Abcc1 (ATP binding cassette subfamily C member 1) - Rat Genome Database

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Gene: Abcc1 (ATP binding cassette subfamily C member 1) Rattus norvegicus
Analyze
Symbol: Abcc1
Name: ATP binding cassette subfamily C member 1
RGD ID: 3112
Description: Enables several functions, including ATPase-coupled transmembrane transporter activity; glutathione transmembrane transporter activity; and long-chain fatty acid transporter activity. Involved in several processes, including glutathione transmembrane transport; lipid transport; and xenobiotic detoxification by transmembrane export across the plasma membrane. Located in basolateral plasma membrane and cytoplasm. Is integral component of plasma membrane. Human ortholog(s) of this gene implicated in autosomal dominant nonsyndromic deafness 77 and chronic obstructive pulmonary disease. Orthologous to human ABCC1 (ATP binding cassette subfamily C member 1); PARTICIPATES IN docetaxel pharmacodynamics pathway; doxorubicin pharmacokinetics pathway; irinotecan pharmacodynamics pathway; INTERACTS WITH (+)-pilocarpine; (R)-adrenaline; 17beta-estradiol 3-benzoate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Abcc1a; ATP-binding cassette sub-family C ( CFTR/MRP) member 1a; ATP-binding cassette sub-family C (CFTR/MRP) member 1 (multiple drug resistance-associated protein); ATP-binding cassette sub-family C member 1; ATP-binding cassette, sub-family C ( CFTR/MRP), member 1a; ATP-binding cassette, sub-family C (CFTR/MRP), member 1; ATP-binding cassette, sub-family C, member 1-like; ATP-binding cassette, subfamily C (CFTR/MRP), member 1; Avcc1a; glutathione-S-conjugate-translocating ATPase ABCC1; leukotriene C(4) transporter; LOC100362747; LOC100365034; LOC103693258; LTC4 transporter; Mrp; Mrp1; multidrug resistance protein; Multidrug resistance protein 1; multidrug resistance-associated protein 1; multidrug resistance-associated protein 1-like; multiple drug resistance-associated protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.210528,961 - 655,179 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl10531,812 - 655,114 (-)Ensembl
Rnor_6.010549,537 - 672,235 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10549,883 - 672,196 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01011,232,233 - 11,354,931 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.410452,239 - 575,705 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.110452,238 - 575,705 (-)NCBI
Celera1011,130,945 - 11,246,232 (-)NCBICelera
Cytogenetic Map10q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-alpha-viniferin  (ISO)
(+)-pilocarpine  (EXP)
(+)-taxifolin  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
(-)-trans-epsilon-viniferin  (ISO)
(25R)-cholest-5-ene-3beta,26-diol  (ISO)
(R)-adrenaline  (EXP)
(S)-colchicine  (ISO)
(S)-naringenin  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (ISO)
15-deoxy-Delta(12,14)-prostaglandin J2  (ISO)
15alpha-hydroxytestosterone  (ISO)
16alpha-hydroxytestosterone  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
17beta-estradiol 17-glucosiduronic acid  (ISO)
17beta-estradiol 3-benzoate  (EXP)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2'-(4-ethoxyphenyl)-5-(4-methylpiperazin-1-yl)-2,5'-bibenzimidazole  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,6-dinitrotoluene  (EXP)
2-(3,4-dimethoxyphenyl)-5-\{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino\}-2-(propan-2-yl)pentanenitrile  (ISO)
2-acetamidofluorene  (EXP)
2-naphthol  (ISO)
2-tert-butylhydroquinone  (ISO)
26-hydroxycholesterol  (ISO)
3',4',7-trihydroxyisoflavone  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
4',5,7-trihydroxy-3'-methoxyflavone  (ISO)
4'-epidoxorubicin  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4-hydroxynon-2-enal  (ISO)
4-nitrophenol  (ISO)
4-nitroquinoline N-oxide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
5-methoxypsoralen  (ISO)
6-carboxyfluorescein  (ISO)
6beta-hydroxytestosterone  (ISO)
8-Br-cAMP  (ISO)
[2,8-bis(trifluoromethyl)quinolin-4-yl]-(2-piperidyl)methanol  (ISO)
abamectin  (ISO)
acetamide  (EXP)
acetic acid [2-[[(5-nitro-2-thiazolyl)amino]-oxomethyl]phenyl] ester  (ISO)
acetochlor  (ISO)
acetylsalicylic acid  (ISO)
actinomycin D  (EXP,ISO)
ADP  (ISO)
aflatoxin B1  (ISO)
afrormosin  (ISO)
aldehydo-D-glucose  (ISO)
allyl alcohol  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
antimony(0)  (ISO)
apigenin  (ISO)
arsane  (ISO)
arsenic acid  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
ATP  (ISO)
baicalein  (ISO)
beclomethasone  (ISO)
benzbromarone  (ISO)
benzene-1,2,4-triol  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[e]pyrene  (ISO)
beta-naphthoflavone  (EXP)
bilirubin IXalpha  (ISO)
biochanin A  (ISO)
biopterin  (ISO)
bisdemethoxycurcumin  (ISO)
bisphenol A  (EXP,ISO)
bortezomib  (ISO)
butan-1-ol  (ISO)
butanal  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
calcein  (ISO)
calcein am  (ISO)
calcitriol  (ISO)
camptothecin  (ISO)
cannabidiol  (ISO)
Cannabinol  (ISO)
carbamazepine  (EXP)
carbon nanotube  (ISO)
carboplatin  (ISO)
celecoxib  (ISO)
chenodeoxycholic acid  (ISO)
chlorambucil  (ISO)
chlorogenic acid  (ISO)
chloroprene  (ISO)
chloroquine  (ISO)
chlorpropham  (ISO)
chlorpyrifos  (ISO)
cholic acid  (ISO)
choline  (EXP,ISO)
chromium(6+)  (ISO)
chrysin  (ISO)
cisplatin  (EXP,ISO)
clobetasol  (ISO)
clothianidin  (ISO)
cobalt dichloride  (EXP)
copper(II) sulfate  (ISO)
Cuprizon  (EXP)
curcumin  (ISO)
cyclophosphamide  (ISO)
cyclosporin A  (ISO)
cytarabine  (ISO)
D-glucose  (ISO)
daidzein  (ISO)
daunorubicin  (ISO)
delta-tocotrienol  (ISO)
demethoxycurcumin  (ISO)
deoxycholic acid  (ISO)
dexamethasone  (EXP,ISO)
diallyl disulfide  (ISO)
Diallyl sulfide  (ISO)
diallyl trisulfide  (ISO)
diarsenic trioxide  (ISO)
dibenzo[a,l]pyrene  (ISO)
dichlorine  (EXP)
dicrotophos  (ISO)
dieldrin  (EXP)
dimethylarsinic acid  (EXP,ISO)
dimethylarsinous acid  (ISO)
diosmetin  (ISO)
dipotassium bis[mu-tartrato(4-)]diantimonate(2-) trihydrate  (ISO)
disulfiram  (ISO)
diuron  (EXP)
doxorubicin  (EXP,ISO)
emamectin  (ISO)
eriodictyol  (ISO)
etacrynic acid  (ISO)
etoposide  (ISO)
fenitrothion  (ISO)
flavone  (ISO)
flavonoids  (ISO)
Fluo-3  (ISO)
folic acid  (ISO)
formononetin  (ISO)
fosinopril  (ISO)
galangin  (ISO)
gallocatechin  (ISO)
gamma-tocopherol  (ISO)
geneticin  (ISO)
genistein  (EXP,ISO)
ginsenoside Re  (ISO)
ginsenoside Rg1  (ISO)
glucose  (ISO)
glutathione  (EXP,ISO)
glutathione disulfide  (EXP,ISO)
glyburide  (ISO)
glycochenodeoxycholic acid  (ISO)
glycocholic acid  (ISO)
glycodeoxycholic acid  (ISO)
glycyrrhetinate  (ISO)
glycyrrhetinic acid  (ISO)
glyphosate  (ISO)
gold atom  (ISO)
gold(0)  (ISO)
Grepafloxacin  (ISO)
haloperidol  (ISO)
heparin  (ISO)
heptachlor  (EXP)
hesperetin  (ISO)
hexadecanoic acid  (ISO)
hydrogen peroxide  (ISO)
hypericin  (ISO)
hypochlorous acid  (ISO)
idarubicin  (ISO)
indole-3-methanol  (EXP)
indometacin  (EXP,ISO)
irinotecan  (ISO)
iron atom  (ISO)
iron(0)  (ISO)
iron(III) nitrilotriacetate  (ISO)
isoflavones  (ISO)
isoniazide  (EXP)
isoorientin  (ISO)
isorhamnetin  (ISO)
ivermectin  (ISO)
kaempferol  (ISO)
ketoconazole  (ISO)
L-ascorbic acid  (ISO)
L-methionine  (EXP,ISO)
lead diacetate  (EXP,ISO)
leflunomide  (ISO)
leukotriene C4  (ISO)
levetiracetam  (EXP)
lipopolysaccharide  (EXP,ISO)
lithocholic acid  (ISO)
lithocholic acid sulfate  (ISO)
loratadine  (ISO)
lovastatin  (ISO)
luteolin  (ISO)
LY294002  (EXP)
mebendazole  (ISO)
mefloquine  (ISO)
melphalan  (ISO)
mercury atom  (EXP,ISO)
mercury dichloride  (EXP,ISO)
mercury(0)  (EXP,ISO)
methapyrilene  (ISO)
methotrexate  (EXP,ISO)
methoxsalen  (ISO)
methoxychlor  (ISO)
methylarsonic acid  (EXP,ISO)
metiram  (ISO)
mitomycin C  (ISO)
MK 571  (EXP,ISO)
montelukast  (ISO)
morin  (ISO)
myricetin  (ISO)
N-acetyl-L-cysteine  (ISO)
N-ethylmaleimide  (ISO)
nelfinavir  (ISO)
nemorubicin  (ISO)
nickel atom  (ISO)
nickel dichloride  (EXP)
nickel sulfate  (ISO)
nimesulide  (ISO)
nimustine  (ISO)
nitric oxide  (ISO)
nobiletin  (ISO)
notoginsenoside R1  (ISO)
NS-398  (ISO)
oltipraz  (ISO)
ozone  (EXP)
paclitaxel  (ISO)
paracetamol  (EXP,ISO)
paraquat  (ISO)
Pentoxifylline  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenethyl caffeate  (ISO)
phenobarbital  (EXP)
phenothiazines  (ISO)
phenytoin  (EXP)
PhIP  (ISO)
phorbol 13-acetate 12-myristate  (EXP,ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
probenecid  (EXP,ISO)
prodigiosin  (ISO)
prostaglandins E  (ISO)
puromycin  (ISO)
quercetin  (EXP,ISO)
raloxifene  (ISO)
resveratrol  (ISO)
rifampicin  (ISO)
robinetin  (ISO)
robinin  (ISO)
romidepsin  (ISO)
S-(2,4-dinitrophenyl)glutathione  (ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (ISO)
saquinavir  (ISO)
SB 203580  (ISO)
Se-methyl-L-selenocysteine  (ISO)
Se-methylselenocysteine  (ISO)
senecionine  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
silver(1+) nitrate  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (EXP,ISO)
sodium azide  (ISO)
sodium chloride  (ISO)
sodium dichromate  (EXP,ISO)
sodium dodecyl sulfate  (ISO)
sodium fluoride  (ISO)
sodium stibogluconate  (ISO)
sorafenib  (ISO)
soybean oil  (EXP)
streptozocin  (ISO)
sulfinpyrazone  (EXP,ISO)
sulforaphane  (ISO)
sulindac  (ISO)
superoxide  (ISO)
tamoxifen  (ISO)
tartrazine  (ISO)
taurocholic acid  (ISO)
taurodeoxycholic acid  (ISO)
tauroursodeoxycholic acid  (ISO)
taxane  (ISO)
Technetium tc 99m sestamibi  (ISO)
temozolomide  (ISO)
teniposide  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
thiethylperazine  (ISO)
thioacetamide  (EXP)
Thiotepa  (ISO)
tiagabine  (EXP)
titanium dioxide  (ISO)
tocopherol  (ISO)
toluene  (EXP)
topiramate  (EXP)
triclosan  (ISO)
trimethylarsine oxide  (EXP)
triptonide  (ISO)
tunicamycin  (ISO)
ursodeoxycholic acid  (EXP,ISO)
vadimezan  (ISO)
valproic acid  (EXP,ISO)
venlafaxine hydrochloride  (ISO)
verapamil  (ISO)
vincaleukoblastine  (EXP,ISO)
vinclozolin  (EXP)
vincristine  (EXP,ISO)
zafirlukast  (ISO)
zearalenone  (EXP,ISO)
zidovudine  (ISO)
zileuton  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
1. Buchler M, etal., J Biol Chem 1996 Jun 21;271(25):15091-8.
2. Budulac SE, etal., Respir Res. 2010 May 20;11:60.
3. Costa VM, etal., Chem Res Toxicol. 2009 Jan;22(1):129-135.
4. Dallas S, etal., J Pharmacol Exp Ther. 2003 Oct;307(1):282-90. Epub 2003 Jul 31.
5. Falcao AS, etal., Neuroscience. 2007 Feb 9;144(3):878-88. Epub 2006 Dec 4.
6. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
7. GOA data from the GO Consortium
8. Hagenbuch B, etal., News Physiol Sci 2002 Dec;17:231-4.
9. Halwachs S, etal., Mol Pharmacol. 2011 Oct;80(4):621-9. doi: 10.1124/mol.111.072421. Epub 2011 Jul 7.
10. Hirrlinger J, etal., J Neurochem 2001 Jan;76(2):627-36.
11. Hirrlinger J, etal., J Neurosci Res. 2002 Aug 1;69(3):318-26.
12. Hurbain I, etal., Pediatr Res. 2003 Nov;54(5):627-34. Epub 2003 Aug 20.
13. Klein DM, etal., Drug Metab Dispos. 2014 Jan;42(1):89-93. doi: 10.1124/dmd.113.054577. Epub 2013 Oct 15.
14. Krohn M, etal., Brain. 2015 Aug;138(Pt 8):2370-82. doi: 10.1093/brain/awv137. Epub 2015 May 18.
15. MGD data from the GO Consortium
16. Mitra P, etal., Proc Natl Acad Sci U S A. 2006 Oct 31;103(44):16394-9. Epub 2006 Oct 18.
17. Nunoya K, etal., Drug Metab Dispos. 2003 Aug;31(8):1016-26.
18. Patel LN, etal., J Pharm Sci. 2008 Jun;97(6):2340-9.
19. Pei QL, etal., Hepatol Res. 2002 Jan;22(1):58-64.
20. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
21. Pipeline to import SMPDB annotations from SMPDB into RGD
22. RGD automated data pipeline
23. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
24. RGD automated import pipeline for gene-chemical interactions
25. Roberts LM, etal., Neuroscience. 2008 Aug 13;155(2):423-38. Epub 2008 Jun 13.
26. Schultz MJ, etal., J Immunol. 2001 Mar 15;166(6):4059-64.
27. Takayanagi S and Ishikawa T, J Exp Ther Oncol. 2003 May-Jun;3(3):136-46.
28. van der Deen M, etal., Virchows Arch. 2006 Dec;449(6):682-8. Epub 2006 Oct 27.
29. Yang Z, etal., AAPS J. 2004;6(1):77-85.
30. Yang Z, etal., AAPS PharmSci 2002;4(3):E15.
31. Yang Z, etal., AAPS PharmSci. 2004 Mar 9;6(1):E8.
32. Yoshioka M, etal., Am J Physiol Lung Cell Mol Physiol. 2009 Jan;296(1):L30-6. Epub 2008 Oct 17.
Additional References at PubMed
PMID:7559771   PMID:7961706   PMID:9281595   PMID:9359705   PMID:11689020   PMID:12951053   PMID:14623264   PMID:15328029   PMID:15999530   PMID:16170839   PMID:16868918   PMID:16946557  
PMID:17669244   PMID:18057958   PMID:18290326   PMID:18485102   PMID:18509883   PMID:18680196   PMID:19879335   PMID:19897579   PMID:19946888   PMID:20051532   PMID:20458337   PMID:21297965  
PMID:21495913   PMID:21803151   PMID:22015764   PMID:22563480   PMID:22883408   PMID:23474709   PMID:23940624   PMID:25543328   PMID:25986174   PMID:26200696   PMID:28298215   PMID:28577929  


Genomics

Candidate Gene Status
Abcc1 is a candidate Gene for QTL Hcar1
Comparative Map Data
Abcc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.210528,961 - 655,179 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl10531,812 - 655,114 (-)Ensembl
Rnor_6.010549,537 - 672,235 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10549,883 - 672,196 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01011,232,233 - 11,354,931 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.410452,239 - 575,705 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.110452,238 - 575,705 (-)NCBI
Celera1011,130,945 - 11,246,232 (-)NCBICelera
Cytogenetic Map10q11NCBI
ABCC1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1615,949,138 - 16,143,257 (+)EnsemblGRCh38hg38GRCh38
GRCh381615,949,616 - 16,143,062 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371616,043,473 - 16,236,910 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361615,950,935 - 16,144,432 (+)NCBINCBI36hg18NCBI36
Build 341615,950,934 - 16,143,774NCBI
Celera1615,781,784 - 15,917,085 (+)NCBI
Cytogenetic Map16p13.11NCBI
HuRef1615,436,705 - 15,630,893 (+)NCBIHuRef
CHM1_11616,185,916 - 16,321,192 (+)NCBICHM1_1
Abcc1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391614,179,317 - 14,292,743 (+)NCBIGRCm39mm39
GRCm39 Ensembl1614,179,422 - 14,293,601 (+)Ensembl
GRCm381614,361,453 - 14,474,878 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1614,361,558 - 14,475,737 (+)EnsemblGRCm38mm10GRCm38
MGSCv371614,361,653 - 14,474,968 (+)NCBIGRCm37mm9NCBIm37
MGSCv361614,275,138 - 14,388,453 (+)NCBImm8
Celera1614,966,079 - 15,077,783 (+)NCBICelera
Cytogenetic Map16A1NCBI
Abcc1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955442729,316 - 860,290 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955442729,322 - 858,826 (+)NCBIChiLan1.0ChiLan1.0
ABCC1
(Pan paniscus - bonobo/pygmy chimpanzee)		 No map positions available.
ABCC1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1627,855,702 - 27,950,140 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl627,855,702 - 27,989,331 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha629,219,306 - 29,353,121 (-)NCBI
ROS_Cfam_1.0628,018,483 - 28,152,589 (-)NCBI
ROS_Cfam_1.0 Ensembl628,010,824 - 28,152,766 (-)Ensembl
UMICH_Zoey_3.1627,821,973 - 27,955,836 (-)NCBI
UNSW_CanFamBas_1.0627,711,967 - 27,845,729 (-)NCBI
UU_Cfam_GSD_1.0628,117,166 - 28,251,282 (-)NCBI
Abcc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344115,297,821 - 115,369,238 (+)NCBI
SpeTri2.0NW_0049365013,400,971 - 3,467,061 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ABCC1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl328,360,868 - 28,485,477 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1328,360,868 - 28,472,940 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2329,082,788 - 29,172,693 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ABCC1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1514,972,589 - 15,164,594 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl514,972,646 - 15,164,567 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606814,816,018 - 14,953,501 (-)NCBIVero_WHO_p1.0
Abcc1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624782449,217 - 590,306 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH142203  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map10q11UniSTS
AU047602  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21929,362,322 - 29,362,552 (+)MAPPERmRatBN7.2
mRatBN7.210630,276 - 630,875 (+)MAPPERmRatBN7.2
Rnor_6.010647,530 - 648,128NCBIRnor6.0
Rnor_6.01933,035,230 - 33,035,459NCBIRnor6.0
Rnor_5.01943,927,425 - 43,927,654UniSTSRnor5.0
Rnor_5.01011,330,226 - 11,330,824UniSTSRnor5.0
RGSC_v3.41931,264,701 - 31,264,930UniSTSRGSC3.4
RGSC_v3.410550,874 - 551,472UniSTSRGSC3.4
Celera1928,861,530 - 28,861,755UniSTS
Celera1011,221,486 - 11,222,084UniSTS
Cytogenetic Map19q11UniSTS
Cytogenetic Map10q11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10124158324Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135225947Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:257
Count of miRNA genes:144
Interacting mature miRNAs:156
Transcripts:ENSRNOT00000041358, ENSRNOT00000044108
Prediction methods:Microtar, 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 1 5 18 2 19 2 8 8 68 28 36 11 8
Low 2 38 37 37 37 3 6 7 5
Below cutoff 2 2 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000044108   ⟹   ENSRNOP00000044445
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl10531,812 - 655,114 (-)Ensembl
Rnor_6.0 Ensembl10549,883 - 672,196 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000103910   ⟹   ENSRNOP00000091802
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl10531,812 - 655,114 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000115220   ⟹   ENSRNOP00000087096
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl10531,812 - 616,211 (-)Ensembl
RefSeq Acc Id: NM_022281   ⟹   NP_071617
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.210531,812 - 655,114 (-)NCBI
Rnor_6.010549,537 - 672,235 (-)NCBI
Rnor_5.01011,232,233 - 11,354,931 (-)NCBI
RGSC_v3.410452,239 - 575,705 (-)RGD
Celera1011,130,945 - 11,246,232 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039085193   ⟹   XP_038941121
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.210528,961 - 655,179 (-)NCBI
RefSeq Acc Id: XM_039085194   ⟹   XP_038941122
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.210528,961 - 655,179 (-)NCBI
RefSeq Acc Id: XM_039085195   ⟹   XP_038941123
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.210528,961 - 655,090 (-)NCBI
RefSeq Acc Id: XM_039085196   ⟹   XP_038941124
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.210528,961 - 566,085 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_071617   ⟸   NM_022281
- UniProtKB: Q8CG09 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000044445   ⟸   ENSRNOT00000044108
RefSeq Acc Id: XP_038941121   ⟸   XM_039085193
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038941122   ⟸   XM_039085194
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038941123   ⟸   XM_039085195
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038941124   ⟸   XM_039085196
- Peptide Label: isoform X4
RefSeq Acc Id: ENSRNOP00000087096   ⟸   ENSRNOT00000115220
RefSeq Acc Id: ENSRNOP00000091802   ⟸   ENSRNOT00000103910
Protein Domains
ABC transmembrane type-1   ABC transporter

Transcriptome

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

Promoters
RGD ID:13696919
Promoter ID:EPDNEW_R7444
Type:multiple initiation site
Name:Abcc1_1
Description:ATP binding cassette subfamily C member 1
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_6.010672,214 - 672,274EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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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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