Human Gene PTPN2 (ENST00000309660.10_12) from GENCODE V47lift37
  Description: protein tyrosine phosphatase non-receptor type 2, transcript variant 1 (from RefSeq NM_002828.4)
Gencode Transcript: ENST00000309660.10_12
Gencode Gene: ENSG00000175354.20_16
Transcript (Including UTRs)
   Position: hg19 chr18:12,792,151-12,884,236 Size: 92,086 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg19 chr18:12,794,277-12,884,140 Size: 89,864 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr18:12,792,151-12,884,236)mRNA (may differ from genome)Protein (415 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PTN2_HUMAN
DESCRIPTION: RecName: Full=Tyrosine-protein phosphatase non-receptor type 2; EC=3.1.3.48; AltName: Full=T-cell protein-tyrosine phosphatase; Short=TCPTP;
CATALYTIC ACTIVITY: Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate.
SUBUNIT: Interacts with FAM82A2. Isoform PTPB interacts with TMED9.
INTERACTION: P10912:GHR; NbExp=8; IntAct=EBI-984930, EBI-286316; P49755:TMED10; NbExp=5; IntAct=EBI-4409481, EBI-998422; Q9BVK6:TMED9; NbExp=5; IntAct=EBI-4409481, EBI-1056827;
SUBCELLULAR LOCATION: Cytoplasm.
SUBCELLULAR LOCATION: Isoform PTPB: Endoplasmic reticulum.
SUBCELLULAR LOCATION: Isoform PTPA: Nucleus.
TISSUE SPECIFICITY: Isoform PTPA is probably the major isoform. Isoform PTPB is expressed in T-cells and in placenta.
SIMILARITY: Belongs to the protein-tyrosine phosphatase family. Non-receptor class 1 subfamily.
SIMILARITY: Contains 1 tyrosine-protein phosphatase domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: PTPN2
Diseases sorted by gene-association score: rheumatoid factor-negative juvenile idiopathic arthritis* (25), oligoarticular juvenile idiopathic arthritis* (10), anonychia congenita (7), bubonic plague (6)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 11.14 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 244.14 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -43.3096-0.451 Picture PostScript Text
3' UTR -557.202126-0.262 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000387 - Tyr/Dual-specificity_Pase
IPR016130 - Tyr_Pase_AS
IPR012265 - Tyr_Pase_non-rcpt_typ-1/2
IPR000242 - Tyr_Pase_rcpt/non-rcpt

Pfam Domains:
PF00102 - Protein-tyrosine phosphatase

SCOP Domains:
52799 - (Phosphotyrosine protein) phosphatases II

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1L8K - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P17706
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004721 phosphoprotein phosphatase activity
GO:0004725 protein tyrosine phosphatase activity
GO:0004726 non-membrane spanning protein tyrosine phosphatase activity
GO:0005178 integrin binding
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0016791 phosphatase activity
GO:0019901 protein kinase binding
GO:0019905 syntaxin binding
GO:0030971 receptor tyrosine kinase binding
GO:0097677 STAT family protein binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006470 protein dephosphorylation
GO:0008285 negative regulation of cell proliferation
GO:0008286 insulin receptor signaling pathway
GO:0010804 negative regulation of tumor necrosis factor-mediated signaling pathway
GO:0010888 negative regulation of lipid storage
GO:0016311 dephosphorylation
GO:0030183 B cell differentiation
GO:0030217 T cell differentiation
GO:0030218 erythrocyte differentiation
GO:0035335 peptidyl-tyrosine dephosphorylation
GO:0042059 negative regulation of epidermal growth factor receptor signaling pathway
GO:0042532 negative regulation of tyrosine phosphorylation of STAT protein
GO:0042593 glucose homeostasis
GO:0045650 negative regulation of macrophage differentiation
GO:0045722 positive regulation of gluconeogenesis
GO:0046627 negative regulation of insulin receptor signaling pathway
GO:0050728 negative regulation of inflammatory response
GO:0050860 negative regulation of T cell receptor signaling pathway
GO:0050922 negative regulation of chemotaxis
GO:0060334 regulation of interferon-gamma-mediated signaling pathway
GO:0060336 negative regulation of interferon-gamma-mediated signaling pathway
GO:0060339 negative regulation of type I interferon-mediated signaling pathway
GO:0061099 negative regulation of protein tyrosine kinase activity
GO:0070104 negative regulation of interleukin-6-mediated signaling pathway
GO:0070373 negative regulation of ERK1 and ERK2 cascade
GO:0071345 cellular response to cytokine stimulus
GO:1902202 regulation of hepatocyte growth factor receptor signaling pathway
GO:1902206 negative regulation of interleukin-2-mediated signaling pathway
GO:1902215 negative regulation of interleukin-4-mediated signaling pathway
GO:1902227 negative regulation of macrophage colony-stimulating factor signaling pathway
GO:1902233 negative regulation of positive thymic T cell selection
GO:1902237 positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway
GO:1903899 positive regulation of PERK-mediated unfolded protein response
GO:2000587 negative regulation of platelet-derived growth factor receptor-beta signaling pathway

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005793 endoplasmic reticulum-Golgi intermediate compartment
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  AK290649 - Homo sapiens cDNA FLJ77075 complete cds, highly similar to Homo sapiens protein tyrosine phosphatase, non-receptor type 2 (PTPN2), transcript variant 2, mRNA.
LF385256 - JP 2014500723-A/192759: Polycomb-Associated Non-Coding RNAs.
BC008244 - Homo sapiens protein tyrosine phosphatase, non-receptor type 2, mRNA (cDNA clone MGC:9389 IMAGE:3872164), complete cds.
AK225706 - Homo sapiens mRNA for protein tyrosine phosphatase, non-receptor type 2 isoform 2 variant, clone: TMS01102.
BC016727 - Homo sapiens protein tyrosine phosphatase, non-receptor type 2, mRNA (cDNA clone MGC:24459 IMAGE:4081330), complete cds.
HQ447463 - Synthetic construct Homo sapiens clone IMAGE:100070792; CCSB015047_02 protein tyrosine phosphatase, non-receptor type 2 (PTPN2) gene, encodes complete protein.
JF432521 - Synthetic construct Homo sapiens clone IMAGE:100073743 protein tyrosine phosphatase, non-receptor type 2 (PTPN2) gene, encodes complete protein.
KJ891946 - Synthetic construct Homo sapiens clone ccsbBroadEn_01340 PTPN2 gene, encodes complete protein.
KJ905884 - Synthetic construct Homo sapiens clone ccsbBroadEn_15554 PTPN2 gene, encodes complete protein.
M25393 - Human protein tyrosine phosphatase (PTPase) mRNA, complete cds.
AK292570 - Homo sapiens cDNA FLJ75808 complete cds, highly similar to Homo sapiens protein tyrosine phosphatase, non-receptor type 2 (PTPN2), transcript variant 1, mRNA.
AB590517 - Synthetic construct DNA, clone: pFN21AE0933, Homo sapiens PTPN2 gene for protein tyrosine phosphatase, non-receptor type 2, without stop codon, in Flexi system.
CU678897 - Synthetic construct Homo sapiens gateway clone IMAGE:100022635 5' read PTPN2 mRNA.
MA620833 - JP 2018138019-A/192759: Polycomb-Associated Non-Coding RNAs.
M80737 - Human cytoplasmic phosphotyrosine phosphatase mRNA.
M81478 - Human cytoplasmic phosphtyrosine phosphatase mRNA.
AB209569 - Homo sapiens mRNA for protein tyrosine phosphatase, non-receptor type 2 isoform 1 variant protein.
JD058312 - Sequence 39336 from Patent EP1572962.
JD144145 - Sequence 125169 from Patent EP1572962.
JD404867 - Sequence 385891 from Patent EP1572962.
JD536185 - Sequence 517209 from Patent EP1572962.
JD100925 - Sequence 81949 from Patent EP1572962.
JD140128 - Sequence 121152 from Patent EP1572962.
JD538348 - Sequence 519372 from Patent EP1572962.
JD112401 - Sequence 93425 from Patent EP1572962.
JD144662 - Sequence 125686 from Patent EP1572962.
JD542817 - Sequence 523841 from Patent EP1572962.
JD542819 - Sequence 523843 from Patent EP1572962.
JD212799 - Sequence 193823 from Patent EP1572962.
JD542816 - Sequence 523840 from Patent EP1572962.
JD376047 - Sequence 357071 from Patent EP1572962.
JD497752 - Sequence 478776 from Patent EP1572962.
JD142554 - Sequence 123578 from Patent EP1572962.
JD222900 - Sequence 203924 from Patent EP1572962.
JD112400 - Sequence 93424 from Patent EP1572962.
JD222899 - Sequence 203923 from Patent EP1572962.
JD089526 - Sequence 70550 from Patent EP1572962.
JD112075 - Sequence 93099 from Patent EP1572962.
JD511531 - Sequence 492555 from Patent EP1572962.
JD491637 - Sequence 472661 from Patent EP1572962.
DQ572286 - Homo sapiens piRNA piR-40398, complete sequence.
LF343838 - JP 2014500723-A/151341: Polycomb-Associated Non-Coding RNAs.
JD280506 - Sequence 261530 from Patent EP1572962.
JD313053 - Sequence 294077 from Patent EP1572962.
JD091827 - Sequence 72851 from Patent EP1572962.
JD359512 - Sequence 340536 from Patent EP1572962.
JD185247 - Sequence 166271 from Patent EP1572962.
JD352611 - Sequence 333635 from Patent EP1572962.
LF343839 - JP 2014500723-A/151342: Polycomb-Associated Non-Coding RNAs.
LF343840 - JP 2014500723-A/151343: Polycomb-Associated Non-Coding RNAs.
LF343841 - JP 2014500723-A/151344: Polycomb-Associated Non-Coding RNAs.
LF343842 - JP 2014500723-A/151345: Polycomb-Associated Non-Coding RNAs.
MA579415 - JP 2018138019-A/151341: Polycomb-Associated Non-Coding RNAs.
MA579416 - JP 2018138019-A/151342: Polycomb-Associated Non-Coding RNAs.
MA579417 - JP 2018138019-A/151343: Polycomb-Associated Non-Coding RNAs.
MA579418 - JP 2018138019-A/151344: Polycomb-Associated Non-Coding RNAs.
MA579419 - JP 2018138019-A/151345: Polycomb-Associated Non-Coding RNAs.
LF343845 - JP 2014500723-A/151348: Polycomb-Associated Non-Coding RNAs.
MA579422 - JP 2018138019-A/151348: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P17706 (Reactome details) participates in the following event(s):

R-HSA-6807027 PTPN1 and PTPN2 dephosphorylate MET
R-HSA-9008059 Interleukin-37 signaling
R-HSA-6807004 Negative regulation of MET activity
R-HSA-446652 Interleukin-1 family signaling
R-HSA-6806834 Signaling by MET
R-HSA-449147 Signaling by Interleukins
R-HSA-9006934 Signaling by Receptor Tyrosine Kinases
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-162582 Signal Transduction
R-HSA-168256 Immune System
R-HSA-997326 Dephosphorylation of p-STAT1 dimer by nuclear isoform of TCPTP
R-HSA-877312 Regulation of IFNG signaling
R-HSA-877300 Interferon gamma signaling
R-HSA-913531 Interferon Signaling
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: A8K955, A8MXU3, ENST00000309660.1, ENST00000309660.2, ENST00000309660.3, ENST00000309660.4, ENST00000309660.5, ENST00000309660.6, ENST00000309660.7, ENST00000309660.8, ENST00000309660.9, K7ENG3, NM_002828, P17706, PTN2_HUMAN, PTPT, Q96AU5, Q96HR2, uc317ooo.1, uc317ooo.2
UCSC ID: ENST00000309660.10_12
RefSeq Accession: NM_002828.4
Protein: P17706 (aka PTN2_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.