Cyp3a23-3a1 (cytochrome P450, family 3, subfamily a, polypeptide 23-polypeptide 1) - Rat Genome Database

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Gene: Cyp3a23-3a1 (cytochrome P450, family 3, subfamily a, polypeptide 23-polypeptide 1) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Cyp3a23-3a1
Name: cytochrome P450, family 3, subfamily a, polypeptide 23-polypeptide 1
RGD ID: 628626
Description: Enables demethylase activity and testosterone 6-beta-hydroxylase activity. Involved in several processes, including oxidative demethylation; response to cadmium ion; and response to dexamethasone. Located in endoplasmic reticulum membrane. Biomarker of cholestasis and mental depression. Human ortholog(s) of this gene implicated in B-lymphoblastic leukemia/lymphoma; acute lymphoblastic leukemia; chronic myeloid leukemia; and essential hypertension. Orthologous to human CYP3A5 (cytochrome P450 family 3 subfamily A member 5); PARTICIPATES IN tamoxifen pharmacokinetics pathway; linoleic acid metabolic pathway; phase I biotransformation pathway via cytochrome P450; INTERACTS WITH 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 1,2,4-trichlorobenzene; 1,2-dichloroethene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: cDEX; CYP; Cyp3a1; CYP3A23; Cyp3a23/3a1; Cyp3a3; CYPIIIA1; cytochrome P-450; cytochrome P-450PCN (PNCN inducible); cytochrome P450 3A1; cytochrome P450 3A1-like; cytochrome P450, family 3, subfamily a, polypeptide 1; cytochrome P450, family 3, subfamily a, polypeptide 23/polypeptide 1; cytochrome P450, subfamily 3A, polypeptide 3; Cytochrome P450, subfamily IIIA, polypeptide 3; cytochrome P450-PCN1; cytochrome P450/6 beta B; LOC100910877; MGC108757; P450 IIIA; P450-PCN1; RL33
RGD Orthologs
Alliance Genes
More Info homologs ...
Allele / Splice: Cyp3a23-3a1em1Myliu  
Genetic Models: SD-Cyp3a23/3a1em1Myliu,Cyp3a2em1Myliu
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2129,256,159 - 9,285,020 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl129,254,475 - 9,285,030 (-)Ensembl
Rnor_6.01211,053,888 - 11,082,742 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1211,655,402 - 11,733,136 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01213,145,742 - 13,174,596 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4129,567,120 - 9,595,974 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1129,596,712 - 9,625,890 (-)NCBI
Celera1211,063,015 - 11,090,937 (-)NCBICelera
RH 3.4 Map12117.0RGD
Cytogenetic Map12p11NCBI
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
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP)
1,2,4-trichlorobenzene  (EXP)
1,2-dichloroethene  (EXP)
1-naphthyl isothiocyanate  (EXP)
17beta-estradiol  (EXP)
2,2',4,4',5,5'-hexachlorobiphenyl  (EXP)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,2',5,5'-tetrachlorobiphenyl  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (EXP)
2-acetamidofluorene  (EXP)
3-methylcholanthrene  (EXP)
3-oxo-5beta-cholanic acid  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
4'-tert-Butyl-2',6'-dimethyl-3',5'-dinitroacetophenone  (EXP)
4-nitrophenol  (EXP)
4-nonylphenol  (EXP)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (EXP)
6-propyl-2-thiouracil  (EXP)
acetonitrile  (EXP)
Acetyl tributyl citrate  (EXP)
acrylamide  (EXP)
actinomycin D  (EXP)
alachlor  (EXP)
alkaloid  (EXP)
alpha-hexachlorocyclohexane  (EXP)
alprazolam  (EXP)
amiodarone  (EXP)
amitraz  (EXP)
amitriptyline  (EXP)
andrographolide  (EXP)
anthocyanin  (EXP)
Aroclor 1254  (EXP)
arsenite(3-)  (EXP)
atorvastatin calcium  (EXP)
benzbromarone  (EXP)
benzene  (EXP)
benzophenone  (EXP)
beta-naphthoflavone  (EXP)
bexarotene  (EXP)
bilobalide  (EXP)
bis(2-chloroethyl) sulfide  (EXP)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP)
bitertanol  (EXP)
Bromadiolone  (EXP)
bromuconazole  (EXP)
calcitriol  (EXP)
capsaicin  (EXP)
carbamazepine  (EXP)
carvedilol  (EXP)
chalcone  (EXP)
chenodeoxycholic acid  (EXP)
chloroform  (EXP)
chlorohydrocarbon  (EXP)
chlorpyrifos  (EXP)
chlorzoxazone  (EXP)
choline  (EXP)
ciprofibrate  (EXP)
ciprofloxacin  (EXP)
cisplatin  (EXP)
clofibrate  (EXP)
clofibric acid  (EXP)
clomipramine  (EXP)
clothianidin  (EXP)
clotrimazole  (EXP)
cocaine  (EXP)
cordycepin  (EXP)
cortisol  (EXP)
cycloheximide  (EXP)
cyclophosphamide  (EXP)
cyhalothrin  (EXP)
cypermethrin  (EXP)
cyproconazole  (EXP)
DDD  (EXP)
DDE  (EXP)
decabromodiphenyl ether  (EXP)
dehydroepiandrosterone  (EXP)
dexamethasone  (EXP)
dextromethorphan  (EXP)
Diallyl sulfide  (EXP)
dibenziodolium  (EXP)
dibutyl phthalate  (EXP)
diclofenac  (EXP)
dicofol  (EXP)
diflubenzuron  (EXP)
dimethyl sulfoxide  (EXP)
dimethylarsinic acid  (EXP)
diuron  (EXP)
enilconazole  (EXP)
epoxiconazole  (EXP)
erythromycin estolate  (EXP)
ethanol  (EXP)
ethoxyquin  (EXP)
farnesol  (EXP)
felbamate  (EXP)
fenofibrate  (EXP)
fenvalerate  (EXP)
fipronil  (EXP)
fipronil-sulfone  (EXP)
fluconazole  (EXP)
Furafylline  (EXP)
furan  (EXP)
gabapentin  (EXP)
gamma-hexachlorocyclohexane  (EXP)
genistein  (EXP)
gentamycin  (EXP)
Ginkgolide A  (EXP)
glafenine  (EXP)
glutathione  (EXP)
hexachlorobenzene  (EXP)
huperzine A  (EXP)
ifosfamide  (EXP)
imipramine  (EXP)
indole-3-methanol  (EXP)
indometacin  (EXP)
isoniazide  (EXP)
ketamine  (EXP)
ketoconazole  (EXP)
L-ethionine  (EXP)
L-methionine  (EXP)
lactacystin  (EXP)
lamotrigine  (EXP)
Lasiocarpine  (EXP)
leflunomide  (EXP)
lithocholic acid  (EXP)
mangiferin  (EXP)
metazachlor  (EXP)
methapyrilene  (EXP)
methotrexate  (EXP)
methoxsalen  (EXP)
methoxychlor  (EXP)
methylmercury chloride  (EXP)
miconazole  (EXP)
midazolam  (EXP)
mifepristone  (EXP)
monocrotaline  (EXP)
musk xylene  (EXP)
N'-(2,4-dimethylphenyl)-N-methylformamidine  (EXP)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (EXP)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP)
N-Vinyl-2-pyrrolidone  (EXP)
NADP zwitterion  (EXP)
NADP(+)  (EXP)
nelfinavir  (EXP)
nemorubicin  (EXP)
nevirapine  (EXP)
Nicardipine  (EXP)
nifedipine  (EXP)
Nonylphenol  (EXP)
octamethylcyclotetrasiloxane  (EXP)
okadaic acid  (EXP)
oltipraz  (EXP)
omeprazole  (EXP)
oxycodone  (EXP)
paracetamol  (EXP)
Paraoxon-methyl  (EXP)
parathion-methyl  (EXP)
PCB138  (EXP)
pentachlorobenzene  (EXP)
pentachlorophenol  (EXP)
perfluorobutyric acid  (EXP)
perfluorodecanoic acid  (EXP)
perfluorooctane-1-sulfonic acid  (EXP)
perfluorooctanoic acid  (EXP)
permethrin  (EXP)
phenacetin  (EXP)
phenobarbital  (EXP)
phenytoin  (EXP)
phthalic acid  (EXP)
pioglitazone  (EXP)
pirinixic acid  (EXP)
poly(I:C)  (EXP)
pravastatin  (EXP)
pregnenolone 16alpha-carbonitrile  (EXP)
prochloraz  (EXP)
progesterone  (EXP)
propiconazole  (EXP)
pyrazinecarboxamide  (EXP)
pyrene  (EXP)
pyridine  (EXP)
rifampicin  (EXP)
ritonavir  (EXP)
rotenone  (EXP)
sodium arsenite  (EXP)
spironolactone  (EXP)
stilbene oxide  (EXP)
Sudan III  (EXP)
sulfoxaflor  (EXP)
tamoxifen  (EXP)
tert-butyl ethyl ether  (EXP)
Tesaglitazar  (EXP)
testosterone  (EXP)
tetrachloromethane  (EXP)
thiacloprid  (EXP)
thioacetamide  (EXP)
toremifene  (EXP)
trabectedin  (EXP)
trans-1,2-dichloroethene  (EXP)
trans-chalcone  (EXP)
triadimefon  (EXP)
trichloroethene  (EXP)
triclosan  (EXP)
trifluralin  (EXP)
triphenyl phosphate  (EXP)
Triptolide  (EXP)
troglitazone  (EXP)
troleandomycin  (EXP)
uranium atom  (EXP)
ursodeoxycholic acid  (EXP)
valdecoxib  (EXP)
valproic acid  (EXP)
vinclozolin  (EXP)
zaragozic acid A  (EXP)
zearalenone  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
1. Gabbia D, etal., World J Gastroenterol. 2017 Nov 14;23(42):7519-7530. doi: 10.3748/wjg.v23.i42.7519.
2. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. Gonzalez FJ, etal., J Biol Chem 1985 Jun 25;260(12):7435-41.
4. Hunter SR, etal., Drug Metab Dispos. 2017 Feb;45(2):118-129. doi: 10.1124/dmd.116.073833. Epub 2016 Nov 16.
5. Kim SY, etal., Chem Res Toxicol. 2003 Sep;16(9):1138-44.
6. Koga N, etal., Biol Pharm Bull. 2007 Dec;30(12):2317-23.
7. Kotsovolou O, etal., Prog Neuropsychopharmacol Biol Psychiatry. 2010 Aug 16;34(6):1075-84. Epub 2010 Jun 4.
8. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
9. Mei Q, etal., J Pharm Sci. 2004 Oct;93(10):2488-96.
10. Nagata K, etal., Arch Biochem Biophys. 1999 Feb 15;362(2):242-53.
11. OMIM Disease Annotation Pipeline
12. Peng FC, etal., J Toxicol Environ Health A. 2005 Nov 12;68(21):1871-88.
13. Pipeline to import KEGG annotations from KEGG into RGD
14. Plewka A, etal., Arch Toxicol. 2004 Apr;78(4):194-200. Epub 2003 Nov 1.
15. Projean D, etal., Pharm Res. 2005 Jan;22(1):62-70.
16. Rekka E, etal., Biochem Pharmacol 2002 Aug 15;64(4):633-43.
17. RGD automated data pipeline
18. RGD automated import pipeline for gene-chemical interactions
19. Ronis MJ, etal., Exp Biol Med (Maywood). 2006 Jan;231(1):60-9.
20. Souidi M, etal., Toxicology. 2005 Oct 15;214(1-2):113-22.
21. Sun G, etal., Xenobiotica. 2007 Feb;37(2):180-93.
22. Van den Broek PJ, etal., Experientia 1996 Sep 15;52(9):851-5.
Additional References at PubMed
PMID:1298226   PMID:1372436   PMID:1417000   PMID:1731631   PMID:2398038   PMID:3875783   PMID:7528203   PMID:7681660   PMID:8274011   PMID:11901229   PMID:12477932   PMID:15979568  
PMID:16461430   PMID:19435144   PMID:19504095   PMID:19848203   PMID:20599767   PMID:22159698   PMID:22822673   PMID:23235327   PMID:23762486   PMID:24212381   PMID:25302309   PMID:25989892  
PMID:26900149   PMID:27899252   PMID:28532222   PMID:29381299   PMID:30811654  


Genomics

Position Markers
RH94398  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2129,255,993 - 9,256,161 (+)MAPPERmRatBN7.2
Rnor_6.01211,703,772 - 11,703,939NCBIRnor6.0
Rnor_6.01211,053,723 - 11,053,890NCBIRnor6.0
Rnor_5.01213,145,577 - 13,145,744UniSTSRnor5.0
Rnor_5.01213,766,697 - 13,766,864UniSTSRnor5.0
RGSC_v3.4129,566,955 - 9,567,122UniSTSRGSC3.4
Celera1211,062,850 - 11,063,017UniSTS
Cytogenetic Map12p11UniSTS
RH132534  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2129,256,029 - 9,256,241 (+)MAPPERmRatBN7.2
Rnor_6.01211,703,808 - 11,704,019NCBIRnor6.0
Rnor_6.01211,053,759 - 11,053,970NCBIRnor6.0
Rnor_5.01213,766,733 - 13,766,944UniSTSRnor5.0
Rnor_5.01213,145,613 - 13,145,824UniSTSRnor5.0
RGSC_v3.4129,566,991 - 9,567,202UniSTSRGSC3.4
Celera1211,062,886 - 11,063,097UniSTS
RH 3.4 Map12102.2UniSTS
Cytogenetic Map12p11UniSTS
RH142381  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2129,285,598 - 9,285,757 (+)MAPPERmRatBN7.2
Rnor_6.01211,733,681 - 11,733,839NCBIRnor6.0
Rnor_6.01211,083,321 - 11,083,479NCBIRnor6.0
Rnor_5.01213,796,606 - 13,796,764UniSTSRnor5.0
Rnor_5.01213,175,175 - 13,175,333UniSTSRnor5.0
RGSC_v3.4129,596,553 - 9,596,711UniSTSRGSC3.4
Celera1211,091,516 - 11,091,674UniSTS
RH 3.4 Map12117.0UniSTS
Cytogenetic Map12p11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300174Bw15Body weight QTL 152.93body mass (VT:0001259)body weight loss (CMO:0001399)1219318387Rat
2312418Kidm41Kidney mass QTL 413.70.0001kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)12119611090Rat
10755457Coatc14Coat color QTL 140.01759coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)12122591684Rat
6893681Bw109Body weight QTL 1092.30.004body mass (VT:0001259)body weight (CMO:0000012)12123297788Rat
1581516Cm56Cardiac mass QTL 564.20.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)12129333307Rat
1598855Bp294Blood pressure QTL 2943.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12134851688Rat
7411660Foco28Food consumption QTL 2810.90.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
9590086Insglur6Insulin/glucose ratio QTL 618.970.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)12142110980Rat
8694179Bw150Body weight QTL 1502.90.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
7411586Foco5Food consumption QTL 55.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411595Foco9Food consumption QTL 940.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411545Bw128Body weight QTL 1285.20.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)12142110980Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)12142450532Rat
737979Pia22Pristane induced arthritis QTL 2253.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12144465750Rat
634351Apr5Acute phase response QTL 56.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)12144503507Rat
2302042Pia38Pristane induced arthritis QTL 383.50.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)12144503507Rat
634350Apr4Acute phase response QTL 46orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)12117200546172005Rat
724526Uae3Urinary albumin excretion QTL 34.90.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)12390696910373166Rat
8552918Pigfal7Plasma insulin-like growth factor 1 level QTL 7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449546669029Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)6556449546669029Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
8552964Pigfal17Plasma insulin-like growth factor 1 level QTL 173.5blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449546669029Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
8552912Pigfal6Plasma insulin-like growth factor 1 level QTL 65blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449846669029Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)12610757946669029Rat
1600391Edcs2Endometrial carcinoma susceptibility QTL23.50.01uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)12683319017870186Rat
1302792Scl21Serum cholesterol level QTL 213.80.0011blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)12719673046669029Rat
2293086Iddm30Insulin dependent diabetes mellitus QTL 303.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)12844949028302290Rat
61331Eau2Experimental allergic uveoretinitis QTL 20.0005uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)12852542328064601Rat


Genetic Models
This gene Cyp3a23-3a1 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:181
Count of miRNA genes:139
Interacting mature miRNAs:156
Transcripts:ENSRNOT00000075671
Prediction methods:Miranda
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

circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High 4 4 4
Medium 20 20 20 1
Low 2 16 13 1 13 2 2 2 4 3 2
Below cutoff 2 7 12 3 3 13 8 15 5 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000051244   ⟹   ENSRNOP00000041138
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl129,015,383 - 9,285,008 (-)Ensembl
Rnor_6.0 Ensembl1211,703,598 - 11,733,099 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000087257   ⟹   ENSRNOP00000068625
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl129,207,980 - 9,230,043 (-)Ensembl
Rnor_6.0 Ensembl1211,655,402 - 11,733,136 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000099867   ⟹   ENSRNOP00000094020
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl129,207,980 - 9,230,043 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000100533   ⟹   ENSRNOP00000082425
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl129,254,475 - 9,285,030 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000104663   ⟹   ENSRNOP00000084206
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl129,254,475 - 9,283,058 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000118926   ⟹   ENSRNOP00000088335
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl129,254,475 - 9,282,915 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000119539   ⟹   ENSRNOP00000087895
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl129,254,475 - 9,283,058 (-)Ensembl
RefSeq Acc Id: NM_013105   ⟹   NP_037237
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2129,256,159 - 9,285,020 (-)NCBI
Rnor_6.01211,053,888 - 11,082,742 (-)NCBI
Rnor_5.01213,145,742 - 13,174,596 (-)NCBI
RGSC_v3.4129,567,120 - 9,595,974 (-)RGD
Celera1211,063,015 - 11,090,937 (-)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_037237   ⟸   NM_013105
- UniProtKB: Q06884 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000068625   ⟸   ENSRNOT00000087257
RefSeq Acc Id: ENSRNOP00000041138   ⟸   ENSRNOT00000051244
RefSeq Acc Id: ENSRNOP00000084206   ⟸   ENSRNOT00000104663
RefSeq Acc Id: ENSRNOP00000082425   ⟸   ENSRNOT00000100533
RefSeq Acc Id: ENSRNOP00000088335   ⟸   ENSRNOT00000118926
RefSeq Acc Id: ENSRNOP00000087895   ⟸   ENSRNOT00000119539
RefSeq Acc Id: ENSRNOP00000094020   ⟸   ENSRNOT00000099867

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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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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
F344/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
F344/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
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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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
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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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)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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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)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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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: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
12 9575874 9575875 G T snv FHH/EurMcwi (MCW)
12 9583982 9583983 C G snv SS/JrHsdMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:628626 AgrOrtholog
  RGD:6495986 AgrOrtholog
Ensembl Genes ENSRNOG00000032560 Ensembl, UniProtKB/TrEMBL
  ENSRNOG00000067532 Ensembl
Ensembl Protein ENSRNOP00000041138 UniProtKB/TrEMBL
  ENSRNOP00000068625 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000051244 UniProtKB/TrEMBL
  ENSRNOT00000087257 UniProtKB/TrEMBL
Gene3D-CATH 1.10.630.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7370410 IMAGE-MGC_LOAD
InterPro Cyt_P450 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cyt_P450_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cyt_P450_E_CYP3A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cyt_P450_E_grp-II UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cyt_P450_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25642 UniProtKB/TrEMBL
MGC_CLONE MGC:108757 IMAGE-MGC_LOAD
NCBI Gene 25642 ENTREZGENE
Pfam p450 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB CYP3A4 RGD
PhenoGen Cyp3a23-3a1 PhenoGen
PRINTS EP450II UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EP450IICYP3A 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
TIGR TC205966
UniProt A0A0G2JT98_RAT UniProtKB/TrEMBL
  CP3A1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q06884 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary Q64580 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Cyp3a23-3a1  cytochrome P450, family 3, subfamily a, polypeptide 23-polypeptide 1  LOC100910877  cytochrome P450 3A1-like  Data Merged 737654 PROVISIONAL
2020-04-16 Cyp3a23-3a1  cytochrome P450, family 3, subfamily a, polypeptide 23-polypeptide 1  Cyp3a23-3a1  cytochrome P450, family 3, subfamily a, polypeptide 23/polypeptide 1  Name changed 629549 APPROVED
2020-04-16 Cyp3a23-3a1  cytochrome P450, family 3, subfamily a, polypeptide 23/polypeptide 1  Cyp3a23/3a1  cytochrome P450, family 3, subfamily a, polypeptide 23/polypeptide 1  Symbol changed 629549 APPROVED
2012-07-05 LOC100910877  cytochrome P450 3A1-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-09-08 Cyp3a23/3a1  cytochrome P450, family 3, subfamily a, polypeptide 23/polypeptide 1  Cyp3a23/3a1_retired  cytochrome P450, family 3, subfamily a, polypeptide 23/polypeptide 1_retired  Data Merged 737654 APPROVED
2007-09-21 Cyp3a23/3a1  cytochrome P450, family 3, subfamily a, polypeptide 23/polypeptide 1  Cyp3a1  cytochrome P450, family 3, subfamily a, polypeptide 1  Symbol and Name updated 1299863 APPROVED
2007-09-21 Cyp3a23/3a1_retired  cytochrome P450, family 3, subfamily a, polypeptide 23/polypeptide 1_retired  Cyp3a23/3a1  cytochrome P450, family 3, subfamily a, polypeptide 23/polypeptide 1  Symbol and Name updated 1299863 PROVISIONAL
2007-07-06 Cyp3a23/3a1  cytochrome P450, family 3, subfamily a, polypeptide 23/polypeptide 1  Cyp3a3  cytochrome P450, subfamily 3A, polypeptide 3  Name updated 1299863 APPROVED
2005-09-08 Cyp3a1  cytochrome P450, family 3, subfamily a, polypeptide 1  Cyp3A1  cytochrome P-450PCN (PNCN inducible)  Symbol and Name updated to reflect Human and Mouse nomenclature 1299863 APPROVED
2003-02-27 Cyp3A1  cytochrome P-450PCN (PNCN inducible)      Symbol and Name status set to provisional 70820 PROVISIONAL
2002-11-06 Cyp3a3  cytochrome P450, subfamily 3A, polypeptide 3    Cytochrome P450, subfamily IIIA, polypeptide 3  Name updated 625702 APPROVED
2002-06-10 Cyp3a3  Cytochrome P450, subfamily IIIA, polypeptide 3      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_drugs induced strongly by pregnenolone 16 alpha-carbonitrile and dexamethasone (DEX) and weakly by phenobarbital (PB) and triacetyloleandomycin 1298860
gene_expression expressed in liver 1298860