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: Exhibits 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. Localizes to several cellular components, including excitatory synapse; growth cone; and 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: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25131,741,959 - 131,824,000 (-)NCBI
Rnor_6.0 Ensembl5137,036,935 - 137,112,927 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.05137,036,936 - 137,112,930 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
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)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
aldrin  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
amiodarone  (EXP,ISO)
ammonium chloride  (EXP)
arsenite(3-)  (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)
dexamethasone  (ISO)
dicrotophos  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
fenofibrate  (EXP)
flavonoids  (EXP)
flutamide  (EXP)
folic acid  (ISO)
fonofos  (ISO)
formaldehyde  (ISO)
glutathione  (EXP)
graphite  (EXP)
indometacin  (ISO)
isoprenaline  (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)
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)
sodium arsenite  (ISO)
sodium dichromate  (ISO)
sodium fluoride  (ISO)
Soman  (EXP)
sulindac sulfide  (ISO)
tamibarotene  (ISO)
terbufos  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
trichloroethene  (EXP)
trichostatin A  (ISO)
Triptolide  (EXP)
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 (-)NCBI
Rnor_6.0 Ensembl5137,036,935 - 137,112,927 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.05137,036,936 - 137,112,930 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
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
CanFam3.1 Ensembl1516,591,308 - 16,666,673 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11516,590,908 - 16,666,673 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Ptprf
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12089,192,426 - 89,284,989 (-)NCBI
ChlSab1.1 Ensembl2089,191,660 - 89,284,970 (-)Ensembl
Ptprf
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248922,825,771 - 2,932,854 (+)NCBI

Position Markers
RH130809  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
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
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
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 (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535788756147487820Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540777918154732375Rat
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)547745646167946134Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)551418671147487820Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)556991667137729065Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)561086525149030144Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)561612600168109659Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)571552569157225114Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)584963058173504662Rat
631527Tls1T-lymphoma susceptibility QTL 100.001thymus integrity trait (VT:0010555)post-insult time to onset of T-cell lymphoma (CMO:0001907)593273130138273130Rat
61452Ciaa5CIA Autoantibody QTL 53.5blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)597921932149030144Rat
1331796Thshl2Thyroid stimulating hormone level QTL 22.3blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)5100723739153577831Rat
2317753Glom24Glomerulus QTL 243.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)5101265591141912026Rat
1358187Emca1Estrogen-induced mammary cancer QTL 14.4mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)5102945579154732228Rat
1578673Bmd13Bone mineral density QTL 134.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)5107119214152119214Rat
2317056Wbc3White blood cell count QTL 32.510.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)5111278451156278451Rat
1549838Bss4Bone structure and strength QTL 49.2femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)5112279412157279412Rat
7207481Bss106Bone structure and strength QTL 1067.9femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5112279412157279412Rat
7207486Bss109Bone structure and strength QTL 109femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)5112279412157279412Rat
7207488Bss110Bone structure and strength QTL 18.4femur strength trait (VT:0010010)femur stiffness (CMO:0001674)5112279412157279412Rat
7207491Bss112Bone structure and strength QTL 1127femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)5112279412157279412Rat
1298089Scl14Serum cholesterol level QTL 145.80.0004blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)5114140832159140832Rat
1598847Cm62Cardiac mass QTL 623.4heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5114140832159140832Rat
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)5116767924161767924Rat
8694198Abfw3Abdominal fat weight QTL 316.130.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)5116767924161767924Rat
8694389Bw160Body weight QTL 1606.170.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)5116767924161767924Rat
8694441Bw169Body weight QTL 16917.610.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)5116767924161767924Rat
1581510Cm54Cardiac mass QTL 543.40.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)5125455818149568944Rat
2293642Bss37Bone structure and strength QTL 374.640.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5125455818157225114Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5128687766173687766Rat
7394710Emca12Estrogen-induced mammary cancer QTL 12mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5129038716139099229Rat
1300122Wbc1White blood cell count QTL 12.75leukocyte quantity (VT:0000217)total white blood cell count (CMO:0000365)5130531300145726262Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5131077716173707219Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5132551937173707219Rat
1581505Rf54Renal function QTL 54kidney physiology trait (VT:0002136)kidney 20-HETE level (CMO:0001854)5133313668138454239Rat
7365049Bp359Blood pressure QTL 359arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5133351969140120264Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5133943857173707219Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5133943857173707219Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5134197905173707219Rat
1331803Rf32Renal function QTL 322.798kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)5134502121149030144Rat
70156Niddm30Non-insulin dependent diabetes mellitus QTL 303.98blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)5134502140157212422Rat
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)5134712342173707219Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5134712342173707219Rat
738018Anxrr4Anxiety related response QTL 45.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)5136354114173707219Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5136640731173707219Rat

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_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
Rnor_6.0 Ensembl5137,037,731 - 137,104,993 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000078302   ⟹   ENSRNOP00000068583
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl5137,036,935 - 137,112,927 (-)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_017593447   ⟹   XP_017448936
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05137,036,936 - 137,112,930 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593448   ⟹   XP_017448937
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05137,036,936 - 137,112,930 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593449   ⟹   XP_017448938
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05137,036,936 - 137,112,930 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593450   ⟹   XP_017448939
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05137,036,936 - 137,112,930 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593451   ⟹   XP_017448940
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05137,036,936 - 137,112,930 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593452   ⟹   XP_017448941
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05137,036,952 - 137,112,930 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593453   ⟹   XP_017448942
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05137,036,936 - 137,112,930 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593454   ⟹   XP_017448943
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05137,036,952 - 137,112,930 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593455   ⟹   XP_017448944
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05137,036,952 - 137,112,930 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593456   ⟹   XP_017448945
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05137,036,936 - 137,112,930 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593457   ⟹   XP_017448946
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05137,036,952 - 137,112,930 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593458   ⟹   XP_017448947
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05137,036,936 - 137,112,930 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593459   ⟹   XP_017448948
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05137,036,936 - 137,112,930 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593460   ⟹   XP_017448949
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05137,036,936 - 137,112,930 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593461   ⟹   XP_017448950
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05137,036,936 - 137,112,930 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593462   ⟹   XP_017448951
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05137,036,952 - 137,112,930 (-)NCBI
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: XP_017448950   ⟸   XM_017593461
- Peptide Label: isoform X15
- Sequence:
RefSeq Acc Id: XP_017448942   ⟸   XM_017593453
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_017448940   ⟸   XM_017593451
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017448938   ⟸   XM_017593449
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017448949   ⟸   XM_017593460
- Peptide Label: isoform X14
- Sequence:
RefSeq Acc Id: XP_017448937   ⟸   XM_017593448
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017448948   ⟸   XM_017593459
- Peptide Label: isoform X13
- Sequence:
RefSeq Acc Id: XP_017448945   ⟸   XM_017593456
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: XP_017448939   ⟸   XM_017593450
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017448947   ⟸   XM_017593458
- Peptide Label: isoform X12
- Sequence:
RefSeq Acc Id: XP_017448936   ⟸   XM_017593447
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017448951   ⟸   XM_017593462
- Peptide Label: isoform X16
- Sequence:
RefSeq Acc Id: XP_017448946   ⟸   XM_017593457
- Peptide Label: isoform X11
- Sequence:
RefSeq Acc Id: XP_017448944   ⟸   XM_017593455
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_017448943   ⟸   XM_017593454
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_017448941   ⟸   XM_017593452
- Peptide Label: isoform X6
- 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
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 (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (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
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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/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
LE/Stm (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
LEW/Crl (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
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
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
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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
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 (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
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
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 (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 (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
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 (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 (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/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 (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
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
5 137054676 137054677 C T snv FHL/EurMcwi (RGD), LN/MavRrrc (RGD), FHH/EurMcwi (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3453 AgrOrtholog
Ensembl Genes ENSRNOG00000019977 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000027271 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000068583 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000027271 ENTREZGENE, 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