Ptpn6 (protein tyrosine phosphatase, non-receptor type 6) - Rat Genome Database

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Gene: Ptpn6 (protein tyrosine phosphatase, non-receptor type 6) Rattus norvegicus
Analyze
Symbol: Ptpn6
Name: protein tyrosine phosphatase, non-receptor type 6
RGD ID: 620660
Description: Exhibits natural killer cell lectin-like receptor binding activity. Involved in response to wounding. Predicted to localize to several cellular components, including alpha-beta T cell receptor complex; cell-cell junction; and nuclear lumen. Orthologous to human PTPN6 (protein tyrosine phosphatase non-receptor type 6); PARTICIPATES IN angiotensin II signaling pathway via AT2 receptor; epidermal growth factor/neuregulin signaling pathway; erythropoietin signaling pathway; INTERACTS WITH 2,6-dinitrotoluene; 3H-1,2-dithiole-3-thione; acetamide.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: MGC124580; protein-tyrosine phosphatase SHP-1; Ptph6; SH2 phosphatase 1; Shp-1; tyrosine-protein phosphatase non-receptor type 6
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
mRatBN7.24157,526,034 - 157,550,783 (-)NCBI
Rnor_6.0 Ensembl4157,239,142 - 157,263,890 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.04157,239,141 - 157,263,890 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.04224,256,737 - 224,281,486 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44160,843,699 - 160,868,856 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14161,088,634 - 161,113,792 (-)NCBI
Celera4146,264,696 - 146,289,049 (-)NCBICelera
Cytogenetic Map4q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-diaminotoluene  (ISO)
2,6-dinitrotoluene  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
5-aza-2'-deoxycytidine  (ISO)
acetamide  (EXP)
acrylamide  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
all-trans-retinol  (EXP)
ammonium chloride  (EXP)
anthranilic acid  (ISO)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP)
bortezomib  (ISO)
carbon nanotube  (ISO)
chlordecone  (ISO)
chloroprene  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
copper(II) sulfate  (ISO)
curcumin  (ISO)
cyclosporin A  (ISO)
diarsenic trioxide  (ISO)
elemental selenium  (ISO)
emodin  (ISO)
endosulfan  (EXP)
ethanol  (EXP,ISO)
flavonoids  (EXP)
fonofos  (ISO)
gentamycin  (EXP)
hydrogen peroxide  (ISO)
lead diacetate  (ISO)
lipopolysaccharide  (ISO)
methoxyacetic acid  (EXP)
methoxychlor  (EXP)
nickel atom  (ISO)
nickel sulfate  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
parathion  (ISO)
PD123319  (EXP)
pirinixic acid  (ISO)
potassium dichromate  (ISO)
raloxifene  (ISO)
selenium atom  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (EXP)
sodium chloride  (ISO)
sodium stibogluconate  (ISO)
Soman  (EXP)
terbufos  (ISO)
tetrachloromethane  (ISO)
tetraphene  (ISO)
titanium dioxide  (ISO)
Tributyltin oxide  (EXP,ISO)
trimethyltin  (ISO)
valproic acid  (ISO)
valsartan  (EXP)
vinclozolin  (EXP)
vitamin E  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
abortive mitotic cell cycle  (IEA,ISO)
B cell receptor signaling pathway  (IEA,ISO)
cell differentiation  (ISO,ISS)
epididymis development  (IEA,ISO)
hematopoietic progenitor cell differentiation  (IEA,ISO)
intracellular signal transduction  (IEA,ISO)
megakaryocyte development  (IEA,ISO)
natural killer cell mediated cytotoxicity  (IEA,ISO)
negative regulation of humoral immune response mediated by circulating immunoglobulin  (IEA,ISO)
negative regulation of interleukin-6 production  (IEA,ISO)
negative regulation of MAP kinase activity  (IEA,ISO)
negative regulation of MAPK cascade  (ISO)
negative regulation of peptidyl-tyrosine phosphorylation  (IEA,ISO)
negative regulation of T cell proliferation  (IEA,ISO)
negative regulation of T cell receptor signaling pathway  (IEA,ISO)
negative regulation of tumor necrosis factor production  (IEA,ISO)
peptidyl-tyrosine dephosphorylation  (IEA,ISO)
peptidyl-tyrosine phosphorylation  (IEA,ISO)
platelet aggregation  (IEA,ISO)
platelet formation  (IEA,ISO)
positive regulation of cell adhesion mediated by integrin  (IEA,ISO)
positive regulation of cell population proliferation  (IEA,ISO)
positive regulation of phosphatidylinositol 3-kinase signaling  (IEA,ISO)
protein dephosphorylation  (ISO,ISS,TAS)
regulation of B cell differentiation  (IEA,ISO)
regulation of ERK1 and ERK2 cascade  (IEA,ISO,ISS)
regulation of G1/S transition of mitotic cell cycle  (IEA,ISO)
regulation of release of sequestered calcium ion into cytosol  (IEA,ISO)
response to wounding  (IEP)

Cellular Component

References

Additional References at PubMed
PMID:1302222   PMID:6971254   PMID:8632004   PMID:8943354   PMID:9064344   PMID:9254656   PMID:9285411   PMID:10206955   PMID:10229828   PMID:10556798   PMID:10585470   PMID:10940933  
PMID:11162587   PMID:11266449   PMID:11986327   PMID:12051764   PMID:12163025   PMID:12221292   PMID:12477932   PMID:14684844   PMID:15115663   PMID:15341919   PMID:16159885   PMID:16223786  
PMID:16814162   PMID:17068200   PMID:17562706   PMID:17954568   PMID:18294464   PMID:18680145   PMID:18802077   PMID:19056867   PMID:19749791   PMID:19838216   PMID:19948503   PMID:20458337  
PMID:21166153   PMID:22077594   PMID:22120166   PMID:22499584   PMID:23509158   PMID:23509253   PMID:23793062   PMID:24029230   PMID:24140598   PMID:24225419   PMID:25007834   PMID:25404734  
PMID:25790452   PMID:27323684   PMID:29758384   PMID:31967332  


Genomics

Comparative Map Data
Ptpn6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24157,526,034 - 157,550,783 (-)NCBI
Rnor_6.0 Ensembl4157,239,142 - 157,263,890 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.04157,239,141 - 157,263,890 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.04224,256,737 - 224,281,486 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44160,843,699 - 160,868,856 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14161,088,634 - 161,113,792 (-)NCBI
Celera4146,264,696 - 146,289,049 (-)NCBICelera
Cytogenetic Map4q42NCBI
PTPN6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl126,946,468 - 6,961,316 (+)EnsemblGRCh38hg38GRCh38
GRCh38126,946,577 - 6,961,316 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37127,055,740 - 7,070,479 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36126,926,001 - 6,940,740 (+)NCBINCBI36hg18NCBI36
Build 34126,930,762 - 6,940,740NCBI
Celera128,674,361 - 8,691,497 (+)NCBI
Cytogenetic Map12p13.31NCBI
HuRef126,911,844 - 6,928,943 (+)NCBIHuRef
CHM1_1127,054,727 - 7,069,431 (+)NCBICHM1_1
Ptpn6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396124,697,670 - 124,715,672 (-)NCBIGRCm39mm39
GRCm39 Ensembl6124,697,670 - 124,715,677 (-)Ensembl
GRCm386124,720,707 - 124,738,709 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6124,720,707 - 124,738,714 (-)EnsemblGRCm38mm10GRCm38
MGSCv376124,670,736 - 124,688,727 (-)NCBIGRCm37mm9NCBIm37
MGSCv366124,686,336 - 124,698,725 (-)NCBImm8
Celera6126,402,447 - 126,420,442 (-)NCBICelera
Cytogenetic Map6F2NCBI
cM Map659.17NCBI
Ptpn6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554134,525,954 - 4,547,177 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554134,525,954 - 4,547,177 (+)NCBIChiLan1.0ChiLan1.0
PTPN6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1126,991,099 - 7,008,830 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl126,991,099 - 7,008,830 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0127,075,879 - 7,093,041 (+)NCBIMhudiblu_PPA_v0panPan3
PTPN6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12738,084,976 - 38,101,552 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2738,084,980 - 38,101,937 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha278,519,708 - 8,531,714 (+)NCBI
ROS_Cfam_1.02738,437,567 - 38,449,584 (-)NCBI
UMICH_Zoey_3.12738,312,457 - 38,324,047 (-)NCBI
UNSW_CanFamBas_1.02738,353,429 - 38,365,020 (-)NCBI
UU_Cfam_GSD_1.0277,998,465 - 8,010,486 (+)NCBI
Ptpn6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945102,196,659 - 102,217,158 (-)NCBI
SpeTri2.0NW_004936709864,206 - 884,630 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PTPN6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl563,762,112 - 63,808,350 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1563,762,109 - 63,779,086 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2566,198,250 - 66,215,843 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PTPN6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1116,977,480 - 6,994,525 (+)NCBI
ChlSab1.1 Ensembl116,984,710 - 6,994,545 (+)Ensembl
Vero_WHO_p1.0NW_0236660631,223,213 - 1,240,430 (-)NCBI
Ptpn6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248603,580,225 - 3,595,403 (+)NCBI

Position Markers
AI411273  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24157,526,457 - 157,526,963 (+)MAPPER
Rnor_6.04157,239,565 - 157,240,070NCBIRnor6.0
Rnor_5.04224,257,161 - 224,257,666UniSTSRnor5.0
RGSC_v3.44160,844,123 - 160,844,628UniSTSRGSC3.4
Celera4146,265,120 - 146,265,625UniSTS
RH 3.4 Map41003.4UniSTS
Cytogenetic Map4q42UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61446Coreg2Compensatory renal growth QTL 23.5kidney mass (VT:0002707)compensatory renal growth score (CMO:0001894)4147274055157294090Rat
61451Ciaa4CIA Autoantibody QTL 43.1blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)4125884464168047091Rat
724535Cm18Cardiac mass QTL 182.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)4117926139162926139Rat
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4131834282176834282Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4136351734180689124Rat
1331759Hrtrt13Heart rate QTL 133.54628heart pumping trait (VT:2000009)heart rate (CMO:0000002)4108876717169215811Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4105971071168047091Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)463537179157286626Rat
631683Bp116Blood pressure QTL 1160.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4123111827168111827Rat
737978Pia23Pristane induced arthritis QTL 235.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131532269168047091Rat
1331802Srn5Serum renin concentration QTL 53.045renin activity (VT:0005581)plasma renin activity level (CMO:0000116)4116726724157291438Rat
1582237Kidm34Kidney mass QTL 3440.0001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)4146942075168998263Rat
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4136351734174694858Rat
631511Pia7Pristane induced arthritis QTL 74.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131532269168047091Rat
1581574Eae20Experimental allergic encephalomyelitis QTL 207.8nervous system integrity trait (VT:0010566)percentage of study population developing experimental autoimmune encephalomyelitis during a period of time (CMO:0001047)4152482121158564471Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4136908430182878540Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)494893247168046938Rat
634342Cia24Collagen induced arthritis QTL 244.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4145373934176509907Rat
634347Hcar8Hepatocarcinoma resistance QTL 85.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)4123478354168478354Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)484475257178931073Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)4137171018182171018Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)47850904182171018Rat
1358364Sradr4Stress Responsive Adrenal Weight QTL 44.92adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)4128602727173602727Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)486438317168047091Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (CMO:0000132)4134917642179917642Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4131864442176864442Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4136351734174694858Rat
61422Cia13Collagen induced arthritis QTL 134.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4132455408168047091Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4145547014184226339Rat
6478720Alc23Alcohol consumption QTL 230.00509drinking behavior trait (VT:0001422)ethanol drink intake rate to body weight ratio (CMO:0001616)4155386197184226339Rat
6478728Anxrr36Anxiety related response QTL 360.01061locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155386197184226339Rat
6478733Anxrr37Anxiety related response QTL 370.00095locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155386197184226339Rat
6478737Anxrr38Anxiety related response QTL 380.00159locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155386197184226339Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4145547014184226339Rat
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4145547014184226339Rat
6478757Anxrr44Anxiety related response QTL 440.01087locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155386197184226339Rat
6478778Anxrr51Anxiety related response QTL 510.25384locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4123587009168587009Rat
6478782Anxrr52Anxiety related response QTL 520.02091locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155386197184226339Rat
6478785Anxrr53Anxiety related response QTL 530.01397locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155386197184226339Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4145547014184226339Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4145547014184226339Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4124442168169442168Rat
10053718Scort25Serum corticosterone level QTL 252.150.0097blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4156855449184226339Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4146497452184226339Rat
10755501Bp390Blood pressure QTL 3902.5arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)423850384169318094Rat
12798519Anxrr54Anxiety related response QTL 542.540.05locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4112807675157807675Rat
12798525Anxrr57Anxiety related response QTL 573.210.05locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4146086918168047091Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:41
Count of miRNA genes:39
Interacting mature miRNAs:41
Transcripts:ENSRNOT00000065416
Prediction methods:Miranda, Rnahybrid
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 1 50 41 19 41 28 19 11
Low 42 7 8 11 74 7 22 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000065416   ⟹   ENSRNOP00000059867
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl4157,239,142 - 157,263,890 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000079947   ⟹   ENSRNOP00000071714
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl4157,239,269 - 157,252,565 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000082739   ⟹   ENSRNOP00000071320
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl4157,239,143 - 157,252,104 (-)Ensembl
RefSeq Acc Id: NM_053908   ⟹   NP_446360
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24157,526,034 - 157,550,783 (-)NCBI
Rnor_6.04157,239,141 - 157,263,890 (-)NCBI
Rnor_5.04224,256,737 - 224,281,486 (-)NCBI
RGSC_v3.44160,843,699 - 160,868,856 (-)RGD
Celera4146,264,696 - 146,289,049 (-)RGD
Sequence:
RefSeq Acc Id: XM_039106947   ⟹   XP_038962875
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24157,526,036 - 157,538,992 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_446360   ⟸   NM_053908
- Sequence:
RefSeq Acc Id: ENSRNOP00000071320   ⟸   ENSRNOT00000082739
RefSeq Acc Id: ENSRNOP00000071714   ⟸   ENSRNOT00000079947
RefSeq Acc Id: ENSRNOP00000059867   ⟸   ENSRNOT00000065416
RefSeq Acc Id: XP_038962875   ⟸   XM_039106947
- Peptide Label: isoform X1
Transcriptome

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

Promoters
RGD ID:13693393
Promoter ID:EPDNEW_R3911
Type:initiation region
Name:Ptpn6_1
Description:protein tyrosine phosphatase, non-receptor type 6
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_6.04157,252,095 - 157,252,155EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
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 (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/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:620660 AgrOrtholog
Ensembl Genes ENSRNOG00000014294 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000059867 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000071320 UniProtKB/TrEMBL
  ENSRNOP00000071714 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000065416 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000079947 UniProtKB/TrEMBL
  ENSRNOT00000082739 UniProtKB/TrEMBL
Gene3D-CATH 3.30.505.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.90.190.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7932620 IMAGE-MGC_LOAD
InterPro Prot-tyrosine_phosphatase-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTPase_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH2_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tyr_Pase_AS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tyr_Pase_cat UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tyr_Pase_non-rcpt_typ-6/11 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TYR_PHOSPHATASE_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:116689 UniProtKB/Swiss-Prot
MGC_CLONE MGC:124580 IMAGE-MGC_LOAD
NCBI Gene 116689 ENTREZGENE
Pfam SH2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Y_phosphatase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PTPN6 RGD
PhenoGen Ptpn6 PhenoGen
PIRSF Tyr-Ptase_nr_6 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PRINTS PRTYPHPHTASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH2DOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE SH2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  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
  SH2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF52799 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF55550 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K064_RAT UniProtKB/TrEMBL
  A0A0G2K163_RAT UniProtKB/TrEMBL
  G3V9T9_RAT UniProtKB/TrEMBL
  P81718 ENTREZGENE, UniProtKB/Swiss-Prot
  Q499N7_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-01-20 Ptpn6  protein tyrosine phosphatase, non-receptor type 6  Ptph6    Symbol updated 1299863 APPROVED
2002-08-07 Ptph6  protein tyrosine phosphatase, non-receptor type 6      Symbol and Name status set to provisional 70820 PROVISIONAL