Mt1 (metallothionein 1) - Rat Genome Database

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Gene: Mt1 (metallothionein 1) Rattus norvegicus
Analyze
Symbol: Mt1
Name: metallothionein 1
RGD ID: 3117
Description: Predicted to enable copper ion binding activity and zinc ion binding activity. Involved in response to cadmium ion and response to zinc ion. Predicted to be located in cytosol and lysosome. Predicted to be active in cytoplasm and nucleus. Biomarker of kidney failure; median neuropathy; and transient cerebral ischemia. Orthologous to human MT1A (metallothionein 1A); INTERACTS WITH 1,2,4-trimethylbenzene; 1,3,5-trinitro-1,3,5-triazinane; 1-naphthyl isothiocyanate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Metallothionein; Metallothionein 1 A; metallothionein 1a; metallothionein-1; metallothionein-I; Mt; MT-1; MT-I; Mt1a
RGD Orthologs
Human
Mouse
Pig
Alliance Genes
More Info more info ...
Related Pseudogenes: LOC100125598   Mt1-ps1   Mt1-ps2  
Allele / Splice: Mt1-ps1   Mt1-ps2  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21910,826,032 - 10,827,048 (-)NCBImRatBN7.2
Rnor_6.0 Ensembl1778,793,336 - 78,793,724 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01911,301,991 - 11,303,007 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01911,277,133 - 11,278,149 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41911,261,631 - 11,262,647 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11911,266,456 - 11,267,404 (-)NCBI
Celera1910,711,989 - 10,713,005 (-)NCBICelera
RH 3.4 Map19128.1RGD
Cytogenetic Map19p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-selegiline  (ISO)
(2,4,5-trichlorophenoxy)acetic acid  (ISO)
(R)-lipoic acid  (ISO)
1,2,4-trimethylbenzene  (EXP)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1,3,5-trinitro-1,3,5-triazinane  (EXP)
1,4-benzoquinone  (ISO)
1,4-dithiothreitol  (ISO)
1-(5-isoquinolinesulfonyl)-2-methylpiperazine  (ISO)
1-naphthyl isothiocyanate  (EXP,ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2-acetamidofluorene  (EXP)
2-amino-4,6-dinitrotoluene  (EXP)
2-butoxyethanol  (ISO)
2-hydroxypropanoic acid  (ISO)
2-nitrofluorene  (EXP)
2-tert-butylhydroquinone  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP,ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-\{1-[3-(dimethylamino)propyl]-1H-indol-3-yl\}-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-tert-butyl-4-hydroxyanisole  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (EXP,ISO)
4,4'-sulfonyldiphenol  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (EXP)
4-amino-2,6-dinitrotoluene  (EXP)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-(2-methylpiperazine-1-sulfonyl)isoquinoline  (ISO)
5-aza-2'-deoxycytidine  (EXP,ISO)
6-aminonicotinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (EXP)
[6]-Shogaol  (ISO)
acetamide  (EXP)
acetazolamide  (ISO)
acetohydrazide  (ISO)
acetylacetonate  (ISO)
acetylsalicylic acid  (EXP,ISO)
acrylamide  (EXP)
actinomycin D  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (EXP,ISO)
aldehydo-D-glucose  (EXP)
aldosterone  (EXP)
aldrin  (ISO)
all-trans-retinoic acid  (ISO)
alpha-naphthoflavone  (ISO)
amlodipine  (EXP)
ammonium chloride  (EXP)
amphetamine  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
arecoline  (ISO)
Aroclor 1254  (EXP)
arsane  (EXP,ISO)
arsenic atom  (EXP,ISO)
arsenic trichloride  (ISO)
arsenite(3-)  (EXP,ISO)
arsenous acid  (ISO)
atrazine  (ISO)
Azaspiracid  (ISO)
bacitracin  (EXP)
barium chloride  (EXP)
benzene  (EXP)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
benzoic acid  (ISO)
benzyl cinnamate  (ISO)
beta-naphthoflavone  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bromobenzene  (EXP)
buspirone  (EXP)
buta-1,3-diene  (ISO)
cadmium atom  (EXP,ISO)
cadmium dichloride  (EXP,ISO)
cadmium sulfate  (ISO)
Calcimycin  (EXP)
calmidazolium  (EXP)
cannabidiol  (ISO)
carbon nanotube  (ISO)
carbonyl cyanide p-trifluoromethoxyphenylhydrazone  (ISO)
carboplatin  (EXP)
carrageenan  (ISO)
cefaloridine  (EXP)
cerium trichloride  (ISO)
chloroethene  (ISO)
chlorogenic acid  (EXP)
chloropicrin  (ISO)
chloroprene  (ISO)
chlorpromazine  (EXP)
cholesterol  (ISO)
cholic acid  (ISO)
choline  (ISO)
chromium(6+)  (ISO)
chrysene  (ISO)
ciguatoxin CTX1B  (ISO)
cisplatin  (EXP,ISO)
citric acid  (EXP)
clofibrate  (EXP,ISO)
cobalt dichloride  (EXP,ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) chloride  (EXP,ISO)
copper(II) sulfate  (EXP,ISO)
corticosterone  (EXP)
cortisol  (EXP)
coumarin  (EXP)
crocidolite asbestos  (ISO)
CU-O LINKAGE  (ISO)
curcumin  (EXP)
cycloheximide  (ISO)
cytarabine  (ISO)
D-gluconic acid  (ISO)
D-glucose  (EXP)
daunorubicin  (EXP)
decabromodiphenyl ether  (EXP)
dexamethasone  (EXP,ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
diclofenac  (ISO)
dicoumarol  (ISO)
diethyl maleate  (ISO)
diethylstilbestrol  (EXP,ISO)
dimethylarsinic acid  (EXP,ISO)
dioxygen  (EXP,ISO)
diphenylcyclopropenone  (ISO)
diquat  (ISO)
disodium selenite  (ISO)
disulfiram  (ISO)
dopamine  (ISO)
doramapimod  (ISO)
doxorubicin  (EXP,ISO)
ethanol  (EXP,ISO)
ethylenediaminetetraacetic acid  (ISO)
ethylmercuric chloride  (ISO)
ferroheme b  (ISO)
folic acid  (EXP,ISO)
fumonisin B1  (ISO)
furan  (EXP)
furosemide  (ISO)
gamma-hexachlorocyclohexane  (EXP)
genistein  (ISO)
genistein 7-O-beta-D-glucoside  (ISO)
glafenine  (EXP)
glucose  (EXP)
glutathione  (EXP,ISO)
glycerol  (ISO)
glycidol  (EXP)
glyphosate  (EXP)
graphene oxide  (ISO)
griseofulvin  (ISO)
heme b  (ISO)
hexachlorobenzene  (EXP)
hexadecanoic acid  (EXP)
homocysteine  (EXP)
hydrogen peroxide  (ISO)
hydroquinone  (ISO)
hydroxycitronellal  (ISO)
irinotecan  (EXP)
iron atom  (EXP,ISO)
iron trichloride  (ISO)
iron(0)  (EXP,ISO)
iron(2+) sulfate (anhydrous)  (EXP)
iron(III) nitrilotriacetate  (ISO)
isoprenaline  (ISO)
kainic acid  (EXP,ISO)
ketamine  (EXP)
ketoconazole  (EXP)
L-1,4-dithiothreitol  (ISO)
L-ascorbic acid  (EXP)
L-methionine  (ISO)
lead diacetate  (EXP,ISO)
lead nitrate  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
lead(II) chloride  (EXP,ISO)
leflunomide  (EXP)
linsidomine  (ISO)
lipoic acid  (ISO)
lipopolysaccharide  (ISO)
lithocholic acid  (EXP,ISO)
LY294002  (ISO)
maneb  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (EXP)
manganese(II) sulfate  (EXP)
melatonin  (EXP)
menadione  (ISO)
Mercuric oxide  (ISO)
mercury atom  (EXP,ISO)
mercury dichloride  (EXP,ISO)
mercury(0)  (EXP,ISO)
mesoporphyrin IX  (ISO)
metformin  (EXP)
methamphetamine  (EXP)
methapyrilene  (EXP)
methotrexate  (EXP)
methyl methanesulfonate  (EXP)
methylmercury chloride  (EXP,ISO)
metyrapone  (EXP)
microcystin-LR  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
Monobutylphthalate  (ISO)
motexafin gadolinium  (ISO)
N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine  (EXP,ISO)
N-(6-acetamidohexyl)acetamide  (ISO)
N-acetyl-L-cysteine  (EXP,ISO)
N-methyl-4-phenylpyridinium  (EXP)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-methyl-N-nitrosourea  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
N-nitrosodimethylamine  (EXP)
nefazodone  (EXP)
nickel atom  (ISO)
nickel dichloride  (EXP,ISO)
nickel subsulfide  (ISO)
nickel sulfate  (EXP,ISO)
nitric oxide  (ISO)
nitroprusside  (ISO)
ochratoxin A  (EXP,ISO)
okadaic acid  (ISO)
oleanolic acid  (EXP,ISO)
oleic acid  (EXP)
oxaliplatin  (EXP,ISO)
ozone  (EXP,ISO)
paracetamol  (EXP,ISO)
paraquat  (EXP,ISO)
parathion  (ISO)
pentetic acid  (EXP)
phalloidin  (ISO)
phenacetin  (EXP)
phenformin  (EXP)
phenobarbital  (EXP,ISO)
phenylarsine oxide  (ISO)
phenylhydrazine  (EXP)
PhIP  (EXP)
phorbol 13-acetate 12-myristate  (ISO)
phorone  (EXP)
phosgene  (ISO)
piperonyl butoxide  (EXP)
pirinixic acid  (EXP,ISO)
poly(vinylpyrrolidone)  (EXP)
potassium bromate  (ISO)
potassium chloride  (EXP)
potassium dichromate  (EXP,ISO)
pregnenolone 16alpha-carbonitrile  (EXP,ISO)
progesterone  (EXP,ISO)
Ptaquiloside  (ISO)
pyrithione  (ISO)
quartz  (ISO)
quercetin  (EXP)
rac-lactic acid  (ISO)
reactive oxygen species  (ISO)
resveratrol  (ISO)
riddelliine  (EXP)
Ro 31-8220  (ISO)
rotenone  (EXP,ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (EXP,ISO)
salicylic acid  (ISO)
SB 203580  (ISO)
serotonin  (ISO)
serpentine asbestos  (ISO)
silicon dioxide  (EXP,ISO)
silver atom  (EXP,ISO)
silver(0)  (EXP,ISO)
silver(1+) nitrate  (ISO)
simvastatin  (EXP)
sodium arsenate  (EXP,ISO)
sodium arsenite  (EXP,ISO)
sodium chloride  (EXP)
sodium dichromate  (EXP,ISO)
sodium dodecyl sulfate  (ISO)
sodium propionate  (EXP)
Soman  (EXP)
spironolactone  (EXP)
staurosporine  (ISO)
streptozocin  (EXP)
succimer  (EXP,ISO)
tamibarotene  (ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (EXP)
tetrachloroethene  (ISO)
tetrachloromethane  (EXP,ISO)
thapsigargin  (ISO)
thimerosal  (ISO)
thioacetamide  (EXP,ISO)
thiosalicylic acid  (ISO)
titanium dioxide  (EXP,ISO)
toluene  (EXP)
topotecan  (EXP)
triadimefon  (ISO)
tributylstannane  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
trifluoperazine  (EXP)
triphenyl phosphate  (EXP)
Triptolide  (EXP)
triptonide  (ISO)
troglitazone  (EXP,ISO)
trovafloxacin  (EXP,ISO)
tunicamycin  (ISO)
undecane  (EXP)
valproic acid  (EXP,ISO)
vanadium atom  (EXP)
vanadium(0)  (EXP)
vanadyl sulfate  (EXP)
vancomycin  (EXP,ISO)
vanillin  (ISO)
vitamin E  (EXP,ISO)
wortmannin  (ISO)
zinc acetate  (ISO)
zinc atom  (EXP,ISO)
zinc dichloride  (EXP,ISO)
zinc pyrithione  (ISO)
zinc sulfate  (EXP,ISO)
zinc(0)  (EXP,ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cellular_component  (ND)
cytoplasm  (IBA,ISS)
cytosol  (ISO)
lysosome  (ISO)
nucleus  (IBA,ISS)

Molecular Function

References

References - curated
1. Andersen RD, etal., DNA 1983;2(1):15-22.
2. Brambila E, etal., Biol Trace Elem Res. 1999 Nov;70(2):173-82.
3. Caballero B, etal., J Pineal Res. 2008 Oct;45(3):302-11. doi: 10.1111/j.1600-079X.2008.00591.x. Epub 2008 Apr 13.
4. Campagne MV, etal., J Neurosci. 2000 Jul 15;20(14):5200-7.
5. Espey LL, etal., Biol Reprod 2003 May;68(5):1895-902.
6. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
7. Gilmour PS, etal., J Toxicol Environ Health A. 2006 Nov;69(22):2011-32.
8. GOA data from the GO Consortium
9. Grunblatt E, etal., J Alzheimers Dis. 2006 Aug;9(3):261-71.
10. Ignacio S, etal., Ann N Y Acad Sci. 2005 Aug;1053:121-36.
11. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
12. Lanza C, etal., J Neurochem. 2009 Sep;110(5):1674-84. Epub 2009 Jul 8.
13. Lanza C, etal., J Neurosci Res. 2012 Apr;90(4):842-8. doi: 10.1002/jnr.22778. Epub 2012 Jan 18.
14. Lu A, etal., J Cereb Blood Flow Metab. 2006 Feb;26(2):230-52.
15. Manso Y, etal., Cell Mol Life Sci. 2012 Nov;69(21):3665-81. doi: 10.1007/s00018-012-1045-y. Epub 2012 Jul 6.
16. Mercer JF and Hudson P, Biosci Rep 1982 Oct;2(10):761-8.
17. MGD data from the GO Consortium
18. Mocchegiani E, etal., Brain Res Bull 2004 Mar 15;63(2):133-42.
19. Morales AI, etal., Toxicol Appl Pharmacol. 2006 Jan 1;210(1-2):128-35. Epub 2005 Oct 14.
20. Mukhopadhyay D, etal., Syst Biol Reprod Med. 2009 Dec;55(5-6):188-92. doi: 10.3109/19396360903114429.
21. NCBI rat LocusLink and RefSeq merged data July 26, 2002
22. Piedboeuf B, etal., Am J Respir Cell Mol Biol. 1994 Feb;10(2):123-32.
23. RGD automated data pipeline
24. RGD automated import pipeline for gene-chemical interactions
25. RGD comprehensive gene curation
26. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
27. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
28. Tsuruma K, etal., Invest Ophthalmol Vis Sci. 2012 Nov 29;53(12):7896-903. doi: 10.1167/iovs.12-10165.
Additional References at PubMed
PMID:1942051   PMID:2959527   PMID:3023830   PMID:3184190   PMID:3653102   PMID:3945804   PMID:6470004   PMID:6853483   PMID:8640230   PMID:9358851   PMID:11168427   PMID:11792622  
PMID:12130647   PMID:12458661   PMID:12692462   PMID:14690533   PMID:15033980   PMID:15062872   PMID:15126248   PMID:15475485   PMID:15489334   PMID:15623840   PMID:15650329   PMID:15884113  
PMID:16827180   PMID:17008879   PMID:17896077   PMID:17974098   PMID:18350280   PMID:18605988   PMID:19103603   PMID:19148152   PMID:19490425   PMID:19767886   PMID:20109269   PMID:20945050  
PMID:21154237   PMID:21264950   PMID:21359432   PMID:21409224   PMID:22100509   PMID:22571646   PMID:22703381   PMID:23291980   PMID:23726995   PMID:24489578   PMID:24807795   PMID:25947372  
PMID:26884304   PMID:27147436   PMID:27173051   PMID:27523482   PMID:27939232   PMID:28377323   PMID:28760087   PMID:32495853  


Genomics

Comparative Map Data
Mt1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21910,826,032 - 10,827,048 (-)NCBImRatBN7.2
Rnor_6.0 Ensembl1778,793,336 - 78,793,724 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01911,301,991 - 11,303,007 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01911,277,133 - 11,278,149 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41911,261,631 - 11,262,647 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11911,266,456 - 11,267,404 (-)NCBI
Celera1910,711,989 - 10,713,005 (-)NCBICelera
RH 3.4 Map19128.1RGD
Cytogenetic Map19p12NCBI
MT1A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1656,638,666 - 56,640,087 (+)EnsemblGRCh38hg38GRCh38
GRCh381656,638,666 - 56,640,087 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371656,672,578 - 56,673,999 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361655,230,079 - 55,231,500 (+)NCBINCBI36hg18NCBI36
Build 341655,230,081 - 55,231,498NCBI
Celera1641,170,031 - 41,171,454 (+)NCBI
Cytogenetic Map16q13NCBI
HuRef1642,542,032 - 42,543,455 (+)NCBIHuRef
CHM1_11658,079,506 - 58,080,929 (+)NCBICHM1_1
Mt1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39894,905,214 - 94,906,955 (+)NCBIGRCm39mm39
GRCm39 Ensembl894,905,710 - 94,906,955 (+)Ensembl
GRCm38894,178,883 - 94,180,327 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl894,179,082 - 94,180,327 (+)EnsemblGRCm38mm10GRCm38
MGSCv37896,702,989 - 96,704,227 (+)NCBIGRCm37mm9NCBIm37
MGSCv36897,068,356 - 97,069,453 (+)NCBImm8
Celera898,511,203 - 98,512,441 (+)NCBICelera
Cytogenetic Map8C5NCBI
cM Map846.34NCBI
MT1A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl618,660,642 - 18,673,766 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1618,672,016 - 18,673,673 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2626,383,569 - 26,411,799 (+)NCBISscrofa10.2Sscrofa10.2susScr3

Position Markers
D19Arb7  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21910,827,691 - 10,827,970 (+)MAPPERmRatBN7.2
Rnor_6.01911,303,651 - 11,303,927NCBIRnor6.0
Celera1910,713,649 - 10,713,920UniSTS
Cytogenetic Map19p12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7411590Foco7Food consumption QTL 76.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)19124688055Rat
10054132Srcrt9Stress Responsive Cort QTL 92.870.0017blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19127355345Rat
631678Cm9Cardiac mass QTL 94.270.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)19128982497Rat
631681Cm12Cardiac mass QTL 123.330.00053heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)19128982497Rat
1549847Bss8Bone structure and strength QTL 84lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)19131963836Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19136824771Rat
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19136824771Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19136824771Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19136824771Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)1956937445569374Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)1956937445569374Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19218792746708701Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19231612147316121Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19320477748204777Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19745724942983518Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19997775339654489Rat
631840Niddm38Non-insulin dependent diabetes mellitus QTL 383.86blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)191032318023069265Rat


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 22 22 21 5 6
Medium 3 35 36 20 19 20 57 30 35 6
Low 8 8 11 17 5 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_138826 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC128848 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF411318 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC058442 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474006 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ255899 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209933 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210006 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210086 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210225 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210276 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210404 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210505 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210574 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210578 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210592 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210741 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210753 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210805 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210924 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210951 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211060 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211146 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211312 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211350 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217792 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218077 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218157 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218299 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218315 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218775 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219348 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219744 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220235 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220411 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220645 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221163 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221173 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221343 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221498 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221507 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221511 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221516 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221571 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221639 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221768 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221874 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221960 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222065 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222070 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222149 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222220 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222329 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222341 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222400 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222420 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222436 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222448 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222605 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222614 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222637 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222674 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222691 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222786 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222845 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222891 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222907 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222910 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222929 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222950 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222957 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223018 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223045 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223097 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223170 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223179 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223313 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223425 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223452 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228316 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228334 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228356 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228476 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228561 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228573 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228587 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228632 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228764 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228920 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228980 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229627 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229826 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229982 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  J00750 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000303 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M11794 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M24327 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000057898   ⟹   ENSRNOP00000054706
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1778,793,336 - 78,793,724 (+)Ensembl
RefSeq Acc Id: NM_138826   ⟹   NP_620181
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21910,826,032 - 10,827,048 (-)NCBI
Rnor_6.01911,301,991 - 11,303,007 (-)NCBI
Rnor_5.01911,277,133 - 11,278,149 (-)NCBI
RGSC_v3.41911,261,631 - 11,262,647 (-)RGD
Celera1910,711,989 - 10,713,005 (-)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_620181   ⟸   NM_138826
- UniProtKB: P02803 (UniProtKB/Swiss-Prot),   Q53Z83 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000054706   ⟸   ENSRNOT00000057898
Protein Domains
G_PROTEIN_RECEP_F1_2

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
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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)
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)
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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)
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)
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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
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3117 AgrOrtholog
Ensembl Genes ENSRNOG00000038047 Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000054706 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000057898 UniProtKB/Swiss-Prot
Gene3D-CATH 4.10.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:6891030 IMAGE-MGC_LOAD