Cyp2b1 (cytochrome P450, family 2, subfamily b, polypeptide 1) - Rat Genome Database

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Gene: Cyp2b1 (cytochrome P450, family 2, subfamily b, polypeptide 1) Rattus norvegicus
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Symbol: Cyp2b1
Name: cytochrome P450, family 2, subfamily b, polypeptide 1
RGD ID: 2466
Description: Enables Hsp70 protein binding activity; Hsp90 protein binding activity; and steroid hydroxylase activity. Involved in several processes, including response to calcium ion; response to insulin; and response to sulfur dioxide. Located in mitochondrial inner membrane. Biomarker of mental depression and obesity. Human ortholog(s) of this gene implicated in acute myeloid leukemia; human immunodeficiency virus infectious disease; and tuberculosis. Orthologous to human CYP2B6 (cytochrome P450 family 2 subfamily B member 6); PARTICIPATES IN arachidonic acid metabolic pathway; phase I biotransformation pathway via cytochrome P450; retinol metabolic pathway; INTERACTS WITH (+)-artemisinin; (-)-cotinine; (R)-camphor.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Cyp2b-1; Cypbe; CYPIIB1; cytochrome P450 2B1; Cytochrome P450, subfamily IIB (phenobarbital-inducible) (b, e); cytochrome P450-B; cytochrome P450-LM2; cytochrome P450-PB1; cytochrome P450-PB2; cytochrome P450b; MGC188065; P450-B; P450-LM2; P450-PB1 and P450-PB2; P450b
RGD Orthologs
Mouse
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2181,518,387 - 81,544,999 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl181,518,408 - 81,542,052 (+)Ensembl
Rnor_6.0799,142,431 - 99,183,540 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl799,142,450 - 99,181,783 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0799,752,108 - 99,777,546 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4181,266,828 - 81,290,471 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1181,341,201 - 81,344,952 (+)NCBI
Celera175,950,659 - 75,974,302 (+)NCBICelera
Cytogenetic Map7q33NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-artemisinin  (EXP,ISO)
(+)-catechin  (ISO)
(+)-epicatechin-3-O-gallate  (ISO)
(-)-anisomycin  (ISO)
(-)-cotinine  (EXP)
(-)-epigallocatechin 3-gallate  (ISO)
(R)-camphor  (EXP)
(R,R,R)-alpha-tocopherol  (ISO)
(S)-nicotine  (EXP)
1,1,1-Trichloro-2-(4-hydroxyphenyl)-2-(4-methoxyphenyl)ethane  (EXP)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (ISO)
1,2,4,5-tetrachlorobenzene  (EXP)
1,2-dichloroethane  (ISO)
1,2-dichloroethene  (EXP)
1,2-dimethylhydrazine  (EXP)
1,4-benzoquinone  (EXP)
1,4-dichlorobenzene  (EXP,ISO)
1,4-dioxane  (EXP)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
19-Nor-17alpha-pregn-5(10)-en-20-yne-3alpha,17beta-diol  (EXP)
2,2',3,3',6,6'-hexachlorobiphenyl  (EXP,ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (EXP,ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP,ISO)
2,2',5,5'-tetrachlorobiphenyl  (EXP)
2,3',4,4',5-Pentachlorobiphenyl  (EXP)
2,3,4,3',4'-Pentachlorobiphenyl  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-Triphenyl-1-hexene  (ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (EXP)
2,6-di-tert-butyl-4-methylphenol  (EXP)
2-(3,4-dimethoxyphenyl)-5-\{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino\}-2-(propan-2-yl)pentanenitrile  (ISO)
2-acetamidofluorene  (EXP)
2-nitrotoluene  (ISO)
2-Oxohexane  (EXP)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP,ISO)
3,3',5,5'-tetrabromobisphenol A  (EXP)
3,3'-diindolylmethane  (EXP)
3,5-diethoxycarbonyl-1,4-dihydrocollidine  (ISO)
3-methylbenzyl alcohol  (EXP)
3-methylcholanthrene  (EXP,ISO)
4'-tert-Butyl-2',6'-dimethyl-3',5'-dinitroacetophenone  (EXP,ISO)
4,4'-diaminodiphenylmethane  (EXP)
4,4'-methylene-bis-(2-chloroaniline)  (EXP)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (EXP)
4-nonylphenol  (ISO)
4-Vinylcyclohexene  (EXP)
5,5-diethylbarbituric acid  (EXP)
5,7-dihydroxy-4'-methoxyflavone  (EXP)
5-fluorouracil  (EXP)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (EXP,ISO)
5-methoxyindole  (ISO)
5alpha-androst-16-en-3alpha-ol  (ISO)
6-propyl-2-thiouracil  (ISO)
7,12-dimethyltetraphene  (EXP)
acephate  (ISO)
acetone  (EXP)
acetonitrile  (EXP)
acifluorfen  (ISO)
actinomycin D  (ISO)
aflatoxin B1  (EXP,ISO)
AICA ribonucleotide  (EXP)
alachlor  (EXP)
all-trans-retinoic acid  (ISO)
allyl alcohol  (EXP)
allyl isothiocyanate  (ISO)
alpha-hexachlorocyclohexane  (EXP)
alpha-pinene  (EXP)
amiodarone  (ISO)
amitraz  (EXP)
amitriptyline  (EXP)
amitrole  (EXP)
ammonium chloride  (EXP)
andrographolide  (ISO)
androst-4-ene-3,17-dione  (ISO)
androstane  (ISO)
aniline  (EXP)
Aroclor 1254  (EXP)
aspartame  (EXP)
atorvastatin calcium  (ISO)
atrazine  (ISO)
barbiturates  (EXP)
benzene  (EXP)
benzo[a]pyrene  (EXP,ISO)
benzo[b]fluoranthene  (ISO)
Benzo[k]fluoranthene  (ISO)
benzophenone  (EXP)
berberine  (ISO)
bergomottin  (ISO)
beta-hexachlorocyclohexane  (ISO)
beta-myrcene  (EXP)
beta-naphthoflavone  (EXP,ISO)
bexarotene  (EXP)
bilobalide  (EXP)
biphenyl-4-amine  (EXP)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bitertanol  (EXP)
bromodichloromethane  (EXP)
bromuconazole  (EXP)
brucine  (EXP)
bupropion  (EXP,ISO)
buta-1,3-diene  (ISO)
butylated hydroxyanisole  (ISO)
Butylbenzyl phthalate  (EXP,ISO)
Butylparaben  (EXP)
C.I. Natural Red 20  (EXP)
camphor  (EXP)
cannabidiol  (ISO)
captan  (ISO)
carbamazepine  (EXP)
carbon monoxide  (EXP)
Chalepensin  (ISO)
chloral hydrate  (EXP)
chlordecone  (EXP,ISO)
chlorobenzene  (EXP)
chlorpromazine  (ISO)
chlorpyrifos  (EXP,ISO)
chlorzoxazone  (EXP)
cholesterol  (ISO)
cholic acid  (ISO)
choline  (EXP,ISO)
chrysin  (ISO)
ciguatoxin CTX1B  (ISO)
ciprofibrate  (EXP,ISO)
citral  (EXP)
citronellal  (EXP)
climbazole  (EXP)
clofibrate  (EXP,ISO)
clofibric acid  (EXP)
clonazepam  (EXP)
clotrimazole  (EXP,ISO)
cobalt dichloride  (ISO)
cortisol  (EXP)
crocidolite asbestos  (ISO)
cumene hydroperoxide  (EXP)
curcumin  (EXP)
cyanocob(III)alamin  (ISO)
cyclophosphamide  (EXP,ISO)
cyhalothrin  (EXP)
cylindrospermopsin  (ISO)
cypermethrin  (EXP,ISO)
cyproconazole  (EXP,ISO)
cyproterone  (ISO)
cyproterone acetate  (ISO)
DDD  (EXP)
DDE  (EXP)
DDT  (EXP,ISO)
decabromodiphenyl ether  (EXP,ISO)
deoxycholic acid  (EXP)
dexamethasone  (EXP,ISO)
dextran sulfate  (EXP,ISO)
dextromethorphan  (ISO)
Diallyl sulfide  (EXP,ISO)
diallyl trisulfide  (EXP)
diazepam  (EXP,ISO)
dibutyl phthalate  (EXP)
diclofenac  (ISO)
dicofol  (EXP)
Dicyclohexyl phthalate  (EXP)
dieldrin  (ISO)
diethyl phthalate  (EXP)
diethyldithiocarbamic acid  (EXP)
diethylstilbestrol  (EXP)
dihydroergotamine  (ISO)
diiodine  (ISO)
Dimethyl phthalate  (EXP)
dimethyl sulfoxide  (EXP,ISO)
dimethylarsinic acid  (EXP)
dioxygen  (EXP)
dipropyl phthalate  (EXP)
disulfiram  (EXP)
elemental selenium  (ISO)
endosulfan  (EXP,ISO)
enilconazole  (ISO)
epoxiconazole  (EXP,ISO)
Erionite  (ISO)
estriol  (ISO)
estrone  (ISO)
ethanol  (EXP,ISO)
ethoxyquin  (ISO)
ethylbenzene  (EXP)
ethylparaben  (EXP)
farnesol  (EXP)
fenarimol  (ISO)
fenbuconazole  (ISO)
fenofibrate  (EXP,ISO)
fenvalerate  (EXP)
fipronil  (EXP,ISO)
fluconazole  (ISO)
flumequine  (ISO)
fluoren-9-one  (EXP)
fluorene  (EXP)
folic acid  (ISO)
fulvestrant  (ISO)
gadolinium trichloride  (EXP)
gallocatechin  (ISO)
gamma-hexachlorocyclohexane  (EXP)
gamma-terpinene  (EXP)
geranial  (EXP)
ginsenoside Rg1  (EXP)
glafenine  (EXP)
glycine betaine  (ISO)
griseofulvin  (ISO)
guggulsterone  (ISO)
GW 7647  (EXP)
hemin  (EXP)
hexachlorobenzene  (EXP)
hexane  (EXP)
hydrogen peroxide  (EXP)
hydroquinone  (EXP)
Hydroxybupropion  (EXP)
ifosfamide  (EXP)
imperatorin  (ISO)
indole-3-methanol  (EXP)
isopimpinellin  (ISO)
isoprenaline  (ISO)
Isosafrole  (EXP)
ivermectin  (ISO)
ketamine  (EXP)
ketoconazole  (EXP,ISO)
kojic acid  (ISO)
L-ascorbic acid  (ISO)
L-methionine  (ISO)
lansoprazole  (EXP)
lead diacetate  (ISO)
limonene  (EXP)
linuron  (EXP)
lithocholic acid  (ISO)
m-tolualdehyde  (EXP)
m-xylene  (EXP)
mangiferin  (EXP)
Meclizine  (ISO)
MeIQx  (ISO)
mephenytoin  (ISO)
mercury dichloride  (ISO)
metazachlor  (EXP)
metformin  (ISO)
methoxsalen  (EXP,ISO)
methoxychlor  (EXP,ISO)
methylarsonic acid  (EXP)
metolachlor  (EXP)
metyrapone  (EXP)
midazolam  (ISO)
mifepristone  (EXP)
mirex  (EXP,ISO)
mitomycin C  (EXP)
monobenzyl phthalate  (EXP)
Monobutylphthalate  (EXP)
monocrotaline  (ISO)
monosodium L-glutamate  (ISO)
musk xylene  (EXP,ISO)
N'-(2,4-dimethylphenyl)-N-methylformamidine  (EXP)
N,N-diethyl-m-toluamide  (EXP)
N-acetyl-L-cysteine  (EXP)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-Nitrosodi-n-butylamine  (EXP)
N-Nitrosodi-n-propylamine  (EXP)
N-nitrosodiethylamine  (EXP,ISO)
N-Vinyl-2-pyrrolidone  (EXP)
NADP zwitterion  (EXP)
NADP(+)  (EXP)
nevirapine  (EXP)
nickel atom  (ISO)
nickel sulfate  (ISO)
nicotine  (EXP)
nifedipine  (ISO)
nitrapyrin  (ISO)
Nonylphenol  (ISO)
o-xylene  (EXP)
Octachlorostyrene  (ISO)
octamethylcyclotetrasiloxane  (EXP)
okadaic acid  (EXP,ISO)
oleanolic acid  (ISO)
oltipraz  (EXP,ISO)
omeprazole  (EXP,ISO)
ortho-Aminoazotoluene  (ISO)
Oxadiazon  (ISO)
oxazepam  (EXP,ISO)
oxolane  (ISO)
Oxyfluorfen  (ISO)
ozone  (ISO)
p-menthan-3-ol  (ISO)
p-xylene  (EXP)
pantoprazole  (EXP)
paracetamol  (EXP)
paraquat  (EXP)
parathion  (EXP)
parathion-methyl  (EXP)
PCB138  (EXP)
pentachlorobenzene  (EXP)
pentane-2,3-dione  (EXP)
pentobarbital  (EXP)
perfluorobutanesulfonic acid  (ISO)
perfluorodecanoic acid  (ISO)
perfluorododecanoic acid  (ISO)
perfluoroheptanoic acid  (ISO)
perfluorohexanesulfonic acid  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
perfluorooctanoic acid  (EXP,ISO)
perfluoroundecanoic acid  (ISO)
permethrin  (EXP,ISO)
phenanthrene  (ISO)
phenethyl caffeate  (EXP)
phenformin  (EXP)
phenobarbital  (EXP,ISO)
phenol  (EXP)
phenytoin  (EXP,ISO)
phlorizin  (ISO)
phorone  (EXP,ISO)
pioglitazone  (EXP,ISO)
piperonyl butoxide  (EXP,ISO)
pirinixic acid  (EXP,ISO)
pravastatin  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP,ISO)
prochloraz  (EXP,ISO)
progesterone  (ISO)
propachlor  (EXP)
propiconazole  (EXP,ISO)
propylbenzene  (EXP)
propylparaben  (EXP)
propyzamide  (EXP,ISO)
purpurin  (ISO)
pyrazinecarboxamide  (EXP)
pyrene  (EXP,ISO)
pyrethrins  (EXP)
pyridine  (EXP,ISO)
quercetin  (ISO)
quinidine  (ISO)
reactive oxygen species  (EXP)
resveratrol  (EXP,ISO)
retinyl acetate  (ISO)
Retrorsine  (EXP)
rifampicin  (ISO)
rotenone  (EXP)
selenium atom  (ISO)
senecionine  (ISO)
Shikonin  (EXP)
sodium arsenite  (EXP)
sodium chromate  (EXP)
sodium dichromate  (EXP,ISO)
stilbene oxide  (EXP)
streptozocin  (EXP,ISO)
strychnine  (EXP)
styrene  (EXP)
styrene oxide  (EXP)
succimer  (ISO)
Sudan III  (EXP)
sulfasalazine  (ISO)
sulfoxaflor  (EXP,ISO)
tacrine  (EXP)
tamoxifen  (ISO)
tebuconazole  (EXP,ISO)
tert-butanol  (ISO)
tert-butyl ethyl ether  (EXP)
testosterone  (EXP,ISO)
tetrachloroethene  (EXP)
tetrachloromethane  (EXP,ISO)
tetrahydrocurcumin  (ISO)
thiabendazole  (EXP)
thiacloprid  (ISO)
thiophanate-methyl  (EXP,ISO)
Thiotepa  (EXP)
titanium dioxide  (ISO)
toluene  (EXP)
toluene 2,4-diisocyanate  (EXP)
toxaphene  (ISO)
trans-1,2-dichloroethene  (EXP)
tremolite asbestos  (ISO)
triadimefon  (EXP,ISO)
trichloroethene  (ISO)
triclocarban  (ISO)
triclosan  (EXP)
trimethylarsine oxide  (EXP)
triphenyl phosphate  (EXP,ISO)
Triptolide  (EXP,ISO)
triptonide  (ISO)
troglitazone  (EXP,ISO)
uranium atom  (EXP)
ursodeoxycholic acid  (EXP,ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
verapamil  (ISO)
verteporfin  (ISO)
vinclozolin  (EXP,ISO)
warfarin  (ISO)
zaragozic acid A  (ISO)
zinc atom  (ISO)
zinc protoporphyrin  (EXP)
zinc(0)  (ISO)
ziram  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Alterman MA and Hanzlik RP, FEBS Lett 2002 Feb 13;512(1-3):319-22.
2. Anandatheerthavarada HK, etal., J Biol Chem. 2009 Jun 19;284(25):17352-63. doi: 10.1074/jbc.M109.007492. Epub 2009 Apr 28.
3. Czekaj P, etal., Acta Biochim Pol 2000;47(4):1115-27.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. Gavrilovich Zgoda V, etal., Arch Biochem Biophys 2002 Dec 1;408(1):58-68.
6. Gilbert EA, etal., J Neural Transm 2003 Oct;110(10):1091-101.
7. Hanna IH, etal., Biochemistry. 1998 Jan 6;37(1):311-8.
8. Hirasawa F, etal., Biomed Res. 2008 Dec;28(6):323-30.
9. John GH, etal., Arch Biochem Biophys. 1994 Nov 1;314(2):367-75.
10. Konstandi M, etal., J Appl Toxicol. 2008 Sep 16.
11. Kotsovolou O, etal., Prog Neuropsychopharmacol Biol Psychiatry. 2010 Aug 16;34(6):1075-84. Epub 2010 Jun 4.
12. Lee SH and Lee SM, Shock. 2005 Feb;23(2):144-9.
13. Lupp A, etal., Arzneimittelforschung. 2008;58(5):225-41.
14. Mochizuki M, etal., J Toxicol Sci. 2008 Aug;33(3):307-14.
15. NCBI rat LocusLink and RefSeq merged data July 26, 2002
16. Pan J, etal., Xenobiotica 2002 Sep;32(9):739-47.
17. Pipeline to import KEGG annotations from KEGG into RGD
18. Qin GH and Meng ZQ, Wei Sheng Yan Jiu. 2006 Sep;35(5):554-6.
19. RGD automated data pipeline
20. RGD automated import pipeline for gene-chemical interactions
21. Samudre KR, etal., Biochem Biophys Res Commun 2002 Mar 29;292(2):312-7.
22. Shaw PM, etal., Biochim Biophys Acta 1996 Feb 7;1305(1-2):54-8.
23. Sindhu RK, etal., Free Radic Res. 2006 Sep;40(9):921-8.
24. Zangar RC, etal., J Pharmacol Exp Ther. 1999 Sep;290(3):1436-41.
25. Zhao H, etal., Environ Health Perspect. 2006 Aug;114(8):1253-8.
Additional References at PubMed
PMID:109438   PMID:2539047   PMID:2583091   PMID:2989270   PMID:3838174   PMID:3928374   PMID:6300027   PMID:6306654   PMID:6953431   PMID:8142377   PMID:12164868   PMID:12477932  
PMID:14722249   PMID:15572372   PMID:15774478   PMID:15813386   PMID:16418063   PMID:17560764   PMID:17646928   PMID:17697118   PMID:19702544   PMID:20166883   PMID:20407477   PMID:20947506  
PMID:21467745   PMID:22612225   PMID:22905390   PMID:23012479   PMID:24368200   PMID:24727239   PMID:25036135   PMID:25052003   PMID:26913515   PMID:28532222   PMID:31049204  


Genomics

Candidate Gene Status
Cyp2b1 is a candidate Gene for QTL Tcas6
Comparative Map Data
Cyp2b1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2181,518,387 - 81,544,999 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl181,518,408 - 81,542,052 (+)Ensembl
Rnor_6.0799,142,431 - 99,183,540 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl799,142,450 - 99,181,783 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0799,752,108 - 99,777,546 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4181,266,828 - 81,290,471 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1181,341,201 - 81,344,952 (+)NCBI
Celera175,950,659 - 75,974,302 (+)NCBICelera
Cytogenetic Map7q33NCBI
Cyp2b10
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39725,597,083 - 25,626,049 (+)NCBIGRCm39mm39
GRCm39 Ensembl725,597,045 - 25,626,049 (+)Ensembl
GRCm38725,897,658 - 25,926,624 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl725,897,620 - 25,926,624 (+)EnsemblGRCm38mm10GRCm38
MGSCv37726,682,683 - 26,711,643 (+)NCBIGRCm37mm9NCBIm37
MGSCv36725,606,424 - 25,635,384 (+)NCBImm8
Celera720,506,748 - 20,536,205 (+)NCBICelera
Cytogenetic Map7A3NCBI
cM Map714.11NCBI

Position Markers
D1Hmgc4  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2181,518,043 - 81,518,167 (+)MAPPERmRatBN7.2
mRatBN7.2181,594,162 - 81,594,314 (+)MAPPERmRatBN7.2
Rnor_6.0183,103,516 - 83,103,667NCBIRnor6.0
Rnor_6.0799,142,086 - 99,142,209NCBIRnor6.0
Rnor_5.0184,360,827 - 84,360,978UniSTSRnor5.0
Rnor_5.0799,736,092 - 99,736,215UniSTSRnor5.0
RGSC_v3.4181,345,016 - 81,345,167UniSTSRGSC3.4
RGSC_v3.4181,342,475 - 81,345,421RGDRGSC3.4
RGSC_v3.4181,266,464 - 81,266,587UniSTSRGSC3.4
Celera176,026,306 - 76,026,457UniSTS
Celera175,950,295 - 75,950,418UniSTS
RH 3.4 Map1827.8UniSTS
RH 3.4 Map1827.8RGD
Cytogenetic Map1q21UniSTS
D1Wox48  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2181,594,189 - 81,594,416 (+)MAPPERmRatBN7.2
mRatBN7.2181,518,070 - 81,518,269 (+)MAPPERmRatBN7.2
Rnor_6.0799,142,113 - 99,142,311NCBIRnor6.0
Rnor_6.0183,103,543 - 83,103,769NCBIRnor6.0
Rnor_5.0799,736,119 - 99,736,317UniSTSRnor5.0
Rnor_5.0184,360,854 - 84,361,080UniSTSRnor5.0
RGSC_v3.4181,266,491 - 81,266,689UniSTSRGSC3.4
RGSC_v3.4181,345,043 - 81,345,269UniSTSRGSC3.4
Celera176,026,333 - 76,026,559UniSTS
Celera175,950,322 - 75,950,520UniSTS
Cytogenetic Map1q21UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)150910886060548Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15925874115540829Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)11148131282174945Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)11148131282174945Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)11148131282174945Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)11148131282174945Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)122340647102268831Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)130882023123479925Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132356093162846471Rat
1300172Bp172Blood pressure QTL 1723.56arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)13273727390665040Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132737458199368955Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143284731118944897Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143284731118944897Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143284731118944897Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)143284731118944897Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143284731118944897Rat
2302059Pia36Pristane induced arthritis QTL 363.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)14333300288333002Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)148963584144267916Rat
4889962Bss94Bone structure and strength QTL 943.8tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)14936146582174945Rat
1578649Bmd8Bone mineral density QTL 84.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)14939317294393172Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149393172159356837Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149393289199050459Rat
6903308Scl36Serum cholesterol QTL 3620.0125blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)15386304190532583Rat
4889919Bss86Bone structure and strength QTL 864.1tibia area (VT:1000281)tibia midshaft total cross-sectional area (CMO:0001715)15389511782174945Rat
4889929Bss87Bone structure and strength QTL 876.7tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)15389511782174945Rat
61342Bp27Blood pressure QTL 273.40.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)15673266898773277Rat
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)156949932101949932Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)157336763151090257Rat
1300121Hrtrt1Heart rate QTL 13.7heart pumping trait (VT:2000009)heart rate (CMO:0000002)165789093115540829Rat
7421628Bp361Blood pressure QTL 3610.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)166023617118608521Rat
631512Scl6Serum cholesterol level QTL 69.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)17219768090508767Rat
1358192Ept13Estrogen-induced pituitary tumorigenesis QTL 133.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)177494165122494165Rat
10054135Gmadr2Adrenal mass QTL 21.970.0129adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)177857876122857876Rat
1549903Bp267Blood pressure QTL 267arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)177876254106047988Rat
61344Bp29Blood pressure QTL 297.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)178350581123350581Rat
7411712Strs4Sensitivity to stroke QTL 48.7cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)178430536123430536Rat
61433Cia2Collagen induced arthritis QTL 25joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)17843075491209302Rat
1582234Gluco18Glucose level QTL 183.40.0003blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)178479925123479925Rat
4889494Scort2Serum corticosterone level QTL 24.2blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)180592172125592172Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:44
Count of miRNA genes:43
Interacting mature miRNAs:43
Transcripts:ENSRNOT00000044127
Prediction methods: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 17 17 17 11
Low 1 10 8 2 8 1 1 2 5 1
Below cutoff 2 16 23 10 11 10 7 8 6 7 18 7

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001134844 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008765491 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008765492 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008765493 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594657 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095056 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AH002161 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ320166 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC166502 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473979 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  J00719 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000033 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M26854 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M26855 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M37134 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U30327 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000047540   ⟹   ENSRNOP00000045196
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl181,518,408 - 81,542,052 (+)Ensembl
RefSeq Acc Id: NM_001134844   ⟹   NP_001128316
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2181,518,408 - 81,542,053 (+)NCBI
Rnor_6.0799,158,102 - 99,181,774 (+)NCBI
Rnor_5.0799,752,108 - 99,777,546 (+)NCBI
RGSC_v3.4181,266,828 - 81,290,471 (+)RGD
Celera175,950,659 - 75,974,302 (+)RGD
Sequence:
RefSeq Acc Id: XM_039095056   ⟹   XP_038950984
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2181,518,387 - 81,544,999 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001128316   ⟸   NM_001134844
- Peptide Label: precursor
- UniProtKB: B2GV28 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_038950984   ⟸   XM_039095056
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000045196   ⟸   ENSRNOT00000047540

Transcriptome

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


Strain Variation

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2466 AgrOrtholog
Ensembl Genes ENSRNOG00000033680 Ensembl, UniProtKB/TrEMBL
  ENSRNOG00000063855 Ensembl
Ensembl Protein ENSRNOP00000049925 UniProtKB/TrEMBL
  ENSRNOP00000074625 UniProtKB/TrEMBL
  ENSRNOP00000075638 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000044127 UniProtKB/TrEMBL
  ENSRNOT00000079036 UniProtKB/TrEMBL
  ENSRNOT00000091923 UniProtKB/TrEMBL
Gene3D-CATH 1.10.630.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Cyt_P450 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cyt_P450_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cyt_P450_E_grp-I UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cyt_P450_E_grp-I_CYP2B-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cyt_P450_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24300 UniProtKB/TrEMBL
NCBI Gene 24300 ENTREZGENE
Pfam p450 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cyp2b1 PhenoGen
PRINTS EP450I UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EP450ICYP2B UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P450 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CYTOCHROME_P450 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48264 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A140UHW7_RAT UniProtKB/TrEMBL
  B2GV28 ENTREZGENE, UniProtKB/TrEMBL
  CP2B1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary F1MAD8 UniProtKB/TrEMBL
  Q64584 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2007-09-27 Cyp2j5-ps  cytochrome P450, family 2, subfamily b, polypeptide 1  Cyp2b1  Cytochrome P450, family 2, subfamily b, polypeptide 1  Name updated 1299863 PROVISIONAL
2006-02-09 Cyp2b1  Cytochrome P450, family 2, subfamily b, polypeptide 1      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-05-03   Cytochrome P450, family 2, subfamily b, polypeptide 1  Cyp2b1  Cytochrome P450, subfamily IIB (phenobarbital-inducible) (b, e)  Name updated 1299863 APPROVED
2002-06-10 Cyp2b1  Cytochrome P450, subfamily IIB (phenobarbital-inducible) (b, e)      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed after exposure to nicotine in liver and lung by time- and tissue-specific mechanisms 1298848
gene_function participates in hydoxylation of decanoic acid and other fatty acids 1298849
gene_process metabolizes nicotine and activates carcinogens 1298848
gene_regulation interaction with the positive response element is essential for the PB-mediated translocation of cytosolic protein complexes into the nucleus 625556
gene_regulation transcription is phenobarbitol- and Aroclor 1254- (ARO) inducible 1298850
gene_regulation promoter region contains recognition sites for HNF3, AP-1, NF-kappa B and various STAT proteins (+27 to -3878) 1298850
gene_transcript promoter region contains both positive (-69 to -98 bp) and negative response elements for phenobarbitone (PB) 625556