Ptpn1 (protein tyrosine phosphatase, non-receptor type 1) - Rat Genome Database

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Gene: Ptpn1 (protein tyrosine phosphatase, non-receptor type 1) Rattus norvegicus
Analyze
Symbol: Ptpn1
Name: protein tyrosine phosphatase, non-receptor type 1
RGD ID: 61965
Description: Enables insulin receptor binding activity; protein phosphatase 2A binding activity; and protein tyrosine phosphatase activity. Involved in protein dephosphorylation and regulation of insulin receptor signaling pathway. Located in cytoplasmic vesicle; cytosol; and mitochondrion. Human ortholog(s) of this gene implicated in type 2 diabetes mellitus. Orthologous to human PTPN1 (protein tyrosine phosphatase non-receptor type 1); PARTICIPATES IN insulin signaling pathway; epidermal growth factor/neuregulin signaling pathway; insulin-like growth factor signaling pathway; INTERACTS WITH 1,4-dithiothreitol; 17alpha-ethynylestradiol; 2,2',5,5'-tetrachlorobiphenyl.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: MGC93562; protein-tyrosine phosphatase; protein-tyrosine phosphatase 1B; Ptp; PTP-1B; tyrosine-protein phosphatase non-receptor type 1
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
mRatBN7.23156,638,811 - 156,687,503 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl3156,638,769 - 156,687,504 (+)Ensembl
Rnor_6.03164,665,462 - 164,711,936 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3164,665,532 - 164,711,848 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03170,816,897 - 170,866,071 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43159,070,473 - 159,116,792 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13158,976,466 - 159,025,198 (+)NCBI
Celera3155,215,176 - 155,261,496 (+)NCBICelera
Cytogenetic Map3q42NCBI
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
(+)-catechin  (ISO)
1,2-dimethylhydrazine  (ISO)
1,2-naphthoquinone  (ISO)
1,4-dithiothreitol  (EXP,ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
2-methylcholine  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
3-chloropropane-1,2-diol  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (EXP)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-nitrophenyl phosphate  (ISO)
9,10-phenanthroquinone  (ISO)
acetamide  (EXP)
acrolein  (ISO)
ADP  (EXP)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
ammonium chloride  (EXP)
anthranilic acid  (ISO)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
arsenous acid  (ISO)
Bardoxolone methyl  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzoic acid  (ISO)
bisphenol A  (EXP)
calcitriol  (ISO)
carbon nanotube  (ISO)
chlordecone  (ISO)
chloropicrin  (ISO)
chromium atom  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
coumestrol  (ISO)
Cryptotanshinone  (ISO)
Cuprizon  (EXP)
decabromodiphenyl ether  (EXP)
dexamethasone  (EXP)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
diclofenac  (ISO)
Didymin  (ISO)
dimethylarsinous acid  (ISO)
disodium selenite  (ISO)
elemental selenium  (EXP)
ethanol  (ISO)
flavonoids  (EXP)
folic acid  (ISO)
fucosterol  (ISO)
genistein  (EXP)
glycidol  (EXP)
hexadecanoic acid  (ISO)
hydrogen peroxide  (EXP)
isoliquiritigenin  (ISO)
ivermectin  (ISO)
L-1,4-dithiothreitol  (EXP,ISO)
lipopolysaccharide  (ISO)
LY294002  (ISO)
metformin  (ISO)
methylglyoxal  (ISO)
methylmercury chloride  (ISO)
morin  (ISO)
N-acetyl-L-cysteine  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP)
nitrofen  (EXP)
paracetamol  (ISO)
phenethyl caffeate  (EXP)
pirinixic acid  (ISO)
pyrithione  (ISO)
resveratrol  (ISO)
rotenone  (ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (EXP)
selenic acid  (ISO)
selenium atom  (EXP)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
streptozocin  (ISO)
tamoxifen  (ISO)
tetrachloromethane  (ISO)
tetrathiomolybdate(2-)  (ISO)
thapsigargin  (ISO)
thiazolidines  (ISO)
triptonide  (ISO)
tris(picolinato)chromium  (EXP)
tunicamycin  (ISO)
ursolic acid  (ISO)
valproic acid  (ISO)
vanadyl sulfate  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
zinc atom  (ISO)
zinc sulfate  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

References - curated
1. Ahmad F and Goldstein BJ, Biochim Biophys Acta. 1995 Apr 5;1248(1):57-69.
2. Arachiche A, etal., J Biol Chem. 2008 Sep 5;283(36):24406-11. doi: 10.1074/jbc.M709217200. Epub 2008 Jun 26.
3. Di Paola R, etal., Am J Hum Genet. 2002 Mar;70(3):806-12. Epub 2002 Feb 6.
4. Guan KL, etal., Proc Natl Acad Sci U S A 1990 Feb;87(4):1501-5.
5. Harris DL and Joyce NC, Mol Vis. 2007 May 24;13:785-96.
6. Hirata AE, etal., Life Sci. 2003 Aug 1;73(11):1369-81.
7. Liu F, etal., J Biol Chem. 1996 Dec 6;271(49):31290-5.
8. Lund IK, etal., J Mol Endocrinol. 2005 Apr;34(2):339-51.
9. MGD data from the GO Consortium
10. Milarski KL, etal., J Biol Chem. 1993 Nov 5;268(31):23634-9.
11. NCBI rat LocusLink and RefSeq merged data July 26, 2002
12. OMIM Disease Annotation Pipeline
13. Pipeline to import KEGG annotations from KEGG into RGD
14. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
15. RGD automated data pipeline
16. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
17. RGD automated import pipeline for gene-chemical interactions
18. Shi K, etal., Biochem Biophys Res Commun. 2007 Nov 23;363(3):626-32. Epub 2007 Sep 17.
19. Shimizu S, etal., J Biol Chem. 2003 Oct 31;278(44):43095-101. Epub 2003 Aug 26.
20. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
21. Valentino L and Pierre J, Biochem Pharmacol. 2006 Mar 14;71(6):713-21. Epub 2006 Jan 19.
22. Youngren JF Cell Mol Life Sci. 2007 Apr;64(7-8):873-91.
23. Zhang ZY, etal., J Biol Chem. 1996 Mar 8;271(10):5386-92.
24. Zhang ZY, etal., Proc Natl Acad Sci U S A. 1993 May 15;90(10):4446-50.
25. Zhen X, etal., Mol Pharmacol 2002 Dec;62(6):1356-63.
Additional References at PubMed
PMID:1599438   PMID:1739967   PMID:11434923   PMID:12477932   PMID:12902327   PMID:14966296   PMID:15271661   PMID:15465829   PMID:15489334   PMID:15632081   PMID:16373608   PMID:16946481  
PMID:17008371   PMID:17038557   PMID:18074158   PMID:18281274   PMID:18456732   PMID:18566118   PMID:18819921   PMID:19605464   PMID:20979831   PMID:21057040   PMID:21063895   PMID:21135139  
PMID:21216966   PMID:21707536   PMID:22045810   PMID:22166493   PMID:22169477   PMID:22569287   PMID:22658674   PMID:22829592   PMID:22844492   PMID:23283996   PMID:23481236   PMID:23639442  
PMID:24225419   PMID:25056348   PMID:25352433   PMID:25391857   PMID:25468996   PMID:25894283   PMID:25998537   PMID:25999679   PMID:26099503   PMID:27461362   PMID:28229972   PMID:28246125  
PMID:28403933   PMID:29929988   PMID:30644128   PMID:30947960   PMID:31502193   PMID:31894853   PMID:32042410  


Genomics

Candidate Gene Status
Ptpn1 is a candidate Gene for QTL Eau4
Ptpn1 is a candidate Gene for QTL Slep7
Ptpn1 is a candidate Gene for QTL Bw94
Ptpn1 is a candidate Gene for QTL Scl63
Comparative Map Data
Ptpn1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23156,638,811 - 156,687,503 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl3156,638,769 - 156,687,504 (+)Ensembl
Rnor_6.03164,665,462 - 164,711,936 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3164,665,532 - 164,711,848 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03170,816,897 - 170,866,071 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43159,070,473 - 159,116,792 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13158,976,466 - 159,025,198 (+)NCBI
Celera3155,215,176 - 155,261,496 (+)NCBICelera
Cytogenetic Map3q42NCBI
PTPN1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2050,510,321 - 50,585,241 (+)EnsemblGRCh38hg38GRCh38
GRCh382050,510,383 - 50,585,241 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372049,126,920 - 49,201,778 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362048,560,298 - 48,634,495 (+)NCBINCBI36hg18NCBI36
Build 342048,560,297 - 48,634,491NCBI
Celera2045,831,156 - 45,905,376 (+)NCBI
Cytogenetic Map20q13.13NCBI
HuRef2045,875,585 - 45,950,061 (+)NCBIHuRef
CHM1_12049,031,996 - 49,106,433 (+)NCBICHM1_1
Ptpn1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392167,772,670 - 167,821,305 (+)NCBIGRCm39mm39
GRCm39 Ensembl2167,773,977 - 167,821,305 (+)Ensembl
GRCm382167,930,750 - 167,979,385 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2167,932,057 - 167,979,385 (+)EnsemblGRCm38mm10GRCm38
MGSCv372167,757,827 - 167,804,885 (+)NCBIGRCm37mm9NCBIm37
MGSCv362167,623,579 - 167,668,124 (+)NCBImm8
Celera2173,874,374 - 173,921,508 (+)NCBICelera
Cytogenetic Map2H3NCBI
Ptpn1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554457,754,319 - 7,819,275 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554457,754,313 - 7,819,229 (-)NCBIChiLan1.0ChiLan1.0
PTPN1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12047,983,098 - 48,057,421 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2047,983,098 - 48,057,421 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02046,854,918 - 46,929,509 (+)NCBIMhudiblu_PPA_v0panPan3
PTPN1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12436,936,469 - 37,010,929 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2436,936,298 - 37,003,720 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2436,179,442 - 36,246,435 (+)NCBI
ROS_Cfam_1.02437,642,503 - 37,713,189 (+)NCBI
UMICH_Zoey_3.12436,882,533 - 36,949,558 (+)NCBI
UNSW_CanFamBas_1.02437,016,127 - 37,083,208 (+)NCBI
UU_Cfam_GSD_1.02437,560,457 - 37,627,492 (+)NCBI
Ptpn1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640188,603,904 - 188,630,208 (-)NCBI
SpeTri2.0NW_0049365144,065,455 - 4,083,847 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PTPN1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1752,017,104 - 52,086,736 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11752,017,100 - 52,086,747 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21758,450,256 - 58,474,772 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PTPN1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1213,385,681 - 13,459,180 (-)NCBI
ChlSab1.1 Ensembl213,387,727 - 13,459,105 (-)Ensembl
Vero_WHO_p1.0NW_02366605061,816,170 - 61,890,307 (-)NCBI
Ptpn1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247905,070,537 - 5,135,243 (-)NCBI

Position Markers
D3Wox6  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23156,687,232 - 156,687,364 (+)MAPPERmRatBN7.2
Rnor_6.03164,714,373 - 164,714,502NCBIRnor6.0
Rnor_5.03170,865,803 - 170,865,932UniSTSRnor5.0
RGSC_v3.43159,118,892 - 159,119,022RGDRGSC3.4
RGSC_v3.43159,118,893 - 159,119,022UniSTSRGSC3.4
RGSC_v3.13159,024,928 - 159,025,058RGD
Celera3155,263,597 - 155,263,726UniSTS
RH 3.4 Map31480.0UniSTS
RH 3.4 Map31480.0RGD
RH 2.0 Map31003.1RGD
Cytogenetic Map3q42UniSTS
D3Wox42  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23156,687,086 - 156,687,374 (+)MAPPERmRatBN7.2
Rnor_6.03164,714,227 - 164,714,512NCBIRnor6.0
Rnor_5.03170,865,657 - 170,865,942UniSTSRnor5.0
RGSC_v3.43159,118,747 - 159,119,032UniSTSRGSC3.4
Celera3155,263,451 - 155,263,736UniSTS
Cytogenetic Map3q42UniSTS
RH131447  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23156,687,584 - 156,687,765 (+)MAPPERmRatBN7.2
Rnor_6.03164,714,723 - 164,714,903NCBIRnor6.0
Rnor_5.03170,866,153 - 170,866,333UniSTSRnor5.0
RGSC_v3.43159,119,243 - 159,119,423UniSTSRGSC3.4
Celera3155,263,947 - 155,264,127UniSTS
RH 3.4 Map31478.0UniSTS
Cytogenetic Map3q42UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
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)343827364169034231Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
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)359242096157323038Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)394856903159898684Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)398535386161695835Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3112681431157681431Rat
1576306Schws3Schwannoma susceptibility QTL 30.001nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)3118839124163839124Rat
1598877Bp285Blood pressure QTL 2851.50.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3120538241165538241Rat
1300159Kidm4Kidney mass QTL 43.83kidney mass (VT:0002707)right kidney wet weight to body weight ratio (CMO:0001953)3121056165157309487Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3122438700167438700Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3124122556169034231Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3127162703168026850Rat
631673Iddm13Insulin dependent diabetes mellitus QTL 131.30.663blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)3130193298161695983Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3130656562169034231Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3130656562169034231Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3131635904169034231Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3137398739169034231Rat
8552952Pigfal13Plasma insulin-like growth factor 1 level QTL 13blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)3138799500169034231Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3141074471169034231Rat
1331726Bp208Blood pressure QTL 2083.129arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3141339013162184794Rat
2317883Alcrsp26Alcohol response QTL 261.80.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)3145526770169034231Rat
12879871Am7Aortic mass QTL 70.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)3145925360166177555Rat
12879872Cm97Cardiac mass QTL 970.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3145925360166177555Rat
12879873Cm96Cardiac mass QTL 960.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)3145925360166177555Rat
12879874Cm98Cardiac mass QTL 980.005heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)3145925360166177555Rat
12879875Kidm64Kidney mass QTL 640.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3145925360166177555Rat
12879876Bw182Body weight QTL 1820.003body mass (VT:0001259)body weight (CMO:0000012)3145925360166177555Rat
2301411Bp320Blood pressure QTL 3200.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3145925360166177555Rat
1300113Bp176Blood pressure QTL 1763.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3145956084157309487Rat
1598854Memor10Memory QTL 102exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)3145956084161299569Rat
8552791Vie2Viral induced encephalitis QTL 24.1brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)3145956084169034231Rat
1578666Vnigr1Vascular neointimal growth QTL 14.6artery morphology trait (VT:0002191)artery lumen area (CMO:0001409)3149040888168026850Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:452
Count of miRNA genes:233
Interacting mature miRNAs:282
Transcripts:ENSRNOT00000014309
Prediction methods:Microtar, Miranda, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 34 42 26 19 26 2 74 31 41 11
Low 9 15 15 15 8 9 4 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000014309   ⟹   ENSRNOP00000014309
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3156,638,769 - 156,687,504 (+)Ensembl
Rnor_6.0 Ensembl3164,665,532 - 164,711,848 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000106950   ⟹   ENSRNOP00000077114
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3156,638,769 - 156,687,504 (+)Ensembl
RefSeq Acc Id: NM_012637   ⟹   NP_036769
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23156,638,811 - 156,685,132 (+)NCBI
Rnor_6.03164,665,532 - 164,711,853 (+)NCBI
Rnor_5.03170,816,897 - 170,866,071 (+)NCBI
RGSC_v3.43159,070,473 - 159,116,792 (+)RGD
Celera3155,215,176 - 155,261,496 (+)RGD
Sequence:
RefSeq Acc Id: XM_039104281   ⟹   XP_038960209
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23156,663,707 - 156,687,503 (+)NCBI
RefSeq Acc Id: XM_039104282   ⟹   XP_038960210
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23156,663,685 - 156,687,503 (+)NCBI
RefSeq Acc Id: XM_039104283   ⟹   XP_038960211
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23156,662,919 - 156,683,397 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_036769   ⟸   NM_012637
- UniProtKB: P20417 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000014309   ⟸   ENSRNOT00000014309
RefSeq Acc Id: XP_038960211   ⟸   XM_039104283
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038960210   ⟸   XM_039104282
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038960209   ⟸   XM_039104281
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000077114   ⟸   ENSRNOT00000106950
Transcriptome

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

Promoters
RGD ID:13692695
Promoter ID:EPDNEW_R3220
Type:initiation region
Name:Ptpn1_1
Description:protein tyrosine phosphatase, non-receptor type 1
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_6.03164,665,480 - 164,665,540EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (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
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (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
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-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)
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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/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
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)
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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
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
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)
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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
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)
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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
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
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)
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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
HXB20/IpcvMcwi (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
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)
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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
LE/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
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 (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
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
LEXF10A/StmMcwi (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
LEXF11/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
LEXF1A/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
LEXF1C/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
LEXF2B/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
LEXF3/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
LEXF4/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
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
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)
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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/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
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
LN/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
M520/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
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
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)
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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 (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
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
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)
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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
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
SHR/OlalpcvMcwi (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
SHRSP/A3NCrl (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
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 (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: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (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
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
WAG/RijCrl (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: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (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
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 (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
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 (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:61965 AgrOrtholog
Ensembl Genes ENSRNOG00000010574 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000014309 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000014309 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.90.190.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7135855 IMAGE-MGC_LOAD
InterPro Prot-tyrosine_phosphatase-like UniProtKB/Swiss-Prot
  PTPase_domain UniProtKB/Swiss-Prot
  Ptpn1/Ptpn2 UniProtKB/Swiss-Prot
  Tyr_Pase_AS UniProtKB/Swiss-Prot
  Tyr_Pase_cat UniProtKB/Swiss-Prot
  TYR_PHOSPHATASE_dom UniProtKB/Swiss-Prot
KEGG Report rno:24697 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93562 IMAGE-MGC_LOAD
NCBI Gene 24697 ENTREZGENE
Pfam Y_phosphatase UniProtKB/Swiss-Prot
PhenoGen Ptpn1 PhenoGen
PIRSF Tyr-Ptase_nr1 UniProtKB/Swiss-Prot
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 TC206132
UniProt P20417 ENTREZGENE, UniProtKB/Swiss-Prot
  Q99ND7_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Ptpn1  protein tyrosine phosphatase, non-receptor type 1      Name updated 70584 APPROVED
2001-06-12 Ptp  Protein-tyrosine phosphatase      Symbol withdrawn, duplicate of Ptpn1 (RGD:61965) 67953 WITHDRAWN

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in the central nervous system with the highest expression in the hippocampus 61723