Thbs1 (thrombospondin 1) - Rat Genome Database

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Gene: Thbs1 (thrombospondin 1) Rattus norvegicus
Analyze
Symbol: Thbs1
Name: thrombospondin 1
RGD ID: 1588455
Description: Enables transforming growth factor beta binding activity. Involved in several processes, including cellular response to tumor necrosis factor; positive regulation of transforming growth factor beta production; and response to testosterone. Located in cytoplasm and extracellular space. Biomarker of diabetic retinopathy; heart disease; myocardial infarction; and prostate cancer. Human ortholog(s) of this gene implicated in cholangiocarcinoma; pancreatic cancer; and pancreatic ductal carcinoma. Orthologous to human THBS1 (thrombospondin 1); PARTICIPATES IN syndecan signaling pathway; cell-extracellular matrix signaling pathway; malaria pathway; INTERACTS WITH (S)-colchicine; 1-naphthyl isothiocyanate; 17beta-estradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: thrombospondin-1; TSP-1; Tsp1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23105,056,286 - 105,071,445 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl3105,056,292 - 105,071,440 (+)Ensembl
Rnor_6.03109,862,120 - 109,873,466 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3109,862,117 - 109,873,466 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03116,411,045 - 116,422,101 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera3103,978,436 - 103,990,486 (+)NCBICelera
Cytogenetic Map3q35NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-colchicine  (EXP)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
1-naphthyl isothiocyanate  (EXP,ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2,4-dinitrobenzenesulfonic acid  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
6alpha-methylprednisolone  (ISO)
9-cis-retinoic acid  (ISO)
acetylsalicylic acid  (ISO)
ADP  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (EXP,ISO)
all-trans-4-oxoretinoic acid  (ISO)
all-trans-retinoic acid  (ISO)
alpha-hexylcinnamaldehyde  (ISO)
amphetamine  (EXP)
andrographolide  (ISO)
aripiprazole  (ISO)
aristolochic acid  (ISO)
arsenite(3-)  (ISO)
aspartame  (ISO)
atorvastatin calcium  (ISO)
axitinib  (EXP)
benzalkonium chloride  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (ISO)
beta-naphthoflavone  (EXP,ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bleomycin A2  (ISO)
boron nitride  (ISO)
busulfan  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
camptothecin  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
chloropicrin  (ISO)
chloroprene  (ISO)
choline  (ISO)
chrysene  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
clofibric acid  (EXP)
clopidogrel  (ISO)
cobalt dichloride  (EXP,ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
curcumin  (ISO)
cycloheximide  (ISO)
cyclophosphamide  (EXP,ISO)
cyclosporin A  (ISO)
cytarabine  (ISO)
D-glucose  (EXP,ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
dibenz[a,h]anthracene  (ISO)
dibutyl phthalate  (ISO)
dicrotophos  (ISO)
diethyl malate  (ISO)
diethyl maleate  (EXP)
diethylstilbestrol  (ISO)
dimethylarsinous acid  (ISO)
dopamine  (EXP)
dorsomorphin  (ISO)
doxifluridine  (ISO)
doxorubicin  (ISO)
Enterolactone  (ISO)
equol  (ISO)
ethanol  (ISO)
fenamidone  (ISO)
fenoldopam  (EXP)
folic acid  (ISO)
fulvestrant  (ISO)
furosemide  (EXP)
geldanamycin  (ISO)
genistein  (ISO)
gentamycin  (EXP)
glucose  (EXP,ISO)
glyphosate  (ISO)
hydrogen peroxide  (ISO)
ibuprofen  (ISO)
indometacin  (ISO)
irinotecan  (ISO)
isotretinoin  (ISO)
ivermectin  (ISO)
L-methionine  (ISO)
lead diacetate  (ISO)
leflunomide  (ISO)
Licochalcone B  (ISO)
magnesium atom  (ISO)
manganese(II) chloride  (ISO)
medroxyprogesterone acetate  (ISO)
mercury dibromide  (ISO)
mercury dichloride  (EXP)
methotrexate  (ISO)
methylmercury chloride  (ISO)
metoprolol  (EXP)
mifepristone  (ISO)
mono(2-ethylhexyl) phthalate  (EXP)
monosodium L-glutamate  (ISO)
N-acetyl-L-cysteine  (EXP)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-nitrosodiethylamine  (EXP)
nickel atom  (ISO)
nickel sulfate  (ISO)
okadaic acid  (ISO)
ozone  (ISO)
p-chloromercuribenzoic acid  (ISO)
paracetamol  (ISO)
paraquat  (EXP,ISO)
paricalcitol  (ISO)
perfluorononanoic acid  (ISO)
phenformin  (EXP)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
phosgene  (ISO)
phosphorus atom  (ISO)
phosphorus(.)  (ISO)
phthalaldehyde  (ISO)
pioglitazone  (EXP)
pirinixic acid  (ISO)
prednisolone  (ISO)
progesterone  (ISO)
protein kinase inhibitor  (ISO)
quercetin  (ISO)
raloxifene  (ISO)
resveratrol  (EXP)
rotenone  (EXP)
SB 203580  (ISO)
SB 431542  (ISO)
serpentine asbestos  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (ISO)
sodium arsenite  (ISO)
sodium aurothiomalate  (ISO)
sodium fluoride  (ISO)
Soman  (EXP)
streptozocin  (EXP)
succimer  (ISO)
sulindac sulfide  (ISO)
T-2 toxin  (ISO)
tamoxifen  (ISO)
temozolomide  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
tetraphene  (ISO)
thioacetamide  (EXP)
ticlopidine  (ISO)
titanium dioxide  (ISO)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
trovafloxacin  (ISO)
valproic acid  (ISO)
vincaleukoblastine  (EXP)
vincristine  (EXP)
vorinostat  (ISO)
zearalenone  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
behavioral response to pain  (ISO)
blood vessel morphogenesis  (ISO)
cell migration  (ISO)
cellular response to growth factor stimulus  (IEP)
cellular response to nitric oxide  (ISO)
cellular response to tumor necrosis factor  (IEP)
chronic inflammatory response  (ISO)
endocardial cushion development  (ISO)
engulfment of apoptotic cell  (ISO)
growth plate cartilage development  (ISO)
immune response  (ISO)
inflammatory response  (ISO)
monocyte aggregation  (ISO)
negative regulation of angiogenesis  (IBA,IDA,ISO)
negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II  (ISO)
negative regulation of apoptotic process  (ISO)
negative regulation of blood vessel endothelial cell migration  (ISO)
negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis  (ISO)
negative regulation of cell migration involved in sprouting angiogenesis  (ISO)
negative regulation of cell-matrix adhesion  (ISO)
negative regulation of cGMP-mediated signaling  (ISO)
negative regulation of cysteine-type endopeptidase activity involved in apoptotic process  (ISO)
negative regulation of dendritic cell antigen processing and presentation  (ISO)
negative regulation of endothelial cell chemotaxis  (ISO)
negative regulation of endothelial cell migration  (ISO)
negative regulation of endothelial cell proliferation  (ISO)
negative regulation of fibrinolysis  (ISO)
negative regulation of fibroblast growth factor receptor signaling pathway  (ISO)
negative regulation of interleukin-12 production  (ISO)
negative regulation of long-chain fatty acid import across plasma membrane  (ISO)
negative regulation of nitric oxide mediated signal transduction  (ISO)
negative regulation of plasminogen activation  (ISO)
negative regulation of sprouting angiogenesis  (ISO)
outflow tract morphogenesis  (ISO)
peptide cross-linking  (ISO)
positive regulation of angiogenesis  (ISO)
positive regulation of blood coagulation  (ISO)
positive regulation of blood vessel endothelial cell migration  (ISO)
positive regulation of cell migration  (ISO)
positive regulation of cell population proliferation  (ISO)
positive regulation of cell-substrate adhesion  (ISO)
positive regulation of chemotaxis  (ISO)
positive regulation of endothelial cell apoptotic process  (ISO)
positive regulation of endothelial cell migration  (ISO)
positive regulation of extrinsic apoptotic signaling pathway via death domain receptors  (ISO)
positive regulation of fibroblast migration  (ISO)
positive regulation of macrophage activation  (ISO)
positive regulation of macrophage chemotaxis  (ISO)
positive regulation of MAP kinase activity  (IEA,ISO)
positive regulation of phosphorylation  (ISO)
positive regulation of protein kinase B signaling  (ISO)
positive regulation of reactive oxygen species metabolic process  (ISO)
positive regulation of smooth muscle cell proliferation  (ISO)
positive regulation of transforming growth factor beta production  (IMP)
positive regulation of transforming growth factor beta receptor signaling pathway  (ISO)
positive regulation of translation  (ISO)
positive regulation of tumor necrosis factor production  (ISO)
regulation of cell cycle  (ISO)
response to calcium ion  (ISO)
response to endoplasmic reticulum stress  (ISO)
response to glucose  (ISO)
response to magnesium ion  (ISO)
response to mechanical stimulus  (IMP)
response to testosterone  (IEP)
response to xenobiotic stimulus  (ISO)
sprouting angiogenesis  (ISO)

References

References - curated
1. Abu-Farha M, etal., PLoS One. 2013 Sep 24;8(9):e75342. doi: 10.1371/journal.pone.0075342. eCollection 2013.
2. Aishima S, etal., Int J Surg Pathol. 2002 Jan;10(1):47-56.
3. Anderson CR, etal., Am J Pathol. 2008 Oct;173(4):1220-8. Epub 2008 Sep 4.
4. Belmadani S, etal., Am J Pathol. 2007 Sep;171(3):777-89. Epub 2007 Jul 19.
5. Breitkopf K, etal., Gut. 2005 May;54(5):673-81.
6. Colombel M, etal., Cancer Res. 2005 Jan 1;65(1):300-8.
7. Daniel C, etal., Diabetes. 2007 Dec;56(12):2982-9. Epub 2007 Sep 18.
8. Fang XQ, etal., Chin Med J (Engl). 2009 Jul 20;122(14):1631-5.
9. Fraser DD, etal., Crit Care Explor. 2020 Jun 22;2(6):e0144. doi: 10.1097/CCE.0000000000000144. eCollection 2020 Jun.
10. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
11. Lee S, etal., Am J Pathol. 2002 Sep;161(3):1015-22.
12. Melnikov AA, etal., J Surg Oncol. 2009 Feb 1;99(2):119-22.
13. Ohtani Y, etal., Int J Oncol. 1999 Sep;15(3):453-7.
14. Okada K, etal., Biomed Res. 2010;31(1):13-9.
15. Pipeline to import KEGG annotations from KEGG into RGD
16. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
17. RGD automated data pipeline
18. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
19. RGD automated import pipeline for gene-chemical interactions
20. Sezaki S, etal., Exp Biol Med (Maywood). 2005 Oct;230(9):621-30.
21. Shariat SF, etal., J Urol. 2010 May;183(5):1744-50. doi: 10.1016/j.juro.2010.01.018. Epub 2010 Mar 17.
22. Tang D, etal., Oncol Rep. 2006 Mar;15(3):525-32.
23. Tobita K, etal., Int J Oncol. 2002 Dec;21(6):1189-95.
24. Tran MD and Neary JT, Proc Natl Acad Sci U S A. 2006 Jun 13;103(24):9321-6. Epub 2006 Jun 5.
25. Ueki T, etal., Cancer Res. 2000 Apr 1;60(7):1835-9.
26. Vallbo C and Damber JE, Acta Oncol. 2005;44(3):293-8.
27. Wang JY, etal., Fen Zi Xi Bao Sheng Wu Xue Bao. 2006 Oct;39(5):431-7.
28. Yan M, etal., Pathobiology. 2004;71(5):253-60.
29. Yehualaeshet T, etal., Am J Pathol. 1999 Sep;155(3):841-51.
30. Zhang X, etal., Cancer Lett. 2007 Mar 8;247(1):143-9. Epub 2006 Jun 6.
31. Zhong M, etal., Zhonghua Xin Xue Guan Bing Za Zhi. 2006 Mar;34(3):217-21.
32. Zhou HJ, etal., J Neurosurg. 2010 Feb 5.
Additional References at PubMed
PMID:101549   PMID:2435757   PMID:3084490   PMID:3997886   PMID:6341993   PMID:6438154   PMID:6693501   PMID:6777381   PMID:8288588   PMID:9006956   PMID:9657149   PMID:11961406  
PMID:12498716   PMID:12511771   PMID:12882934   PMID:12937160   PMID:14717916   PMID:15184388   PMID:15700281   PMID:15963261   PMID:16019429   PMID:16150726   PMID:16294224   PMID:16310163  
PMID:16502470   PMID:16882710   PMID:17381066   PMID:17413041   PMID:17416590   PMID:17596205   PMID:17879962   PMID:17996481   PMID:18045834   PMID:18096704   PMID:18407596   PMID:18467703  
PMID:18555217   PMID:18575624   PMID:18653767   PMID:18674744   PMID:18722097   PMID:18726995   PMID:18757424   PMID:18757743   PMID:18940719   PMID:19056867   PMID:19127780   PMID:19189070  
PMID:19199708   PMID:19278574   PMID:19342245   PMID:19571575   PMID:19734591   PMID:19738618   PMID:19818485   PMID:19821086   PMID:20016205   PMID:20026598   PMID:20080874   PMID:20215829  
PMID:20524210   PMID:20551380   PMID:20878350   PMID:20889977   PMID:21152035   PMID:21362503   PMID:21394550   PMID:21422735   PMID:22206666   PMID:22418977   PMID:22455124   PMID:22682248  
PMID:22745497   PMID:22776902   PMID:23009856   PMID:23043906   PMID:23087362   PMID:23144964   PMID:23376485   PMID:23533145   PMID:23541831   PMID:23658023   PMID:23843515   PMID:23979707  
PMID:24006456   PMID:24121060   PMID:24177325   PMID:24615654   PMID:25387836   PMID:25660232   PMID:25884585   PMID:25958163   PMID:26092525   PMID:26395742   PMID:27068509   PMID:27588705  
PMID:27735996   PMID:28124060   PMID:28228282   PMID:29408825   PMID:29683384   PMID:30360646   PMID:30537736   PMID:30720765  


Genomics

Comparative Map Data
Thbs1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23105,056,286 - 105,071,445 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl3105,056,292 - 105,071,440 (+)Ensembl
Rnor_6.03109,862,120 - 109,873,466 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3109,862,117 - 109,873,466 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03116,411,045 - 116,422,101 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera3103,978,436 - 103,990,486 (+)NCBICelera
Cytogenetic Map3q35NCBI
THBS1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1539,581,079 - 39,599,466 (+)EnsemblGRCh38hg38GRCh38
GRCh381539,581,079 - 39,599,466 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371539,873,280 - 39,891,667 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361537,660,572 - 37,676,960 (+)NCBINCBI36hg18NCBI36
Build 341537,660,571 - 37,676,959NCBI
Celera1516,636,119 - 16,652,508 (+)NCBI
Cytogenetic Map15q14NCBI
HuRef1516,716,691 - 16,733,080 (+)NCBIHuRef
CHM1_11539,992,660 - 40,009,050 (+)NCBICHM1_1
Thbs1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392117,942,357 - 117,957,614 (+)NCBIGRCm39mm39
GRCm39 Ensembl2117,942,357 - 117,957,614 (+)Ensembl
GRCm382118,111,876 - 118,127,133 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2118,111,876 - 118,127,133 (+)EnsemblGRCm38mm10GRCm38
MGSCv372117,937,658 - 117,952,869 (+)NCBIGRCm37mm9NCBIm37
MGSCv362119,046,897 - 119,061,990 (+)NCBImm8
MGSCv362117,803,363 - 117,818,574 (+)NCBImm8
Celera2119,257,347 - 119,271,479 (+)NCBICelera
Cytogenetic Map2E5NCBI
cM Map259.34NCBI
Thbs1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554166,489,451 - 6,506,419 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554166,490,034 - 6,506,419 (+)NCBIChiLan1.0ChiLan1.0
THBS1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11536,776,756 - 36,793,469 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1536,776,756 - 36,793,170 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01518,521,802 - 18,538,172 (+)NCBIMhudiblu_PPA_v0panPan3
THBS1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1306,770,212 - 6,786,875 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl306,769,470 - 6,784,915 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha306,824,809 - 6,841,468 (+)NCBI
ROS_Cfam_1.0306,896,290 - 6,912,963 (+)NCBI
UMICH_Zoey_3.1306,820,232 - 6,836,894 (+)NCBI
UNSW_CanFamBas_1.0306,926,083 - 6,942,777 (+)NCBI
UU_Cfam_GSD_1.0307,055,241 - 7,071,904 (+)NCBI
Thbs1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864085,216,385 - 85,233,062 (+)NCBI
SpeTri2.0NW_0049364713,064,466 - 3,081,125 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
THBS1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1131,728,781 - 131,746,115 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11131,728,781 - 131,746,098 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21146,905,998 - 146,923,315 (-)NCBISscrofa10.2Sscrofa10.2susScr3
THBS1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12643,410,693 - 43,427,816 (-)NCBI
ChlSab1.1 Ensembl2643,410,580 - 43,427,812 (-)Ensembl
Vero_WHO_p1.0NW_02366604897,515,387 - 97,532,504 (+)NCBI
Thbs1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248046,849,660 - 6,866,164 (+)NCBI

Position Markers
M87276  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23105,069,602 - 105,069,776 (+)MAPPERmRatBN7.2
Rnor_6.03109,873,417 - 109,873,590NCBIRnor6.0
Rnor_5.03116,422,052 - 116,422,225UniSTSRnor5.0
Celera3103,990,437 - 103,990,610UniSTS
PMC152639P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23105,068,151 - 105,068,227 (+)MAPPERmRatBN7.2
Rnor_6.03109,871,965 - 109,872,040NCBIRnor6.0
Rnor_5.03116,420,600 - 116,420,675UniSTSRnor5.0
Celera3103,988,986 - 103,989,061UniSTS
Thbs1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03109,867,214 - 109,867,537NCBIRnor6.0
Rnor_5.03116,415,849 - 116,416,172UniSTSRnor5.0
Celera3103,984,219 - 103,984,549UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)329463235118376539Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)338192233133483320Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)343827364121056321Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
1358186Ept2Estrogen-induced pituitary tumorigenesis QTL 28.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)347233430110362260Rat
2292613Ept16Estrogen-induced pituitary tumorigenesis QTL 168.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)347233430110362260Rat
631665Bw8Body weight QTL 85.5body mass (VT:0001259)body weight (CMO:0000012)350437042119183768Rat
724523Tsu1Thymus enlargement suppressive QTL 13.84thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)350437504115638231Rat
1582218Bw74Body weight QTL 743.90.0021body mass (VT:0001259)body weight (CMO:0000012)353184593115665732Rat
1582238Bw68Body weight QTL 683.20.0064body mass (VT:0001259)body weight (CMO:0000012)353184593115665732Rat
1582239Epfw1Epididymal fat weight QTL 14.50.0006epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)353184593115665732Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)359242096157323038Rat
1300111Rf12Renal function QTL 123.78renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)361017749121056321Rat
1582210Bw71Body weight QTL 713.30.0012body mass (VT:0001259)body weight (CMO:0000012)364655305115665732Rat
1582221Kidm30Kidney mass QTL 303.50.0008kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)364655305115665732Rat
12879848Bw181Body weght QTL 1810.015body mass (VT:0001259)body weight (CMO:0000012)370348525121056321Rat
2301414Kidm37Kidney mass QTL 370.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)370653097121056321Rat
1600376Arunc5Aerobic running capacity QTL 50.21exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)373376539118376539Rat
1581546Pur13Proteinuria QTL 132.930.0335total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)378196190146592722Rat
2302273Gluco35Glucose level QTL 355.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)380800231114297550Rat
631649Bp123Blood pressure QTL 1233.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)389772419134772419Rat
8694437Bw167Body weight QTL 16722.460.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)391797474136797474Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)394856903159898684Rat
724532Cm17Cardiac mass QTL 172heart mass (VT:0007028)calculated heart weight (CMO:0000073)395735366140735366Rat
1582219Bw63Body weight QTL 633.80.001body mass (VT:0001259)body weight (CMO:0000012)396127817115665732Rat
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)397084464142084464Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)397551417147415807Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)398535386161695835Rat
1582216Bw65Body weight QTL 656.3body mass (VT:0001259)body weight (CMO:0000012)3102200529115665732Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:54
Count of miRNA genes:48
Interacting mature miRNAs:54
Transcripts:ENSRNOT00000070912
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 28 25 22 11 22 6 7 39 35 33 11 6
Low 1 15 31 18 8 18 2 4 35 8 2
Below cutoff 1 1 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000070912   ⟹   ENSRNOP00000066041
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3109,862,120 - 109,873,466 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000083351   ⟹   ENSRNOP00000069322
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3105,056,292 - 105,071,440 (+)Ensembl
Rnor_6.0 Ensembl3109,862,117 - 109,872,871 (+)Ensembl
RefSeq Acc Id: NM_001013062   ⟹   NP_001013080
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23105,057,009 - 105,069,652 (+)NCBI
Rnor_6.03109,862,120 - 109,873,466 (+)NCBI
Rnor_5.03116,411,045 - 116,422,101 (+)NCBI
Celera3103,978,436 - 103,990,486 (+)RGD
Sequence:
RefSeq Acc Id: XM_039105644   ⟹   XP_038961572
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23105,056,286 - 105,071,445 (+)NCBI
RefSeq Acc Id: XM_039105645   ⟹   XP_038961573
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23105,056,286 - 105,071,445 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001013080 (Get FASTA)   NCBI Sequence Viewer  
  XP_038961572 (Get FASTA)   NCBI Sequence Viewer  
  XP_038961573 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAQ14549 (Get FASTA)   NCBI Sequence Viewer  
  EDL79850 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001013080   ⟸   NM_001013062
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: ENSRNOP00000066041   ⟸   ENSRNOT00000070912
RefSeq Acc Id: ENSRNOP00000069322   ⟸   ENSRNOT00000083351
RefSeq Acc Id: XP_038961572   ⟸   XM_039105644
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038961573   ⟸   XM_039105645
- Peptide Label: isoform X2
Protein Domains
EGF-like   TSP C-terminal   VWFC

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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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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)
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
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:1588455 AgrOrtholog
Ensembl Genes ENSRNOG00000045829 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000066041 UniProtKB/TrEMBL
  ENSRNOP00000069322 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000070912 UniProtKB/TrEMBL
  ENSRNOT00000083351 UniProtKB/TrEMBL
Gene3D-CATH 2.20.100.10 UniProtKB/TrEMBL
  4.10.1080.10 UniProtKB/TrEMBL
InterPro ConA-like_subgrp UniProtKB/TrEMBL
  EG-like_dom UniProtKB/TrEMBL
  EGF-like_Ca-bd UniProtKB/TrEMBL
  Laminin_G UniProtKB/TrEMBL
  Thrombospondin-1 UniProtKB/TrEMBL
  Thrombospondin_1_rpt UniProtKB/TrEMBL
  Thrombospondin_3-like_rpt UniProtKB/TrEMBL
  Thrombospondin_3_rpt UniProtKB/TrEMBL
  Thrombospondin_C UniProtKB/TrEMBL
  TSP1_rpt_sf UniProtKB/TrEMBL
  TSP_type-3_rpt UniProtKB/TrEMBL
  VWF_C UniProtKB/TrEMBL
KEGG Report rno:445442 UniProtKB/TrEMBL
NCBI Gene 445442 ENTREZGENE
PANTHER PTHR10199:SF78 UniProtKB/TrEMBL
Pfam TSP_1 UniProtKB/TrEMBL
  TSP_3 UniProtKB/TrEMBL
  TSP_C UniProtKB/TrEMBL
  VWC UniProtKB/TrEMBL
PhenoGen Thbs1 PhenoGen
PROSITE EGF_2 UniProtKB/TrEMBL
  EGF_3 UniProtKB/TrEMBL
  TSP1 UniProtKB/TrEMBL
  TSP3 UniProtKB/TrEMBL
  TSP_CTER UniProtKB/TrEMBL
  VWFC_1 UniProtKB/TrEMBL
  VWFC_2 UniProtKB/TrEMBL
SMART EGF UniProtKB/TrEMBL
  EGF_CA UniProtKB/TrEMBL
  TSP1 UniProtKB/TrEMBL
  TSPN UniProtKB/TrEMBL
  VWC UniProtKB/TrEMBL
Superfamily-SCOP ConA_like_lec_gl UniProtKB/TrEMBL
  SSF103647 UniProtKB/TrEMBL
  TSP1 UniProtKB/TrEMBL
UniProt A0A0G2JV24_RAT UniProtKB/TrEMBL
  M0R979_RAT UniProtKB/TrEMBL
  Q71SA3_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-11-19 Thbs1  thrombospondin 1      Symbol and Name status set to provisional 70820 PROVISIONAL