Human Gene PTPN13 (uc003hqc.1) Description and Page Index
  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 chr4:87,689,667-87,726,522 Size: 36,856 Total Exon Count: 16 Strand: +
Coding Region
   Position: hg19 chr4:87,692,423-87,726,521 Size: 34,099 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr4:87,689,667-87,726,522)mRNA (may differ from genome)Protein (614 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
PubMedStanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
DESCRIPTION: SubName: Full=Putative uncharacterized protein DKFZp686J1497; Flags: Fragment;
SIMILARITY: Contains 3 PDZ (DHR) domains.

-  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
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-  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
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-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -405.311668-0.243 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
IPR001478 - PDZ

Pfam Domains:
PF00595 - PDZ domain (Also known as DHR or GLGF)

SCOP Domains:
50156 - PDZ domain-like
52799 - (Phosphotyrosine protein) phosphatases II

ModBase Predicted Comparative 3D Structure on Q6AWB9
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     

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004725 protein tyrosine phosphatase activity

Biological Process:
GO:0006470 protein dephosphorylation
GO:0035335 peptidyl-tyrosine dephosphorylation

-  Descriptions from all associated GenBank mRNAs
  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.
BX647553 - Homo sapiens mRNA; cDNA DKFZp686J1497 (from clone DKFZp686J1497).
MA765599 - JP 2017514519-A/165: Small ncRNAs as biomarkers.

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

-  Other Names for This Gene
  Alternate Gene Symbols: BX647553, DKFZp686J1497, NM_080684, NP_542415, Q6AWB9, Q6AWB9_HUMAN
UCSC ID: uc003hqc.1
RefSeq Accession: NM_080684
Protein: Q6AWB9

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: BX647553.1
exon count: 16CDS single in 3' UTR: no RNA size: 3487
ORF size: 1842CDS single in intron: no Alignment % ID: 99.91
txCdsPredict score: 3101.50frame shift in genome: no % Coverage: 99.48
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: no retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 1255# 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.