Ptprn (protein tyrosine phosphatase, receptor type, N) - Rat Genome Database

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Gene: Ptprn (protein tyrosine phosphatase, receptor type, N) Rattus norvegicus
Analyze
Symbol: Ptprn
Name: protein tyrosine phosphatase, receptor type, N
RGD ID: 620777
Description: Exhibits GTPase binding activity. Involved in several processes, including positive regulation of type B pancreatic cell proliferation; response to cAMP; and response to estrogen. Localizes to several cellular components, including axon terminus; neuronal cell body; and secretory granule. Colocalizes with Golgi apparatus; endosome; and plasma membrane. Used to study type 1 diabetes mellitus. Human ortholog(s) of this gene implicated in type 1 diabetes mellitus. Orthologous to human PTPRN (protein tyrosine phosphatase receptor type N); PARTICIPATES IN type 1 diabetes mellitus pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 3,3',4,4',5-pentachlorobiphenyl.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: 105 kDa islet cell antigen; BEM-3; brain-enriched membrane-associated protein tyrosine phosphatase; Ia-2; ICA105; ICA512; PTP IA-2; PTPLP; R-PTP-N; receptor-type tyrosine-protein phosphatase-like N
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
mRatBN7.2976,741,010 - 76,756,704 (-)NCBI
Rnor_6.0 Ensembl982,446,633 - 82,461,903 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0982,446,626 - 82,462,314 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0982,215,889 - 82,231,560 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4974,528,095 - 74,542,756 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1974,675,076 - 74,689,738 (-)NCBI
Celera974,311,913 - 74,326,515 (-)NCBICelera
Cytogenetic Map9q33NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-chloropropane-1,2-diol  (EXP)
acetamide  (EXP)
acrylamide  (EXP)
aflatoxin B1  (EXP,ISO)
all-trans-retinoic acid  (ISO)
amiodarone  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP)
Butylbenzyl phthalate  (EXP)
calcitriol  (ISO)
choline  (ISO)
dibutyl phthalate  (EXP)
diethyl phthalate  (EXP)
diisobutyl phthalate  (EXP)
diisononyl phthalate  (EXP)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
finasteride  (EXP)
folic acid  (ISO)
furan  (EXP)
genistein  (EXP)
irinotecan  (ISO)
ketamine  (EXP)
L-methionine  (ISO)
lead diacetate  (EXP)
lead(0)  (ISO)
lead(2+)  (ISO)
leflunomide  (EXP)
methoxychlor  (EXP)
miconazole  (EXP)
N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine  (ISO)
N-methyl-4-phenylpyridinium  (EXP,ISO)
orphenadrine  (EXP)
pravastatin  (EXP,ISO)
propanal  (ISO)
quercetin  (ISO)
rotenone  (EXP)
serpentine asbestos  (ISO)
sodium arsenite  (ISO)
Soman  (EXP)
sulindac  (EXP)
sunitinib  (ISO)
tamibarotene  (ISO)
tetrachloromethane  (EXP,ISO)
tributylstannane  (EXP)
trichloroethene  (EXP)
triptonide  (ISO)
valdecoxib  (EXP)
valproic acid  (EXP,ISO)
WIN 55212-2  (ISO)
zaragozic acid A  (EXP,ISO)
zinc atom  (ISO)
zinc sulfate  (ISO)
zinc(0)  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:7887886   PMID:8878556   PMID:11086001   PMID:12031972   PMID:15596545   PMID:16269463   PMID:16622421   PMID:18048354   PMID:21732083   PMID:23087044   PMID:24843546   PMID:25561468  
PMID:30053369   PMID:30979722  


Genomics

Comparative Map Data
Ptprn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2976,741,010 - 76,756,704 (-)NCBI
Rnor_6.0 Ensembl982,446,633 - 82,461,903 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0982,446,626 - 82,462,314 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0982,215,889 - 82,231,560 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4974,528,095 - 74,542,756 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1974,675,076 - 74,689,738 (-)NCBI
Celera974,311,913 - 74,326,515 (-)NCBICelera
Cytogenetic Map9q33NCBI
PTPRN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2219,289,623 - 219,309,648 (-)EnsemblGRCh38hg38GRCh38
GRCh382219,289,623 - 219,309,404 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372220,154,345 - 220,174,123 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362219,862,589 - 219,882,387 (-)NCBINCBI36hg18NCBI36
Build 342219,979,851 - 219,999,648NCBI
Celera2213,924,192 - 213,944,148 (-)NCBI
Cytogenetic Map2q35NCBI
HuRef2212,007,432 - 212,027,331 (-)NCBIHuRef
CHM1_12220,160,193 - 220,180,139 (-)NCBICHM1_1
Ptprn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39175,223,679 - 75,241,437 (-)NCBIGRCm39mm39
GRCm39 Ensembl175,223,671 - 75,241,146 (-)Ensembl
GRCm38175,247,035 - 75,264,497 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl175,247,027 - 75,264,502 (-)EnsemblGRCm38mm10GRCm38
MGSCv37175,243,616 - 75,260,783 (-)NCBIGRCm37mm9NCBIm37
MGSCv36175,130,189 - 75,147,297 (-)NCBImm8
Celera175,737,937 - 75,755,020 (-)NCBICelera
Cytogenetic Map1C4NCBI
cM Map138.64NCBI
Ptprn
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545314,126,416 - 14,145,347 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495545314,126,416 - 14,145,347 (+)NCBIChiLan1.0ChiLan1.0
PTPRN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B225,138,283 - 225,158,118 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B225,138,887 - 225,206,700 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B106,547,156 - 106,567,056 (-)NCBIMhudiblu_PPA_v0panPan3
PTPRN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13725,835,590 - 25,854,050 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3725,836,118 - 25,869,931 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3726,661,448 - 26,679,881 (-)NCBI
ROS_Cfam_1.03725,850,814 - 25,869,258 (-)NCBI
UMICH_Zoey_3.13725,755,175 - 25,773,586 (-)NCBI
UNSW_CanFamBas_1.03725,690,528 - 25,708,945 (-)NCBI
UU_Cfam_GSD_1.03725,711,218 - 25,729,647 (-)NCBI
Ptprn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303175,355,937 - 175,374,833 (-)NCBI
SpeTri2.0NW_0049365691,698,718 - 1,717,639 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PTPRN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15121,329,288 - 121,349,276 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115121,329,284 - 121,349,228 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215134,364,686 - 134,384,609 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PTPRN
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110105,196,508 - 105,216,665 (-)NCBI
ChlSab1.1 Ensembl10105,196,505 - 105,216,525 (-)Ensembl
Ptprn
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248235,710,669 - 5,734,739 (+)NCBI

Position Markers
D9Mco68  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2976,742,351 - 76,742,539 (+)MAPPER
Rnor_6.0982,447,968 - 82,448,155NCBIRnor6.0
Rnor_5.0982,217,229 - 82,217,416UniSTSRnor5.0
RGSC_v3.4974,528,930 - 74,529,117UniSTSRGSC3.4
Celera974,312,748 - 74,312,935UniSTS
Cytogenetic Map9q33UniSTS
D9Mco44  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2976,757,822 - 76,758,010 (+)MAPPER
Rnor_6.0982,463,433 - 82,463,620NCBIRnor6.0
Rnor_5.0982,232,694 - 82,232,881UniSTSRnor5.0
RGSC_v3.4974,544,448 - 74,544,635UniSTSRGSC3.4
Celera974,328,207 - 74,328,394UniSTS
Cytogenetic Map9q33UniSTS
RH131806  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2976,741,156 - 76,741,349 (+)MAPPER
Rnor_6.0982,446,773 - 82,446,965NCBIRnor6.0
Rnor_5.0982,216,034 - 82,216,226UniSTSRnor5.0
RGSC_v3.4974,527,735 - 74,527,927UniSTSRGSC3.4
Celera974,311,553 - 74,311,745UniSTS
Cytogenetic Map9q33UniSTS
X74438  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2976,741,016 - 76,741,112 (+)MAPPER
Rnor_6.0982,446,633 - 82,446,728NCBIRnor6.0
Rnor_5.0982,215,894 - 82,215,989UniSTSRnor5.0
RGSC_v3.4974,527,595 - 74,527,690UniSTSRGSC3.4
Celera974,311,413 - 74,311,508UniSTS
Cytogenetic Map9q33UniSTS
MARC_8095-8096:996688286:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2976,745,650 - 76,746,337 (+)MAPPER
Rnor_6.0982,451,265 - 82,451,951NCBIRnor6.0
Rnor_5.0982,220,526 - 82,221,212UniSTSRnor5.0
RGSC_v3.4974,532,227 - 74,532,913UniSTSRGSC3.4
Celera974,316,045 - 74,316,731UniSTS
Cytogenetic Map9q33UniSTS
PTPRN_1350  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2976,741,022 - 76,741,590 (+)MAPPER
Rnor_6.0982,446,639 - 82,447,206NCBIRnor6.0
Rnor_5.0982,215,900 - 82,216,467UniSTSRnor5.0
RGSC_v3.4974,527,601 - 74,528,168UniSTSRGSC3.4
Celera974,311,419 - 74,311,986UniSTS
Cytogenetic Map9q33UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9105522293442944Rat
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92569234292741406Rat
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)92748615588333183Rat
70218Cm28Cardiac mass QTL 288.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)92907507983686404Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)929075079122095297Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)929466970107878528Rat
7411571Bw138Body weight QTL 13814.30.001body mass (VT:0001259)body weight gain (CMO:0000420)93764235182642351Rat
7411656Foco26Food consumption QTL 269.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)93764235182642351Rat
1598834Memor11Memory QTL 112.5exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)94126103490024806Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)94126103498606834Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)941261034102531865Rat
6903941Pur31Proteinuria QTL 310.036total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)94657976991579769Rat
11353949Bp393Blood pressure QTL 393arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94657976991579769Rat
61352Bp34Blood pressure QTL 345arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94695242783686153Rat
10058949Gmadr5Adrenal mass QTL 520.014adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)94724896594124663Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)95417754299177542Rat
2303170Bp332Blood pressure QTL 3323.730.027arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)96081029882732466Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)961186278106186278Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)96173092382890620Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)96173092382890620Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)96173092382890620Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)963270073107878387Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)966757444112943287Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)96745166499920892Rat
1578757Pur6Proteinuria QTL 63.30.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)96745166499920892Rat
61385Edpm9Estrogen-dependent pituitary mass QTL 93.430.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)970241351115241351Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)970942881115942881Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)981411073119983851Rat
1581517Bp284Blood pressure QTL 284arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)98235603082477136Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:88
Count of miRNA genes:71
Interacting mature miRNAs:80
Transcripts:ENSRNOT00000026654
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 4 2 2 72 13 4
Low 3 32 45 31 11 31 3 3 2 22 37 9 3
Below cutoff 11 8 8 8 8 5 7 2 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000026654   ⟹   ENSRNOP00000026654
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl982,446,633 - 82,461,903 (-)Ensembl
RefSeq Acc Id: NM_053881   ⟹   NP_446333
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2976,741,517 - 76,756,131 (-)NCBI
Rnor_6.0982,447,133 - 82,461,741 (-)NCBI
Rnor_5.0982,215,889 - 82,231,560 (-)NCBI
RGSC_v3.4974,528,095 - 74,542,756 (-)RGD
Celera974,311,913 - 74,326,515 (-)RGD
Sequence:
RefSeq Acc Id: XM_006245134   ⟹   XP_006245196
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2976,741,023 - 76,756,215 (-)NCBI
Rnor_6.0982,446,626 - 82,461,822 (-)NCBI
Rnor_5.0982,215,889 - 82,231,560 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017596229   ⟹   XP_017451718
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2976,741,010 - 76,756,704 (-)NCBI
Rnor_6.0982,446,626 - 82,462,314 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017596230   ⟹   XP_017451719
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2976,741,023 - 76,756,704 (-)NCBI
Rnor_6.0982,446,626 - 82,462,314 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017596231   ⟹   XP_017451720
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0982,446,626 - 82,459,859 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039082907   ⟹   XP_038938835
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2976,741,023 - 76,755,830 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_446333   ⟸   NM_053881
- Peptide Label: precursor
- UniProtKB: Q63259 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006245196   ⟸   XM_006245134
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017451719   ⟸   XM_017596230
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017451718   ⟸   XM_017596229
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017451720   ⟸   XM_017596231
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000026654   ⟸   ENSRNOT00000026654
RefSeq Acc Id: XP_038938835   ⟸   XM_039082907
- Peptide Label: isoform X4
Transcriptome

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

Promoters
RGD ID:13696777
Promoter ID:EPDNEW_R7301
Type:initiation region
Name:Ptprn_1
Description:protein tyrosine phosphatase, receptor type, N
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_6.0982,461,769 - 82,461,829EPDNEW

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)
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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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620777 AgrOrtholog
Ensembl Genes ENSRNOG00000019587 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000026654 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000026654 ENTREZGENE, 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:116660 UniProtKB/Swiss-Prot
NCBI Gene 116660 ENTREZGENE
PANTHER PTHR46106 UniProtKB/Swiss-Prot
Pfam Receptor_IA-2 UniProtKB/Swiss-Prot
  RESP18 UniProtKB/Swiss-Prot
  Y_phosphatase UniProtKB/Swiss-Prot
PhenoGen Ptprn 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
UniProt PTPRN_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q62883 UniProtKB/Swiss-Prot
  Q63795 UniProtKB/Swiss-Prot
  Q64643 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Ptprn  protein tyrosine phosphatase, receptor type, N      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Ptprn  protein tyrosine phosphatase, receptor type, N      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_disease autoantibodies to the cytoplasmic domain occur in 55{75% of newly diagnosed patients with type 1 diabetes 628454
gene_expression expressed in neurons and in pancreatic islets 628454
gene_physical_interaction binds to beta2-syntrophin and neuronal nitric oxide synthase 628454
gene_process connects the secretory granules with the actin cytoskeleton and the nitric oxide signaling pathways in beta-cells 628454
gene_process may regulate the beta- cell function 628454
gene_product member of the protein tyrosine phosphatase family 628454
gene_product membrane protein of the secretory vesicles 628454
gene_regulation expression is inhibited by IL-1b, TNF-alpha, and IFN-gamma 628454