Ptprf (protein tyrosine phosphatase, receptor type, F) - Rat Genome Database

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Gene: Ptprf (protein tyrosine phosphatase, receptor type, F) Rattus norvegicus
Analyze
Symbol: Ptprf
Name: protein tyrosine phosphatase, receptor type, F
RGD ID: 3453
Description: Enables phosphate ion binding activity; signaling receptor binding activity; and transmembrane receptor protein tyrosine phosphatase activity. Involved in several processes, including homophilic cell adhesion via plasma membrane adhesion molecules; negative regulation of signal transduction; and regulation of cell projection organization. Located in several cellular components, including excitatory synapse; growth cone; and neuronal cell body. Is integral component of postsynaptic density membrane. Biomarker of obesity. Human ortholog(s) of this gene implicated in hyperinsulinism. Orthologous to human PTPRF (protein tyrosine phosphatase receptor type F); PARTICIPATES IN insulin signaling pathway; INTERACTS WITH (+)-schisandrin B; 1,3-dinitrobenzene; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LAR; LARFN5C; leukocyte antigen-related (LAR) PTP receptor; leukocyte common antigen related; protein tyrosine phosphatase receptor-type F; receptor-type tyrosine-protein phosphatase F
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
mRatBN7.25131,741,959 - 131,824,000 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl5131,742,754 - 131,810,023 (-)Ensembl
Rnor_6.05137,036,936 - 137,112,930 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5137,036,935 - 137,112,927 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05140,825,315 - 140,901,672 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45138,671,725 - 138,739,002 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15138,676,940 - 138,744,228 (-)NCBI
Celera5130,289,962 - 130,357,275 (-)NCBICelera
Cytogenetic Map5q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
1,2-dimethylhydrazine  (ISO)
1,3-dinitrobenzene  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (EXP)
6-propyl-2-thiouracil  (EXP)
8-Br-cAMP  (ISO)
acetamide  (EXP)
acrolein  (ISO)
acrylamide  (EXP,ISO)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
aldrin  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
amiodarone  (EXP,ISO)
ammonium chloride  (EXP)
antimycin A  (ISO)
arsenite(3-)  (ISO)
azoxystrobin  (ISO)
benzbromarone  (EXP)
benzene  (EXP)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
buspirone  (EXP)
cadmium dichloride  (EXP)
calcitriol  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
casticin  (ISO)
chloropicrin  (ISO)
chlorpyrifos  (EXP)
choline  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
clobetasol  (ISO)
clofibrate  (EXP,ISO)
clofibric acid  (EXP)
cobalt dichloride  (ISO)
coumestrol  (ISO)
cyclosporin A  (ISO)
deguelin  (ISO)
dexamethasone  (ISO)
dicrotophos  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
fenofibrate  (EXP)
fipronil  (EXP)
flavonoids  (EXP)
flutamide  (EXP)
folic acid  (ISO)
fonofos  (ISO)
formaldehyde  (ISO)
gallic acid  (ISO)
glutathione  (EXP)
graphite  (EXP)
indometacin  (ISO)
isoprenaline  (ISO)
ivermectin  (ISO)
L-ethionine  (EXP)
L-methionine  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
methapyrilene  (EXP,ISO)
methylmercury(1+)  (EXP)
N-nitrosodiethylamine  (EXP)
nefazodone  (EXP)
nimesulide  (EXP)
omeprazole  (EXP)
oxaliplatin  (EXP)
ozone  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
paraquat  (EXP)
parathion  (ISO)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
perfluorooctanoic acid  (EXP,ISO)
phenobarbital  (ISO)
phenylephrine  (EXP)
pirinixic acid  (EXP,ISO)
potassium dichromate  (ISO)
propiconazole  (ISO)
resveratrol  (ISO)
rotenone  (EXP,ISO)
sodium arsenite  (ISO)
sodium dichromate  (ISO)
sodium fluoride  (ISO)
Soman  (EXP)
sulindac sulfide  (ISO)
tamibarotene  (ISO)
temozolomide  (ISO)
terbufos  (ISO)
tetrachloromethane  (EXP,ISO)
thifluzamide  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
trichloroethene  (EXP)
trichostatin A  (ISO)
Triptolide  (EXP)
triptonide  (ISO)
troglitazone  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Ahmad F and Goldstein BJ, Biochim Biophys Acta. 1995 Apr 5;1248(1):57-69.
2. Ahmad F and Goldstein BJ, Metabolism. 1995 Sep;44(9):1175-84.
3. Ahmad F, etal., J Clin Invest. 1995 Jun;95(6):2806-12.
4. Ahmad F, etal., J Clin Invest. 1997 Jul 15;100(2):449-58.
5. Calera MR, etal., J Biol Chem. 2000 Mar 3;275(9):6308-12.
6. Choi Y, etal., Sci Rep. 2016 May 26;6:26676. doi: 10.1038/srep26676.
7. Dunah AW, etal., Nat Neurosci. 2005 Apr;8(4):458-67. Epub 2005 Mar 6.
8. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
9. GOA data from the GO Consortium
10. Honkaniemi J, etal., Brain Res Mol Brain Res. 1998 Sep 18;60(1):1-12.
11. Kulas DT, etal., J Biol Chem. 1996 Jan 12;271(2):748-54.
12. Kwon SK, etal., J Biol Chem. 2010 Apr 30;285(18):13966-78. doi: 10.1074/jbc.M109.061127. Epub 2010 Feb 6.
13. Li C, etal., Endocrinology. 2006 Feb;147(2):912-8. Epub 2005 Nov 3.
14. Longo FM, etal., J Biol Chem 1993 Dec 15;268(35):26503-11.
15. Machide M, etal., J Biol Chem. 2006 Mar 31;281(13):8765-72. Epub 2006 Jan 16.
16. MGD data from the GO Consortium
17. Miscio G, etal., J Mol Med. 2004 Jul;82(7):459-66. Epub 2004 May 19.
18. NCBI rat LocusLink and RefSeq merged data July 26, 2002
19. Pipeline to import KEGG annotations from KEGG into RGD
20. Pot DA, etal., J Biol Chem 1991 Oct 15;266(29):19688-96.
21. RGD automated data pipeline
22. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
23. RGD automated import pipeline for gene-chemical interactions
24. Streuli M, etal., J Exp Med 1988 Nov 1;168(5):1523-30.
25. Tagami S, etal., Tohoku J Exp Med. 2002 Jul;197(3):169-81.
26. Tang S, etal., Diabetes. 2001 Jan;50(1):83-90.
27. Tisi MA, etal., J Neurobiol. 2000 Mar;42(4):477-86.
28. Weng LP, etal., Curr Biol. 1998 Feb 26;8(5):247-56.
29. Yang T, etal., J Neurosci 2003 Apr 15;23(8):3353-63.
30. Youngren JF Cell Mol Life Sci. 2007 Apr;64(7-8):873-91.
31. Zabolotny JM, etal., Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):5187-92. Epub 2001 Apr 17.
32. Zhang JS and Longo FM, J Cell Biol 1995 Feb;128(3):415-31.
33. Zhang JS, etal., Mol Cell Neurosci. 1998 Apr;10(5-6):271-86.
34. Zhang WR, etal., Biochem J 1994 Aug 15;302 ( Pt 1):39-47.
Additional References at PubMed
PMID:10338209   PMID:11438588   PMID:15555919   PMID:15878970   PMID:19199708   PMID:19252495   PMID:19356234   PMID:21976490   PMID:23358419   PMID:23376485   PMID:23791195   PMID:23986473  
PMID:26321637   PMID:28752900   PMID:30394599  


Genomics

Comparative Map Data
Ptprf
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25131,741,959 - 131,824,000 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl5131,742,754 - 131,810,023 (-)Ensembl
Rnor_6.05137,036,936 - 137,112,930 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5137,036,935 - 137,112,927 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05140,825,315 - 140,901,672 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45138,671,725 - 138,739,002 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15138,676,940 - 138,744,228 (-)NCBI
Celera5130,289,962 - 130,357,275 (-)NCBICelera
Cytogenetic Map5q36NCBI
PTPRF
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl143,525,187 - 43,623,666 (+)EnsemblGRCh38hg38GRCh38
GRCh38143,522,238 - 43,623,666 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37143,991,708 - 44,089,337 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36143,769,134 - 43,861,930 (+)NCBINCBI36hg18NCBI36
Build 34143,665,639 - 43,758,427NCBI
Celera142,278,501 - 42,371,223 (+)NCBI
Cytogenetic Map1p34.2NCBI
HuRef142,115,737 - 42,210,000 (+)NCBIHuRef
CHM1_1144,112,964 - 44,205,662 (+)NCBICHM1_1
Ptprf
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394118,065,410 - 118,148,602 (-)NCBIGRCm39mm39
GRCm39 Ensembl4118,065,410 - 118,148,602 (-)Ensembl
GRCm384118,208,213 - 118,291,405 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4118,208,213 - 118,291,405 (-)EnsemblGRCm38mm10GRCm38
MGSCv374117,880,818 - 117,964,002 (-)NCBIGRCm37mm9NCBIm37
MGSCv364117,707,733 - 117,775,378 (-)NCBImm8
Celera4116,924,108 - 117,000,571 (-)NCBICelera
Cytogenetic Map4D2.1NCBI
Ptprf
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555373,096,603 - 3,185,682 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555373,096,601 - 3,185,682 (+)NCBIChiLan1.0ChiLan1.0
PTPRF
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1144,202,298 - 44,299,309 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl144,220,991 - 44,297,647 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0142,878,344 - 42,923,539 (+)NCBIMhudiblu_PPA_v0panPan3
PTPRF
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11516,590,908 - 16,666,673 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1516,591,308 - 16,666,673 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1516,715,596 - 16,802,435 (-)NCBI
ROS_Cfam_1.01516,749,545 - 16,780,639 (-)NCBI
UMICH_Zoey_3.11516,547,414 - 16,635,530 (-)NCBI
UNSW_CanFamBas_1.01516,616,690 - 16,703,670 (-)NCBI
UU_Cfam_GSD_1.01516,689,993 - 16,777,132 (-)NCBI
Ptprf
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505859,083,308 - 59,159,896 (+)NCBI
SpeTri2.0NW_00493647424,908,103 - 24,984,678 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PTPRF
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6167,656,680 - 167,743,721 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.16167,656,674 - 167,743,750 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.26155,043,861 - 155,112,457 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PTPRF
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12089,192,426 - 89,284,989 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2089,191,660 - 89,284,970 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603327,638,913 - 27,731,698 (+)NCBIVero_WHO_p1.0
Ptprf
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248922,825,771 - 2,932,854 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH130809  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25131,741,998 - 131,742,190 (+)MAPPERmRatBN7.2
Rnor_6.05137,036,976 - 137,037,167NCBIRnor6.0
Rnor_5.05140,825,355 - 140,825,546UniSTSRnor5.0
RGSC_v3.45138,670,985 - 138,671,176UniSTSRGSC3.4
Celera5130,289,222 - 130,289,413UniSTS
RH 3.4 Map5858.2UniSTS
Cytogenetic Map5q36UniSTS
RH139045  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25131,742,936 - 131,743,120 (+)MAPPERmRatBN7.2
Rnor_6.05137,037,914 - 137,038,097NCBIRnor6.0
Rnor_5.05140,826,293 - 140,826,476UniSTSRnor5.0
RGSC_v3.45138,671,923 - 138,672,106UniSTSRGSC3.4
Celera5130,290,160 - 130,290,343UniSTS
RH 3.4 Map5858.2UniSTS
Cytogenetic Map5q36UniSTS
fj50d02.y1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25131,745,458 - 131,745,796 (+)MAPPERmRatBN7.2
Rnor_6.05137,040,436 - 137,040,773NCBIRnor6.0
Rnor_5.05140,828,815 - 140,829,152UniSTSRnor5.0
RGSC_v3.45138,674,445 - 138,674,782UniSTSRGSC3.4
Celera5130,292,682 - 130,293,019UniSTS
Cytogenetic Map5q36UniSTS
UniSTS:224908  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25131,743,133 - 131,743,310 (+)MAPPERmRatBN7.2
Rnor_6.05137,038,111 - 137,038,287NCBIRnor6.0
Rnor_5.05140,826,490 - 140,826,666UniSTSRnor5.0
RGSC_v3.45138,672,120 - 138,672,296UniSTSRGSC3.4
Celera5130,290,357 - 130,290,533UniSTS
Cytogenetic Map5q36UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535189153141643988Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)550328551141643988Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555805606132207589Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)559793399143070159Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)569540295151018848Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
7411601Foco12Food consumption QTL 1219.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)587468046132468046Rat
7411564Bw135Body weight QTL 1350.001body mass (VT:0001259)body weight gain (CMO:0000420)587468046132468046Rat
7411582Foco3Food consumption QTL 37.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)587468046132468046Rat
6903316Bw113Body weight QTL 11320.0103body mass (VT:0001259)body weight (CMO:0000012)587765973132765973Rat
631527Tls1T-lymphoma susceptibility QTL 100.001thymus integrity trait (VT:0010555)post-insult time to onset of T-cell lymphoma (CMO:0001907)590450144135450144Rat
61452Ciaa5CIA Autoantibody QTL 53.5blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)594858972143070159Rat
1331796Thshl2Thyroid stimulating hormone level QTL 22.3blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)597059760147465714Rat
2317753Glom24Glomerulus QTL 243.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)597570330136479578Rat
1358187Emca1Estrogen-induced mammary cancer QTL 14.4mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)599216724148607142Rat
1578673Bmd13Bone mineral density QTL 134.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)5103689353148689353Rat
2317056Wbc3White blood cell count QTL 32.510.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)5105999803150999803Rat
7207488Bss110Bone structure and strength QTL 18.4femur strength trait (VT:0010010)femur stiffness (CMO:0001674)5106906205151906205Rat
7207491Bss112Bone structure and strength QTL 1127femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)5106906205151906205Rat
7207481Bss106Bone structure and strength QTL 1067.9femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5106906205151906205Rat
7207486Bss109Bone structure and strength QTL 109femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)5106906205151906205Rat
1549838Bss4Bone structure and strength QTL 49.2femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)5106906205151906205Rat
1298089Scl14Serum cholesterol level QTL 145.80.0004blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)5108845856153845856Rat
1598847Cm62Cardiac mass QTL 623.4heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5108845856153845856Rat
8657050Bw146Body weight QTL 14619.840.001body mass (VT:0001259)body weight gain (CMO:0000420)5108938288153938288Rat
8694441Bw169Body weight QTL 16917.610.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)5111416838156416838Rat
8694198Abfw3Abdominal fat weight QTL 316.130.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)5111416838156416838Rat
8694389Bw160Body weight QTL 1606.170.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)5111416838156416838Rat
8552960Pigfal15Plasma insulin-like growth factor 1 level QTL 15blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5111416838156416838Rat
1581510Cm54Cardiac mass QTL 543.40.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)5120740824143608494Rat
2293642Bss37Bone structure and strength QTL 374.640.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5120740824151018848Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5121846814166846814Rat
7394710Emca12Estrogen-induced mammary cancer QTL 12mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5124160767133749643Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5124965598166875058Rat
1300122Wbc1White blood cell count QTL 12.75leukocyte quantity (VT:0000217)total white blood cell count (CMO:0000365)5125392826139989768Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5126424772166875058Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5127798274166875058Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5127798274166875058Rat
1581505Rf54Renal function QTL 54kidney physiology trait (VT:0002136)kidney 20-HETE level (CMO:0001854)5128033842133011550Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5128506074166875058Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5128506074166875058Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5128924607166875058Rat
1331803Rf32Renal function QTL 322.798kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)5129132428143070159Rat
70156Niddm30Non-insulin dependent diabetes mellitus QTL 303.98blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)5129132447151006154Rat
738018Anxrr4Anxiety related response QTL 45.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)5130130159166875058Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5131345754166875058Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:118
Count of miRNA genes:98
Interacting mature miRNAs:116
Transcripts:ENSRNOT00000027271
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 3 26 57 41 15 41 74 35 37 11
Low 17 4 8 11 4 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_019249 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593447 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593448 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593449 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593450 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593451 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593452 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593453 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593454 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593455 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593456 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593457 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593458 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593459 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593460 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593461 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593462 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110153 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110154 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110155 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110156 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110157 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110158 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110159 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110160 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110161 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110163 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110164 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110165 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110166 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110167 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110168 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110169 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110170 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110171 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110172 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110174 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110175 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110176 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110177 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH474008 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000162 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  L11586 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M60103 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U00477 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X83505 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000027271   ⟹   ENSRNOP00000027271
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5131,742,754 - 131,810,023 (-)Ensembl
Rnor_6.0 Ensembl5137,037,731 - 137,104,993 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000078302   ⟹   ENSRNOP00000068583
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5131,742,754 - 131,810,023 (-)Ensembl
Rnor_6.0 Ensembl5137,036,935 - 137,112,927 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000102268   ⟹   ENSRNOP00000082730
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5131,742,754 - 131,810,023 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000108252   ⟹   ENSRNOP00000083289
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5131,742,754 - 131,810,023 (-)Ensembl
RefSeq Acc Id: NM_019249   ⟹   NP_062122
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25131,742,739 - 131,810,023 (-)NCBI
Rnor_6.05137,037,716 - 137,104,993 (-)NCBI
Rnor_5.05140,825,315 - 140,901,672 (-)NCBI
RGSC_v3.45138,671,725 - 138,739,002 (-)RGD
Celera5130,289,962 - 130,357,275 (-)RGD
Sequence:
RefSeq Acc Id: XM_039110153   ⟹   XP_038966081
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25131,741,959 - 131,824,000 (-)NCBI
RefSeq Acc Id: XM_039110154   ⟹   XP_038966082
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25131,741,959 - 131,824,000 (-)NCBI
RefSeq Acc Id: XM_039110155   ⟹   XP_038966083
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25131,741,959 - 131,824,000 (-)NCBI
RefSeq Acc Id: XM_039110156   ⟹   XP_038966084
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25131,741,959 - 131,824,000 (-)NCBI
RefSeq Acc Id: XM_039110157   ⟹   XP_038966085
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25131,741,959 - 131,824,000 (-)NCBI
RefSeq Acc Id: XM_039110158   ⟹   XP_038966086
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25131,741,975 - 131,824,000 (-)NCBI
RefSeq Acc Id: XM_039110159   ⟹   XP_038966087
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25131,741,959 - 131,824,000 (-)NCBI
RefSeq Acc Id: XM_039110160   ⟹   XP_038966088
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25131,741,975 - 131,824,000 (-)NCBI
RefSeq Acc Id: XM_039110161   ⟹   XP_038966089
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25131,741,975 - 131,824,000 (-)NCBI
RefSeq Acc Id: XM_039110163   ⟹   XP_038966091
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25131,741,975 - 131,824,000 (-)NCBI
RefSeq Acc Id: XM_039110164   ⟹   XP_038966092
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25131,741,959 - 131,824,000 (-)NCBI
RefSeq Acc Id: XM_039110165   ⟹   XP_038966093
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25131,741,959 - 131,802,132 (-)NCBI
RefSeq Acc Id: XM_039110166   ⟹   XP_038966094
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25131,741,959 - 131,824,000 (-)NCBI
RefSeq Acc Id: XM_039110167   ⟹   XP_038966095
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25131,741,959 - 131,824,000 (-)NCBI
RefSeq Acc Id: XM_039110168   ⟹   XP_038966096
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25131,741,975 - 131,824,000 (-)NCBI
RefSeq Acc Id: XM_039110169   ⟹   XP_038966097
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25131,741,959 - 131,824,000 (-)NCBI
RefSeq Acc Id: XM_039110170   ⟹   XP_038966098
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25131,741,959 - 131,824,000 (-)NCBI
RefSeq Acc Id: XM_039110171   ⟹   XP_038966099
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25131,741,959 - 131,824,000 (-)NCBI
RefSeq Acc Id: XM_039110172   ⟹   XP_038966100
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25131,741,959 - 131,824,000 (-)NCBI
RefSeq Acc Id: XM_039110174   ⟹   XP_038966102
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25131,741,959 - 131,824,000 (-)NCBI
RefSeq Acc Id: XM_039110175   ⟹   XP_038966103
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25131,741,975 - 131,824,000 (-)NCBI
RefSeq Acc Id: XM_039110176   ⟹   XP_038966104
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25131,741,959 - 131,760,939 (-)NCBI
RefSeq Acc Id: XM_039110177   ⟹   XP_038966105
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25131,741,959 - 131,823,926 (-)NCBI
Protein Sequences
Protein RefSeqs NP_062122 (Get FASTA)   NCBI Sequence Viewer  
  XP_038966081 (Get FASTA)   NCBI Sequence Viewer  
  XP_038966082 (Get FASTA)   NCBI Sequence Viewer  
  XP_038966083 (Get FASTA)   NCBI Sequence Viewer  
  XP_038966084 (Get FASTA)   NCBI Sequence Viewer  
  XP_038966085 (Get FASTA)   NCBI Sequence Viewer  
  XP_038966086 (Get FASTA)   NCBI Sequence Viewer  
  XP_038966087 (Get FASTA)   NCBI Sequence Viewer  
  XP_038966088 (Get FASTA)   NCBI Sequence Viewer  
  XP_038966089 (Get FASTA)   NCBI Sequence Viewer  
  XP_038966091 (Get FASTA)   NCBI Sequence Viewer  
  XP_038966092 (Get FASTA)   NCBI Sequence Viewer  
  XP_038966093 (Get FASTA)   NCBI Sequence Viewer  
  XP_038966094 (Get FASTA)   NCBI Sequence Viewer  
  XP_038966095 (Get FASTA)   NCBI Sequence Viewer  
  XP_038966096 (Get FASTA)   NCBI Sequence Viewer  
  XP_038966097 (Get FASTA)   NCBI Sequence Viewer  
  XP_038966098 (Get FASTA)   NCBI Sequence Viewer  
  XP_038966099 (Get FASTA)   NCBI Sequence Viewer  
  XP_038966100 (Get FASTA)   NCBI Sequence Viewer  
  XP_038966102 (Get FASTA)   NCBI Sequence Viewer  
  XP_038966103 (Get FASTA)   NCBI Sequence Viewer  
  XP_038966104 (Get FASTA)   NCBI Sequence Viewer  
  XP_038966105 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA41510 (Get FASTA)   NCBI Sequence Viewer  
  AAC04306 (Get FASTA)   NCBI Sequence Viewer  
  AAC37655 (Get FASTA)   NCBI Sequence Viewer  
  CAA58495 (Get FASTA)   NCBI Sequence Viewer  
  EDL90187 (Get FASTA)   NCBI Sequence Viewer  
  Q64604 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_062122   ⟸   NM_019249
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: ENSRNOP00000068583   ⟸   ENSRNOT00000078302
RefSeq Acc Id: ENSRNOP00000027271   ⟸   ENSRNOT00000027271
RefSeq Acc Id: XP_038966095   ⟸   XM_039110167
- Peptide Label: isoform X14
RefSeq Acc Id: XP_038966102   ⟸   XM_039110174
- Peptide Label: isoform X20
RefSeq Acc Id: XP_038966087   ⟸   XM_039110159
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038966085   ⟸   XM_039110157
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038966083   ⟸   XM_039110155
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038966100   ⟸   XM_039110172
- Peptide Label: isoform X19
RefSeq Acc Id: XP_038966082   ⟸   XM_039110154
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038966099   ⟸   XM_039110171
- Peptide Label: isoform X18
RefSeq Acc Id: XP_038966094   ⟸   XM_039110166
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038966098   ⟸   XM_039110170
- Peptide Label: isoform X17
RefSeq Acc Id: XP_038966084   ⟸   XM_039110156
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038966097   ⟸   XM_039110169
- Peptide Label: isoform X16
RefSeq Acc Id: XP_038966092   ⟸   XM_039110164
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038966081   ⟸   XM_039110153
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038966105   ⟸   XM_039110177
- Peptide Label: isoform X23
RefSeq Acc Id: XP_038966093   ⟸   XM_039110165
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038966104   ⟸   XM_039110176
- Peptide Label: isoform X22
RefSeq Acc Id: XP_038966103   ⟸   XM_039110175
- Peptide Label: isoform X21
RefSeq Acc Id: XP_038966096   ⟸   XM_039110168
- Peptide Label: isoform X15
RefSeq Acc Id: XP_038966091   ⟸   XM_039110163
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038966089   ⟸   XM_039110161
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038966088   ⟸   XM_039110160
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038966086   ⟸   XM_039110158
- Peptide Label: isoform X6
RefSeq Acc Id: ENSRNOP00000083289   ⟸   ENSRNOT00000108252
RefSeq Acc Id: ENSRNOP00000082730   ⟸   ENSRNOT00000102268
Protein Domains
Fibronectin type-III   Ig-like   Ig-like C2-type   TYR_PHOSPHATASE_2   Tyrosine-protein phosphatase

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)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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)
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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)
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)
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
MNS/Gib (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
MR/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
MR/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
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)
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
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)
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
SHRSP/A3NCrl (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
SHRSP/Gcrc (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
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)
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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
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)
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
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
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)
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/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
WKY/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
WKY/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
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)
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
WN/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
WN/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
Damaging Variants


Assembly: Rnor_6.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
5 137054676 137054677 C T snv FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), GH/OmrMcwi (MCW), FHH/EurMcwi (RGD), FHH/EurMcwi (2019), LN/MavRrrcAek (2020), SR/JrHsd (2020), SR/JrHsd (MCW), FHL/EurMcwi (RGD), LN/MavRrrc (RGD), LH/MavRrrcAek (2020)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3453 AgrOrtholog
Ensembl Genes ENSRNOG00000019977 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000027271 UniProtKB/TrEMBL
  ENSRNOP00000068583 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000027271 UniProtKB/TrEMBL
  ENSRNOT00000078302 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.90.190.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro FN3_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FN3_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_I-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_sub UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_sub2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Prot-tyrosine_phosphatase-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTPase_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tyr_Pase_AS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tyr_Pase_cat UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TYR_PHOSPHATASE_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:360406 UniProtKB/Swiss-Prot
NCBI Gene 360406 ENTREZGENE
Pfam fn3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  I-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Y_phosphatase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ptprf PhenoGen
PRINTS PRTYPHPHTASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE FN3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IG_LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TYR_PHOSPHATASE_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TYR_PHOSPHATASE_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TYR_PHOSPHATASE_PTP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART FN3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IGc2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTPc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTPc_motif UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00409 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF49265 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF52799 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JT62_RAT UniProtKB/TrEMBL
  G3V8P4_RAT UniProtKB/TrEMBL
  PTPRF_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q4JFJ1 UniProtKB/Swiss-Prot
  Q63294 UniProtKB/Swiss-Prot
  Q63295 UniProtKB/Swiss-Prot
  Q63296 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Ptprf  protein tyrosine phosphatase, receptor type, F      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression mRNA expressed in brain 633826