Ptpra (protein tyrosine phosphatase, receptor type, A) - Rat Genome Database

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Gene: Ptpra (protein tyrosine phosphatase, receptor type, A) Rattus norvegicus
Analyze
Symbol: Ptpra
Name: protein tyrosine phosphatase, receptor type, A
RGD ID: 3450
Description: Exhibits protein tyrosine phosphatase activity. Involved in oligodendrocyte differentiation and positive regulation of oligodendrocyte differentiation. Localizes to intracellular membrane-bounded organelle and plasma membrane. Orthologous to human PTPRA (protein tyrosine phosphatase receptor type A); PARTICIPATES IN insulin signaling pathway; INTERACTS WITH atrazine; bis(2-chloroethyl) sulfide; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LRP; MGC93561; protein tyrosine phosphatase alpha; protein-tyrosine phosphatase alpha; R-PTP-alpha; receptor-type tyrosine-protein phosphatase alpha
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: PtpraTn(sb-T2/Bart3)2.261Mcwi  
Genetic Models: F344-PtpraTn(sb-T2/Bart3)2.261Mcwi
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23117,650,146 - 117,759,744 (+)NCBI
Rnor_6.0 Ensembl3122,976,104 - 123,084,863 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.03122,976,066 - 123,084,585 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.03129,475,237 - 129,582,992 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43118,061,713 - 118,171,300 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13118,022,615 - 118,077,164 (+)NCBI
Celera3116,464,194 - 116,570,590 (+)NCBICelera
Cytogenetic Map3q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease 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:12826681   PMID:12912911   PMID:14733908   PMID:15978577   PMID:16899073   PMID:18768480   PMID:20458337   PMID:23382219  


Genomics

Comparative Map Data
Ptpra
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23117,650,146 - 117,759,744 (+)NCBI
Rnor_6.0 Ensembl3122,976,104 - 123,084,863 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.03122,976,066 - 123,084,585 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.03129,475,237 - 129,582,992 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43118,061,713 - 118,171,300 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13118,022,615 - 118,077,164 (+)NCBI
Celera3116,464,194 - 116,570,590 (+)NCBICelera
Cytogenetic Map3q36NCBI
PTPRA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl202,864,184 - 3,039,076 (+)EnsemblGRCh38hg38GRCh38
GRCh38202,864,184 - 3,038,669 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37202,844,830 - 3,019,315 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36202,792,841 - 2,967,315 (+)NCBINCBI36hg18NCBI36
Build 34202,851,852 - 2,967,314NCBI
Celera202,907,196 - 3,081,302 (+)NCBI
Cytogenetic Map20p13NCBI
HuRef202,793,748 - 2,965,653 (+)NCBIHuRef
CHM1_1202,844,843 - 3,014,144 (+)NCBICHM1_1
Ptpra
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392130,292,198 - 130,396,220 (+)NCBIGRCm39mm39
GRCm39 Ensembl2130,292,198 - 130,398,044 (+)Ensembl
GRCm382130,450,278 - 130,554,300 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2130,450,278 - 130,556,124 (+)EnsemblGRCm38mm10GRCm38
MGSCv372130,276,014 - 130,380,036 (+)NCBIGRCm37mm9NCBIm37
MGSCv362130,194,915 - 130,245,464 (+)NCBImm8
Celera2131,674,730 - 131,778,720 (+)NCBICelera
Cytogenetic Map2F1NCBI
cM Map263.23NCBI
Ptpra
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541513,819,717 - 13,967,068 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541513,819,934 - 13,967,068 (+)NCBIChiLan1.0ChiLan1.0
PTPRA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1202,726,657 - 2,888,195 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl202,801,905 - 2,888,195 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0202,962,701 - 3,125,282 (+)NCBIMhudiblu_PPA_v0panPan3
PTPRA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12418,224,355 - 18,395,650 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2418,224,801 - 18,296,350 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2418,052,684 - 18,223,899 (-)NCBI
ROS_Cfam_1.02418,643,403 - 18,815,534 (-)NCBI
UMICH_Zoey_3.12418,236,577 - 18,408,752 (-)NCBI
UNSW_CanFamBas_1.02418,349,051 - 18,519,508 (-)NCBI
UU_Cfam_GSD_1.02418,677,051 - 18,848,067 (-)NCBI
Ptpra
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640167,313,690 - 167,441,022 (-)NCBI
SpeTri2.0NW_00493648515,745,054 - 15,872,377 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PTPRA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1732,633,612 - 32,797,104 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11732,638,494 - 32,797,110 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21737,008,987 - 37,167,722 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PTPRA
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1233,559,634 - 33,724,446 (+)NCBI
ChlSab1.1 Ensembl233,559,697 - 33,722,137 (+)Ensembl
Vero_WHO_p1.0NW_02366607110,789,232 - 10,956,158 (-)NCBI
Ptpra
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247413,997,853 - 4,155,130 (+)NCBI

Position Markers
BE108511  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03123,084,673 - 123,084,866NCBIRnor6.0
Rnor_5.03129,582,801 - 129,582,994UniSTSRnor5.0
RGSC_v3.43118,171,401 - 118,171,594UniSTSRGSC3.4
Celera3116,570,691 - 116,570,884UniSTS
RH 3.4 Map31001.2UniSTS
Cytogenetic Map3q36UniSTS
AU047115  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03123,058,055 - 123,058,320NCBIRnor6.0
Rnor_5.03129,556,183 - 129,556,448UniSTSRnor5.0
RGSC_v3.43118,143,790 - 118,144,055UniSTSRGSC3.4
Celera3116,545,174 - 116,545,439UniSTS
Cytogenetic Map3q36UniSTS
RH134950  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03123,037,794 - 123,037,989NCBIRnor6.0
Rnor_5.03129,535,922 - 129,536,117UniSTSRnor5.0
RGSC_v3.43118,123,530 - 118,123,725UniSTSRGSC3.4
Celera3116,524,913 - 116,525,108UniSTS
RH 3.4 Map31000.7UniSTS
Cytogenetic Map3q36UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)310639528127023997Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)310639528127023997Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)330114912123700444Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)330846101172879276Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)339248391140271184Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)343295930163640485Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)343295930163640485Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)345406058127023997Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)345406058177699992Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)348561928155263151Rat
631665Bw8Body weight QTL 85.5body mass (VT:0001259)body weight (CMO:0000012)351821836124513579Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)358204463170534769Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)361241033165369047Rat
1300111Rf12Renal function QTL 123.78renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)362922868127023997Rat
12879848Bw181Body weght QTL 1810.015body mass (VT:0001259)body weight (CMO:0000012)372672290127023997Rat
2301414Kidm37Kidney mass QTL 370.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)372973445127023997Rat
1600376Arunc5Aerobic running capacity QTL 50.21exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)378700444123700444Rat
1581546Pur13Proteinuria QTL 132.930.0335total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)381136227154416635Rat
7387306Bw124Body weight QTL 1243.20.0003body mass (VT:0001259)body weight (CMO:0000012)388910015133910015Rat
631649Bp123Blood pressure QTL 1233.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)394788365139788365Rat
8694437Bw167Body weight QTL 16722.460.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)397009185142009185Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)399465522168732722Rat
724532Cm17Cardiac mass QTL 172heart mass (VT:0007028)calculated heart weight (CMO:0000073)3101058963146058963Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)3102152812155263151Rat
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)3102466149147466149Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)3103141814176418101Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)3103141814176418101Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3103141814176418101Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)3103141944170934860Rat
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3114376250159376250Rat
1331758Bp207Blood pressure QTL 2072.848arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3117303473141971336Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3119471263164471263Rat
1358204Insglur1Insulin/glucose ratio QTL 13.8blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)3120917788141971336Rat
1358204Insglur1Insulin/glucose ratio QTL 13.8blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)3120917788141971336Rat


Genetic Models
This gene Ptpra is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:249
Count of miRNA genes:171
Interacting mature miRNAs:192
Transcripts:ENSRNOT00000055801
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 3 43 56 40 19 40 6 6 74 35 38 11 6
Low 1 1 1 2 5 3 2
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000055801   ⟹   ENSRNOP00000052657
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3122,976,104 - 123,084,569 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000080379   ⟹   ENSRNOP00000069583
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3123,031,307 - 123,084,863 (+)Ensembl
RefSeq Acc Id: NM_012763   ⟹   NP_036895
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23117,650,183 - 117,759,731 (+)NCBI
Rnor_6.03122,976,104 - 123,084,572 (+)NCBI
Rnor_5.03129,475,237 - 129,582,992 (+)NCBI
RGSC_v3.43118,061,713 - 118,171,300 (+)RGD
Celera3116,464,194 - 116,570,590 (+)RGD
Sequence:
RefSeq Acc Id: XM_006235006   ⟹   XP_006235068
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23117,650,146 - 117,759,744 (+)NCBI
Rnor_6.03122,976,066 - 123,084,585 (+)NCBI
Rnor_5.03129,475,237 - 129,582,992 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006235007   ⟹   XP_006235069
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03122,992,798 - 123,084,585 (+)NCBI
Rnor_5.03129,475,237 - 129,582,992 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039104340   ⟹   XP_038960268
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23117,650,203 - 117,759,744 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_036895   ⟸   NM_012763
- Peptide Label: precursor
- UniProtKB: Q66HJ7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006235068   ⟸   XM_006235006
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006235069   ⟸   XM_006235007
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000069583   ⟸   ENSRNOT00000080379
RefSeq Acc Id: ENSRNOP00000052657   ⟸   ENSRNOT00000055801
RefSeq Acc Id: XP_038960268   ⟸   XM_039104340
- Peptide Label: isoform X1
Transcriptome

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

Promoters
RGD ID:13692434
Promoter ID:EPDNEW_R2958
Type:multiple initiation site
Name:Ptpra_1
Description:protein tyrosine phosphatase, receptor type, A
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_6.03122,976,086 - 122,976,146EPDNEW

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)
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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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
3 129571241 129571242 T C snv ACI/EurMcwi (MCW), ZFDM (KyushuU), GH/OmrMcwi (MCW), SBH/Ygl (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SR/JrHsd (MCW), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), Crl:SD (UDEL), IS/Kyo (KyushuU), BUF/MNa (KyushuU), NIG-III/Hok (KyushuU), F344/DuCrlCrlj (KyushuU), LE/Stm (KyushuU), HTX/Kyo (KyushuU), F344/NSlc (KyushuU), RCS/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU), F344/Stm (KyushuU), HWY/Slc (KyushuU), F344/Jcl (KyushuU), BDIX/NemOda (KyushuU), DOB/Oda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), KFRS3B/Kyo (KyushuU), ZF (KyushuU), COP/CrCrl (MCW & UW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
3 123073113 123073114 T C snv CDS, WKY/NHsd (RGD), Buf/N (MCW), F344/NRrrc (MCW), M520/N (MCW), MR/N (MCW), WKY/N (MCW), FHL/EurMcwi (RGD), ACI/EurMcwi (RGD), BBDP/Wor (RGD), F344/NCrl (RGD), FHH/EurMcwi (RGD), LE/Stm (RGD), LEW/Crl (RGD), LEW/NCrlBR (RGD), MNS/Gib (RGD), SBH/Ygl (RGD), SHR/NHsd (RGD), SHRSP/Gcrc (RGD), SR/JrHsd (RGD), WAG/Rij (RGD), WKY/NCrl (RGD), WKY/Gcrc (RGD), ACI/N (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
3 118157700 118157701 G A snv SS/JrHsdMcwi (MCW)
3 118158825 118158826 T C snv DA/BklArbNsi (ICAHN), SHRSP/Gcrc (MDC), ACI/N (KNAW), BUF/N (KNAW), F344/NRrrc (KNAW), LE/Stm (KNAW), M520/N (KNAW), MR/N (KNAW), WKY/N (KNAW), SHR/OlaIpcv (KNAW), ACI/EurMcwi (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SR/JrHsd (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), ACI/EurMcwi (ICL), BBDP/WorN (ICL), F344/NCrl (ICL), LE/Stm (ICL), FHH/EurMcwi (ICL), FHL/EurMcwi (ICL), LEW/Crl (ICL), LEW/NCrl (ICL), MHS/Gib (ICL), MNS/Gib (ICL), SBH/Ygl (ICL), SHR/OlaIpcv (ICL), SHR/NHsd (ICL), SHRSP/Gcrc (ICL), SR/JrHsd (ICL), WAG/Rij (ICL), WKY/Gcrc (ICL), WKY/NHsd (ICL), WKY/NCrl (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich), LCR/2Mco (UMich), F344/NHsd (ICAHN), SHR/OlaIpcv (ICL), FHH/EurMcwi (MDC)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3450 AgrOrtholog
Ensembl Genes ENSRNOG00000021223 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000052657 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000069583 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000055801 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000080379 UniProtKB/TrEMBL
Gene3D-CATH 3.90.190.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7107006 IMAGE-MGC_LOAD
InterPro Prot-tyrosine_phosphatase-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTPase_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tyr_Pase_AS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tyr_Pase_cat UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tyr_Pase_rcpt_a/e-type UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tyr_Pase_rcpt_alpha UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TYR_PHOSPHATASE_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25167 UniProtKB/TrEMBL
MGC_CLONE MGC:93561 IMAGE-MGC_LOAD
NCBI Gene 25167 ENTREZGENE
PANTHER PTHR19134:SF433 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Y_phosphatase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ptpra PhenoGen
PIRSF PTPR_alpha UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTPR_alpha_epsilon UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PRINTS PRTYPHPHTASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE TYR_PHOSPHATASE_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TYR_PHOSPHATASE_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TYR_PHOSPHATASE_PTP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART PTPc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTPc_motif UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF52799 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC229590
Transposagen Ptpra Transposagen
UniProt A0A0G2JVR0_RAT UniProtKB/TrEMBL
  PTPRA_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q66HJ7 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary F1M833 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Ptpra  Protein tyrosine phosphatase, receptor type, A      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains has two intracellular PTPase domains 633823
gene_regulation expression is inhibited by treatment with Il6 or Il1 633823