Human Gene PTPN13 (uc003hqb.3)
  Description: Homo sapiens protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase) (PTPN13), transcript variant 3, mRNA.
RefSeq Summary (NM_080684): The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This PTP is a large intracellular protein. It has a catalytic PTP domain at its C-terminus and two major structural domains: a region with five PDZ domains and a FERM domain that binds to plasma membrane and cytoskeletal elements. This PTP was found to interact with, and dephosphorylate, Fas receptor and IkappaBalpha through the PDZ domains. This suggests it has a role in Fas mediated programmed cell death. This PTP was also shown to interact with GTPase-activating protein, and thus may function as a regulator of Rho signaling pathways. Four alternatively spliced transcript variants, which encode distinct proteins, have been reported. [provided by RefSeq, Oct 2008].
Transcript (Including UTRs)
   Position: hg19 chr4:87,515,468-87,736,328 Size: 220,861 Total Exon Count: 45 Strand: +
Coding Region
   Position: hg19 chr4:87,556,410-87,735,704 Size: 179,295 Coding Exon Count: 44 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:87,515,468-87,736,328)mRNA (may differ from genome)Protein (2294 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMalacardsMGI
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PTPN13
CDC HuGE Published Literature: PTPN13
Positive Disease Associations: Tunica Media
Related Studies:
  1. Tunica Media
    , , . [PubMed 0]
  2. Tunica Media
    , , . [PubMed 0]
  3. Tunica Media
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: PTPN13
Diseases sorted by gene-association score: amyloidosis, hereditary, transthyretin-related (6), tropical spastic paraparesis (6), colorectal cancer (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  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: 22.12 RPKM in Skin - Not Sun Exposed (Suprapubic)
Total median expression: 333.24 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 -246.20480-0.513 Picture PostScript Text
3' UTR -128.92624-0.207 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
  Pfam Domains:
PF00102 - Protein-tyrosine phosphatase
PF00373 - FERM central domain
PF00595 - PDZ domain (Also known as DHR or GLGF)
PF09379 - FERM N-terminal domain
PF09380 - FERM C-terminal PH-like domain
PF16599 - Unstructured linker region on PTN13 protein between PDZ

SCOP Domains:
47031 - Second domain of FERM
101690 - PAZ domain
50156 - PDZ domain-like
50729 - PH domain-like
52799 - (Phosphotyrosine protein) phosphatases II
54236 - Ubiquitin-like

ModBase Predicted Comparative 3D Structure on Q12923-2
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 Details     
Gene Sorter     
      
      
      

-  Descriptions from all associated GenBank mRNAs
  AK056151 - Homo sapiens cDNA FLJ31589 fis, clone NT2RI2002266, highly similar to Protein tyrosine phosphatase (PTP-BAS, type 1).
BC139915 - Homo sapiens cDNA clone IMAGE:40148027.
X80289 - H.sapiens PTPL1 mRNA for protein tyrosine phosphatase.
D21209 - Homo sapiens PTP-BAS mRNA for protein tyrosine phosphatase type 1, complete cds.
D21210 - Homo sapiens PTP-BAS mRNA for protein tyrosine phosphatase type 2, complete cds.
D21211 - Homo sapiens PTP-BAS mRNA for protein tyrosine phosphatase type 3, complete cds.
U12128 - Human protein tyrosine phosphatase 1E (PTP1E) mRNA, complete cds.
BC140777 - Homo sapiens protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase), mRNA (cDNA clone MGC:176454 IMAGE:9021645), complete cds.
BC144520 - Homo sapiens cDNA clone IMAGE:9053047, containing frame-shift errors.
AB208904 - Homo sapiens mRNA for protein tyrosine phosphatase, non-receptor type 13 isoform 2 variant protein.
X79676 - H.sapiens PNP1 mRNA.
L34583 - Homo sapiens (clone HFAP10) tyrosine phosphatase mRNA, partial cds.
AF233323 - Homo sapiens Fas-associated phosphatase-1 mRNA, partial cds.
BC039610 - Homo sapiens protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase), mRNA (cDNA clone IMAGE:5495336), partial cds.
U12132 - Human protein-tyrosine phosphatase (hPTP1E) mRNA, 5' UTR.
U12129 - Human protein-tyrosine phosphatase (hPTP1E) mRNA, 5'UTR sequence.
U12130 - Human protein-tyrosine phosphatase (hPTP1E) mRNA, 5'UTR sequence.
U12131 - Human protein-tyrosine phosphatase (hPTP1E) mRNA, 5'UTR sequence.
JD384896 - Sequence 365920 from Patent EP1572962.
BX647553 - Homo sapiens mRNA; cDNA DKFZp686J1497 (from clone DKFZp686J1497).
JD187269 - Sequence 168293 from Patent EP1572962.
JD149156 - Sequence 130180 from Patent EP1572962.
JD383055 - Sequence 364079 from Patent EP1572962.
JD383056 - Sequence 364080 from Patent EP1572962.
JD064845 - Sequence 45869 from Patent EP1572962.
JD448824 - Sequence 429848 from Patent EP1572962.
JD504454 - Sequence 485478 from Patent EP1572962.
JD361728 - Sequence 342752 from Patent EP1572962.
JD237701 - Sequence 218725 from Patent EP1572962.
JD359296 - Sequence 340320 from Patent EP1572962.
JD528253 - Sequence 509277 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_fasPathway - FAS signaling pathway ( CD95 )

Reactome (by CSHL, EBI, and GO)

Protein Q12923 (Reactome details) participates in the following event(s):

R-HSA-8870332 PTPN13:PLEKHA1,2 bind PI(3,4)P2
R-HSA-9008059 Interleukin-37 signaling
R-HSA-1660499 Synthesis of PIPs at the plasma membrane
R-HSA-446652 Interleukin-1 family signaling
R-HSA-1483255 PI Metabolism
R-HSA-449147 Signaling by Interleukins
R-HSA-1483257 Phospholipid metabolism
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-556833 Metabolism of lipids
R-HSA-168256 Immune System
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: NM_080684, NP_542415, PNP1, PTP1E, PTPL1, Q12923-2
UCSC ID: uc003hqb.3
RefSeq Accession: NM_080684
Protein: Q12923-2, splice isoform of Q12923 CCDS: CCDS47096.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_080684.2
exon count: 45CDS single in 3' UTR: no RNA size: 8000
ORF size: 6885CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 10316.00frame shift in genome: no % Coverage: 99.86
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.