Human Gene PTPN6 (ENST00000318974.14_8) from GENCODE V47lift37
  Description: protein tyrosine phosphatase non-receptor type 6, transcript variant 1 (from RefSeq NM_002831.6)
Gencode Transcript: ENST00000318974.14_8
Gencode Gene: ENSG00000111679.17_12
Transcript (Including UTRs)
   Position: hg19 chr12:7,060,519-7,070,479 Size: 9,961 Total Exon Count: 16 Strand: +
Coding Region
   Position: hg19 chr12:7,060,676-7,070,083 Size: 9,408 Coding Exon Count: 15 

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 (chr12:7,060,519-7,070,479)mRNA (may differ from genome)Protein (595 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PTN6_HUMAN
DESCRIPTION: RecName: Full=Tyrosine-protein phosphatase non-receptor type 6; EC=3.1.3.48; AltName: Full=Hematopoietic cell protein-tyrosine phosphatase; AltName: Full=Protein-tyrosine phosphatase 1C; Short=PTP-1C; AltName: Full=Protein-tyrosine phosphatase SHP-1; AltName: Full=SH-PTP1;
FUNCTION: Modulates signaling by tyrosine phosphorylated cell surface receptors such as KIT and the EGF receptor/EGFR. The SH2 regions may interact with other cellular components to modulate its own phosphatase activity against interacting substrates. Together with MTUS1, induces UBE2V2 expression upon angiotensin II stimulation. Plays a key role in hematopoiesis.
CATALYTIC ACTIVITY: Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate.
SUBUNIT: Monomer. Interacts with MTUS1 (By similarity). Interacts with MILR1 (tyrosine-phosphorylated). Interacts with KIT (By similarity). Binds PTPNS1, LILRB1 and LILRB2. Interacts with FCRL2, FCRL3, FCRL4, CD300LF, CDK2 and CD84. Interacts with KIR2DL1; the interaction is enhanced by ARRB2. Interacts (via SH2 1 domain) with ROS1; the interaction is direct and promotes ROS1 dephosphorylation. Interacts with EGFR; inhibits EGFR-dependent activation of MAPK/ERK. Interacts with LYN. Interacts with the tyrosine phosphorylated form of PDPK1.
INTERACTION: P20273:CD22; NbExp=4; IntAct=EBI-78260, EBI-78277; P11049:CD37; NbExp=4; IntAct=EBI-78260, EBI-6139068; Q9UKJ1:PILRA; NbExp=5; IntAct=EBI-78260, EBI-965833;
SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Note=In neurons, translocates into the nucleus after treatment with angiotensin II (By similarity). Shuttles between the cytoplasm and nucleus via its association with PDPK1.
TISSUE SPECIFICITY: Isoform 1 is expressed in hematopoietic cells. Isoform 2 is expressed in non-hematopoietic cells.
DOMAIN: The N-terminal SH2 domain functions as an auto-inhibitory domain, blocking the catalytic domain in the ligand-free close conformation.
PTM: Phosphorylated on tyrosine residues. Binding of KITLG/SCF to KIT increases tyrosine phosphorylation (By similarity). Phosphorylation at Tyr-564 enhances phosphatase activity.
SIMILARITY: Belongs to the protein-tyrosine phosphatase family. Non-receptor class 2 subfamily.
SIMILARITY: Contains 2 SH2 domains.
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: PTPN6
Diseases sorted by gene-association score: cd45 deficiency (21)

-  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: 188.86 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 769.83 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 -64.60157-0.411 Picture PostScript Text
3' UTR -56.70216-0.263 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
IPR000980 - SH2
IPR000387 - Tyr/Dual-specificity_Pase
IPR016130 - Tyr_Pase_AS
IPR012152 - Tyr_Pase_non-rcpt_typ-6/11
IPR000242 - Tyr_Pase_rcpt/non-rcpt

Pfam Domains:
PF00017 - SH2 domain
PF00102 - Protein-tyrosine phosphatase

SCOP Domains:
52799 - (Phosphotyrosine protein) phosphatases II
55550 - SH2 domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1FPR - X-ray MuPIT 1GWZ - X-ray MuPIT 1X6C - NMR MuPIT 2B3O - X-ray MuPIT 2RMX - NMR MuPIT 2YU7 - NMR MuPIT 3PS5 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P29350
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    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001784 phosphotyrosine binding
GO:0004721 phosphoprotein phosphatase activity
GO:0004725 protein tyrosine phosphatase activity
GO:0005001 transmembrane receptor protein tyrosine phosphatase activity
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0016791 phosphatase activity
GO:0017124 SH3 domain binding
GO:0019901 protein kinase binding
GO:0042169 SH2 domain binding
GO:0050839 cell adhesion molecule binding

Biological Process:
GO:0002244 hematopoietic progenitor cell differentiation
GO:0002924 negative regulation of humoral immune response mediated by circulating immunoglobulin
GO:0006470 protein dephosphorylation
GO:0006915 apoptotic process
GO:0007186 G-protein coupled receptor signaling pathway
GO:0008283 cell proliferation
GO:0008284 positive regulation of cell proliferation
GO:0008285 negative regulation of cell proliferation
GO:0014068 positive regulation of phosphatidylinositol 3-kinase signaling
GO:0016311 dephosphorylation
GO:0018108 peptidyl-tyrosine phosphorylation
GO:0019221 cytokine-mediated signaling pathway
GO:0030154 cell differentiation
GO:0030168 platelet activation
GO:0030220 platelet formation
GO:0031295 T cell costimulation
GO:0033277 abortive mitotic cell cycle
GO:0033630 positive regulation of cell adhesion mediated by integrin
GO:0035335 peptidyl-tyrosine dephosphorylation
GO:0035556 intracellular signal transduction
GO:0035855 megakaryocyte development
GO:0042130 negative regulation of T cell proliferation
GO:0042267 natural killer cell mediated cytotoxicity
GO:0043312 neutrophil degranulation
GO:0043407 negative regulation of MAP kinase activity
GO:0043409 negative regulation of MAPK cascade
GO:0045577 regulation of B cell differentiation
GO:0050732 negative regulation of peptidyl-tyrosine phosphorylation
GO:0050853 B cell receptor signaling pathway
GO:0050859 negative regulation of B cell receptor signaling pathway
GO:0050860 negative regulation of T cell receptor signaling pathway
GO:0050900 leukocyte migration
GO:0051279 regulation of release of sequestered calcium ion into cytosol
GO:0060338 regulation of type I interferon-mediated signaling pathway
GO:0070372 regulation of ERK1 and ERK2 cascade
GO:0070527 platelet aggregation
GO:0071345 cellular response to cytokine stimulus
GO:2000045 regulation of G1/S transition of mitotic cell cycle

Cellular Component:
GO:0005576 extracellular region
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005911 cell-cell junction
GO:0016020 membrane
GO:0032991 macromolecular complex
GO:0035580 specific granule lumen
GO:0042105 alpha-beta T cell receptor complex
GO:0070062 extracellular exosome
GO:1904724 tertiary granule lumen


-  Descriptions from all associated GenBank mRNAs
  LF207386 - JP 2014500723-A/14889: Polycomb-Associated Non-Coding RNAs.
AK313379 - Homo sapiens cDNA, FLJ93911, Homo sapiens protein tyrosine phosphatase, non-receptor type 6 (PTPN6), transcript variant 2, mRNA.
BC002523 - Homo sapiens protein tyrosine phosphatase, non-receptor type 6, mRNA (cDNA clone MGC:2332 IMAGE:3140265), complete cds.
BC007667 - Homo sapiens protein tyrosine phosphatase, non-receptor type 6, mRNA (cDNA clone MGC:2331 IMAGE:3138804), complete cds.
X62055 - H.sapiens PTP1C mRNA for protein-tyrosine phosphatase 1C.
AK300167 - Homo sapiens cDNA FLJ59423 complete cds, highly similar to Tyrosine-protein phosphatase non-receptor type6 (EC 3.1.3.48).
CU675749 - Synthetic construct Homo sapiens gateway clone IMAGE:100020369 5' read PTPN6 mRNA.
AB590143 - Synthetic construct DNA, clone: pFN21AE1329, Homo sapiens PTPN6 gene for protein tyrosine phosphatase, non-receptor type 6, without stop codon, in Flexi system.
BT007390 - Homo sapiens protein tyrosine phosphatase, non-receptor type 6 mRNA, complete cds.
DQ891946 - Synthetic construct clone IMAGE:100004576; FLH181669.01X; RZPDo839F11136D protein tyrosine phosphatase, non-receptor type 6 (PTPN6) gene, encodes complete protein.
DQ895133 - Synthetic construct Homo sapiens clone IMAGE:100009593; FLH181665.01L; RZPDo839F11135D protein tyrosine phosphatase, non-receptor type 6 (PTPN6) gene, encodes complete protein.
KJ891948 - Synthetic construct Homo sapiens clone ccsbBroadEn_01342 PTPN6 gene, encodes complete protein.
AK308230 - Homo sapiens cDNA, FLJ98178.
AK298470 - Homo sapiens cDNA FLJ60320 complete cds, highly similar to Tyrosine-protein phosphatase non-receptor type6 (EC 3.1.3.48).
JD497042 - Sequence 478066 from Patent EP1572962.
JD187127 - Sequence 168151 from Patent EP1572962.
M77273 - Human tyrosine phosphatase mRNA, complete cds.
AK223629 - Homo sapiens mRNA for protein tyrosine phosphatase, non-receptor type 6 isoform 1 variant, clone: FCC135A04.
AK290421 - Homo sapiens cDNA FLJ77053 complete cds, highly similar to Homo sapiens protein tyrosine phosphatase, non-receptor type 6 (PTPN6), transcript variant 1, mRNA.
JD394802 - Sequence 375826 from Patent EP1572962.
AK309037 - Homo sapiens cDNA, FLJ99078.
M74903 - Human hematopoietic cell phosphatase mRNA, complete cds.
JD422773 - Sequence 403797 from Patent EP1572962.
JD399491 - Sequence 380515 from Patent EP1572962.
AF178946 - Homo sapiens 70 kDa SHP-1L protein mRNA, complete cds.
DL492187 - Novel nucleic acids.
LF365808 - JP 2014500723-A/173311: Polycomb-Associated Non-Coding RNAs.
LF365807 - JP 2014500723-A/173310: Polycomb-Associated Non-Coding RNAs.
JD042499 - Sequence 23523 from Patent EP1572962.
JD168599 - Sequence 149623 from Patent EP1572962.
JD370336 - Sequence 351360 from Patent EP1572962.
JD172680 - Sequence 153704 from Patent EP1572962.
JD450352 - Sequence 431376 from Patent EP1572962.
JD220973 - Sequence 201997 from Patent EP1572962.
LF365805 - JP 2014500723-A/173308: Polycomb-Associated Non-Coding RNAs.
LF365804 - JP 2014500723-A/173307: Polycomb-Associated Non-Coding RNAs.
JD456937 - Sequence 437961 from Patent EP1572962.
JD455385 - Sequence 436409 from Patent EP1572962.
MA601385 - JP 2018138019-A/173311: Polycomb-Associated Non-Coding RNAs.
MA601384 - JP 2018138019-A/173310: Polycomb-Associated Non-Coding RNAs.
MA601382 - JP 2018138019-A/173308: Polycomb-Associated Non-Coding RNAs.
MA601381 - JP 2018138019-A/173307: Polycomb-Associated Non-Coding RNAs.
MA442963 - JP 2018138019-A/14889: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_epoPathway - EPO Signaling Pathway
h_ghPathway - Growth Hormone Signaling Pathway
h_il2rbPathway - IL-2 Receptor Beta Chain in T cell Activation
h_il3Pathway - IL 3 signaling pathway
h_nkcellsPathway - Ras-Independent pathway in NK cell-mediated cytotoxicity

Reactome (by CSHL, EBI, and GO)

Protein P29350 (Reactome details) participates in the following event(s):

R-HSA-205306 Interaction of SHP1 and KIT
R-HSA-210277 Interaction of PECAM-1 and SHP-1
R-HSA-1168839 SHP1 (PTPN6) binds JAK2 in the receptor complex
R-HSA-5690701 SHP1 binds p-CD22
R-HSA-913424 The SHC1:SHIP1 complex is stabilized by GRB2
R-HSA-1169188 SHP1 (PTPN6) dephosphorylates JAK2
R-HSA-389759 Interaction of SHP-1 or SHP-2 with phospho PD-1
R-HSA-389941 SHP-1 and SHP-2 bind pBTLA
R-HSA-391150 p-4Y-SIRPA:CD47 binds PTPN6,PTPN11
R-HSA-909738 SHP1 and SHP2 bind the common beta chain
R-HSA-5684169 G6B binds PTPN6,PTPN11
R-HSA-997314 Dephosphorylation of JAK1 by SHP1
R-HSA-6798749 Exocytosis of specific granule lumen proteins
R-HSA-6798745 Exocytosis of tertiary granule lumen proteins
R-HSA-914036 SHP1 and SHP2 dephosphorylate Y628 of IL3RB
R-HSA-877308 Dephosphorylation of JAKs by PTPs
R-HSA-389758 Dephosphorylation of CD3-zeta by PD-1 bound phosphatases
R-HSA-1433559 Regulation of KIT signaling
R-HSA-210990 PECAM1 interactions
R-HSA-432142 Platelet sensitization by LDL
R-HSA-982772 Growth hormone receptor signaling
R-HSA-5690714 CD22 mediated BCR regulation
R-HSA-912526 Interleukin receptor SHC signaling
R-HSA-389948 PD-1 signaling
R-HSA-388841 Costimulation by the CD28 family
R-HSA-391160 Signal regulatory protein family interactions
R-HSA-512988 Interleukin-3, 5 and GM-CSF signaling
R-HSA-114604 GPVI-mediated activation cascade
R-HSA-1433557 Signaling by SCF-KIT
R-HSA-202733 Cell surface interactions at the vascular wall
R-HSA-418346 Platelet homeostasis
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-983705 Signaling by the B Cell Receptor (BCR)
R-HSA-912694 Regulation of IFNA signaling
R-HSA-6798695 Neutrophil degranulation
R-HSA-9008059 Interleukin-37 signaling
R-HSA-451927 Interleukin-2 family signaling
R-HSA-1280218 Adaptive Immune System
R-HSA-1500931 Cell-Cell communication
R-HSA-449147 Signaling by Interleukins
R-HSA-76002 Platelet activation, signaling and aggregation
R-HSA-877312 Regulation of IFNG signaling
R-HSA-9006934 Signaling by Receptor Tyrosine Kinases
R-HSA-109582 Hemostasis
R-HSA-168256 Immune System
R-HSA-909733 Interferon alpha/beta signaling
R-HSA-168249 Innate Immune System
R-HSA-446652 Interleukin-1 family signaling
R-HSA-877300 Interferon gamma signaling
R-HSA-162582 Signal Transduction
R-HSA-913531 Interferon Signaling

-  Other Names for This Gene
  Alternate Gene Symbols: A8K306, ENST00000318974.1, ENST00000318974.10, ENST00000318974.11, ENST00000318974.12, ENST00000318974.13, ENST00000318974.2, ENST00000318974.3, ENST00000318974.4, ENST00000318974.5, ENST00000318974.6, ENST00000318974.7, ENST00000318974.8, ENST00000318974.9, G3V0F8, HCP, NM_002831, P29350, PTN6_HUMAN, PTP1C, Q969V8, Q9UK67, uc317qoj.1, uc317qoj.2
UCSC ID: ENST00000318974.14_8
RefSeq Accession: NM_002831.6
Protein: P29350 (aka PTN6_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.