Ptprc (protein tyrosine phosphatase, receptor type, C) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Ptprc (protein tyrosine phosphatase, receptor type, C) Rattus norvegicus
Analyze
Symbol: Ptprc
Name: protein tyrosine phosphatase, receptor type, C
RGD ID: 3451
Description: Exhibits protein tyrosine phosphatase activity. Involved in T cell receptor signaling pathway; regulation of gene expression; and response to gamma radiation. Localizes to cell surface and integral component of plasma membrane. Human ortholog(s) of this gene implicated in hepatitis C; multiple sclerosis; severe combined immunodeficiency; and severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-positive, Nk cell-positive. Orthologous to human PTPRC (protein tyrosine phosphatase receptor type C); PARTICIPATES IN Fc gamma receptor mediated signaling pathway; primary immunodeficiency pathway; T cell receptor signaling pathway; INTERACTS WITH 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: CD45; L-CA; Lca; leucocyte common antigen; leukocyte common antigen; leukocyte common antigen A; leukocyte common antigen B; Protein tyrosine phosphatase, receptor-type, c polypeptide; receptor-type tyrosine-protein phosphatase C; RT7; T200; T200 glycoprotein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Is Marker For: Strains:   BBDP.WF-(D13Rat124-D13Mgh5)/Sunn   BBDP.BBDR-Gimap5, WF-(D13Rat124-D13Mgh5)/Sunn  
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21349,596,193 - 49,708,283 (-)NCBI
Rnor_6.0 Ensembl1355,061,562 - 55,173,692 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01355,061,561 - 55,174,150 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01360,094,038 - 60,205,773 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41351,246,163 - 51,357,995 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11351,261,097 - 51,309,893 (-)NCBI
Celera1349,881,478 - 49,993,142 (-)NCBICelera
Cytogenetic Map13q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP,ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP)
17beta-estradiol 3-benzoate  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2-acetamidofluorene  (EXP)
2-butoxyethanol  (ISO)
3-chloropropane-1,2-diol  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (EXP)
5-azacytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acrolein  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
allyl methyl disulfide  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
beauvericin  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
bexarotene  (EXP)
bis(2-chloroethyl) sulfide  (EXP)
bisphenol A  (EXP,ISO)
buta-1,3-diene  (ISO)
cadmium atom  (ISO)
Calcimycin  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
chloroprene  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
cyclophosphamide  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
diclofenac  (ISO)
diethylstilbestrol  (ISO)
dimethylarsinous acid  (ISO)
enniatin  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
folpet  (ISO)
formaldehyde  (ISO)
furan  (EXP)
genistein  (ISO)
gentamycin  (EXP)
glycidol  (EXP)
histamine  (ISO)
isotretinoin  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
lipopolysaccharide  (ISO)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
N-ethyl-N-nitrosourea  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodimethylamine  (EXP)
nickel atom  (ISO)
nitrofen  (EXP)
ozone  (ISO)
paracetamol  (ISO)
pirinixic acid  (EXP,ISO)
silicon dioxide  (ISO)
sirolimus  (ISO)
sodium dichromate  (ISO)
Soman  (EXP)
succimer  (ISO)
tamibarotene  (ISO)
tebuconazole  (ISO)
testosterone  (EXP)
tetrachloromethane  (EXP,ISO)
titanium dioxide  (ISO)
Tributyltin oxide  (ISO)
triprolidine  (ISO)
Triptolide  (EXP)
triptonide  (ISO)
tungsten  (ISO)
vancomycin  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of MAPK activity  (ISO)
B cell differentiation  (ISO)
B cell proliferation  (ISO,ISS)
B cell receptor signaling pathway  (ISO,ISS)
bone marrow development  (ISO)
calcium-mediated signaling using intracellular calcium source  (ISO)
cell cycle phase transition  (ISO)
cellular response to extracellular stimulus  (ISO)
defense response to virus  (ISO,ISS)
dephosphorylation  (ISO,ISS)
hematopoietic progenitor cell differentiation  (ISO)
heterotypic cell-cell adhesion  (ISO)
leukocyte cell-cell adhesion  (ISO)
natural killer cell differentiation  (ISO)
negative regulation of cell adhesion involved in substrate-bound cell migration  (ISO)
negative regulation of cytokine-mediated signaling pathway  (ISO,ISS)
negative regulation of ERK1 and ERK2 cascade  (ISO)
negative regulation of interleukin-2 production  (ISO)
negative regulation of peptidyl-tyrosine phosphorylation  (ISO)
negative regulation of protein autophosphorylation  (ISO)
negative regulation of protein kinase activity  (IBA,ISO,ISS)
negative regulation of protein tyrosine kinase activity  (ISO)
negative regulation of T cell mediated cytotoxicity  (ISO,ISS)
negative thymic T cell selection  (ISO)
peptidyl-tyrosine dephosphorylation  (IEA)
plasma membrane raft distribution  (ISO)
positive regulation of alpha-beta T cell proliferation  (ISO)
positive regulation of antigen receptor-mediated signaling pathway  (ISO,ISS)
positive regulation of B cell proliferation  (ISO)
positive regulation of ERK1 and ERK2 cascade  (ISO)
positive regulation of extrinsic apoptotic signaling pathway  (ISO)
positive regulation of Fc-gamma receptor signaling pathway involved in phagocytosis  (ISO)
positive regulation of gamma-delta T cell differentiation  (ISO)
positive regulation of hematopoietic stem cell migration  (ISO)
positive regulation of humoral immune response mediated by circulating immunoglobulin  (ISO)
positive regulation of immunoglobulin production  (ISO)
positive regulation of interleukin-2 production  (ISO)
positive regulation of isotype switching to IgG isotypes  (ISO)
positive regulation of MAPK cascade  (ISO)
positive regulation of peptidyl-tyrosine phosphorylation  (IBA,ISO)
positive regulation of protein tyrosine phosphatase activity  (ISO)
positive regulation of stem cell proliferation  (ISO)
positive regulation of T cell differentiation  (ISO)
positive regulation of T cell mediated cytotoxicity  (ISO)
positive regulation of T cell mediated immunity  (ISO)
positive regulation of T cell proliferation  (ISO,ISS)
positive regulation of tumor necrosis factor production  (ISO)
positive thymic T cell selection  (ISO)
protein dephosphorylation  (IBA,ISO,ISS,TAS)
regulation of cell cycle  (ISO,ISS)
regulation of extrinsic apoptotic signaling pathway  (ISO)
regulation of gene expression  (IGI,ISO)
regulation of humoral immune response mediated by circulating immunoglobulin  (ISO)
regulation of interleukin-8 production  (ISO)
regulation of phagocytosis  (ISO)
regulation of protein tyrosine kinase activity  (ISO)
regulation of receptor signaling pathway via JAK-STAT  (ISO)
release of sequestered calcium ion into cytosol  (ISO,ISS)
response to gamma radiation  (IDA)
stem cell development  (ISO)
T cell differentiation  (ISO,ISS)
T cell proliferation  (ISO)
T cell receptor signaling pathway  (IGI,ISO,ISS)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:61878   PMID:1378817   PMID:1793833   PMID:2853967   PMID:6233370   PMID:6610701   PMID:7477352   PMID:7477353   PMID:7499277   PMID:7589135   PMID:7630421   PMID:7688139  
PMID:7743522   PMID:7751624   PMID:7807014   PMID:8041705   PMID:8043862   PMID:8175795   PMID:8334701   PMID:8552190   PMID:8566025   PMID:8566034   PMID:8666928   PMID:8692271  
PMID:8788039   PMID:8889548   PMID:9015183   PMID:9197241   PMID:9208839   PMID:9254656   PMID:9725213   PMID:10358156   PMID:10508267   PMID:10848813   PMID:10943842   PMID:10970857  
PMID:11201744   PMID:11466198   PMID:12100025   PMID:12115612   PMID:12354383   PMID:12519789   PMID:12574355   PMID:12714519   PMID:12900455   PMID:12902479   PMID:14609575   PMID:14625311  
PMID:14990792   PMID:15128768   PMID:15240667   PMID:15557316   PMID:15599401   PMID:15661907   PMID:15795238   PMID:15843532   PMID:15845452   PMID:15909309   PMID:15978577   PMID:16263122  
PMID:16287714   PMID:16455951   PMID:16493007   PMID:17213291   PMID:17277142   PMID:17941951   PMID:18249142   PMID:18628982   PMID:18762567   PMID:19015308   PMID:19838199   PMID:19861679  
PMID:19934022   PMID:19946888   PMID:20458337   PMID:20660734   PMID:20709950   PMID:21166153   PMID:21460847   PMID:21606356   PMID:21911094   PMID:22072979   PMID:22871113   PMID:24029230  
PMID:24337748   PMID:25074919  


Genomics

Comparative Map Data
Ptprc
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21349,596,193 - 49,708,283 (-)NCBI
Rnor_6.0 Ensembl1355,061,562 - 55,173,692 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01355,061,561 - 55,174,150 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01360,094,038 - 60,205,773 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41351,246,163 - 51,357,995 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11351,261,097 - 51,309,893 (-)NCBI
Celera1349,881,478 - 49,993,142 (-)NCBICelera
Cytogenetic Map13q13NCBI
PTPRC
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1198,638,457 - 198,757,476 (+)EnsemblGRCh38hg38GRCh38
GRCh381198,639,025 - 198,757,476 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371198,608,170 - 198,726,605 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361196,874,760 - 196,993,168 (+)NCBINCBI36hg18NCBI36
Build 341195,339,881 - 195,393,989NCBI
Celera1171,730,687 - 171,849,073 (+)NCBI
Cytogenetic Map1q31.3-q32.1NCBI
HuRef1169,775,326 - 169,893,838 (+)NCBIHuRef
CHM1_11200,030,413 - 200,148,903 (+)NCBICHM1_1
Ptprc
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391137,990,597 - 138,103,491 (-)NCBIGRCm39mm39
GRCm39 Ensembl1137,990,599 - 138,103,446 (-)Ensembl
GRCm381138,062,859 - 138,175,756 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1138,062,861 - 138,175,708 (-)EnsemblGRCm38mm10GRCm38
MGSCv371139,959,438 - 140,071,882 (-)NCBIGRCm37mm9NCBIm37
MGSCv361139,879,826 - 139,991,677 (-)NCBImm8
Celera1140,702,480 - 140,816,534 (-)NCBICelera
Cytogenetic Map1E4NCBI
cM Map160.73NCBI
Ptprc
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540635,005,214 - 35,129,552 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540635,005,577 - 35,127,395 (+)NCBIChiLan1.0ChiLan1.0
PTPRC
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11178,555,803 - 178,674,089 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1178,556,104 - 178,672,994 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01174,246,389 - 174,364,893 (+)NCBIMhudiblu_PPA_v0panPan3
PTPRC
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.174,155,876 - 4,282,151 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl74,137,728 - 4,282,124 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha73,841,036 - 3,967,333 (-)NCBI
ROS_Cfam_1.073,809,638 - 3,848,816 (-)NCBI
ROS_Cfam_1.073,851,043 - 3,967,973 (-)NCBI
UMICH_Zoey_3.173,787,560 - 3,913,845 (-)NCBI
UNSW_CanFamBas_1.073,889,732 - 4,015,907 (-)NCBI
UU_Cfam_GSD_1.073,921,322 - 4,047,618 (-)NCBI
Ptprc
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934476,032,103 - 76,143,785 (-)NCBI
SpeTri2.0NW_0049365675,266,653 - 5,378,464 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PTPRC
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1021,466,373 - 21,764,560 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11021,482,984 - 21,601,627 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21026,308,772 - 26,332,086 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PTPRC
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12530,655,014 - 30,777,367 (-)NCBI
ChlSab1.1 Ensembl2530,653,044 - 30,777,303 (-)Ensembl
Ptprc
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247981,700,732 - 1,814,603 (-)NCBI

Position Markers
D13Mit7  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map13q13UniSTS
D13Got34  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21349,709,060 - 49,709,222 (+)MAPPER
Rnor_6.01355,174,550 - 55,174,711NCBIRnor6.0
Rnor_5.01360,206,196 - 60,206,357UniSTSRnor5.0
RGSC_v3.41351,358,852 - 51,359,014RGDRGSC3.4
RGSC_v3.41351,358,853 - 51,359,014UniSTSRGSC3.4
RGSC_v3.11351,372,932 - 51,373,094RGD
Celera1349,994,000 - 49,994,161UniSTS
Cytogenetic Map13q13UniSTS
RH94594  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21349,597,057 - 49,597,218 (+)MAPPER
Rnor_6.01355,062,426 - 55,062,586NCBIRnor6.0
Rnor_5.01360,094,903 - 60,095,063UniSTSRnor5.0
RGSC_v3.41351,247,028 - 51,247,188UniSTSRGSC3.4
Celera1349,882,343 - 49,882,503UniSTS
Cytogenetic Map13q13UniSTS
RH142448  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map13q13UniSTS
RH136913  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21349,596,193 - 49,596,344 (+)MAPPER
Rnor_6.01355,061,562 - 55,061,712NCBIRnor6.0
Rnor_5.01360,094,039 - 60,094,189UniSTSRnor5.0
RGSC_v3.41351,246,164 - 51,246,314UniSTSRGSC3.4
Celera1349,881,479 - 49,881,629UniSTS
Cytogenetic Map13q13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131107975663Rat
1581554Pur11Proteinuria QTL 11urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13901690682995569Rat
1581573Uae36Urinary albumin excretion QTL 36urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13901690682995569Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)1312193394108478121Rat
9589141Insul28Insulin level QTL 2810.820.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)131409633059096330Rat
7411662Foco29Food consumption QTL 2920.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)131409633059096330Rat
2317040Aia21Adjuvant induced arthritis QTL 212.75joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)131462463159624631Rat
2317046Aia8Adjuvant induced arthritis QTL 83.9700000286102295joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)131462463159624631Rat
631645Bp121Blood pressure QTL 1213.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131981081464810814Rat
9589164Gluco66Glucose level QTL 666.670.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)132005247765052477Rat
1331784Bp222Blood pressure QTL 2222.944arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)132148248158537177Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1324502279108770533Rat
61391Bp5Blood pressure QTL 55.6arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)132800833873008338Rat
70170Eae14Experimental allergic encephalomyelitis QTL 140.0024nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)132858445273584452Rat
1558644Cm45Cardiac mass QTL 453.60.002heart mass (VT:0007028)heart wet weight (CMO:0000069)132907693474076934Rat
6893338Cm76Cardiac mass QTL 7600.99heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)132907693474076934Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1335301263107975663Rat
2301962Cm72Cardiac mass QTL 724.12heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)133614753364868393Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133614753399968921Rat
2303563Bw89Body weight QTL 896body mass (VT:0001259)body weight (CMO:0000012)133734634882346348Rat
61340Bp25Blood pressure QTL 254.20.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133937292784372927Rat
10755495Bp387Blood pressure QTL 3873.78arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133950130093652524Rat
4889861Pur29Proteinuria QTL 2913.80.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)134231074486833540Rat
1331750Bp220Blood pressure QTL 2202.98arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)134231074487310744Rat
70220Bp55Blood pressure QTL 555.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)134250834587508345Rat
61349Bp31Blood pressure QTL 315.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)134250834587508345Rat
1549897Stresp12Stress response QTL 123.35stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)134357571788575717Rat
619615Bp80Blood pressure QTL 800.0354arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134567662990676629Rat
6893344Cm79Cardiac mass QTL 791.50.04heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)134905850767207219Rat
12879441Bp396Blood pressure QTL 396arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)135108098996080989Rat
1298066Bp159Blood pressure QTL 1590.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)135156924896569248Rat
71119Thym2Thymus enlargement QTL 23.8thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)135157782490675199Rat


Related Rat Strains
The following Strains have been annotated to Ptprc

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1446
Count of miRNA genes:245
Interacting mature miRNAs:309
Transcripts:ENSRNOT00000000814, ENSRNOT00000029865, ENSRNOT00000029878, ENSRNOT00000060292, ENSRNOT00000064785
Prediction methods:Microtar, Miranda, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 4 17 4 19 4 3 8 11
Low 1 29 40 37 37 8 10 70 32 30 8
Below cutoff 10 1 4 3

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001109887 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001109888 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001109889 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001109890 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_138507 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006249910 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006249912 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769534 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090347 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005492203 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF251010 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AH002194 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AH002195 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BF288130 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BF556033 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CA508247 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB788988 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473958 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CK364357 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CN541893 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CV080346 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220380 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225001 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226583 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230923 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232030 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232152 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234081 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000242 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M25820 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M25821 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M25822 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M25823 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  S40716 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  Y00065 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000000814   ⟹   ENSRNOP00000000814
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1355,061,562 - 55,173,692 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000029865   ⟹   ENSRNOP00000029889
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1355,061,562 - 55,173,692 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000029878   ⟹   ENSRNOP00000030503
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1355,061,562 - 55,173,692 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000060292   ⟹   ENSRNOP00000057042
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1355,061,562 - 55,173,692 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000064785   ⟹   ENSRNOP00000063859
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1355,061,562 - 55,173,692 (-)Ensembl
RefSeq Acc Id: NM_001109887   ⟹   NP_001103357
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21349,596,193 - 49,708,218 (-)NCBI
Rnor_6.01355,061,561 - 55,173,692 (-)NCBI
Rnor_5.01360,094,038 - 60,205,773 (-)NCBI
RGSC_v3.41351,246,163 - 51,357,995 (-)RGD
Celera1349,881,478 - 49,993,142 (-)RGD
Sequence:
RefSeq Acc Id: NM_001109888   ⟹   NP_001103358
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21349,596,193 - 49,708,218 (-)NCBI
Rnor_6.01355,061,561 - 55,173,692 (-)NCBI
Rnor_5.01360,094,038 - 60,205,773 (-)NCBI
RGSC_v3.41351,246,163 - 51,357,995 (-)RGD
Celera1349,881,478 - 49,993,142 (-)RGD
Sequence:
RefSeq Acc Id: NM_001109889   ⟹   NP_001103359
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21349,596,193 - 49,708,218 (-)NCBI
Rnor_6.01355,061,561 - 55,173,692 (-)NCBI
Rnor_5.01360,094,038 - 60,205,773 (-)NCBI
RGSC_v3.41351,246,163 - 51,357,995 (-)RGD
Celera1349,881,478 - 49,993,142 (-)RGD
Sequence:
RefSeq Acc Id: NM_001109890   ⟹   NP_001103360
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21349,596,193 - 49,708,218 (-)NCBI
Rnor_6.01355,061,561 - 55,173,692 (-)NCBI
Rnor_5.01360,094,038 - 60,205,773 (-)NCBI
RGSC_v3.41351,246,163 - 51,357,995 (-)RGD
Celera1349,881,478 - 49,993,142 (-)RGD
Sequence:
RefSeq Acc Id: NM_138507   ⟹   NP_612516
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21349,596,193 - 49,708,218 (-)NCBI
Rnor_6.01355,061,561 - 55,173,692 (-)NCBI
Rnor_5.01360,094,038 - 60,205,773 (-)NCBI
RGSC_v3.41351,246,163 - 51,357,995 (-)RGD
Celera1349,881,478 - 49,993,142 (-)RGD
Sequence:
RefSeq Acc Id: XM_006249910   ⟹   XP_006249972
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01355,061,561 - 55,174,150 (-)NCBI
Rnor_5.01360,094,038 - 60,205,773 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006249912   ⟹   XP_006249974
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21349,596,193 - 49,708,282 (-)NCBI
Rnor_6.01355,061,561 - 55,173,744 (-)NCBI
Rnor_5.01360,094,038 - 60,205,773 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008769534   ⟹   XP_008767756
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21349,596,193 - 49,708,282 (-)NCBI
Rnor_6.01355,061,561 - 55,173,744 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039090347   ⟹   XP_038946275
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21349,596,193 - 49,708,282 (-)NCBI
RefSeq Acc Id: XR_005492203
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21349,605,175 - 49,708,283 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_612516   ⟸   NM_138507
- Peptide Label: isoform 4 precursor
- UniProtKB: P04157 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001103357   ⟸   NM_001109887
- Peptide Label: isoform 3 precursor
- UniProtKB: P04157 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001103358   ⟸   NM_001109888
- Peptide Label: isoform 5 precursor
- UniProtKB: P04157 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001103359   ⟸   NM_001109889
- Peptide Label: isoform 2 precursor
- UniProtKB: P04157 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001103360   ⟸   NM_001109890
- Peptide Label: isoform 1 precursor
- UniProtKB: P04157 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006249972   ⟸   XM_006249910
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006249974   ⟸   XM_006249912
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008767756   ⟸   XM_008769534
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000000814   ⟸   ENSRNOT00000000814
RefSeq Acc Id: ENSRNOP00000057042   ⟸   ENSRNOT00000060292
RefSeq Acc Id: ENSRNOP00000029889   ⟸   ENSRNOT00000029865
RefSeq Acc Id: ENSRNOP00000030503   ⟸   ENSRNOT00000029878
RefSeq Acc Id: ENSRNOP00000063859   ⟸   ENSRNOT00000064785
RefSeq Acc Id: XP_038946275   ⟸   XM_039090347
- Peptide Label: isoform X3
Transcriptome

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

Promoters
RGD ID:13698859
Promoter ID:EPDNEW_R9384
Type:initiation region
Name:Ptprc_1
Description:protein tyrosine phosphatase, receptor type, C
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01355,173,661 - 55,173,721EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
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 (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/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 (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)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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 (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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
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
M520/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
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 (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
SBH/Ygl (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: 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)
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: 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)
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
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 (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)
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/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)
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/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 (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 (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 (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_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
13 60126687 60126688 C G snv SHRSP/Gcrc (KNAW), F344/Stm (KyushuU), F344/NSlc (KyushuU), F344/DuCrlCrlj (KyushuU), BUF/MNa (KyushuU), LE/OrlBarth (UDEL), WN/N (KNAW), F344/NHsd (KNAW), F344/NCrl (KNAW), F344/NRrrc (SOLiD) (KNAW), WKY/NHsd (KNAW), WKY/NCrl (KNAW), WKY/N (KNAW), WKY/Gcrc (KNAW), F344/NRrrc (Illumina) (KNAW), F344/Jcl (KyushuU), SHR/OlaIpcvPrin (KNAW), SHR/OlaIpcv (KNAW), SHR/NHsd (KNAW), SHR/NCrlPrin (KNAW), SR/JrHsd (KNAW), LN/MavRrrc (KNAW), LL/MavRrrc (KNAW), LH/MavRrrc (KNAW), SR/JrHsd (MCW)
13 60137340 60137341 T A snv NIG-III/Hok (KyushuU), GH/OmrMcwi (MCW), SBH/Ygl (MCW), FHH/EurMcwi (MCW), SBN/Ygl (MCW), BUF/N (KNAW), MHS/Gib (KNAW), SBH/Ygl (KNAW), SBN/Ygl (KNAW), HTX/Kyo (KyushuU), MNS/Gib (KNAW), FHH/EurMcwi (KNAW)
13 60141104 60141105 C G snv SBH/Ygl (KNAW), GH/OmrMcwi (MCW), FHH/EurMcwi (KNAW), SBN/Ygl (MCW), MNS/Gib (KNAW), HTX/Kyo (KyushuU), SBH/Ygl (MCW), BUF/N (KNAW), NIG-III/Hok (KyushuU), MHS/Gib (KNAW), FHH/EurMcwi (MCW), SBN/Ygl (KNAW)
13 60143647 60143648 A G snv FHH/EurMcwi (KNAW), BUF/N (KNAW), SBH/Ygl (MCW), MNS/Gib (KNAW), MHS/Gib (KNAW), SBN/Ygl (KNAW), FHH/EurMcwi (MCW), NIG-III/Hok (KyushuU), SBH/Ygl (KNAW), GH/OmrMcwi (MCW), SBN/Ygl (MCW), HTX/Kyo (KyushuU)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
13 55094283 55094284 C G snv F344/NCrl (RGD), WKY/Gcrc (RGD), WKY/NCrl (RGD), SR/JrHsd (RGD), SHRSP/Gcrc (RGD), SHR/NHsd (RGD), LL/MavRrrc (RGD), LN/MavRrrc (RGD), LH/MavRrrc (RGD), WKY/NHsd (RGD), WN/N (MCW), WKY/N (MCW), F344/NRrrc (MCW), SR/JrHsd (MCW)
13 55104936 55104937 T A snv GH/OmrMcwi (MCW), FHH/EurMcwi (RGD), MNS/Gib (RGD), MHS/Gib (RGD), SBN/Ygl (RGD), SBH/Ygl (RGD), SBN/Ygl (MCW), CDR, FHH/EurMcwi (MCW), SBH/Ygl (MCW), Buf/N (MCW)
13 55108700 55108701 C G snv CDR, SBN/Ygl (MCW), MNS/Gib (RGD), Buf/N (MCW), GH/OmrMcwi (MCW), SBN/Ygl (RGD), SBH/Ygl (RGD), SBH/Ygl (MCW), FHH/EurMcwi (RGD), FHH/EurMcwi (MCW)
13 55111243 55111244 A G snv SBH/Ygl (MCW), FHH/EurMcwi (MCW), SBN/Ygl (MCW), MNS/Gib (RGD), MHS/Gib (RGD), SBN/Ygl (RGD), FHH/EurMcwi (RGD), SBH/Ygl (RGD), Buf/N (MCW), GH/OmrMcwi (MCW), CDR


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
13 51278892 51278893 C G snv SHR/OlaIpcv (ICL), HCR/2Mco (UMich), LL/MavRrrc (ICL), LH/MavRrrc (ICL), SHRSP/Gcrc (MDC), LCR/1Mco (UMich), HCR/1Mco (UMich), SHR/OlaIpcv (ICL), F344/NRrrc (KNAW), WKY/N (KNAW), WN/N (KNAW), SHR/OlaIpcv (KNAW), WKY/NCrl (ICL), WKY/NHsd (ICL), F344/NHsd (ICAHN), SR/JrHsd (MCW), WKY/Gcrc (ICL), LCR/2Mco (UMich), SR/JrHsd (ICL), F344/NCrl (ICL), SHRSP/Gcrc (ICL), SHR/NHsd (ICL), LN/MavRrrc (ICL)
13 51289446 51289447 T A snv FHH/EurMcwi (ICL), GH/OmrMcwi (MCW), FHH/EurMcwi (MCW), BUF/N (KNAW), FHH/EurMcwi (MDC), SBN/Ygl (ICL), SBH/Ygl (ICL), MNS/Gib (ICL), MHS/Gib (ICL)
13 51293210 51293211 C G snv HCR/2Mco (UMich), FHH/EurMcwi (MCW), LCR/2Mco (UMich), MNS/Gib (ICL), FHH/EurMcwi (MDC), SBN/Ygl (ICL), GH/OmrMcwi (MCW), MHS/Gib (ICL), LCR/1Mco (UMich), BUF/N (KNAW), FHH/EurMcwi (ICL), SBH/Ygl (ICL)
13 51295753 51295754 A G snv MNS/Gib (ICL), HCR/2Mco (UMich), BUF/N (KNAW), LCR/1Mco (UMich), HCR/1Mco (UMich), FHH/EurMcwi (MCW), GH/OmrMcwi (MCW), FHH/EurMcwi (ICL), MHS/Gib (ICL), FHH/EurMcwi (MDC), SBN/Ygl (ICL), SBH/Ygl (ICL), LCR/2Mco (UMich)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3451 AgrOrtholog
Ensembl Genes ENSRNOG00000000655 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000000814 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000029889 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000030503 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000057042 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000063859 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000000814 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000029865 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000029878 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000060292 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000064785 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot
  3.90.190.10 UniProtKB/Swiss-Prot
InterPro FN3_dom UniProtKB/Swiss-Prot
  FN3_sf UniProtKB/Swiss-Prot
  Ig-like_fold UniProtKB/Swiss-Prot
  Prot-tyrosine_phosphatase-like UniProtKB/Swiss-Prot
  PTP_recept_N UniProtKB/Swiss-Prot
  PTPase_domain UniProtKB/Swiss-Prot
  Ptprc UniProtKB/Swiss-Prot
  Tyr_Pase_AS UniProtKB/Swiss-Prot
  Tyr_Pase_cat UniProtKB/Swiss-Prot
  TYR_PHOSPHATASE_dom UniProtKB/Swiss-Prot
KEGG Report rno:24699 UniProtKB/Swiss-Prot
NCBI Gene 24699 ENTREZGENE
Pfam CD45 UniProtKB/Swiss-Prot
  fn3 UniProtKB/Swiss-Prot
  PTP_N UniProtKB/Swiss-Prot
  Y_phosphatase UniProtKB/Swiss-Prot
PharmGKB PTPRC RGD
PhenoGen Ptprc PhenoGen
PIRSF Leukocyte_common_antigen UniProtKB/Swiss-Prot
PRINTS PRTYPHPHTASE UniProtKB/Swiss-Prot
PROSITE FN3 UniProtKB/Swiss-Prot
  TYR_PHOSPHATASE_1 UniProtKB/Swiss-Prot
  TYR_PHOSPHATASE_2 UniProtKB/Swiss-Prot
  TYR_PHOSPHATASE_PTP UniProtKB/Swiss-Prot
SMART FN3 UniProtKB/Swiss-Prot
  PTPc UniProtKB/Swiss-Prot
  PTPc_motif UniProtKB/Swiss-Prot
Superfamily-SCOP SSF49265 UniProtKB/Swiss-Prot
  SSF52799 UniProtKB/Swiss-Prot
UniProt P04157 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Ptprc  Protein tyrosine phosphatase, receptor-type, c polypeptide (antigen Cd45, leukocyte-common antigen/T200 glycoprotein) also RT7      Symbol and Name status set to approved 70586 APPROVED