., Biochem Biophys Res Commun 2002 Jan 11;290(1):518-25.
41. Vos TA, etal., Hepatology. 1998 Dec;28(6):1637-44.
42. Wakabayashi Y, etal., Mol Biol Cell. 2004 Jul;15(7):3485-96. doi: 10.1091/mbc.e03-10-0737. Epub 2004 Apr 30.
43. Wang L, etal., J Clin Invest. 2002 Oct;110(7):965-72.
44. Xu W, etal., Toxicol Appl Pharmacol. 2017 Jan 15;315:23-34. doi: 10.1016/j.taap.2016.12.001. Epub 2016 Dec 6.
45. Yabuuchi H, etal., Biopharm Drug Dispos. 2008 Nov;29(8):441-8. doi: 10.1002/bdd.629.
46. Zhang Y, etal., J Biol Chem. 2012 Jul 13;287(29):24784-94. doi: 10.1074/jbc.M111.329318. Epub 2012 May 22.
Additional References at PubMed
PMID:11279518   PMID:12068294   PMID:12538788   PMID:15040800   PMID:15763547   PMID:17384956   PMID:17615179   PMID:17855769   PMID:17916651   PMID:17947449   PMID:18551070   PMID:19056867  
PMID:20147439   PMID:20702406   PMID:21748767   PMID:22057277   PMID:23096566   PMID:23108811   PMID:23200860   PMID:23376485   PMID:24002920   PMID:26646631   PMID:27237619   PMID:28645914  
PMID:30068870   PMID:31746430  


Genomics

Comparative Map Data
Abcb11
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2354,016,854 - 54,112,797 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl354,017,127 - 54,112,730 (-)Ensembl
Rnor_6.0355,480,024 - 55,587,946 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl355,480,024 - 55,587,946 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0362,091,490 - 62,092,502 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0362,106,821 - 62,195,528 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera353,579,155 - 53,674,029 (-)NCBICelera
Cytogenetic Map3q21NCBI
ABCB11
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2168,915,498 - 169,031,324 (-)EnsemblGRCh38hg38GRCh38
GRCh382168,915,468 - 169,031,396 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372169,777,291 - 169,887,834 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362169,487,695 - 169,596,079 (-)NCBINCBI36hg18NCBI36
Build 342169,604,955 - 169,713,340NCBI
Celera2163,404,770 - 163,513,162 (-)NCBI
Cytogenetic Map2q31.1NCBI
HuRef2161,675,981 - 161,784,996 (-)NCBIHuRef
CHM1_12169,785,291 - 169,893,825 (-)NCBICHM1_1
Abcb11
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39269,068,626 - 69,172,960 (-)NCBIGRCm39mm39
GRCm39 Ensembl269,068,626 - 69,172,960 (-)Ensembl
GRCm38269,238,282 - 69,342,616 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl269,238,282 - 69,342,616 (-)EnsemblGRCm38mm10GRCm38
MGSCv37269,076,339 - 69,180,673 (-)NCBIGRCm37mm9NCBIm37
MGSCv36269,039,121 - 69,143,426 (-)NCBImm8
Celera270,904,503 - 71,008,403 (-)NCBICelera
Cytogenetic Map2C2NCBI
cM Map239.69NCBI
Abcb11
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554495,412,876 - 5,512,701 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554495,412,958 - 5,511,629 (+)NCBIChiLan1.0ChiLan1.0
ABCB11
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B173,664,518 - 173,776,233 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B173,664,518 - 173,776,379 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B56,199,434 - 56,311,773 (-)NCBIMhudiblu_PPA_v0panPan3
ABCB11
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13613,742,895 - 13,835,312 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3613,746,964 - 13,834,974 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3613,757,951 - 13,834,638 (-)NCBI
ROS_Cfam_1.03613,859,241 - 13,951,551 (-)NCBI
UMICH_Zoey_3.13613,948,052 - 14,024,630 (-)NCBI
UNSW_CanFamBas_1.03613,935,894 - 14,012,502 (-)NCBI
UU_Cfam_GSD_1.03614,048,864 - 14,125,753 (-)NCBI
Abcb11
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303131,017,599 - 131,107,385 (-)NCBI
SpeTri2.0NW_00493646910,521,576 - 10,599,005 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ABCB11
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1575,400,766 - 75,486,403 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11575,402,296 - 75,487,092 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21584,505,249 - 84,590,184 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ABCB11
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11054,458,283 - 54,575,943 (-)NCBI
ChlSab1.1 Ensembl1054,459,377 - 54,575,059 (-)Ensembl
Vero_WHO_p1.0NW_023666040144,979,703 - 145,077,569 (+)NCBI
Abcb11
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247876,653,849 - 6,733,058 (-)NCBI

Position Markers
D18061  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2354,017,159 - 54,017,235 (+)MAPPERmRatBN7.2
Rnor_6.0355,480,056 - 55,480,131NCBIRnor6.0
Rnor_5.0362,091,522 - 62,091,597UniSTSRnor5.0
Celera353,579,187 - 53,579,262UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31086191289878372Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
2298542Neuinf11Neuroinflammation QTL 113.9nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)31500542276927699Rat
631676Cm8Cardiac mass QTL 87.030.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)31695470861954708Rat
10450804Scl70Serum cholesterol level QTL 704.70.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)32071409065714090Rat
10450794Scl69Serum cholesterol level QTL 696.30.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)32071409065714090Rat
2302055Pia30Pristane induced arthritis QTL 303.50.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)32793691972936919Rat
9590286Uminl1Urine mineral level QTL 13.50.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)32824968773249687Rat
8694196Abfw2Abdominal fat weight QTL 216.580.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)32824968773249687Rat
8694386Bw159Body weight QTL 1594.520.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)32824968773249687Rat
8552950Pigfal12Plasma insulin-like growth factor 1 level QTL 127.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)32824968773249687Rat
9590136Scort3Serum corticosterone level QTL 323.370.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)32824968773249687Rat
2303593Gluco46Glucose level QTL 463blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)32846857173468571Rat
1354590Despr11Despair related QTL 110.000031locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)32846857173468571Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)329463235118376539Rat
61419Cia11Collagen induced arthritis QTL 115.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)33035677398535386Rat
61356Bp37Blood pressure QTL 373blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)33068464275684642Rat
631647Bp122Blood pressure QTL 1226.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)33068464275684642Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
11565451Bw177Body weight QTL 1770.002body mass (VT:0001259)body weight (CMO:0000012)33142640370668733Rat
11565452Kidm57Kidney mass QTL 570.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)33142640370668733Rat
12879866Cm94Cardiac mass QTL 940.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)33142640370668733Rat
12879867Cm95Cardiac mass QTL 950.047heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)33142640370668733Rat
12879868Am6Aortic mass QTL 60.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)33142640370668733Rat
2301400Cm68Cardiac mass QTL 680.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)33142640370668733Rat
1300169Bp177Blood pressure QTL 1772.96arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)33370334761017857Rat
1354589Bw31Body weight QTL 313.3body mass (VT:0001259)body weight (CMO:0000012)33370334778196190Rat
1354604Bw36Body weight QTL 362.9body mass (VT:0001259)body weight (CMO:0000012)333703347104104347Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)338192233133483320Rat
738019Anxrr10Anxiety related response QTL 103.9exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)33851780383517803Rat
2302276Bw82Body weight QTL 824.32body mass (VT:0001259)body weight (CMO:0000012)33945463762951183Rat
1331777Bw24Body weight QTL 243.503body mass (VT:0001259)body weight (CMO:0000012)33945463789115240Rat
1331795Rf30Renal function QTL 303.708urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)33945463789115240Rat
1354597Kidm13Kidney mass QTL 132.9kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)341874578104104347Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
1300178Hrtrt4Heart rate QTL 43.74heart pumping trait (VT:2000009)heart rate (CMO:0000002)34382736490905114Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)343827364121056321Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
1358186Ept2Estrogen-induced pituitary tumorigenesis QTL 28.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)347233430110362260Rat
2292613Ept16Estrogen-induced pituitary tumorigenesis QTL 168.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)347233430110362260Rat
631665Bw8Body weight QTL 85.5body mass (VT:0001259)body weight (CMO:0000012)350437042119183768Rat
724523Tsu1Thymus enlargement suppressive QTL 13.84thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)350437504115638231Rat
1582249Bw77Body weight QTL 773.20.0025epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)35318459364655484Rat
1582218Bw74Body weight QTL 743.90.0021body mass (VT:0001259)body weight (CMO:0000012)353184593115665732Rat
1582238Bw68Body weight QTL 683.20.0064body mass (VT:0001259)body weight (CMO:0000012)353184593115665732Rat
1582239Epfw1Epididymal fat weight QTL 14.50.0006epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)353184593115665732Rat
61377Edpm3Estrogen-dependent pituitary mass QTL 37.050.038pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)35318469289878207Rat
731180Bp152Blood pressure QTL 1520.03arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)35378111291609953Rat
731180Bp152Blood pressure QTL 1520.03arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)35378111291609953Rat
731180Bp152Blood pressure QTL 1520.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)35378111291609953Rat


Genetic Models
This gene Abcb11 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:40
Count of miRNA genes:36
Interacting mature miRNAs:40
Transcripts:ENSRNOT00000075107
Prediction methods: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 27 27 27
Low 2 24 8 19 8 2 2 1 10 6 7 2
Below cutoff 1 7 6 6 6 6 6 32 9 21 4 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000075107   ⟹   ENSRNOP00000064279
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl354,017,128 - 54,112,730 (-)Ensembl
Rnor_6.0 Ensembl355,480,024 - 55,587,946 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000104145   ⟹   ENSRNOP00000084310
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl354,017,127 - 54,100,973 (-)Ensembl
RefSeq Acc Id: NM_031760   ⟹   NP_113948
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2354,017,128 - 54,112,730 (-)NCBI
Rnor_6.0355,480,024 - 55,587,946 (-)NCBI
Rnor_5.0362,091,490 - 62,092,502 (-)NCBI
Rnor_5.0362,106,821 - 62,195,528 (-)NCBI
Celera353,579,155 - 53,674,029 (-)RGD
Sequence:
RefSeq Acc Id: XM_039105931   ⟹   XP_038961859
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2354,016,854 - 54,112,797 (-)NCBI
RefSeq Acc Id: XM_039105932   ⟹   XP_038961860
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2354,016,854 - 54,112,780 (-)NCBI
RefSeq Acc Id: XM_039105933   ⟹   XP_038961861
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2354,016,854 - 54,095,865 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_113948   ⟸   NM_031760
- UniProtKB: O70127 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000064279   ⟸   ENSRNOT00000075107
RefSeq Acc Id: XP_038961859   ⟸   XM_039105931
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038961860   ⟸   XM_039105932
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038961861   ⟸   XM_039105933
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000084310   ⟸   ENSRNOT00000104145
Transcriptome

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

Promoters
RGD ID:13692112
Promoter ID:EPDNEW_R2637
Type:initiation region
Name:Abcb11_1
Description:ATP binding cassette subfamily B member 11
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_6.0355,587,960 - 55,588,020EPDNEW

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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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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
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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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
SHRSP/Gcrc (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
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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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)