Abcc2 (ATP binding cassette subfamily C member 2) - Rat Genome Database

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Gene: Abcc2 (ATP binding cassette subfamily C member 2) Rattus norvegicus
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Symbol: Abcc2
Name: ATP binding cassette subfamily C member 2
RGD ID: 2366
Description: Enables ABC-type transporter activity; bilirubin transmembrane transporter activity; and protein domain specific binding activity. Involved in several processes, including carboxylic acid transport; cellular response to cytokine stimulus; and cellular response to lipid. Located in brush border membrane and intracellular canaliculus. Used to study Dubin-Johnson syndrome; bilirubin metabolic disorder; cholestasis; end stage renal disease; and visual epilepsy. Biomarker of several diseases, including bilirubin metabolic disorder; fatty liver disease; primary biliary cholangitis; status epilepticus; and type 2 diabetes mellitus. Human ortholog(s) of this gene implicated in bilirubin metabolic disorder (multiple); carcinoma (multiple); drug-induced hepatitis; leukemia (multiple); and non-alcoholic fatty liver disease. Orthologous to human ABCC2 (ATP binding cassette subfamily C member 2); PARTICIPATES IN bile acid signaling pathway; docetaxel pharmacodynamics pathway; doxorubicin pharmacokinetics pathway; INTERACTS WITH (+)-pilocarpine; (-)-epigallocatechin 3-gallate; (S)-colchicine.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: ATP-binding cassette sub-family C member 2; ATP-binding cassette, sub-family C (CFTR/MRP) member 2; ATP-binding cassette, sub-family C (CFTR/MRP), member 2; ATP-binding cassette, subfamily C (CFTR/MRP), member 2; calicular multispecific organic anion transporter; canalicular multidrug resistance protein; canalicular multispecific organic anion transporter; canalicular multispecific organic anion transporter 1; Cmoat; cMRP; cMrp2/cMoat canalicular apical conjugate export pump; mrp; Mrp2; multidrug resistance associated protein 2; multidrug resistance-associated protein 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Abcc2TR-   Abcc2em1Sage  
Genetic Models: SD-Abcc2em1Sage WUN-Abcc2TR-/HsdRrrc
Is Marker For: Strains:   WUN-Abcc2TR-/HsdRrrc  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21242,664,657 - 242,723,239 (+)NCBImRatBN7.2
Rnor_6.0 Ensembl1263,554,453 - 263,613,252 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01263,554,426 - 263,612,556 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01270,999,832 - 271,057,750 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1238,483,399 - 238,539,595 (+)NCBICelera
Cytogenetic Map1q54NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
(-)-epigallocatechin 3-gallate  (EXP)
(2,4,5-trichlorophenoxy)acetic acid  (ISO)
(RS)-coclaurine  (ISO)
(RS)-norcoclaurine  (ISO)
(S)-coclaurine  (ISO)
(S)-colchicine  (EXP)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (ISO)
1,2-dichloroethane  (ISO)
1-[3-(dimethylamino)propyl]-1-(4-fluorophenyl)-1,3-dihydro-2-benzofuran-5-carbonitrile  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
1-naphthyl isothiocyanate  (EXP,ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 17-glucosiduronic acid  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
2',3'-dideoxyadenosine  (EXP)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (EXP)
2-(3,4-dimethoxyphenyl)-5-\{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino\}-2-(propan-2-yl)pentanenitrile  (ISO)
2-acetamidofluorene  (ISO)
2-tert-butylhydroquinone  (EXP,ISO)
3',4',7-trihydroxyisoflavone  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP,ISO)
3-methyl-3H-imidazo[4,5-f]quinolin-2-amine  (ISO)
4'-epidoxorubicin  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (EXP)
4-hydroxynon-2-enal  (EXP,ISO)
5(6)-carboxy-2',7'-dichlorofluorescein  (EXP,ISO)
5-aza-2'-deoxycytidine  (ISO)
5-chloromethylfluorescein diacetate  (ISO)
5-fluorouracil  (ISO)
5-formyltetrahydrofolic acid  (EXP)
5-methoxypsoralen  (ISO)
6-bromoindirubin-3'-oxime  (ISO)
6-carboxyfluorescein  (ISO)
6-propyl-2-thiouracil  (EXP)
8-(4-chlorophenylthio)-cAMP  (ISO)
8-Br-cAMP  (EXP)
8-Epidiosbulbin E acetate  (ISO)
abietic acid  (EXP)
acadesine  (EXP)
acetamide  (EXP)
actinomycin D  (EXP,ISO)
aflatoxin B1  (ISO)
AICA ribonucleotide  (EXP)
aldehydo-D-glucose  (EXP)
alfacalcidol  (ISO)
all-trans-retinoic acid  (ISO)
allyl alcohol  (ISO)
alpha-amanitin  (ISO)
aluminium hydroxide  (EXP)
amiodarone  (EXP)
angelicin  (EXP)
aristolochic acid  (ISO)
Aroclor 1254  (EXP)
arsane  (EXP,ISO)
arsenic atom  (EXP,ISO)
arsenite(3-)  (EXP,ISO)
arsenous acid  (ISO)
atazanavir sulfate  (ISO)
atorvastatin calcium  (EXP,ISO)
ATP  (EXP,ISO)
azathioprine  (EXP,ISO)
aztreonam  (ISO)
benzbromarone  (EXP,ISO)
benzo[a]pyrene  (ISO)
benzoylaconine  (ISO)
benzoylhypaconine  (ISO)
benzoylmesaconine  (ISO)
benzylpenicillin  (EXP,ISO)
beta-hexachlorocyclohexane  (ISO)
beta-naphthoflavone  (EXP,ISO)
bezafibrate  (ISO)
bilirubin IXalpha  (EXP)
biochanin A  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisdemethoxycurcumin  (ISO)
bisphenol A  (EXP,ISO)
Boldine  (EXP)
bortezomib  (ISO)
bosentan  (EXP,ISO)
bromfenac  (ISO)
bromosulfophthalein  (ISO)
bucladesine  (EXP,ISO)
buspirone  (EXP)
buta-1,3-diene  (ISO)
butanal  (ISO)
butylated hydroxyanisole  (ISO)
cadmium dichloride  (EXP,ISO)
caffeine  (ISO)
calcein  (ISO)
calcein am  (EXP,ISO)
calcitriol  (EXP,ISO)
calcium atom  (ISO)
calcium(0)  (ISO)
captan  (ISO)
carbamazepine  (EXP,ISO)
carbon monoxide  (EXP)
carboplatin  (ISO)
carmustine  (ISO)
cefaloridine  (EXP)
cefalotin  (ISO)
celecoxib  (ISO)
cerivastatin  (ISO)
chenodeoxycholic acid  (EXP,ISO)
chlorambucil  (ISO)
chlordecone  (ISO)
chlorogenic acid  (ISO)
chloroquine  (ISO)
chlorpromazine  (EXP)
chlorpyrifos  (ISO)
cholic acid  (ISO)
choline  (EXP,ISO)
chrysin  (ISO)
chrysophanol  (EXP)
ciprofloxacin  (ISO)
cisplatin  (EXP,ISO)
citalopram  (ISO)
clobazam  (EXP)
clofibrate  (EXP,ISO)
clofibric acid  (EXP)
clotrimazole  (ISO)
colforsin daropate hydrochloride  (ISO)
coniferyl aldehyde  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
curcumin  (ISO)
cyazofamid  (ISO)
cyclosporin A  (EXP,ISO)
cyproconazole  (EXP,ISO)
D-glucose  (EXP)
dapsone  (EXP)
daunorubicin  (ISO)
DDE  (ISO)
DDT  (ISO)
demethoxycurcumin  (ISO)
deoxycholic acid  (ISO)
desloratadine  (ISO)
dexamethasone  (EXP,ISO)
dextran sulfate  (ISO)
Diallyl sulfide  (EXP)
diarsenic trioxide  (ISO)
diclofenac  (EXP,ISO)
dicrotophos  (ISO)
dieldrin  (ISO)
diethyl maleate  (ISO)
dimethylarsinic acid  (EXP)
Diosbulbin B  (ISO)
dioscin  (EXP)
diosgenin  (EXP)
dioxygen  (ISO)
dipotassium bis[mu-tartrato(4-)]diantimonate(2-) trihydrate  (EXP)
doramapimod  (ISO)
dorsomorphin  (EXP)
dothiepin  (ISO)
doxorubicin  (EXP,ISO)
DPDPE  (EXP)
E3040  (ISO)
elemental selenium  (EXP)
emodin  (EXP,ISO)
endosulfan  (EXP,ISO)
enilconazole  (ISO)
epoxiconazole  (EXP)
estrone 3-sulfate  (EXP,ISO)
etacrynic acid  (ISO)
ethoxyquin  (ISO)
etoposide  (ISO)
fenofibrate  (EXP)
Fexofenadine hydrochloride  (ISO)
fipronil  (EXP,ISO)
Fluo-3  (EXP)
flutamide  (EXP)
fluvastatin  (EXP,ISO)
formononetin  (EXP,ISO)
fosinopril  (ISO)
fructose  (EXP)
fulvestrant  (EXP,ISO)
furan  (EXP)
furosemide  (EXP,ISO)
fusidic acid  (EXP)
geneticin  (ISO)
genistein  (ISO)
gentamycin  (EXP)
geraniol  (EXP)
Ginkgolide A  (ISO)
ginkgolide B  (ISO)
ginsenoside Rb2  (EXP)
ginsenoside Re  (EXP,ISO)
ginsenoside Rg1  (EXP,ISO)
ginsenoside Rg2  (EXP)
glafenine  (EXP)
glucose  (EXP)
glutathione  (EXP,ISO)
glutathione disulfide  (EXP)
glyburide  (EXP)
glycyrrhetinate  (EXP)
glycyrrhetinic acid  (EXP)
glyphosate  (ISO)
Goe 6976  (EXP,ISO)
guggulsterone  (ISO)
GW 4064  (EXP)
hepoxilin A3  (ISO)
heptachlor  (ISO)
Heptachlor epoxide  (ISO)
hydrogen peroxide  (ISO)
Hypaconitine  (ISO)
imipenem hydrate  (ISO)
indole-3-methanol  (EXP)
indometacin  (EXP,ISO)
irinotecan  (ISO)
iron(III) nitrilotriacetate  (ISO)
isoniazide  (EXP)
ivermectin  (ISO)
ketoconazole  (EXP,ISO)
kojic acid  (EXP)
KT 5720  (EXP,ISO)
L-ascorbic acid  (EXP,ISO)
L-cysteine  (EXP,ISO)
L-methionine  (EXP,ISO)
leukotriene C4  (EXP,ISO)
levetiracetam  (EXP)
lipopolysaccharide  (EXP,ISO)
lithocholic acid  (EXP,ISO)
lopinavir  (ISO)
Loratadine  (ISO)
lovastatin  (EXP,ISO)
luteolin  (ISO)
LY294002  (ISO)
macitentan  (ISO)
manganese(II) chloride  (EXP)
Maprotiline  (EXP)
Meclizine  (ISO)
mercury atom  (EXP,ISO)
mercury dichloride  (EXP,ISO)
mercury(0)  (EXP,ISO)
Mesaconitine  (ISO)
metformin  (ISO)
methapyrilene  (EXP)
methotrexate  (EXP,ISO)
methoxsalen  (ISO)
methylarsonic acid  (EXP,ISO)
methylisothiazolinone  (ISO)
methylmercury chloride  (EXP,ISO)
metiram  (ISO)
metronidazole  (ISO)
microcystin LF  (ISO)
microcystin RR  (ISO)
microcystin-LR  (ISO)
Midecamycin  (EXP,ISO)
mifepristone  (ISO)
MK 571  (EXP,ISO)
mono(2-ethylhexyl) phthalate  (ISO)
mono(glucosyluronic acid)bilirubin  (EXP,ISO)
monosodium L-glutamate  (ISO)
montelukast  (ISO)
myricetin  (ISO)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (EXP,ISO)
N-acetyl-L-cysteine  (ISO)
N-Acetyl-S-(1,2-dichlorovinyl)-cysteine  (ISO)
N-hydroxy-PhIP  (ISO)
N-nitrosodiethylamine  (EXP)
N-Vinyl-2-pyrrolidone  (EXP)
nelfinavir  (ISO)
neomycin  (ISO)
nifedipine  (EXP)
nimesulide  (EXP)
nitric oxide  (EXP,ISO)
nitrogen dioxide  (ISO)
nocodazole  (ISO)
norgestimate  (ISO)
notoginsenoside R1  (EXP,ISO)
obeticholic acid  (EXP,ISO)
ochratoxin A  (EXP,ISO)
olmesartan  (ISO)
oltipraz  (EXP,ISO)
organoselenium compound  (ISO)
orphenadrine  (EXP)
ortho-Aminoazotoluene  (ISO)
p-menthan-3-ol  (ISO)
paclitaxel  (ISO)
pantoprazole  (ISO)
paracetamol  (EXP,ISO)
paroxetine  (ISO)
PCB138  (ISO)
pentachlorophenol  (ISO)
perfluorodecanoic acid  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
perfluorooctanoic acid  (ISO)
perhexiline  (EXP)
phalloidin  (EXP)
phenethyl isothiocyanate  (ISO)
phenobarbital  (EXP,ISO)
phenol red  (EXP)
phenytoin  (EXP,ISO)
PhIP  (EXP,ISO)
phorbol 13-acetate 12-myristate  (EXP)
physcion  (EXP)
piperonyl butoxide  (ISO)
pirinixic acid  (EXP,ISO)
pitavastatin  (EXP,ISO)
pitavastatin(1-)  (EXP,ISO)
platinum  (ISO)
platinum(0)  (ISO)
pravastatin  (EXP,ISO)
pregnenolone 16alpha-carbonitrile  (EXP,ISO)
probenecid  (EXP,ISO)
prochloraz  (EXP)
progesterone  (ISO)
propane-1,2-diol  (ISO)
protein kinase inhibitor  (EXP)
Prulifloxacin  (EXP)
psoralen  (EXP)
pyrazinecarboxamide  (EXP)
pyrrolidines  (EXP)
quercetin  (EXP,ISO)
reactive oxygen species  (EXP)
resveratrol  (EXP,ISO)
rifampicin  (ISO)
robinetin  (ISO)
rosuvastatin calcium  (EXP,ISO)
rubitecan  (ISO)
S-(2,4-dinitrophenyl)glutathione  (EXP,ISO)
S-nitrosoglutathione  (EXP)
saquinavir  (ISO)
selenium atom  (EXP)
senecionine  (ISO)
sevoflurane  (EXP)
simvastatin  (EXP,ISO)
sincalide  (ISO)
sirolimus  (EXP)
sodium arsenate  (EXP,ISO)
sodium arsenite  (EXP,ISO)
sodium chloride  (ISO)
sodium dichromate  (EXP,ISO)
sodium dodecyl sulfate  (ISO)
sodium hydrogencarbonate  (EXP)
sorafenib  (ISO)
soybean oil  (EXP)
spironolactone  (EXP)
stilbene oxide  (EXP)
streptozocin  (EXP,ISO)
succimer  (EXP,ISO)
sulfasalazine  (EXP)
sulfinpyrazone  (ISO)
sulforaphane  (EXP,ISO)
sunitinib  (EXP)
tamoxifen  (EXP,ISO)
taurine  (EXP)
tauro-beta-muricholic acid  (EXP)
taurochenodeoxycholic acid  (EXP)
taurocholic acid  (EXP,ISO)
taurolithocholic acid  (EXP)
tauroursodeoxycholic acid  (EXP)
Temocaprilat  (EXP)
temozolomide  (ISO)
tert-butyl hydroperoxide  (EXP,ISO)
testosterone  (EXP,ISO)
tetrachloromethane  (EXP,ISO)
tetracycline  (EXP)
texas red  (EXP)
thiacloprid  (ISO)
thioacetamide  (EXP)
thiophanate-methyl  (ISO)
thyroxine  (EXP)
tiagabine  (EXP)
ticlopidine  (EXP,ISO)
Tolvaptan  (ISO)
topiramate  (EXP)
topotecan  (ISO)
trans-piceid  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
trimethylarsine oxide  (EXP)
triphenyl phosphate  (EXP)
triptonide  (ISO)
troglitazone  (ISO)
tyrphostin AG 1478  (EXP)
uranium atom  (EXP)
urethane  (ISO)
ursodeoxycholic acid  (EXP,ISO)
vadimezan  (ISO)
valdecoxib  (EXP)
valproic acid  (EXP,ISO)
vancomycin  (EXP,ISO)
verapamil  (ISO)
vincaleukoblastine  (EXP,ISO)
vincristine  (ISO)
vitamin E  (EXP)
wortmannin  (EXP)
Y-27632  (ISO)
Yangonin  (ISO)
yohimbine  (ISO)
zearalenone  (ISO)
ziram  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
antibiotic metabolic process  (IMP)
benzylpenicillin metabolic process  (IMP)
bile acid and bile salt transport  (IEP,ISO,ISS)
bile acid signaling pathway  (IEP)
bilirubin transport  (IMP,ISO)
canalicular bile acid transport  (IMP)
cellular chloride ion homeostasis  (IDA)
cellular response to dexamethasone stimulus  (IEP)
cellular response to interleukin-1  (IEP)
cellular response to interleukin-6  (IEP)
cellular response to lipopolysaccharide  (IEP)
cellular response to tumor necrosis factor  (IEP)
cellular response to xenobiotic stimulus  (IEP)
detoxification of mercury ion  (IMP)
female pregnancy  (IEP)
inflammatory response  (IEP)
leukotriene transport  (IMP,ISO)
mercury ion transport  (IMP)
negative regulation of gene expression  (IMP)
organic anion transport  (IMP,TAS)
prostaglandin transport  (IMP)
regulation of bile acid secretion  (IEP)
regulation of gene expression  (IEP)
response to 17alpha-ethynylestradiol  (IEP)
response to antineoplastic agent  (IEP)
response to arsenic-containing substance  (IEP)
response to estradiol  (IEP)
response to estrogen  (IDA)
response to glucagon  (IEP)
response to heat  (IEP)
response to lipopolysaccharide  (IEP)
response to methotrexate  (IEP)
response to oxidative stress  (IEP)
response to steroid hormone  (IEP)
response to xenobiotic stimulus  (IDA)
thyroid hormone transport  (IMP)
transepithelial transport  (IGI,IMP)
transmembrane transport  (IBA)
xenobiotic catabolic process  (IMP)
xenobiotic detoxification by transmembrane export across the plasma membrane  (IMP)
xenobiotic export  (ISO)
xenobiotic transmembrane transport  (IMP,ISO)
xenobiotic transport across blood-brain barrier  (IGI,IMP)

Cellular Component

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
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25. GOA data from the GO Consortium
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37. Kim MS, etal., Drug Metab Dispos. 2004 Sep;32(9):909-14.
38. Kim SH, etal., Tuberculosis (Edinb). 2012 Jan;92(1):100-4. doi: 10.1016/j.tube.2011.09.007. Epub 2011 Dec 16.
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40. Kojima H, etal., Biochem Biophys Res Commun. 1992 Jul 15;186(1):398-404.
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51. MGD data from the GO Consortium
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74. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
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Additional References at PubMed
PMID:7559771   PMID:9571149   PMID:11093739   PMID:11279518   PMID:11500505   PMID:12068294   PMID:12538788   PMID:12623073   PMID:12883478   PMID:12951053   PMID:13678533   PMID:14636316  
PMID:14724430   PMID:15057914   PMID:15374814   PMID:15504935   PMID:15816878   PMID:16332456   PMID:16537972   PMID:16946557   PMID:17038627   PMID:17065236   PMID:17234897   PMID:17384956  
PMID:17463180   PMID:17467962   PMID:17615179   PMID:17724374   PMID:17825285   PMID:17959626   PMID:17963604   PMID:18159133   PMID:18175959   PMID:18378562   PMID:18538350   PMID:18662814  
PMID:18687803   PMID:18700187   PMID:19010343   PMID:19063911   PMID:19074644   PMID:19156843   PMID:19214140   PMID:19541926   PMID:19581412   PMID:19656454   PMID:19703566   PMID:19944137  
PMID:20676911   PMID:20738239   PMID:20868650   PMID:21131269   PMID:21198435   PMID:21660137   PMID:22057277   PMID:22330094   PMID:22361279   PMID:22446938   PMID:22472606   PMID:22576625  
PMID:22579010   PMID:22613706   PMID:22711747   PMID:22812007   PMID:22925079   PMID:22992436   PMID:23041646   PMID:23096566   PMID:23125159   PMID:23146761   PMID:23442774   PMID:23562342  
PMID:23569176   PMID:25200138   PMID:25813982   PMID:26053941   PMID:26244301   PMID:26254357   PMID:26646631   PMID:27237619   PMID:27780379   PMID:28298215   PMID:29052767   PMID:30068870  


Genomics

Comparative Map Data
Abcc2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21242,664,657 - 242,723,239 (+)NCBImRatBN7.2
Rnor_6.0 Ensembl1263,554,453 - 263,613,252 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01263,554,426 - 263,612,556 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01270,999,832 - 271,057,750 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1238,483,399 - 238,539,595 (+)NCBICelera
Cytogenetic Map1q54NCBI
ABCC2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1099,782,640 - 99,852,594 (+)EnsemblGRCh38hg38GRCh38
GRCh381099,782,602 - 99,853,741 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3710101,542,397 - 101,612,351 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3610101,532,493 - 101,601,571 (+)NCBINCBI36hg18NCBI36
Build 3410101,532,562 - 101,601,571NCBI
Celera1095,279,806 - 95,349,643 (+)NCBI
Cytogenetic Map10q24.2NCBI
HuRef1095,169,835 - 95,239,503 (+)NCBIHuRef
CHM1_110101,824,911 - 101,894,368 (+)NCBICHM1_1
Abcc2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391943,770,747 - 43,826,771 (+)NCBIGRCm39mm39
GRCm39 Ensembl1943,770,631 - 43,829,179 (+)Ensembl
GRCm381943,782,308 - 43,838,332 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1943,782,192 - 43,840,740 (+)EnsemblGRCm38mm10GRCm38
MGSCv371943,856,798 - 43,912,708 (+)NCBIGRCm37mm9NCBIm37
MGSCv361943,835,715 - 43,891,248 (+)NCBImm8
Celera1944,567,463 - 44,621,438 (+)NCBICelera
Cytogenetic Map19C3NCBI
cM Map1936.67NCBI
Abcc2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555075,724,762 - 5,790,812 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555075,724,788 - 5,791,281 (+)NCBIChiLan1.0ChiLan1.0
ABCC2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11099,889,021 - 99,947,452 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1099,889,160 - 99,947,270 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01096,385,534 - 96,458,571 (+)NCBIMhudiblu_PPA_v0panPan3
ABCC2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12812,670,885 - 12,740,124 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2812,670,885 - 12,740,740 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2812,854,192 - 12,923,368 (+)NCBI
ROS_Cfam_1.02813,138,667 - 13,208,016 (+)NCBI
UMICH_Zoey_3.12812,685,440 - 12,754,683 (+)NCBI
UNSW_CanFamBas_1.02812,716,120 - 12,786,599 (+)NCBI
UU_Cfam_GSD_1.02812,857,984 - 12,927,300 (+)NCBI
Abcc2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721334,253,163 - 34,302,933 (-)NCBI
SpeTri2.0NW_004936636292,631 - 341,999 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ABCC2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl14110,955,656 - 111,078,873 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.114110,955,698 - 111,038,898 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.214120,400,787 - 120,484,137 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ABCC2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1992,826,423 - 92,902,389 (+)NCBI
ChlSab1.1 Ensembl992,841,818 - 92,902,265 (+)Ensembl
Vero_WHO_p1.0NW_02366604853,844,985 - 53,909,244 (+)NCBI
Abcc2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473711,593,701 - 11,686,790 (+)NCBI

Position Markers
RH138478  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21242,722,900 - 242,723,106 (+)MAPPERmRatBN7.2
Rnor_6.01263,612,218 - 263,612,423NCBIRnor6.0
Rnor_5.01271,057,427 - 271,057,632UniSTSRnor5.0
Celera1238,539,257 - 238,539,462UniSTS
RH 3.4 Map11618.32UniSTS
Cytogenetic Map1q51UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2292216Bw80Body weight QTL 803.230.0019body mass (VT:0001259)body weight (CMO:0000012)1213533809243914901Rat
70211Niddm24Non-insulin dependent diabetes mellitus QTL 243.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1214647894259647894Rat
631215Stl8Serum triglyceride level QTL 89.270.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1225126575260522016Rat
2302040Pia35Pristane induced arthritis QTL 353.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)1216255568260522016Rat
2302375Bw83Body weight QTL 834.870.0002body mass (VT:0001259)body weight (CMO:0000012)1197697768242697768Rat
2302378Insul11Insulin level QTL 113.25blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1144267353251128347Rat
724531Uae5Urinary albumin excretion QTL 54urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)1150700142252085212Rat
724533Rf51Renal function QTL 515.30.0002kidney plasma flow trait (VT:0005524)renal plasma flow (CMO:0001914)1218753816256448513Rat
724538Kidm1Kidney mass QTL 13.2kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1213707201252085212Rat
724552Glom2Glomerulus QTL 23.30.0001kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)1222363780260522016Rat
734767Niddm57Non-insulin dependent diabetes mellitus QTL 57body mass (VT:0001259)body weight (CMO:0000012)1224054293260122809Rat
734768Niddm59Non-insulin dependent diabetes mellitus QTL 59body mass (VT:0001259)body weight (CMO:0000012)1213843987258843987Rat
734769Niddm58Non-insulin dependent diabetes mellitus QTL 58body mass (VT:0001259)body weight (CMO:0000012)1224569538260122809Rat
1298084Thym4Thymus enlargement QTL 410.68thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)1197814409242814409Rat
631669Iddm9Insulin dependent diabetes mellitus QTL 92.80.039blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1233190394258625266Rat
631690Scl5Serum cholesterol level QTL 52.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1236125214260522016Rat
1354580Scort1Serum corticosterone level QTL 13.4blood corticosterone amount (VT:0005345)blood corticosterone level (CMO:0001172)1156677124256448636Rat
1581544Rf52Renal function QTL 520.05total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)1232156370259647894Rat
731175Uae20Urinary albumin excretion QTL 203.50.0018urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1221264111259647894Rat
738032Hcas5Hepatocarcinoma susceptibility QTL 53.12liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1176426412257976495Rat
631536Lnnr2Liver neoplastic nodule remodeling QTL 22.90.0005liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)1233948574260522016Rat
1598821Rf55Renal function QTL 556.3renal blood flow trait (VT:2000006)ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)1218748008257976495Rat
2300175Bmd40Bone mineral density QTL 4015.40.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)1201554356246554356Rat
2293655Bss36Bone structure and strength QTL 3610.660.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)1201554356246554356Rat
2293674Bss39Bone structure and strength QTL 397.10.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)1201554356246554356Rat
2293694Bss38Bone structure and strength QTL 387.050.0001femur strength trait (VT:0010010)femur stiffness (CMO:0001674)1201554356246554356Rat
2293700Bmd27Bone mineral density QTL 276.60.0001femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1224054293243747962Rat
2293701Bmd34Bone mineral density QTL 348.30.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)1224054293243747962Rat
631836Stl31Serum triglyceride level QTL 314.640.00000487blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)1237147813260522016Rat
631837Niddm35Non-insulin dependent diabetes mellitus QTL 350.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1238699859259647894Rat
631843Bw116Body weight QTL 1164.10.016abdominal adipose amount (VT:1000220)abdominal fat pad weight (CMO:0000088)1224054293260122809Rat
634313Niddm43Non-insulin dependent diabetes mellitus QTL 43blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1199050459259647894Rat
1357335Bw39Body weight QTL 393.3body mass (VT:0001259)body weight (CMO:0000012)1197814409242814409Rat
1357399Bw45Body weight QTL 453.05body mass (VT:0001259)body mass index (BMI) (CMO:0000105)1206329708251329708Rat
1357404Bw42Body weight QTL 424.490.0001body mass (VT:0001259)body weight (CMO:0000012)1206329708251329708Rat
1600363Hc6Hypercalciuria QTL 62.7urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1203995416244113296Rat
1600374Mcs17Mammary carcinoma susceptibility QTL 173mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1197670404242670404Rat
1600388Niddm67Non-insulin dependent diabetes mellitus QTL 675.840.000004blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1195804352257091168Rat
1600392Bw123Body weight QTL 1230.001body mass (VT:0001259)body weight (CMO:0000012)1223201027260522016Rat
1600395Niddm69Non-insulin dependent diabetes mellitus QTL 694.140.0002blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1195804352257091168Rat
1600396Niddm68Non-insulin dependent diabetes mellitus QTL 684.970.0003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1195804352257091168Rat
1600397Edcs4Endometrial carcinoma susceptibility QTL 42.2uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)1206081677251081677Rat
1578759Uae30Urinary albumin excretion QTL 303.30.003urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1150700247252085048Rat
1578763Kidm29Kidney mass QTL 293.30.0001kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1179567751260522016Rat
1578778Pur4Proteinuria QTL 43.30.003total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1150700247252085048Rat
1300108Rf8Renal function QTL 83.75renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1228581588259647894Rat
1354610Bw34Body weight QTL 344.1body mass (VT:0001259)body weight (CMO:0000012)1151162512256448636Rat
1354624Cm35Cardiac mass QTL355.7heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1177227632256448636Rat
1354646Kidm18Kidney mass QTL 185.7kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1151162512256448636Rat
1354652Kidm20Kidney mass QTL 204.3kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1177227632256448636Rat
1354661Bw33Body weight QTL 335.2body mass (VT:0001259)body weight (CMO:0000012)1151162512256448636Rat
1549910Bw54Body weight QTL 540.05body mass (VT:0001259)body weight (CMO:0000012)1214647894259647894Rat
2316896Gluco57Glucose level QTL 577.2blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1228985440245907899Rat
1549837Hcar15Hepatocarcinoma resistance QTL 150.05liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1153136852260522016Rat
1358191Ept10Estrogen-induced pituitary tumorigenesis QTL 103.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)1192825253243914732Rat
2292220Bp306Blood pressure QTL 3063.470.00087arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1164310393243914901Rat
1358890Bp259Blood pressure QTL 2593.06arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1210702053260522016Rat
1358898Bp255Blood pressure QTL 2553.6arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1191019702246062233Rat
61327Eae7Experimental allergic encephalomyelitis QTL 75.6body mass (VT:0001259)change in body weight (CMO:0002045)1216255568260522016Rat
61376Bp42Blood pressure QTL 4223.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1197814409242814409Rat
61400Niddm1Non-insulin dependent diabetes mellitus QTL 111blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1218753689245907899Rat
8655655Arrd2Age-related retinal degeneration QTL 27.79retinal layer morphology trait (VT:0003727)percentage of study population developing retinopathy during a period of time (CMO:0002453)1183970203243914901Rat
7394701Uae46Urinary albumin excretion QTL 463.60.0056urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1201554356246554356Rat
8655855Arrd3Age-related retinal degeneration QTL 33.07lens clarity trait (VT:0001304)cataract incidence/prevalence measurement (CMO:0001585)1183970203243914901Rat
10053715Scort24Serum corticosterone level QTL 242.130.0088blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1221414816260522016Rat
10059587Bw173Body weight QTL 1733.230.025body mass (VT:0001259)body weight (CMO:0000012)1202069611247069611Rat


Related Rat Strains
The following Strains have been annotated to Abcc2


Genetic Models
This gene Abcc2 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:27
Count of miRNA genes:27
Interacting mature miRNAs:27
Transcripts:ENSRNOT00000070861
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 37 37 37 7
Low 2 19 4 11 4 2 2 64 24 13 11 2
Below cutoff 1 41 1 8 6 8 10 4 27 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000070861   ⟹   ENSRNOP00000064799
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1263,554,453 - 263,613,252 (+)Ensembl
RefSeq Acc Id: NM_012833   ⟹   NP_036965
RefSeq Status: REVIEWED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21242,664,657 - 242,723,239 (+)NCBI
Rnor_6.01263,554,426 - 263,612,556 (+)NCBI
Rnor_5.01270,999,832 - 271,057,750 (+)NCBI
Celera1238,483,399 - 238,539,595 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_036965   ⟸   NM_012833
- UniProtKB: Q63120 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000064799   ⟸   ENSRNOT00000070861
Transcriptome

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

Promoters
RGD ID:13690930
Promoter ID:EPDNEW_R1454
Type:initiation region
Name:Abcc2_1
Description:ATP binding cassette subfamily C member 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01263,554,541 - 263,554,601EPDNEW

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)
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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)
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)
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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
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)
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