Gpt (glutamic--pyruvic transaminase) - Rat Genome Database

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Gene: Gpt (glutamic--pyruvic transaminase) Rattus norvegicus
Analyze
Symbol: Gpt
Name: glutamic--pyruvic transaminase
RGD ID: 621720
Description: Involved in cellular response to insulin stimulus; positive regulation of gluconeogenesis; and response to starvation. Located in cytoplasm and extracellular space. Biomarker of type 2 diabetes mellitus. Orthologous to human GPT (glutamic--pyruvic transaminase); PARTICIPATES IN 2-hydroxyglutaric aciduria pathway; alanine metabolic pathway; argininosuccinic aciduria pathway; INTERACTS WITH (+)-schisandrin B; (+)-taxifolin; (-)-epigallocatechin 3-gallate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: alanine aminotransferase 1; ALAT; ALT1; glutamate pyruvate transaminase 1; glutamic pyruvate transaminase; glutamic pyruvic transaminase (alanine aminotrasferase); glutamic pyruvic transaminase 1, soluble; glutamic--alanine transaminase 1; glutamic--pyruvic transaminase 1; glutamic-pyruvate transaminase (alanine aminotransferase); GPT 1; Gpt1
RGD Orthologs
Human
Mouse
Chinchilla
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
mRatBN7.27108,416,646 - 108,419,495 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl7108,416,642 - 108,419,494 (+)Ensembl
Rnor_6.07117,759,083 - 117,761,932 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7117,759,083 - 117,761,931 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07117,745,308 - 117,749,938 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47114,746,054 - 114,748,903 (+)NCBIRGSC3.4rn4RGSC3.4
Celera7104,766,538 - 104,769,387 (+)NCBICelera
Cytogenetic Map7q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (ISO)
(+)-schisandrin B  (EXP)
(+)-taxifolin  (EXP)
(-)-epigallocatechin 3-gallate  (EXP,ISO)
(E)-thiamethoxam  (EXP)
(R)-lipoic acid  (EXP)
(R,R)-tramadol  (EXP)
(R,R,R)-alpha-tocopherol  (EXP)
(S)-naringenin  (EXP)
1,1,2-trichloroethane  (EXP)
1,1-dichloroethene  (ISO)
1,2-dichlorobenzene  (EXP)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1,3-dichloropropan-2-ol  (ISO)
1-(5-isoquinolinesulfonyl)-2-methylpiperazine  (EXP)
1-bromopropane  (ISO)
1-naphthyl isothiocyanate  (EXP,ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
1H-1,2,4-triazole  (EXP)
2',4',6'-trihydroxyacetophenone  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-(3,4-dimethoxyphenyl)-5-\{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino\}-2-(propan-2-yl)pentanenitrile  (EXP)
2-amino-2-deoxy-D-galactopyranose  (EXP,ISO)
2-chloroethanol  (ISO)
2-methoxyethanol  (EXP)
2-methyl-6-(phenylethynyl)pyridine  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP,ISO)
3,3',5,5'-tetrabromobisphenol A  (EXP)
3-chloropropane-1,2-diol  (ISO)
3-hydroxybutyric acid  (ISO)
3-methyladenine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4-hydroxyphenyl retinamide  (ISO)
4-phenylbutyric acid  (EXP,ISO)
5-(2-methylpiperazine-1-sulfonyl)isoquinoline  (EXP)
5-fluorouracil  (EXP,ISO)
6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxamide  (EXP)
6-propyl-2-thiouracil  (EXP)
6alpha-methylprednisolone  (ISO)
7,12-dimethyltetraphene  (EXP)
7,8-dihydroxycoumarin  (EXP)
8-Epidiosbulbin E acetate  (ISO)
9,11,13-octadecatrienoic acid  (EXP)
acephate  (EXP)
acetamide  (EXP)
acetylsalicylic acid  (EXP)
acrolein  (EXP)
acrylamide  (EXP,ISO)
actinomycin D  (EXP)
aflatoxin B1  (EXP,ISO)
aldehydo-D-glucose  (EXP)
alectinib  (ISO)
all-trans-retinol  (EXP)
allethrin  (EXP)
allicin  (ISO)
alloxan  (EXP)
allyl alcohol  (EXP,ISO)
allyl isothiocyanate  (EXP)
allyl methyl disulfide  (ISO)
alpha-amanitin  (ISO)
alpha-galactosylceramide  (ISO)
alpha-linolenic acid  (EXP)
amiodarone  (ISO)
amlexanox  (ISO)
amlodipine  (EXP)
ammonium chloride  (EXP)
Ammothamnine  (EXP)
amodiaquine  (ISO)
andrographolide  (ISO)
Anetholtrithion  (ISO)
angelicin  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (EXP,ISO)
arachidonic acid  (ISO)
aristolochic acid  (EXP)
arsane  (EXP,ISO)
arsenic atom  (EXP,ISO)
arsenous acid  (EXP,ISO)
astragaloside IV  (EXP)
atorvastatin calcium  (EXP,ISO)
azathioprine  (ISO)
azure A  (EXP)
baicalin  (EXP)
bentonite  (EXP)
benzene  (EXP)
benzo[a]pyrene  (ISO)
beraprost  (ISO)
berberine  (EXP,ISO)
beta-naphthoflavone  (EXP)
Betanin  (EXP)
bezafibrate  (ISO)
bicuculline  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
boric acid  (EXP)
boron atom  (EXP)
bosentan  (EXP)
bosutinib  (ISO)
bromobenzene  (EXP,ISO)
bromodichloromethane  (ISO)
brucine  (ISO)
buprenorphine  (EXP)
buspirone  (EXP)
Butralin  (EXP)
cabozantinib  (ISO)
cadmium atom  (EXP,ISO)
cadmium dichloride  (EXP,ISO)
caffeine  (EXP)
calciol  (EXP)
capsaicin  (EXP)
carbofuran  (EXP)
carbon nanotube  (EXP,ISO)
carfilzomib  (ISO)
carnosic acid  (ISO)
carnosine  (EXP)
carvedilol  (EXP)
catalpol  (ISO)
celastrol  (ISO)
celecoxib  (ISO)
ceritinib  (ISO)
ceruletide  (ISO)
charcoal  (EXP)
chelerythrine  (EXP)
chenodeoxycholic acid  (EXP,ISO)
chlordecone  (ISO)
chlorhexidine gluconate  (EXP)
Chlorobenzilate  (EXP)
Chlorodibromomethane  (ISO)
chloroethene  (ISO)
chloroform  (EXP,ISO)
chlorogenic acid  (EXP,ISO)
chloroquine  (ISO)
chlorpyrifos  (EXP,ISO)
choline  (EXP,ISO)
chromium(6+)  (EXP,ISO)
chrysin  (EXP)
ciprofloxacin  (ISO)
cis-caffeic acid  (EXP,ISO)
cisplatin  (EXP,ISO)
citral  (EXP)
clodronic acid  (EXP,ISO)
clotrimazole  (ISO)
cobalt dichloride  (EXP)
cobimetinib  (EXP)
cocaine  (ISO)
coenzyme Q10  (EXP,ISO)
Columbin  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
crizotinib  (ISO)
crocin-1  (EXP)
Cuprizon  (EXP)
curcumin  (EXP,ISO)
Curcumol  (ISO)
cyclophosphamide  (EXP,ISO)
cyclosporin A  (EXP,ISO)
cyhalothrin  (EXP)
cypermethrin  (EXP,ISO)
D-gluconic acid  (EXP)
D-glucose  (EXP)
dabrafenib  (ISO)
dantrolene  (ISO)
dapagliflozin  (EXP)
DDT  (EXP)
decabromodiphenyl ether  (ISO)
dehydroacetic acid  (EXP)
deoxynivalenol  (EXP,ISO)
deoxypodophyllotoxin  (ISO)
dexamethasone  (ISO)
dexmedetomidine  (EXP)
dextromethorphan  (ISO)
diallyl disulfide  (EXP)
Diallyl sulfide  (EXP)
diarsenic trioxide  (EXP,ISO)
dibutyl phthalate  (EXP)
diclofenac  (EXP,ISO)
dicloxacillin  (ISO)
dicofol  (EXP)
dicrotophos  (ISO)
diethyl phthalate  (EXP)
diethylene glycol monoethyl ether  (EXP)
dihydroartemisinin  (ISO)
dimethylmercury  (EXP)
Diosbulbin B  (ISO)
dioscin  (EXP)
dioxygen  (ISO)
diquat  (ISO)
disodium selenite  (EXP,ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
duvoglustat  (ISO)
elemental boron  (EXP)
elemental selenium  (EXP)
ellagic acid  (EXP)
endosulfan  (EXP)
ergothioneine  (EXP)
eriodictyol  (EXP)
eritoran  (ISO)
ethanol  (EXP,ISO)
fenofibrate  (EXP)
fenvalerate  (EXP)
ferroheme b  (ISO)
fipronil  (EXP,ISO)
flucloxacillin  (ISO)
flutamide  (ISO)
folic acid  (EXP,ISO)
fomepizole  (EXP,ISO)
fosinopril  (ISO)
fructose  (EXP,ISO)
fucoidan  (EXP)
fumonisin B1  (ISO)
furan  (EXP)
gadolinium trichloride  (EXP,ISO)
gallic acid  (ISO)
gamma-aminobutyric acid  (ISO)
gamma-hexachlorocyclohexane  (EXP)
gamma-mangostin  (ISO)
Ganoderic acid A  (ISO)
gefitinib  (ISO)
gemfibrozil  (ISO)
Geniposide  (ISO)
genistein  (EXP)
geranial  (EXP)
Ginkgoic acid  (EXP)
Ginkgolide A  (ISO)
ginkgolide B  (ISO)
ginsenoside Rg1  (ISO)
glafenine  (EXP)
glucose  (EXP)
glyburide  (EXP)
glycyrrhetinate  (EXP,ISO)
glycyrrhetinic acid  (EXP,ISO)
glycyrrhizinic acid  (EXP,ISO)
glyphosate  (EXP)
gold atom  (ISO)
gold(0)  (ISO)
Guanabenz  (ISO)
GW 4064  (EXP)
GW 7647  (EXP)
halothane  (ISO)
heme b  (ISO)
heparin  (EXP)
herbacetin  (ISO)
herbicide  (EXP,ISO)
hesperidin  (EXP,ISO)
hexadecanoic acid  (ISO)
homocysteine  (EXP)
hydralazine  (ISO)
hydrogen peroxide  (EXP)
hydrogen sulfide  (EXP)
ibrutinib  (ISO)
idelalisib  (ISO)
imidacloprid  (EXP)
imiprothrin  (EXP)
inulin  (EXP)
irbesartan  (ISO)
iron atom  (EXP,ISO)
iron dextran  (EXP)
iron(0)  (EXP,ISO)
iron(3+) sulfate  (EXP)
isoniazide  (EXP,ISO)
isoproturon  (EXP)
isorhamnetin  (ISO)
kaempferol  (ISO)
ketoconazole  (EXP,ISO)
L-ascorbic acid  (EXP,ISO)
L-methionine  (EXP,ISO)
lapatinib  (ISO)
Lasiocarpine  (EXP)
lead diacetate  (ISO)
lipoic acid  (EXP)
lipopolysaccharide  (EXP,ISO)
liquiritigenin  (EXP)
liquiritin  (EXP)
liraglutide  (EXP)
lithium atom  (EXP)
lithium hydride  (EXP)
lithocholic acid  (ISO)
losartan  (EXP,ISO)
lovastatin  (ISO)
magnesium atom  (EXP)
malathion  (EXP)
Malotilate  (EXP,ISO)
mancozeb  (EXP)
manganese dioxide  (EXP)
mangiferin  (EXP)
melatonin  (EXP)
mercury dichloride  (EXP,ISO)
mesalamine  (EXP)
metformin  (EXP,ISO)
methamphetamine  (EXP)
methapyrilene  (EXP)
methimazole  (EXP,ISO)
methotrexate  (EXP)
methoxsalen  (EXP)
methylmercury chloride  (EXP)
microcystin RR  (ISO)
mifepristone  (ISO)
monocrotaline  (EXP,ISO)
monosodium L-glutamate  (ISO)
morin  (EXP)
muscimol  (ISO)
myricitrin  (ISO)
N,N-dimethylformamide  (ISO)
N,N-dimethylglycine  (ISO)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (EXP)
N-acetyl-L-cysteine  (EXP,ISO)
N-nitrosodiethylamine  (EXP,ISO)
N-nitrosodimethylamine  (EXP,ISO)
N-Nitrosopyrrolidine  (ISO)
naringin  (EXP)
neohesperidin dihydrochalcone  (ISO)
nickel atom  (EXP)
nickel dichloride  (EXP)
nickel sulfate  (EXP,ISO)
nicotinamide  (EXP)
nilotinib  (EXP,ISO)
nimesulide  (EXP)
nobiletin  (EXP)
O-methyleugenol  (ISO)
octamethylcyclotetrasiloxane  (ISO)
octreotide  (EXP)
olaparib  (ISO)
oleanolic acid  (ISO)
oleic acid  (ISO)
oleuropein  (EXP)
orlistat  (EXP)
oroxylin A  (ISO)
osimertinib  (ISO)
Oxadiazon  (ISO)
oxycodone  (EXP)
ozone  (EXP)
palbociclib  (ISO)
paracetamol  (EXP,ISO)
paraquat  (EXP,ISO)
patulin  (ISO)
penconazole  (ISO)
perfluorodecanoic acid  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
perfluorooctanoic acid  (ISO)
perindopril  (ISO)
phenformin  (EXP)
phenobarbital  (EXP)
phenylhydrazine  (EXP,ISO)
phloretin  (ISO)
phorate  (EXP)
pinocembrin  (ISO)
pioglitazone  (EXP)
piperine  (EXP)
pirinixic acid  (ISO)
polymyxin B2  (ISO)
polyphosphates  (ISO)
ponatinib  (ISO)
potassium bromate  (EXP)
potassium dichromate  (EXP,ISO)
progesterone  (EXP)
propacetamol  (ISO)
prostaglandin E2  (ISO)
psoralen  (EXP)
puerarin  (ISO)
pyrazinecarboxamide  (EXP)
quercetin  (EXP,ISO)
quercetin 3-O-beta-D-galactopyranoside  (ISO)
rac-1,2-dichloropropane  (EXP)
regorafenib  (ISO)
resveratrol  (EXP,ISO)
Retrorsine  (ISO)
rifampicin  (ISO)
rimonabant  (EXP,ISO)
rivaroxaban  (EXP)
rosmarinic acid  (EXP)
rotenone  (EXP,ISO)
rottlerin  (EXP,ISO)
Rutecarpine  (ISO)
rutin  (EXP)
ruxolitinib  (ISO)
ryanodine  (ISO)
S-allylcysteine  (EXP,ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (EXP,ISO)
salvianolic acid B  (EXP,ISO)
SB 203580  (ISO)
scopoletin  (EXP)
selenium atom  (EXP)
senecionine  (EXP,ISO)
silibinin  (EXP)
sinapic acid  (EXP)
sirolimus  (EXP,ISO)
sodium arsenate  (EXP)
sodium arsenite  (EXP,ISO)
sodium dichromate  (EXP)
sodium fluoride  (EXP,ISO)
sodium nitrite  (EXP)
sodium sulfite  (ISO)
sodium tungstate  (EXP)
Soman  (EXP)
sorafenib  (ISO)
squalene  (EXP)
stattic  (ISO)
streptozocin  (EXP,ISO)
succimer  (EXP)
sucrose  (EXP)
sulfasalazine  (ISO)
sunitinib  (ISO)
syringic acid  (EXP)
T-2 toxin  (ISO)
tamoxifen  (ISO)
tapentadol  (EXP)
taurine  (EXP,ISO)
telmisartan  (EXP)
tert-butyl hydroperoxide  (EXP,ISO)
Tesaglitazar  (EXP)
testosterone cypionate  (ISO)
tetrachloro-1,4-benzoquinone  (ISO)
tetrachloromethane  (EXP,ISO)
tetrahydrocurcumin  (ISO)
thiacloprid  (EXP)
thiamethoxam  (EXP)
thioacetamide  (EXP,ISO)
thymoquinone  (EXP)
thyroxine  (EXP)
titanium dioxide  (EXP,ISO)
tramadol  (EXP)
trans-caffeic acid  (EXP,ISO)
trelagliptin  (ISO)
trichloroethene  (ISO)
Triptolide  (EXP,ISO)
troglitazone  (EXP)
urethane  (ISO)
ursodeoxycholic acid  (EXP)
ursolic acid  (ISO)
valproic acid  (EXP,ISO)
vancomycin  (ISO)
vandetanib  (ISO)
verapamil  (EXP)
vildagliptin  (ISO)
vitamin D  (ISO)
vitamin E  (EXP)
vitamin K  (EXP)
zearalenone  (ISO)
zidovudine  (EXP)
zinc atom  (EXP)
zinc molecular entity  (EXP)
zinc oxide  (EXP,ISO)
zinc sulfate  (ISO)
zinc(0)  (EXP)
zolmitriptan  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IDA)
extracellular space  (IDA,ISO)

Molecular Function

References

References - curated
1. Al-Said MS, etal., Evid Based Complement Alternat Med. 2016;2016:1867048. doi: 10.1155/2016/1867048. Epub 2016 May 12.
2. Bu Y and Yu J, Zhonghua Yi Xue Za Zhi. 2015 Oct 20;95(39):3180-3.
3. Chen JY, etal., J Ethnopharmacol. 2012 Aug 1;142(3):811-8. doi: 10.1016/j.jep.2012.06.005. Epub 2012 Jun 15.
4. Cui X, etal., Afr J Tradit Complement Altern Med. 2016 Aug 12;13(5):114-122. doi: 10.21010/ajtcam.v13i5.15. eCollection 2016.
5. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6. GOA data from the GO Consortium
7. Guardiola Arévalo A, etal., Gastroenterol Hepatol. 2017 Feb;40(2):59-69. doi: 10.1016/j.gastrohep.2016.11.002. Epub 2016 Dec 20.
8. Guardiola-Arévalo A, etal., Gastroenterol Hepatol. 2018 Mar;41(3):153-162. doi: 10.1016/j.gastrohep.2017.11.003. Epub 2017 Dec 24.
9. Guijarro de Armas MG, etal., Med Clin (Barc). 2015 Jan 20;144(2):55-8. doi: 10.1016/j.medcli.2014.02.018. Epub 2014 Apr 24.
10. Ishiguro M, etal., Biochemistry 1991 Oct 29;30(43):10451-7.
11. Ishiguro M, etal., Biochemistry. 1991 Jun 18;30(24):6048-53.
12. KEGG
13. Kim HJ, etal., Korean J Intern Med. 2019 Jan 23. pii: kjim.2018.214. doi: 10.3904/kjim.2018.214.
14. Lima de Medeiros BJ, etal., Pharmacognosy Res. 2011 Apr;3(2):79-84. doi: 10.4103/0974-8490.81954.
15. Liu R, etal., Liver Int. 2009 Mar;29(3):337-43. doi: 10.1111/j.1478-3231.2008.01862.x. Epub 2008 Aug 14.
16. Mahale AR, etal., J Int Med Res. 2018 Nov;46(11):4447-4454. doi: 10.1177/0300060518793039. Epub 2018 Sep 5.
17. NCBI rat LocusLink and RefSeq merged data July 26, 2002
18. Nishiura T, etal., J Anesth. 1994 Mar;8(1):87-92. doi: 10.1007/BF02482762.
19. Pagliarini R, etal., Cell Rep. 2016 Jun 7;15(10):2292-2300. doi: 10.1016/j.celrep.2016.05.014. Epub 2016 May 26.
20. Pipeline to import KEGG annotations from KEGG into RGD
21. Pipeline to import SMPDB annotations from SMPDB into RGD
22. Qian K, etal., Diabetes Metab Res Rev. 2015 Sep;31(6):562-71. doi: 10.1002/dmrr.2655. Epub 2015 Jun 17.
23. Rafter I, etal., Int J Mol Med. 2012 Nov;30(5):1241-9. doi: 10.3892/ijmm.2012.1106. Epub 2012 Aug 23.
24. RGD automated data pipeline
25. RGD automated import pipeline for gene-chemical interactions
26. RGD comprehensive gene curation
27. Wei YL, etal., Braz J Med Biol Res. 2017 May 15;50(6):e5758. doi: 10.1590/1414-431X20175758.
28. Yang RZ, etal., Hepatology. 2009 Feb;49(2):598-607. doi: 10.1002/hep.22657.
Additional References at PubMed
PMID:11863375   PMID:12477932   PMID:17582939   PMID:18850354   PMID:19050265   PMID:19056867   PMID:27430334  


Genomics

Comparative Map Data
Gpt
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27108,416,646 - 108,419,495 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl7108,416,642 - 108,419,494 (+)Ensembl
Rnor_6.07117,759,083 - 117,761,932 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7117,759,083 - 117,761,931 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07117,745,308 - 117,749,938 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47114,746,054 - 114,748,903 (+)NCBIRGSC3.4rn4RGSC3.4
Celera7104,766,538 - 104,769,387 (+)NCBICelera
Cytogenetic Map7q34NCBI
GPT
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl8144,502,973 - 144,507,174 (+)EnsemblGRCh38hg38GRCh38
GRCh388144,503,068 - 144,507,172 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh378145,728,451 - 145,732,555 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 368145,700,231 - 145,703,357 (+)NCBINCBI36hg18NCBI36
Build 348145,700,232 - 145,703,357NCBI
Celera8141,904,937 - 141,908,027 (+)NCBI
Cytogenetic Map8q24.3NCBI
HuRef8140,842,619 - 140,845,709 (+)NCBIHuRef
CHM1_18145,767,740 - 145,770,746 (+)NCBICHM1_1
Gpt
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391576,580,926 - 76,583,875 (+)NCBIGRCm39mm39
GRCm39 Ensembl1576,579,916 - 76,583,886 (+)Ensembl
GRCm381576,696,726 - 76,699,675 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1576,695,716 - 76,699,686 (+)EnsemblGRCm38mm10GRCm38
MGSCv371576,527,194 - 76,530,105 (+)NCBIGRCm37mm9NCBIm37
MGSCv361576,524,016 - 76,526,930 (+)NCBImm8
Celera1578,190,374 - 78,193,285 (+)NCBICelera
Cytogenetic Map15D3NCBI
cM Map1536.28NCBI
Gpt
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554543,127,997 - 3,132,459 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554543,127,997 - 3,132,459 (+)NCBIChiLan1.0ChiLan1.0
GPT
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11337,923,757 - 37,927,843 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1337,924,422 - 37,926,156 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1337,884,479 - 37,888,507 (+)NCBI
ROS_Cfam_1.01338,397,476 - 38,401,488 (+)NCBI
UMICH_Zoey_3.11338,089,429 - 38,093,531 (+)NCBI
UNSW_CanFamBas_1.01338,197,829 - 38,201,856 (+)NCBI
UU_Cfam_GSD_1.01338,674,294 - 38,678,329 (+)NCBI
Gpt
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303339,711 - 344,808 (-)NCBI
SpeTri2.0NW_0049364707,765,810 - 7,770,837 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GPT
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4297,748 - 320,056 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.14297,747 - 302,498 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24388,746 - 393,520 (-)NCBISscrofa10.2Sscrofa10.2susScr3
GPT
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.18138,716,802 - 138,721,421 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl8138,718,767 - 138,721,251 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660391,133,510 - 1,138,125 (-)NCBIVero_WHO_p1.0
Gpt
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473512,355,476 - 12,359,910 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH134715  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27108,419,461 - 108,419,658 (+)MAPPERmRatBN7.2
Rnor_6.07117,761,899 - 117,762,095NCBIRnor6.0
Rnor_5.07117,749,878 - 117,750,074UniSTSRnor5.0
RGSC_v3.47114,748,870 - 114,749,066UniSTSRGSC3.4
Celera7104,769,354 - 104,769,550UniSTS
RH 3.4 Map7795.4UniSTS
Cytogenetic Map7q34UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat
71114Niddm14Non-insulin dependent diabetes mellitus QTL 144.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)784257275129257275Rat
70159Bp61Blood pressure QTL 610.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7103146217116738842Rat
1331728Bp214Blood pressure QTL 2142.825arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)780221299124373579Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7102297359133492884Rat
1331746Kidm9Kidney mass QTL 93.934kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)780221299112308525Rat
1331768Kidm10Kidney mass QTL 104.62096kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)780221299125221299Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)791412594129807172Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7106571501135012528Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7104603555135012528Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)796670164135012528Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)744421311118198041Rat
631529Tls2T-lymphoma susceptibility QTL 200.001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)780221299109401111Rat
631540Bw9Body weight QTL 94.5body mass (VT:0001259)body weight (CMO:0000012)769736226117455174Rat
2298475Eau6Experimental allergic uveoretinitis QTL 60.0029uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)784257275129257275Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)783153392128153392Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)773829340130221005Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
1357336Gluco6Glucose level QTL 63.4blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)794811326116294265Rat
1357338Stl17Serum triglyceride level QTL 173.23blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)769736356112729554Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)791281130135012528Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)790482196135012528Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)786983365131983365Rat
2316947Rf58Renal function QTL 587.8kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)768938720113886318Rat
2316952Pur22Proteinuria QTL 225.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)768938720113886318Rat
2316955Stl24Serum triglyceride level QTL 247.1blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)768938720113886318Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)781737938126737938Rat
1358361Sradr5Stress Responsive Adrenal Weight QTL 55.55adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)743747012108555253Rat
2313102Bmd79Bone mineral density QTL 792.30.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)794811085116738842Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)741333674119109060Rat
7411654Foco25Food consumption QTL 259.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)775918751120918751Rat
7411607Foco15Food consumption QTL 150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)775918751120918751Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:109
Count of miRNA genes:91
Interacting mature miRNAs:97
Transcripts:ENSRNOT00000050556
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 3 18 38 27 4 27 8 11 74 33 32 11 8
Low 25 19 14 15 14 2 9
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000050556   ⟹   ENSRNOP00000044411
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7108,416,642 - 108,419,494 (+)Ensembl
Rnor_6.0 Ensembl7117,759,083 - 117,761,931 (+)Ensembl
RefSeq Acc Id: NM_031039   ⟹   NP_112301
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27108,416,646 - 108,419,495 (+)NCBI
Rnor_6.07117,759,083 - 117,761,932 (+)NCBI
Rnor_5.07117,745,308 - 117,749,938 (+)NCBI
RGSC_v3.47114,746,054 - 114,748,903 (+)RGD
Celera7104,766,538 - 104,769,387 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_112301   ⟸   NM_031039
- UniProtKB: P25409 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000044411   ⟸   ENSRNOT00000050556

Transcriptome

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

Promoters
RGD ID:13695434
Promoter ID:EPDNEW_R5959
Type:multiple initiation site
Name:Gpt_1
Description:glutamic--pyruvic transaminase
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_6.07117,759,068 - 117,759,128EPDNEW

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)
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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