Ptprn2 (protein tyrosine phosphatase, receptor type N2) - Rat Genome Database

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Gene: Ptprn2 (protein tyrosine phosphatase, receptor type N2) Rattus norvegicus
Analyze
Symbol: Ptprn2
Name: protein tyrosine phosphatase, receptor type N2
RGD ID: 61904
Description: Predicted to enable protein tyrosine phosphatase activity. Involved in negative regulation of GTPase activity. Located in endoplasmic reticulum lumen; secretory granule; and terminal bouton. Is integral component of synaptic vesicle membrane. Human ortholog(s) of this gene implicated in prediabetes syndrome and type 1 diabetes mellitus. Orthologous to human PTPRN2 (protein tyrosine phosphatase receptor type N2); PARTICIPATES IN type 1 diabetes mellitus pathway; INTERACTS WITH 17beta-estradiol; 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: phogrin; protein tyrosine phosphatase receptor-type N polypeptide 2; protein tyrosine phosphatase, receptor type, N polypeptide 2; protein tyrosine phosphatase, receptor-type, N polypeptide 2; PTP NE-6; PTPNE6; R-PTP-N2; receptor-type tyrosine-protein phosphatase N2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.26137,439,572 - 138,191,575 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl6137,439,540 - 138,191,575 (+)Ensembl
Rnor_6.06144,384,773 - 145,133,042 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6144,384,773 - 145,133,042 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06153,312,968 - 154,056,676 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46143,787,884 - 144,549,042 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16143,794,070 - 144,555,221 (+)NCBI
Celera6135,102,182 - 135,845,915 (+)NCBICelera
Cytogenetic Map6q33NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:15788565   PMID:19361477   PMID:20097759   PMID:21732083   PMID:23382219  


Genomics

Comparative Map Data
Ptprn2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.26137,439,572 - 138,191,575 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl6137,439,540 - 138,191,575 (+)Ensembl
Rnor_6.06144,384,773 - 145,133,042 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6144,384,773 - 145,133,042 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06153,312,968 - 154,056,676 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46143,787,884 - 144,549,042 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16143,794,070 - 144,555,221 (+)NCBI
Celera6135,102,182 - 135,845,915 (+)NCBICelera
Cytogenetic Map6q33NCBI
PTPRN2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl7157,539,056 - 158,587,823 (-)EnsemblGRCh38hg38GRCh38
GRCh387157,539,056 - 158,587,823 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh377157,331,750 - 158,380,515 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 367157,024,516 - 158,073,179 (-)NCBINCBI36hg18NCBI36
Build 347156,831,230 - 157,879,894NCBI
Celera7151,758,421 - 152,708,128 (-)NCBI
Cytogenetic Map7q36.3NCBI
HuRef7151,062,797 - 152,022,430 (-)NCBIHuRef
CHM1_17157,340,603 - 158,388,873 (-)NCBICHM1_1
CRA_TCAGchr7v27156,563,177 - 157,584,848 (-)NCBI
Ptprn2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3912116,449,316 - 117,241,787 (+)NCBIGRCm39mm39
GRCm39 Ensembl12116,449,340 - 117,240,469 (+)Ensembl
GRCm3812116,485,695 - 117,278,167 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl12116,485,720 - 117,276,849 (+)EnsemblGRCm38mm10GRCm38
MGSCv3712117,724,193 - 118,516,640 (+)NCBIGRCm37mm9NCBIm37
MGSCv3612110,685,719 - 111,477,358 (+)NCBImm8
MGSCv3612116,927,842 - 117,718,802 (+)NCBImm8
Cytogenetic Map12F2NCBI
cM Map1262.65NCBI
Ptprn2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955579364,748 - 833,729 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955579366,441 - 862,837 (-)NCBIChiLan1.0ChiLan1.0
PTPRN2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.17160,850,042 - 161,756,328 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl7160,851,703 - 161,756,325 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v07149,158,513 - 150,390,077 (-)NCBIMhudiblu_PPA_v0panPan3
PTPRN2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11619,904,468 - 20,562,585 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1619,905,473 - 20,602,680 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1620,472,150 - 21,134,670 (-)NCBI
ROS_Cfam_1.01621,636,514 - 22,361,137 (-)NCBI
UMICH_Zoey_3.11620,003,354 - 20,728,392 (-)NCBI
UNSW_CanFamBas_1.01620,586,565 - 21,312,677 (-)NCBI
UU_Cfam_GSD_1.01620,639,115 - 21,366,802 (-)NCBI
Ptprn2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118752,917 - 1,422,817 (+)NCBI
SpeTri2.0NW_00493679755,217 - 151,201 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PTPRN2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl18721,131 - 1,392,870 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.118721,125 - 1,389,609 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2181,081,388 - 1,085,384 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PTPRN2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.121125,655,787 - 126,622,503 (-)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366607221,894,122 - 23,016,772 (-)NCBIVero_WHO_p1.0
Ptprn2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624800501,884 - 1,116,795 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D6Rat4  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26137,848,730 - 137,848,904 (+)MAPPERmRatBN7.2
Rnor_6.06144,792,505 - 144,792,678NCBIRnor6.0
Rnor_5.06153,718,972 - 153,719,145UniSTSRnor5.0
RGSC_v3.46144,200,728 - 144,200,901UniSTSRGSC3.4
RGSC_v3.46144,200,727 - 144,200,901RGDRGSC3.4
RGSC_v3.16144,206,914 - 144,207,088RGD
Celera6135,504,276 - 135,504,449UniSTS
RH 3.4 Map6923.9RGD
RH 3.4 Map6923.9UniSTS
RH 2.0 Map61203.5RGD
SHRSP x BN Map683.9998RGD
FHH x ACI Map699.32RGD
Cytogenetic Map6q33UniSTS
D6Rat1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26137,801,573 - 137,801,795 (+)MAPPERmRatBN7.2
Rnor_6.06144,745,354 - 144,745,573NCBIRnor6.0
Rnor_5.06153,671,821 - 153,672,040UniSTSRnor5.0
RGSC_v3.46144,152,353 - 144,152,572UniSTSRGSC3.4
RGSC_v3.46144,152,352 - 144,152,572RGDRGSC3.4
RGSC_v3.16144,158,540 - 144,158,759RGD
Celera6135,457,174 - 135,457,393UniSTS
RH 3.4 Map6924.0RGD
RH 3.4 Map6924.0UniSTS
RH 2.0 Map61203.5RGD
SHRSP x BN Map682.8898RGD
FHH x ACI Map695.64RGD
Cytogenetic Map6q33UniSTS
D6Rat215  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26137,511,759 - 137,511,971 (+)MAPPERmRatBN7.2
Rnor_6.06144,456,707 - 144,456,918NCBIRnor6.0
Rnor_5.06153,384,902 - 153,385,113UniSTSRnor5.0
RGSC_v3.46143,860,093 - 143,860,305RGDRGSC3.4
RGSC_v3.46143,860,094 - 143,860,305UniSTSRGSC3.4
RGSC_v3.16143,866,280 - 143,866,492RGD
Celera6135,173,984 - 135,174,195UniSTS
FHH x ACI Map6101.32RGD
FHH x ACI Map6101.32UniSTS
Cytogenetic Map6q33UniSTS
D6Got203  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26138,166,889 - 138,167,082 (+)MAPPERmRatBN7.2
Rnor_6.06145,108,357 - 145,108,549NCBIRnor6.0
Rnor_5.06154,032,025 - 154,032,217UniSTSRnor5.0
RGSC_v3.46144,524,330 - 144,524,522RGDRGSC3.4
RGSC_v3.46144,524,330 - 144,524,522UniSTSRGSC3.4
RGSC_v3.16144,530,517 - 144,530,709RGD
Celera6135,821,151 - 135,821,341UniSTS
RH 3.4 Map6929.0RGD
RH 3.4 Map6929.0UniSTS
RH 2.0 Map61207.9RGD
Cytogenetic Map6q33UniSTS
RH133268  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26138,056,604 - 138,057,914 (+)MAPPERmRatBN7.2
Rnor_6.06144,997,198 - 144,998,545NCBIRnor6.0
Rnor_5.06153,922,415 - 153,923,762UniSTSRnor5.0
RGSC_v3.46144,413,491 - 144,414,838UniSTSRGSC3.4
Celera6135,711,347 - 135,712,690UniSTS
RH 3.4 Map6936.0UniSTS
Cytogenetic Map6q33UniSTS
RH140469  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26138,063,571 - 138,063,671 (+)MAPPERmRatBN7.2
Rnor_6.06145,004,202 - 145,004,301NCBIRnor6.0
Rnor_5.06153,929,419 - 153,929,518UniSTSRnor5.0
RGSC_v3.46144,420,495 - 144,420,594UniSTSRGSC3.4
Celera6135,718,232 - 135,718,331UniSTS
RH 3.4 Map6922.1UniSTS
Cytogenetic Map6q33UniSTS
RH131937  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26137,885,505 - 137,885,703 (+)MAPPERmRatBN7.2
Rnor_6.06144,825,959 - 144,826,156NCBIRnor6.0
Rnor_5.06153,753,404 - 153,753,601UniSTSRnor5.0
RGSC_v3.46144,239,975 - 144,240,172UniSTSRGSC3.4
Celera6135,541,086 - 135,541,283UniSTS
RH 3.4 Map6923.9UniSTS
Cytogenetic Map6q33UniSTS
RH131993  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26138,190,802 - 138,190,988 (+)MAPPERmRatBN7.2
Rnor_6.06145,132,270 - 145,132,455NCBIRnor6.0
Rnor_5.06154,055,904 - 154,056,089UniSTSRnor5.0
RGSC_v3.46144,548,270 - 144,548,455UniSTSRGSC3.4
Celera6135,845,143 - 135,845,328UniSTS
RH 3.4 Map6921.6UniSTS
Cytogenetic Map6q33UniSTS
RH142979  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26138,164,840 - 138,165,127 (+)MAPPERmRatBN7.2
Rnor_6.06145,106,309 - 145,106,595NCBIRnor6.0
Rnor_5.06154,029,977 - 154,030,263UniSTSRnor5.0
RGSC_v3.46144,522,282 - 144,522,568UniSTSRGSC3.4
Celera6135,819,103 - 135,819,389UniSTS
RH 3.4 Map6928.8UniSTS
Cytogenetic Map6q33UniSTS
BF396367  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26138,084,234 - 138,084,396 (+)MAPPERmRatBN7.2
Rnor_6.06145,025,076 - 145,025,237NCBIRnor6.0
Rnor_5.06153,950,186 - 153,950,347UniSTSRnor5.0
RGSC_v3.46144,441,423 - 144,441,584UniSTSRGSC3.4
Celera6135,738,821 - 135,738,982UniSTS
RH 3.4 Map6929.2UniSTS
Cytogenetic Map6q33UniSTS
BE120609  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26138,186,246 - 138,186,414 (+)MAPPERmRatBN7.2
Rnor_6.06145,127,714 - 145,127,881NCBIRnor6.0
Rnor_5.06154,051,348 - 154,051,515UniSTSRnor5.0
RGSC_v3.46144,543,714 - 144,543,881UniSTSRGSC3.4
Celera6135,840,587 - 135,840,754UniSTS
RH 3.4 Map6929.0UniSTS
Cytogenetic Map6q33UniSTS
BF405459  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26138,096,514 - 138,096,652 (+)MAPPERmRatBN7.2
Rnor_6.06145,037,355 - 145,037,492NCBIRnor6.0
Rnor_5.06153,962,465 - 153,962,602UniSTSRnor5.0
RGSC_v3.46144,453,703 - 144,453,840UniSTSRGSC3.4
Celera6135,751,101 - 135,751,238UniSTS
RH 3.4 Map6919.1UniSTS
Cytogenetic Map6q33UniSTS
AU047288  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26137,758,301 - 137,758,476 (+)MAPPERmRatBN7.2
Rnor_6.06144,702,088 - 144,702,264NCBIRnor6.0
Rnor_5.06153,628,555 - 153,628,731UniSTSRnor5.0
RGSC_v3.46144,109,087 - 144,109,263UniSTSRGSC3.4
Celera6135,414,668 - 135,414,822UniSTS
Cytogenetic Map6q33UniSTS
AU048803  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26138,033,163 - 138,033,292 (+)MAPPERmRatBN7.2
Rnor_6.06144,973,761 - 144,973,889NCBIRnor6.0
Rnor_5.06153,898,978 - 153,899,106UniSTSRnor5.0
RGSC_v3.46144,390,054 - 144,390,182UniSTSRGSC3.4
Celera6135,687,998 - 135,688,126UniSTS
Cytogenetic Map6q33UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
61414Pia3Pristane induced arthritis QTL 34.5joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)694968928137848904Rat
12801411Schws8Schwannoma susceptibility QTL 8nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)694968928139968928Rat
8552796Vie3Viral induced encephalitis QTL 32.6brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)696833997140994061Rat
1358355Srcrt4Stress Responsive Cort QTL 46.39blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)6100364669140994061Rat
71111Iddm8Insulin dependent diabetes mellitus QTL 81.90.002blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)6105156861140994061Rat
737976Pia24Pristane induced arthritis QTL 24joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)6112636280140994061Rat
1641917Colcr5Colorectal carcinoma resistance QTL 53.180.0009intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)6122549046137801795Rat
2293085Iddm29Insulin dependent diabetes mellitus QTL 297.66blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)6122549046140286318Rat
61329Eae9Experimental allergic encephalomyelitis QTL 93.7body mass (VT:0001259)change in body weight (CMO:0002045)6122549046140994061Rat
2312560Pur20Proteinuria QTL 202.10.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)6125628133137801795Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:544
Count of miRNA genes:254
Interacting mature miRNAs:321
Transcripts:ENSRNOT00000006942
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 74 1
Low 1 2 24 16 7 16 17 33 8
Below cutoff 37 32 24 11 24 8 8 18 7 3 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000006942   ⟹   ENSRNOP00000006942
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl6137,439,572 - 138,191,575 (+)Ensembl
Rnor_6.0 Ensembl6144,384,773 - 145,133,042 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000116222   ⟹   ENSRNOP00000093030
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl6137,439,540 - 138,191,575 (+)Ensembl
RefSeq Acc Id: NM_031600   ⟹   NP_113788
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26137,439,572 - 138,191,575 (+)NCBI
Rnor_6.06144,384,773 - 145,133,042 (+)NCBI
Rnor_5.06153,312,968 - 154,056,676 (+)NCBI
RGSC_v3.46143,787,884 - 144,549,042 (+)RGD
Celera6135,102,182 - 135,845,915 (+)RGD
Sequence:
RefSeq Acc Id: XM_039111861   ⟹   XP_038967789
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26137,439,658 - 138,191,027 (+)NCBI
RefSeq Acc Id: XM_039111862   ⟹   XP_038967790
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26137,439,658 - 138,189,570 (+)NCBI
RefSeq Acc Id: XM_039111863   ⟹   XP_038967791
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26137,439,658 - 138,189,570 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_113788   ⟸   NM_031600
- Peptide Label: precursor
- UniProtKB: Q63475 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000006942   ⟸   ENSRNOT00000006942
RefSeq Acc Id: XP_038967789   ⟸   XM_039111861
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038967791   ⟸   XM_039111863
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038967790   ⟸   XM_039111862
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000093030   ⟸   ENSRNOT00000116222
Transcriptome

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

Promoters
RGD ID:13694910
Promoter ID:EPDNEW_R5434
Type:initiation region
Name:Ptprn2_1
Description:protein tyrosine phosphatase, receptor type N2
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_6.06144,384,730 - 144,384,790EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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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-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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/RijCrl (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:61904 AgrOrtholog
Ensembl Genes ENSRNOG00000005003 Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000006942 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000006942 UniProtKB/Swiss-Prot
Gene3D-CATH 3.30.70.2470 UniProtKB/Swiss-Prot
  3.90.190.10 UniProtKB/Swiss-Prot
InterPro IA-2/IA-2_beta UniProtKB/Swiss-Prot
  Prot-tyrosine_phosphatase-like UniProtKB/Swiss-Prot
  PTPase_domain UniProtKB/Swiss-Prot
  Receptor_IA-2_dom UniProtKB/Swiss-Prot
  Receptor_IA-2_ectodomain_sf UniProtKB/Swiss-Prot
  RESP18_dom UniProtKB/Swiss-Prot
  Tyr_Pase_AS UniProtKB/Swiss-Prot
  Tyr_Pase_cat UniProtKB/Swiss-Prot
  TYR_PHOSPHATASE_dom UniProtKB/Swiss-Prot
KEGG Report rno:29714 UniProtKB/Swiss-Prot
NCBI Gene 29714 ENTREZGENE
PANTHER PTHR46106 UniProtKB/Swiss-Prot
Pfam Receptor_IA-2 UniProtKB/Swiss-Prot
  RESP18 UniProtKB/Swiss-Prot
  Y_phosphatase UniProtKB/Swiss-Prot
PhenoGen Ptprn2 PhenoGen
PRINTS PRTYPHPHTASE UniProtKB/Swiss-Prot
PROSITE TYR_PHOSPHATASE_1 UniProtKB/Swiss-Prot
  TYR_PHOSPHATASE_2 UniProtKB/Swiss-Prot
  TYR_PHOSPHATASE_PTP UniProtKB/Swiss-Prot
SMART PTPc UniProtKB/Swiss-Prot
  PTPc_motif UniProtKB/Swiss-Prot
Superfamily-SCOP SSF52799 UniProtKB/Swiss-Prot
TIGR TC218024
UniProt PTPR2_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-13 Ptprn2  protein tyrosine phosphatase, receptor type N2  Ptprn2  protein tyrosine phosphatase, receptor type, N polypeptide 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Ptprn2  protein tyrosine phosphatase, receptor type, N polypeptide 2    protein tyrosine phosphatase, receptor-type, N polypeptide 2  Name updated 1299863 APPROVED
2002-06-10 Ptprn2  protein tyrosine phosphatase, receptor-type, N polypeptide 2       Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization localized to insulin secretory granule membranes 61724