Abcb4 (ATP binding cassette subfamily B member 4) - Rat Genome Database

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Gene: Abcb4 (ATP binding cassette subfamily B member 4) Rattus norvegicus
Analyze
Symbol: Abcb4
Name: ATP binding cassette subfamily B member 4
RGD ID: 620248
Description: Predicted to enable ATPase-coupled intramembrane lipid transporter activity; ATPase-coupled transmembrane transporter activity; and xenobiotic transmembrane transporter activity. Involved in response to drug and response to glucocorticoid. Located in Golgi membrane and apical plasma membrane. Biomarker of cholestasis. Human ortholog(s) of this gene implicated in cholestasis (multiple); gallbladder disease; and liver cirrhosis (multiple). Orthologous to human ABCB4 (ATP binding cassette subfamily B member 4); PARTICIPATES IN multidrug resistance protein mediated transport pathway; bile acid transport pathway; INTERACTS WITH (+)-schisandrin B; 1,9-dideoxyforskolin; 1-naphthyl isothiocyanate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: ATP-binding cassette sub-family B (MDR/TAP) member 4 (P-glycoprotein 3/ multidrug resistance 2; ATP-binding cassette sub-family B (MDR/TAP) member 4 (P-glycoprotein 3/ multidrug resistance 2); ATP-binding cassette sub-family B member 4; ATP-binding cassette, sub-family B (MDR/TAP), member 4; ATP-binding cassette, sub-family B (MDR/TAP), member 4 (P-glycoprotein 3/ multidrug resistance 2); ATP-binding cassette, subfamily B (MDR/TAP), member 4; ATP-binding cassette, subfamily B, member 4; Mdr2; multidrug resistance protein 2; multidrug resistance protein 3; P-glycoprotein 2; P-glycoprotein 3; P-glycoprotein 3/ multidrug resistance 2; Pgy3; phosphatidylcholine translocator ABCB4
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2425,150,998 - 25,209,489 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl425,151,953 - 25,209,202 (-)Ensembl
Rnor_6.0422,133,984 - 22,192,687 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl422,133,521 - 22,425,515 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0422,070,806 - 22,128,781 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4421,946,274 - 22,004,328 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1421,946,273 - 22,004,328 (+)NCBI
Celera420,645,103 - 20,702,285 (-)NCBICelera
Cytogenetic Map4q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(2,4,5-trichlorophenoxy)acetic acid  (ISO)
(6aR,9R)-N-[(2S)-1-hydroxybutan-2-yl]-4,7-dimethyl-6,6a,8,9-tetrahydroindolo[4,3-fg]quinoline-9-carboxamide  (ISO)
(RS)-coclaurine  (ISO)
(RS)-norcoclaurine  (ISO)
(S)-coclaurine  (ISO)
1,2-dimethylhydrazine  (ISO)
1,9-dideoxyforskolin  (EXP)
1-[4-(1,3-benzodioxol-5-ylmethyl)-1-piperazinyl]-2-(4-chlorophenoxy)ethanone  (ISO)
1-naphthyl isothiocyanate  (EXP,ISO)
1-phenyl-1-cyclopentanecarboxylic acid 2-[2-(diethylamino)ethoxy]ethyl ester  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
17beta-estradiol 17-glucosiduronic acid  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP,ISO)
2,4-D  (ISO)
2-(3,4-dimethoxyphenyl)-5-\{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino\}-2-(propan-2-yl)pentanenitrile  (EXP,ISO)
3,3',5-triiodo-L-thyronine  (ISO)
3,5-diethoxycarbonyl-1,4-dihydrocollidine  (ISO)
3-\{1-[3-(dimethylamino)propyl]-1H-indol-3-yl\}-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione  (ISO)
3-methylcholanthrene  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (ISO)
adefovir  (EXP)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
all-trans-retinoic acid  (ISO)
alpha-hexachlorocyclohexane  (EXP)
amiodarone  (EXP,ISO)
ammonium chloride  (EXP)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
aspartame  (ISO)
atazanavir sulfate  (ISO)
atorvastatin calcium  (ISO)
azathioprine  (EXP)
beclomethasone  (ISO)
benzarone  (ISO)
benzatropine  (ISO)
benzbromarone  (ISO)
benziodarone  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
benzo[e]pyrene  (ISO)
bezafibrate  (EXP,ISO)
bicalutamide  (ISO)
biperiden  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bosentan  (ISO)
bromosulfophthalein  (EXP)
brompheniramine  (ISO)
buta-1,3-diene  (ISO)
cadmium dichloride  (EXP)
caffeine  (ISO)
calcitriol  (EXP)
carbon nanotube  (ISO)
carboplatin  (EXP)
chenodeoxycholic acid  (EXP,ISO)
chlorphenamine  (ISO)
chlorpromazine  (ISO)
cholesterol  (ISO)
cholic acid  (ISO)
chromium(6+)  (ISO)
ciprofibrate  (ISO)
clemastine  (ISO)
clofibrate  (ISO)
clofibric acid  (EXP,ISO)
colforsin daropate hydrochloride  (ISO)
copper(II) sulfate  (ISO)
cycloheximide  (ISO)
cyclosporin A  (ISO)
deoxycholic acid  (ISO)
dexamethasone  (EXP)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
dibenz[a,h]anthracene  (ISO)
dichloroacetic acid  (ISO)
diclofenac  (ISO)
dihydroergotamine  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
doxycycline  (EXP)
doxylamine  (ISO)
ebrotidine  (ISO)
emodin  (EXP)
entinostat  (ISO)
esmolol  (ISO)
ethanol  (ISO)
fenofibrate  (ISO)
flutamide  (EXP,ISO)
fluvoxamine  (ISO)
fumonisin B1  (ISO)
furan  (EXP)
genistein  (EXP)
gentamycin  (EXP)
glutathione  (ISO)
glyburide  (EXP)
glycochenodeoxycholic acid  (ISO)
glycocholic acid  (ISO)
glycodeoxycholic acid  (ISO)
glycyrrhetinate  (ISO)
glycyrrhetinic acid  (ISO)
gold atom  (ISO)
gold(0)  (ISO)
griseofulvin  (ISO)
guanethidine  (ISO)
guggulsterone  (ISO)
GW 4064  (EXP,ISO)
herbicide  (ISO)
hydroxyzine  (ISO)
indocyanine green  (ISO)
isoprenaline  (EXP,ISO)
ketoconazole  (EXP,ISO)
labetalol  (ISO)
lapatinib  (ISO)
leflunomide  (EXP,ISO)
Licochalcone B  (ISO)
lipopolysaccharide  (EXP,ISO)
lithocholic acid  (ISO)
Loratadine  (ISO)
LY-2157299  (ISO)
metformin  (EXP)
methapyrilene  (EXP,ISO)
methotrexate  (ISO)
methoxsalen  (EXP,ISO)
methyltestosterone  (ISO)
methysergide  (ISO)
monosodium L-glutamate  (ISO)
N,N-diethyl-m-toluamide  (EXP)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (ISO)
N-nitrosodiethylamine  (EXP)
N-Nitrosopyrrolidine  (ISO)
nefazodone  (EXP,ISO)
nitrofurantoin  (ISO)
nomifensine  (ISO)
nortriptyline  (ISO)
O-methyleugenol  (ISO)
obeticholic acid  (EXP,ISO)
omeprazole  (ISO)
oxaliplatin  (EXP)
oxybutynin  (ISO)
oxycodone  (EXP)
paclitaxel  (ISO)
paliperidone palmitate  (ISO)
paracetamol  (ISO)
paraquat  (EXP)
pazopanib  (ISO)
penbutolol  (ISO)
perfluoroheptanoic acid  (ISO)
perfluorohexanesulfonic acid  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
perfluorooctanoic acid  (EXP)
perhexiline  (EXP,ISO)
permethrin  (EXP)
phenazopyridine  (ISO)
phenformin  (EXP)
phenobarbital  (EXP)
Phenoxybenzamine  (ISO)
phentolamine  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
phosphatidylcholine  (ISO)
physcion  (EXP)
pirinixic acid  (ISO)
pravastatin  (EXP)
pregnenolone 16alpha-carbonitrile  (EXP,ISO)
primaquine  (ISO)
procyclidine  (ISO)
procymidone  (EXP)
propiconazole  (ISO)
protriptyline  (ISO)
pyrazinecarboxamide  (EXP)
quercetin  (ISO)
rifampicin  (ISO)
ritonavir  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
senecionine  (ISO)
simvastatin  (EXP,ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
Soman  (EXP)
soybean oil  (EXP)
streptozocin  (EXP)
tacrine  (ISO)
tamoxifen  (EXP,ISO)
tamsulosin  (ISO)
tartrazine  (ISO)
tasosartan  (ISO)
taurocholic acid  (EXP)
Technetium tc 99m sestamibi  (ISO)
tenofovir disoproxil fumarate  (ISO)
tetrachloromethane  (EXP)
tetracycline  (EXP,ISO)
thioacetamide  (EXP)
tipranavir  (ISO)
titanium dioxide  (ISO)
tolterodine tartrate  (ISO)
topotecan  (EXP)
triadimefon  (ISO)
triclosan  (ISO)
triphenyl phosphate  (EXP)
troglitazone  (EXP,ISO)
tungsten  (ISO)
ursodeoxycholic acid  (ISO)
valdecoxib  (EXP)
valproic acid  (EXP,ISO)
verapamil  (EXP,ISO)
vinclozolin  (EXP)
vincristine  (ISO)
vorinostat  (ISO)
Y-27632  (ISO)
yohimbine  (ISO)
zafirlukast  (ISO)
zimeldine  (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. Aronson SJ, etal., J Hepatol. 2019 Jul;71(1):153-162. doi: 10.1016/j.jhep.2019.03.021. Epub 2019 Mar 29.
2. Brown PC, etal., Nucleic Acids Res 1993 Aug 11;21(16):3885-91.
3. de Vree JM, etal., Proc Natl Acad Sci U S A 1998 Jan 6;95(1):282-7.
4. Degiorgio D, etal., J Gastroenterol. 2016 Mar;51(3):271-80. doi: 10.1007/s00535-015-1110-z. Epub 2015 Sep 1.
5. Deuchars KL, etal., Biochim Biophys Acta 1992 Mar 24;1130(2):157-65.
6. Fickert P, etal., Gastroenterology. 2004 Jul;127(1):261-74.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. Gotthardt D, etal., Hepatology. 2008 Oct;48(4):1157-66. doi: 10.1002/hep.22485.
9. Hagenbuch B, etal., News Physiol Sci 2002 Dec;17:231-4.
10. Hooiveld GJ, etal., Gastroenterology. 1999 Sep;117(3):678-87.
11. Hyogo H, etal., Dig Dis Sci. 2001 Oct;46(10):2089-97.
12. Jirsa M, etal., World J Gastroenterol. 2014 May 21;20(19):5867-74. doi: 10.3748/wjg.v20.i19.5867.
13. Kipp H and Arias IM, J Biol Chem. 2000 May 26;275(21):15917-25.
14. Luttringer O, etal., Biochem Pharmacol. 2002 Dec 1;64(11):1637-50.
15. MGD data from the GO Consortium
16. Nakken KE, etal., Scand J Gastroenterol. 2007 Oct;42(10):1245-55. doi: 10.1080/00365520701320521.
17. NCBI rat LocusLink and RefSeq merged data July 26, 2002
18. Ohishi Y, etal., Hepatology. 2008 Sep;48(3):853-62. doi: 10.1002/hep.22382.
19. OMIM Disease Annotation Pipeline
20. Ortiz DF, etal., J Biol Chem 2004 Jul 30;279(31):32761-70. Epub 2004 May 24.
21. Paulusma CC, etal., Science 1996 Feb 23;271(5252):1126-8.
22. Pipeline to import KEGG annotations from KEGG into RGD
23. RGD automated data pipeline
24. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
25. RGD automated import pipeline for gene-chemical interactions
26. Smit JJ, etal., Cell 1993 Nov 5;75(3):451-62.
27. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
28. Tomaiuolo R, etal., Dig Liver Dis. 2009 Nov;41(11):817-22. Epub 2009 May 20.
29. Tygstrup N, etal., Biochem Biophys Res Commun 2002 Jan 11;290(1):518-25.
30. van Waarde WM, etal., Gastroenterology. 2002 Jun;122(7):1842-52.
31. Ziol M, etal., Gastroenterology. 2008 Jul;135(1):131-41. doi: 10.1053/j.gastro.2008.03.044. Epub 2008 Mar 26.
Additional References at PubMed
PMID:1990275   PMID:7948020   PMID:8615769   PMID:8898203   PMID:11279518   PMID:12068294   PMID:17065236   PMID:17523162   PMID:19674157   PMID:20107068   PMID:22324395   PMID:23486593  
PMID:23533145   PMID:24045840   PMID:24806754  


Genomics

Comparative Map Data
Abcb4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2425,150,998 - 25,209,489 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl425,151,953 - 25,209,202 (-)Ensembl
Rnor_6.0422,133,984 - 22,192,687 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl422,133,521 - 22,425,515 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0422,070,806 - 22,128,781 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4421,946,274 - 22,004,328 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1421,946,273 - 22,004,328 (+)NCBI
Celera420,645,103 - 20,702,285 (-)NCBICelera
Cytogenetic Map4q12NCBI
ABCB4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl787,401,696 - 87,480,435 (-)EnsemblGRCh38hg38GRCh38
GRCh38787,398,988 - 87,476,722 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37787,031,012 - 87,104,996 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36786,869,297 - 86,942,955 (-)NCBINCBI36hg18NCBI36
Build 34786,676,016 - 86,754,402NCBI
Celera781,736,239 - 81,809,903 (-)NCBI
Cytogenetic Map7q21.12NCBI
HuRef781,642,357 - 81,716,022 (-)NCBIHuRef
CHM1_1786,961,467 - 87,035,121 (-)NCBICHM1_1
CRA_TCAGchr7v2786,362,871 - 86,436,531 (-)NCBI
Abcb4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3958,943,614 - 9,009,226 (+)NCBIGRCm39mm39
GRCm39 Ensembl58,943,717 - 9,009,231 (+)Ensembl
GRCm3858,893,614 - 8,959,226 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl58,893,717 - 8,959,231 (+)EnsemblGRCm38mm10GRCm38
MGSCv3758,893,721 - 8,959,226 (+)NCBIGRCm37mm9NCBIm37
MGSCv3658,899,723 - 8,965,232 (+)NCBImm8
Celera58,813,446 - 8,878,635 (+)NCBICelera
Cytogenetic Map5A1NCBI
cM Map53.43NCBI
ABCB4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1793,046,085 - 93,119,439 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl793,046,085 - 93,119,439 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0779,395,924 - 79,469,755 (-)NCBIMhudiblu_PPA_v0panPan3
ABCB4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11413,542,610 - 13,614,334 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1413,548,462 - 13,614,571 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1413,114,115 - 13,185,936 (-)NCBI
ROS_Cfam_1.01413,307,604 - 13,379,530 (-)NCBI
UMICH_Zoey_3.11413,510,779 - 13,582,706 (-)NCBI
UNSW_CanFamBas_1.01413,236,739 - 13,308,588 (-)NCBI
UU_Cfam_GSD_1.01413,520,259 - 13,592,210 (-)NCBI
Abcb4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511826,585,866 - 26,661,600 (-)NCBI
SpeTri2.0NW_0049367631,339,849 - 1,415,528 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ABCB4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1993,171,371 - 93,262,124 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.29102,651,665 - 102,741,039 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ABCB4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12161,459,344 - 61,529,017 (+)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604242,535,591 - 42,605,958 (-)NCBIVero_WHO_p1.0


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61351Bp33Blood pressure QTL 330.0018arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4127716890Rat
61408Scl23Serum cholesterol level QTL 230.0005blood HDL phospholipid amount (VT:0010504)serum high density lipoprotein phospholipid level (CMO:0001567)4127716890Rat
724557Plsm1Polydactyly-luxate syndrome (PLS) morphotypes QTL 10.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)4127716890Rat
1641905Colcr1Colorectal carcinoma resistance QTL 14.30.0003intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)4129494328Rat
61333Gluco16Glucose level QTL 164.30.00001adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)4130372989Rat
9589097Slep11Serum leptin concentration QTL 115.090.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)4131934116Rat
8552903Pigfal2Plasma insulin-like growth factor 1 level QTL 27.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)4131934116Rat
9589046Scfw2Subcutaneous fat weight QTL 25.540.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)4131934116Rat
9590100Sffal4Serum free fatty acids level QTL 47.360.05blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)4131934116Rat
738021Hcar13Hepatocarcinoma resistance QTL 134.3liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)4132584199Rat
1357341Gluco5Glucose level QTL 56.4adipocyte free fatty acid secretion trait (VT:0010465)absolute change in adipocyte free fatty acid secretion per unit volume (CMO:0001446)4133250345Rat
1357343Gluco4Glucose level QTL 40.00002adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake to basal glucose uptake ratio (CMO:0000874)4133250345Rat
61415Eae11Experimental allergic encephalomyelitis QTL 112.9nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)4139505420Rat
634323Hc2Hypercalciuria QTL 22.15urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)421079645210796Rat
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4521460278882945Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
2302371Stl22Serum triglyceride level QTL 225.15blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829457114705Rat
1358203Stl19Serum triglyceride level QTL 192.80.002blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829465958103Rat
1358201Gluco12Glucose level QTL121.6adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake (CMO:0000870)4521839229593287Rat
631642Stl2Serum triglyceride level QTL 23.3blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521917856647776Rat
631209Bw2Body weight QTL24.2retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)4994088544463908Rat
1300141Bp178Blood pressure QTL 178arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)41002490139524530Rat
6478724Anxrr35Anxiety related response QTL 350.00449defecation behavior trait (VT:0010462)defecation measurement (CMO:0000997)41008408955084089Rat
6478766Anxrr47Anxiety related response QTL 470.09637locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)41008408955084089Rat
6478769Anxrr48Anxiety related response QTL 480.02514locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)41008408955084089Rat
8694374Bw155Body weight QTL 1553.390.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)41008408955084089Rat
9590304Scort17Serum corticosterone level QTL 174.960.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)41008408955084089Rat
8552906Pigfal3Plasma insulin-like growth factor 1 level QTL 3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)41008408955084089Rat
631261Tcas3Tongue tumor susceptibility QTL 36.88tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)41081417091360527Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
2303585Bw86Body weight QTL 864body mass (VT:0001259)body weight (CMO:0000012)41467806559678065Rat
2313401Anxrr27Anxiety related response QTL 27aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)41793350862933508Rat
70222Eae2Experimental allergic encephalomyelitis QTL 24.3nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)42133334339505420Rat
1354665Stl10Serum triglyceride level QTL 103.57blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)42133334344463908Rat
61412Pia2Pristane induced arthritis QTL 23.9joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)42133334362278020Rat
8552803Bw144Body weight QTL 14416body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)42271068534430484Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:128
Count of miRNA genes:104
Interacting mature miRNAs:110
Transcripts:ENSRNOT00000043822
Prediction methods:Microtar, Miranda, Rnahybrid
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 31 31 7 31 3 4 8
Low 27 26 10 12 10 8 11 70 20 30 3 8
Below cutoff 16 4 12 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000043822   ⟹   ENSRNOP00000042556
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl425,151,956 - 25,209,202 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000094965   ⟹   ENSRNOP00000097106
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl425,151,953 - 25,209,202 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000095305   ⟹   ENSRNOP00000090279
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl425,151,956 - 25,208,984 (-)Ensembl
RefSeq Acc Id: NM_012690   ⟹   NP_036822
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2425,151,956 - 25,209,200 (-)NCBI
Rnor_6.0422,134,805 - 22,192,472 (-)NCBI
Rnor_5.0422,070,806 - 22,128,781 (-)NCBI
RGSC_v3.4421,946,274 - 22,004,328 (+)RGD
Celera420,645,103 - 20,702,285 (-)RGD
Sequence:
RefSeq Acc Id: XM_006235999   ⟹   XP_006236061
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2425,150,998 - 25,203,388 (-)NCBI
Rnor_6.0422,133,984 - 22,186,777 (-)NCBI
Rnor_5.0422,070,806 - 22,128,781 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006236000   ⟹   XP_006236062
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2425,150,998 - 25,203,551 (-)NCBI
Rnor_6.0422,133,984 - 22,186,779 (-)NCBI
Rnor_5.0422,070,806 - 22,128,781 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008762697   ⟹   XP_008760919
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2425,150,998 - 25,209,392 (-)NCBI
Rnor_6.0422,133,984 - 22,192,659 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592474   ⟹   XP_017447963
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2425,150,998 - 25,209,489 (-)NCBI
Rnor_6.0422,133,984 - 22,192,687 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039107075   ⟹   XP_038963003
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2425,150,998 - 25,203,551 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_036822   ⟸   NM_012690
- UniProtKB: Q08201 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006236062   ⟸   XM_006236000
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006236061   ⟸   XM_006235999
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008760919   ⟸   XM_008762697
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017447963   ⟸   XM_017592474
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_038963003   ⟸   XM_039107075
- Peptide Label: isoform X5
RefSeq Acc Id: ENSRNOP00000097106   ⟸   ENSRNOT00000094965
RefSeq Acc Id: ENSRNOP00000042556   ⟸   ENSRNOT00000043822
RefSeq Acc Id: ENSRNOP00000090279   ⟸   ENSRNOT00000095305
Transcriptome

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

Promoters
RGD ID:13692827
Promoter ID:EPDNEW_R3352
Type:initiation region
Name:Abcb1b_2
Description:ATP-binding cassette, subfamily B (MDR/TAP), member 1B
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R3353  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0422,192,467 - 22,192,527EPDNEW

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)
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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)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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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
WKY/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
WKY/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
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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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
WKY/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
WN/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
WN/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
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
4 22135794 22135795 G A snv Buf/N (MCW)
4 22141077 22141078 C T snv F344/NRrrc (MCW), MR/N (MCW), ACI/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620248 AgrOrtholog
Ensembl Genes ENSRNOG00000008012 Ensembl, UniProtKB/TrEMBL
  ENSRNOG00000068001 Ensembl
Ensembl Protein ENSRNOP00000038721 UniProtKB/TrEMBL
  ENSRNOP00000042556 UniProtKB/TrEMBL
  ENSRNOP00000049952 UniProtKB/TrEMBL
  ENSRNOP00000075278 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000037712 UniProtKB/TrEMBL
  ENSRNOT00000043822 UniProtKB/TrEMBL
  ENSRNOT00000047126 UniProtKB/TrEMBL
  ENSRNOT00000082359 UniProtKB/TrEMBL
Gene3D-CATH 1.20.1560.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.40.50.300 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro AAA+_ATPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ABC1_TM_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ABC1_TM_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ABC_transporter-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ABC_transporter_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MDR1 UniProtKB/TrEMBL
  MDR3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Type_I_exporter UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24891 UniProtKB/Swiss-Prot
NCBI Gene 24891 ENTREZGENE
PANTHER PTHR24221 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR24221:SF241 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR24221:SF251 UniProtKB/TrEMBL
Pfam ABC_membrane UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ABC_tran UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB ABCB4 RGD
PhenoGen Abcb4 PhenoGen
PROSITE ABC_TM1F UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ABC_TRANSPORTER_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ABC_TRANSPORTER_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART AAA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF90123 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC210446
UniProt A0A0G2KA64_RAT UniProtKB/TrEMBL
  D4A0Y9_RAT UniProtKB/TrEMBL
  G3V9C8_RAT UniProtKB/TrEMBL
  G3V9J6_RAT UniProtKB/TrEMBL
  MDR3_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q78E07 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-25 Abcb4  ATP binding cassette subfamily B member 4  Abcb4  ATP-binding cassette, subfamily B (MDR/TAP), member 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-11-16 Abcb4  ATP-binding cassette, subfamily B (MDR/TAP), member 4  Abcb4  ATP-binding cassette, sub-family B (MDR/TAP), member 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2003-04-09 Abcb4  ATP-binding cassette, sub-family B (MDR/TAP), member 4      Symbol and Name updated 629477 APPROVED
2003-03-06 Abcb4  ATP-binding cassette, sub-family B (MDR/TAP), member 4  Pgy3  P-glycoprotein 3/ multidrug resistance 2  Data Merged 628472 PROVISIONAL
2002-08-07 Abcb4        Symbol and Name status set to provisional 70820 PROVISIONAL
2002-06-10 Pgy3  P-glycoprotein 3/ multidrug resistance 2      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease increased hepatic expression occurs in streptozotocin induced diabetic rats 724707
gene_expression expression reduced in response to certain types of liver damage 70249
gene_process responsible for decreased drug accumulation in multidrug-resistant cells 724707