Ugt1a1 (UDP glucuronosyltransferase family 1 member A1) - Rat Genome Database

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Gene: Ugt1a1 (UDP glucuronosyltransferase family 1 member A1) Rattus norvegicus
Analyze
Symbol: Ugt1a1
Name: UDP glucuronosyltransferase family 1 member A1
RGD ID: 3935
Description: Enables enzyme binding activity and glucuronosyltransferase activity. Involved in several processes, including biphenyl catabolic process; cellular glucuronidation; and cellular response to lipid. Located in endoplasmic reticulum. Part of cytochrome complex. Used to study Crigler-Najjar syndrome and bilirubin metabolic disorder. Biomarker of hyperthyroidism; type 1 diabetes mellitus; and type 2 diabetes mellitus. Human ortholog(s) of this gene implicated in several diseases, including bilirubin metabolic disorder (multiple); cholecystolithiasis; cholelithiasis; female reproductive organ cancer (multiple); and hepatitis B. Orthologous to human UGT1A1 (UDP glucuronosyltransferase family 1 member A1); PARTICIPATES IN axitinib pharmacokinetics pathway; codeine and morphine pharmacodynamics pathway; codeine and morphine pharmacokinetics pathway; INTERACTS WITH (R,R,R)-alpha-tocopherol; 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: B1; UDP glucuronosyltransferase 1 family, polypeptide A1; UDP glycosyltransferase 1 family, polypeptide A1; UDP-glucuronosyltransferase 1 family member 1; UDP-glucuronosyltransferase 1 family, member 1; UDP-glucuronosyltransferase 1-1; UDP-glucuronosyltransferase 1A1; Udpgt; UDPGT 1-1; Ugt1; UGT1*1; UGT1-01; UGT1.1
RGD Orthologs
Human
Mouse
Alliance Genes
More Info more info ...
Allele / Splice: Ugt1a1j  
Genetic Models: Gunn-Ugt1a1j/BluHsdRrrc Gunn-Ugt1a1j/BluHsd
Is Marker For: Strains:   WIST/Nhg   SD.Gunn-Ugt1a1j/Aon   W.Gunn-Ugt1a1j/Aon  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2988,801,344 - 88,808,465 (+)NCBImRatBN7.2
Rnor_6.0995,295,701 - 95,302,822 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl995,161,157 - 95,302,822 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0994,982,916 - 94,990,037 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4987,091,241 - 87,098,362 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1987,277,121 - 87,284,238 (+)NCBI
Celera986,362,434 - 86,369,556 (+)NCBICelera
Cytogenetic Map9q35NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-taxifolin  (ISO)
(5Z,8Z,11Z,13E)-15-HETE  (ISO)
(R,R,R)-alpha-tocopherol  (EXP)
(S)-naringenin  (ISO)
(Z)-ligustilide  (ISO)
1,4-dioxane  (ISO)
1-Hydroxypyrene  (ISO)
1-naphthyl isothiocyanate  (EXP,ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
2',4,4',6'-tetrahydroxychalcone  (ISO)
2',5'-Dihydroxychalcone  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP,ISO)
2,3,4,7,8-Pentachlorodibenzofuran  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (ISO)
2,4,6-trinitrotoluene  (EXP)
2,4,6-Triphenyl-1-hexene  (ISO)
2,4-Dihydroxychalcone  (ISO)
2-hydroxy-17beta-estradiol  (ISO)
2-hydroxyestrone  (ISO)
2-methoxy-17beta-estradiol  (ISO)
2-tert-butylhydroquinone  (EXP)
20-HETE  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP,ISO)
3,3',5,5'-tetrabromobisphenol A  (EXP)
3,3',5-triiodo-L-thyronine  (EXP)
3-Hydroxybenzo[a]pyrene  (EXP)
3-methyl-3H-imidazo[4,5-f]quinolin-2-amine  (ISO)
3-methylcholanthrene  (EXP,ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyestrone  (ISO)
4-hydroxyphenytoin  (ISO)
4-methylumbelliferone  (ISO)
4-methylumbelliferone beta-D-glucuronide  (ISO)
4-nitrophenol  (ISO)
5,7-dihydroxy-4'-methoxyflavone  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (EXP,ISO)
5-methoxypsoralen  (EXP,ISO)
6-propyl-2-thiouracil  (EXP)
8-Epidiosbulbin E acetate  (ISO)
9-cis-retinoic acid  (EXP)
acetamide  (EXP)
acetylsalicylic acid  (EXP)
afimoxifene  (ISO)
aflatoxin B1  (EXP,ISO)
alizarin  (ISO)
all-trans-retinol  (EXP)
alpha-tocotrienol  (ISO)
amentoflavone  (ISO)
amiodarone  (EXP)
amitriptyline  (EXP)
ammonium chloride  (EXP)
androsterone  (ISO)
Anetholtrithion  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
anthraflavic acid  (ISO)
anthrarobin  (ISO)
apigenin  (ISO)
arachidonic acid  (ISO)
aristolochic acid  (EXP)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
atrazine  (ISO)
belinostat  (ISO)
benzamidoxime  (ISO)
benzbromarone  (EXP)
benzo[a]pyrene  (ISO)
bergomottin  (ISO)
beta-naphthoflavone  (EXP,ISO)
beta-tocopherol  (EXP)
beta-tocotrienol  (ISO)
bilirubin IXalpha  (EXP,ISO)
biochanin A  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
Bisphenol B  (ISO)
bisphenol F  (ISO)
Boldine  (EXP)
Bropirimine  (ISO)
buprenorphine  (ISO)
buta-1,3-diene  (ISO)
butylated hydroxyanisole  (ISO)
butyric acid  (ISO)
C.I. Natural Red 20  (EXP,ISO)
cadmium dichloride  (ISO)
caffeine  (ISO)
calcitriol  (ISO)
calycosin  (ISO)
capsaicin  (ISO)
carbamazepine  (EXP,ISO)
carvedilol  (ISO)
chalcones  (EXP)
chenodeoxycholic acid  (ISO)
chlorpyrifos  (ISO)
chrysen-6-ol  (EXP)
chrysin  (EXP,ISO)
ciprofibrate  (ISO)
cisplatin  (EXP,ISO)
clofibrate  (EXP)
clofibric acid  (ISO)
Clofop  (ISO)
clomipramine  (EXP)
clotrimazole  (ISO)
clozapine  (ISO)
coumarins  (EXP,ISO)
coumestrol  (ISO)
curcumin  (EXP,ISO)
cycloheximide  (ISO)
cyclosporin A  (ISO)
cylindrospermopsin  (ISO)
cyproconazole  (EXP)
daidzein  (ISO)
decabromodiphenyl ether  (EXP)
delta-tocopherol  (EXP)
delta-tocotrienol  (ISO)
deoxycholic acid  (ISO)
dexamethasone  (EXP,ISO)
diallyl disulfide  (EXP)
Diallyl sulfide  (EXP)
diallyl trisulfide  (EXP)
dibenzo[a,l]pyrene  (ISO)
diclofenac  (EXP,ISO)
diethylstilbestrol  (ISO)
diflunisal  (ISO)
dioxygen  (ISO)
dipyridamole  (ISO)
doxorubicin  (EXP)
emodin  (ISO)
endosulfan  (ISO)
entacapone  (ISO)
epoxiconazole  (EXP)
equol  (ISO)
Erucin  (ISO)
Estragole  (ISO)
estriol  (ISO)
estrone  (ISO)
ethoxyquin  (EXP,ISO)
etoposide  (ISO)
eugenol  (ISO)
ezetimibe  (ISO)
farnesol  (ISO)
felbamate  (EXP)
fenofibrate  (ISO)
fipronil  (EXP,ISO)
fipronil-sulfone  (EXP)
fisetin  (ISO)
flavanone  (ISO)
flavonoids  (ISO)
flumequine  (ISO)
flunitrazepam  (ISO)
flurbiprofen  (ISO)
formononetin  (ISO)
fulvestrant  (ISO)
furan  (EXP)
furosemide  (ISO)
fusidic acid  (ISO)
galangin  (ISO)
gamma-hexachlorocyclohexane  (EXP)
gamma-tocopherol  (EXP,ISO)
gemfibrozil  (ISO)
genistein  (ISO)
gentamycin  (EXP)
Ginkgolide A  (ISO)
ginkgolide B  (ISO)
ginsenoside Rg1  (EXP)
glabridin  (ISO)
glycochenodeoxycholic acid  (ISO)
glycocholic acid  (ISO)
glycodeoxycholic acid  (ISO)
Grepafloxacin  (ISO)
griseofulvin  (ISO)
hyperforin  (ISO)
ibuprofen  (ISO)
imipramine  (EXP)
imperatorin  (EXP,ISO)
indometacin  (ISO)
indoxyl sulfate  (ISO)
irinotecan  (EXP,ISO)
isoflavones  (ISO)
isoliquiritigenin  (ISO)
kaempferol  (ISO)
ketoconazole  (EXP,ISO)
ketoprofen  (ISO)
L-ethionine  (EXP)
labetalol  (ISO)
lansoprazole  (EXP)
leflunomide  (ISO)
Licochalcone A  (ISO)
lithocholic acid  (ISO)
luteolin  (ISO)
LY294002  (ISO)
mangiferin  (ISO)
masoprocol  (ISO)
Meclizine  (ISO)
MeIQx  (ISO)
metazachlor  (EXP)
methotrexate  (ISO)
methoxychlor  (ISO)
MK 571  (ISO)
morin  (ISO)
morphine  (ISO)
moxifloxacin  (ISO)
N-butyl-N-(4-hydroxybutyl)nitrosamine  (ISO)
N-hydroxy-PhIP  (ISO)
N-nitrosodiethylamine  (EXP)
naproxen  (ISO)
Niflumic acid  (ISO)
nilotinib  (ISO)
Nor-9-carboxy-delta9-THC  (ISO)
notoginsenoside R1  (ISO)
obeticholic acid  (ISO)
ofloxacin  (ISO)
oltipraz  (ISO)
omeprazole  (EXP,ISO)
ortho-Aminoazotoluene  (ISO)
osimertinib  (ISO)
oxycodone  (EXP)
paclitaxel  (ISO)
pantoprazole  (EXP)
paracetamol  (EXP,ISO)
parathion  (ISO)
perfluorobutyric acid  (EXP)
perfluorodecanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
perfluorooctanoic acid  (ISO)
phenacetin  (EXP)
phenanthrene  (ISO)
phenobarbital  (EXP,ISO)
phenylbutazone  (ISO)
phenytoin  (EXP,ISO)
PhIP  (EXP,ISO)
pioglitazone  (ISO)
pirinixic acid  (EXP,ISO)
plumbagin  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP,ISO)
prochloraz  (EXP)
progesterone  (EXP,ISO)
propacetamol  (ISO)
propiconazole  (EXP)
prostaglandin B1  (ISO)
prostaglandin E2  (EXP)
prostaglandin F2alpha  (EXP)
pterostilbene  (ISO)
puerarin  (ISO)
pyrene  (ISO)
quercetin  (EXP,ISO)
quercetin 3-O-beta-D-galactopyranoside  (ISO)
quinizarin  (ISO)
rabeprazole  (EXP)
resveratrol  (EXP,ISO)
retinyl acetate  (ISO)
rifampicin  (ISO)
ritonavir  (ISO)
robinetin  (ISO)
SB 203580  (ISO)
scopoletin  (ISO)
sevoflurane  (EXP)
Shikonin  (EXP,ISO)
silibinin  (EXP,ISO)
Sitafloxacin  (ISO)
sodium acetate trihydrate  (ISO)
sodium arsenite  (ISO)
sodium propionate  (ISO)
spironolactone  (EXP,ISO)
sulforaphane  (ISO)
sulindac  (ISO)
sulindac sulfide  (ISO)
sulindac sulfone  (ISO)
sunitinib  (EXP)
tamoxifen  (ISO)
taurine  (EXP)
tebuconazole  (ISO)
tert-butyl ethyl ether  (EXP)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
thymol  (ISO)
thymol sulfate(1-)  (ISO)
thyroxine  (EXP)
ticlopidine  (ISO)
tienilic acid  (ISO)
trans-piceid  (ISO)
triadimefon  (EXP)
trichloroethene  (ISO)
trichostatin A  (ISO)
triclocarban  (ISO)
triclosan  (EXP,ISO)
trifluralin  (EXP)
troglitazone  (ISO)
UDP-alpha-D-glucuronic acid  (ISO)
ursodeoxycholic acid  (EXP,ISO)
valproic acid  (EXP,ISO)
vorinostat  (ISO)
warfarin  (ISO)
xanthohumol  (ISO)
zearalenone  (ISO)
zinc atom  (EXP)
zinc(0)  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
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53. Pipeline to import KEGG annotations from KEGG into RGD
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Additional References at PubMed
PMID:1898728   PMID:7603447   PMID:7608130   PMID:7986077   PMID:8554318   PMID:8999837   PMID:9271076   PMID:9488689   PMID:11437649   PMID:12475965   PMID:12477932   PMID:12951053  
PMID:16141793   PMID:17179145   PMID:18004212   PMID:18052087   PMID:19996319   PMID:20056724   PMID:20308471   PMID:20610558   PMID:22447239   PMID:22579593   PMID:23230277   PMID:28479355  
PMID:29131354  


Genomics

Comparative Map Data
Ugt1a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2988,801,344 - 88,808,465 (+)NCBImRatBN7.2
Rnor_6.0995,295,701 - 95,302,822 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl995,161,157 - 95,302,822 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0994,982,916 - 94,990,037 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4987,091,241 - 87,098,362 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1987,277,121 - 87,284,238 (+)NCBI
Celera986,362,434 - 86,369,556 (+)NCBICelera
Cytogenetic Map9q35NCBI
UGT1A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2233,760,270 - 233,773,300 (+)EnsemblGRCh38hg38GRCh38
GRCh382233,760,270 - 233,773,300 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372234,668,916 - 234,681,946 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362234,333,658 - 234,346,684 (+)NCBINCBI36hg18NCBI36
Build 342234,450,918 - 234,463,945NCBI
Celera2228,389,552 - 228,402,577 (+)NCBI
Cytogenetic Map2q37.1NCBI
HuRef2226,468,768 - 226,481,779 (+)NCBIHuRef
CHM1_12234,674,733 - 234,682,899 (+)NCBICHM1_1
Ugt1a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39188,139,681 - 88,147,724 (+)NCBIGRCm39mm39
GRCm39 Ensembl188,139,681 - 88,146,719 (+)Ensembl
GRCm38188,211,959 - 88,220,002 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl188,211,959 - 88,218,997 (+)EnsemblGRCm38mm10GRCm38
MGSCv37190,108,534 - 90,116,577 (+)NCBIGRCm37mm9NCBIm37
MGSCv36190,043,130 - 90,050,148 (+)NCBImm8
Celera191,173,026 - 91,181,062 (+)NCBICelera
Cytogenetic Map1DNCBI
cM Map144.55NCBI

Position Markers
RH94830  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2988,808,140 - 88,808,341 (+)MAPPERmRatBN7.2
Rnor_6.0995,302,498 - 95,302,698NCBIRnor6.0
Rnor_5.0994,989,713 - 94,989,913UniSTSRnor5.0
RGSC_v3.4987,098,038 - 87,098,238UniSTSRGSC3.4
Celera986,369,232 - 86,369,432UniSTS
Cytogenetic Map9q35UniSTS
Cytogenetic Map9q35-q36UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)925268044114175309Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)925661188100929786Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)93696235992058970Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)93696235995410867Rat
11353951Bp394Blood pressure QTL 394arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94464992189649921Rat
12879506Pur33Proteinuria QTL 33total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)94464992189649921Rat
11353957Bmd92Bone mineral density QTL 920.01tibia mineral mass (VT:1000283)volumetric bone mineral density (CMO:0001553)94611419991114199Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94859825193598251Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)956771635101771635Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)958163035100929646Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)961381434104821652Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)96207227596470995Rat
1578757Pur6Proteinuria QTL 63.30.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)96207227596470995Rat
61385Edpm9Estrogen-dependent pituitary mass QTL 93.430.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)963869687108869687Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)964573531109573531Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)975712843111552878Rat
4889852Pur26Proteinuria QTL 26150.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)977813894101597663Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)977813894111552878Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)97927151191616855Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)97927151191616855Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)97927151191616855Rat
724547Cm21Cardiac mass QTL 212.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)979271511102910209Rat
4889943Bss90Bone structure and strength QTL 904.1tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)98636963192058970Rat


Related Rat Strains
The following Strains have been annotated to Ugt1a1


Genetic Models
This gene Ugt1a1 is modified in the following models/strains

Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000025045   ⟹   ENSRNOP00000025045
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl988,801,339 - 88,808,465 (+)Ensembl
Rnor_6.0 Ensembl995,295,701 - 95,302,822 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000025291   ⟹   ENSRNOP00000025292
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl988,762,249 - 88,808,465 (+)Ensembl
Rnor_6.0 Ensembl995,256,627 - 95,302,822 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000025652   ⟹   ENSRNOP00000025652
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl988,739,577 - 88,808,465 (+)Ensembl
Rnor_6.0 Ensembl995,202,632 - 95,302,822 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000032634   ⟹   ENSRNOP00000030374
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl988,747,213 - 88,808,463 (+)Ensembl
Rnor_6.0 Ensembl995,241,609 - 95,302,822 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000045163   ⟹   ENSRNOP00000046507
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl988,780,328 - 88,808,465 (+)Ensembl
Rnor_6.0 Ensembl995,274,707 - 95,302,822 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000063853   ⟹   ENSRNOP00000062958
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl988,791,216 - 88,808,465 (+)Ensembl
Rnor_6.0 Ensembl995,285,592 - 95,302,822 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000066839   ⟹   ENSRNOP00000063634
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl988,713,184 - 88,808,465 (+)Ensembl
Rnor_6.0 Ensembl995,221,474 - 95,302,822 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000071003   ⟹   ENSRNOP00000075547
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl995,233,957 - 95,302,810 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000071200   ⟹   ENSRNOP00000066773
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl988,727,092 - 88,808,453 (+)Ensembl
Rnor_6.0 Ensembl995,161,157 - 95,302,822 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000077416   ⟹   ENSRNOP00000070501
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl995,241,626 - 95,302,816 (+)Ensembl
RefSeq Acc Id: NM_012683   ⟹   NP_036815
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2988,801,344 - 88,808,465 (+)NCBI
Rnor_6.0995,295,701 - 95,302,822 (+)NCBI
Rnor_5.0994,982,916 - 94,990,037 (+)NCBI
RGSC_v3.4987,091,241 - 87,098,362 (+)RGD
Celera986,362,434 - 86,369,556 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_036815   ⟸   NM_012683
- Peptide Label: precursor
- UniProtKB: Q64550 (UniProtKB/Swiss-Prot),   Q5DT04 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000046507   ⟸   ENSRNOT00000045163
RefSeq Acc Id: ENSRNOP00000062958   ⟸   ENSRNOT00000063853
RefSeq Acc Id: ENSRNOP00000075547   ⟸   ENSRNOT00000071003
RefSeq Acc Id: ENSRNOP00000070501   ⟸   ENSRNOT00000077416
RefSeq Acc Id: ENSRNOP00000030374   ⟸   ENSRNOT00000032634
RefSeq Acc Id: ENSRNOP00000066773   ⟸   ENSRNOT00000071200
RefSeq Acc Id: ENSRNOP00000025292   ⟸   ENSRNOT00000025291
RefSeq Acc Id: ENSRNOP00000025652   ⟸   ENSRNOT00000025652
RefSeq Acc Id: ENSRNOP00000063634   ⟸   ENSRNOT00000066839
RefSeq Acc Id: ENSRNOP00000025045   ⟸   ENSRNOT00000025045
Protein Domains
UDPGT

Transcriptome

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

Promoters
RGD ID:13696846
Promoter ID:EPDNEW_R7370
Type:multiple initiation site
Name:Ugt1a7c_3
Description:UDP glucuronosyltransferase 1 family, polypeptide A7C
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R7366  EPDNEW_R7367  EPDNEW_R7368  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0995,295,686 - 95,295,746EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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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)
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)
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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)
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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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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)
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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)
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)
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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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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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)
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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