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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

PTPN20A Gene

protein-coding   GIFtS: 40
GCID: GC10M046550

protein tyrosine phosphatase, non-receptor type 20A

  Search for PTPN20A
in our new
 Human Malady Compendium 
Biological research products
for PTPN20A
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Protein Tyrosine Phosphatase, Non-Receptor Type 20A1 2     EC 3.1.3.483 8
CT1261 2     PTPN20B2
BA142I17.11     Cancer/Testis Antigen 1262
HPTPN201     Tyrosine-Protein Phosphatase Non-Receptor Type 202

External Ids:    HGNC: 234221   Entrez Gene: 6531292   Ensembl: ENSG000002041797   OMIM: 6106305   UniProtKB: Q4JDL33   

Export aliases for PTPN20A gene to outside databases

Previous GC identifers: GC10U900462 GC10M045970 GC10M043492


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for PTPN20A:
The product of this gene belongs to the family of classical tyrosine-specific protein tyrosine phosphatases. Many
protein tyrosine phosphatases have been shown to regulate fundamental cellular processes and several are mutated in
human diseases. Chromosome 10q contains a segmental duplication resulting in multiple copies of the protein tyrosine
phosphatase, non-receptor type 20 gene. The two nearly identical copies are designated as PTPN20A and PTPN20B. A third
copy is only partially duplicated and contains a pseudogene, designated as PTPN20C. This gene encodes the more
centromeric copy, PTPN20A. Multiple alternatively spliced transcript variants encoding different isoforms have been
identified. (provided by RefSeq, Jul 2008)

UniProtKB/Swiss-Prot: PTN20_HUMAN, Q4JDL3
Function: Tyrosine-protein phosphatase targeted to sites of actin polymerization in response of varied extracellular
stimuli. Has tyrosine phosphatase activity towards various tyrosyl phosphorylated substrates




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000010.10  NC_018921.1  NT_031847.8  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the PTPN20A gene promoter:
         MEF-2A   GR   AML1a   FOXC1   MEF-2   aMEF-2   GR-alpha   FOXL1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPTPN20A promoter sequence
   Search SABiosciences Chromatin IP Primers for PTPN20A

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PTPN20A


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 10q11.22   Ensembl cytogenetic band:  10q11.22   HGNC cytogenetic band: 10q11.22

PTPN20A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PTPN20A gene location

GeneLoc information about chromosome 10         GeneLoc Exon Structure

GeneLoc location for GC10M046550:  view genomic region     (about GC identifiers)

Start:
46,549,955 bp from pter      End:
46,641,045 bp from pter
Size:
91,091 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: PTN20_HUMAN, Q4JDL3 (See protein sequence)
Recommended Name: Tyrosine-protein phosphatase non-receptor type 20  
Size: 420 amino acids; 48423 Da
Subcellular location: Nucleus. Cytoplasm. Cytoplasm, cytoskeleton, centrosome. Note=Colocalizes with the
microtubule-organizing center and intracellular membrane compartments
Sequence caution: Sequence=AAW28797.1; Type=Erroneous translation; Note=Wrong choice of frame;
Secondary accessions: A6NNH8 B7ZKV3 Q4JDG6 Q4JDK1 Q4JDK5 Q4JDK6 Q4JDK8 Q4JDK9 Q4JDL0 Q4JDL1 Q4JDL4
Q4JDL5 Q4JDL6 Q4JDL7 Q4JDL8 Q5RJ33 Q5T1G3
Alternative splicing: 15 isoforms:  Q4JDL3-1   Q4JDL3-2   Q4JDL3-3   Q4JDL3-4   Q4JDL3-5   Q4JDL3-6   Q4JDL3-7   Q4JDL3-8   
Q4JDL3-9   Q4JDL3-10   Q4JDL3-11   Q4JDL3-12   Q4JDL3-13   Q4JDL3-14   Q4JDL3-15   (May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay)

Explore the universe of human proteins at neXtProt for PTPN20A: NX_Q4JDL3

Post-translational modifications:

  • Phosphorylated upon DNA damage, probably by ATM or ATR1
  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q4JDL3

  • 4 DME Specific Peptides for PTPN20A (Q4JDL3)
     VVHCSAG  YIATQGP  QRSGMVQT  HCSAGIGR 

    PTPN20A Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (10 alternative transcripts): 
    NP_001035846.1  NP_001035848.1  NP_001035849.1  NP_001035850.1  NP_001035851.1  NP_001035852.1  NP_001035853.1  NP_001035854.1  
    NP_001035855.1  NP_001035856.1  

    ENSEMBL proteins: 
     ENSP00000379071   ENSP00000363466   ENSP00000424491   ENSP00000363459   ENSP00000379077  
     ENSP00000423819   ENSP00000427676   ENSP00000421921   ENSP00000422839   ENSP00000420995  
     ENSP00000426355   ENSP00000425362   ENSP00000424283   ENSP00000425012   ENSP00000421453  
     ENSP00000425912   ENSP00000421404   ENSP00000396009   ENSP00000426681   ENSP00000422384  
     ENSP00000403444   ENSP00000363462   ENSP00000379072   ENSP00000363335   ENSP00000379075  

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    Uscn Proteins for PTPN20A

    Gene Ontology (GO): 4 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--
    GO:0005737cytoplasm IEA--
    GO:0005815microtubule organizing center IEA--
    GO:0005874microtubule IEA--


    PTPN20A for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    PTPN20A for domains           About GeneDecksing

    3 InterPro domains/families:
     IPR016130 Tyr_Pase_AS
     IPR000242 Tyr_Pase_rcpt/non-rcpt
     IPR000387 Tyr/Dual-sp_Pase

    Graphical View of Domain Structure for InterPro Entry Q4JDL3

    ProtoNet protein and cluster: Q4JDL3

    1 Blocks protein family: IPB000242 Protein tyrosine phosphatase signature

    UniProtKB/Swiss-Prot: PTN20_HUMAN, Q4JDL3
    Similarity: Belongs to the protein-tyrosine phosphatase family. Non-receptor class subfamily
    Similarity: Contains 1 tyrosine-protein phosphatase domain


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: PTN20_HUMAN, Q4JDL3
    Function: Tyrosine-protein phosphatase targeted to sites of actin polymerization in response of varied extracellular
    stimuli. Has tyrosine phosphatase activity towards various tyrosyl phosphorylated substrates
    Catalytic activity: Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate

    Enzyme Number (IUBMB): EC 3.1.3.481 2

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    8/14 QIAGEN miScript miRNA Assays for microRNAs that regulate PTPN20A (see all 14):
    hsa-miR-3163 hsa-miR-3152-3p hsa-miR-3607-3p hsa-miR-4272 hsa-miR-1258 hsa-miR-944 hsa-miR-138-2* hsa-miR-3133
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    Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004725protein tyrosine phosphatase activity IEA--
    GO:0004872receptor activity ----


    PTPN20A for ontologies           About GeneDecksing



    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section

    Unified GeneCards pathways  About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1PAK Pathway
    Epithelial Adherens Junctions0.36

    1 Downloadable PowerPoint Slide of QIAGEN Pathway Central Maps for PTPN20A
        Epithelial Adherens Junctions


    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for PTPN20A

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for PTPN20A
    Search CenterWatch for drugs/clinical trials and news about PTPN20A / PTN20 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for PTPN20A gene (10 alternative transcripts): 
    NM_001042387.1  NM_001042389.1  NM_001042390.1  NM_001042391.1  NM_001042392.1  NM_001042393.1  NM_001042394.1  NM_001042395.1  
    NM_001042396.1  NM_001042397.1  

    Unigene Cluster for PTPN20A:

    Protein tyrosine phosphatase, non-receptor type 20A
    Hs.440733  [show with all ESTs]
    Unigene Representative Sequence: NM_001042389
    18/32 Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 32):
    ENST00000374340(uc001jdk.1) ENST00000395721(uc001jde.1 uc001jdg.1 uc009xmw.1 uc001jdp.1)
    ENST00000246887(uc001jdl.1 uc001jdq.1) ENST00000509181(uc001jdu.1)
    ENST00000374346(uc001jcz.1 uc001jdh.1 uc001jdm.1 uc001jdt.1)
    ENST00000508602 ENST00000374339 ENST00000395727 ENST00000509900 ENST00000503851
    ENST00000506080 ENST00000513266 ENST00000502705 ENST00000505814 ENST00000509774
    ENST00000511769 ENST00000513159 ENST00000509599

    miRNA
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    hsa-miR-3163 hsa-miR-3152-3p hsa-miR-3607-3p hsa-miR-4272 hsa-miR-1258 hsa-miR-944 hsa-miR-138-2* hsa-miR-3133
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    Additional cDNA sequence: 

    AL050040.1 AY704141.1 AY704142.1 AY704143.1 AY704144.1 AY704145.1 AY704146.1 AY704147.1 
    AY704148.1 AY704149.1 AY704150.1 AY704151.1 AY704152.1 AY704153.1 AY704154.1 AY704155.1 
    AY704156.1 AY704157.1 AY704158.1 AY753191.1 BC036539.2 BC093750.1 BC113473.1 BC143394.1 
    BC171725.1 BX648913.1 CR933668.1 

    24/25 DOTS entries (see all 25):

    DT.40297888  DT.100745172  DT.121288976  DT.121289160  DT.121285666  DT.121288957  DT.121289024  DT.121289173 
    DT.99940484  DT.121285649  DT.121288951  DT.121289019  DT.121289039  DT.121285664  DT.121285665  DT.121285671 
    DT.121288839  DT.121288848  DT.121288902  DT.121289137  DT.121285645  DT.121288849  DT.121285655  DT.121285661 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    PTPN20A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: --

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    See PTPN20A Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for PTPN20A

    SOURCE GeneReport for Unigene cluster: Hs.440733

    UniProtKB/Swiss-Prot: PTN20_HUMAN, Q4JDL3
    Tissue specificity: Present in many cell lines (at protein level). Widely expressed

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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of eukaryotes.

    Orthologs for PTPN20A gene from 3/13 species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves --
    --
    1(a)
    1 → many
    Un(9215481-9216500)
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons PTP11 tyrosine phosphatase 1 48.35(n)
    36.48(a)
      843516  NM_001036189.1  NP_001031266.1 
    rice
    (Oryza sativa)
    Liliopsida Os12g01748001 hypothetical protein 46.72(n)
    37.24(a)
      4351645  NM_001072821.1  NP_001066289.1 


    ENSEMBL Gene Tree for PTPN20A (if available)
    TreeFam Gene Tree for PTPN20A (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for PTPN20A gene
    PTPN20B1 2  PTPN12  PTPN32  PTPN20C2  FRMPD22  PTPN42  PTPN132  PTPN92  
    PTPN142  PTPN212  PTPN22  
    18/39 SIMAP similar genes for PTPN20A using alignment to 6 protein entries:     PTN20_HUMAN (see all proteins) (see all similar genes):
    DKFZp781P23155    PTPN20    PTPN20B    DKFZp566K0524    DKFZp781C1038    PTPRR
    DKFZp686B1310    LAR    PTPRF    PTPsigma    PTPN13    PTPN2
    PTPRD    PTPRS    DKFZp686E13109    PTPRB    BPTP-2    DKFZp686N0569

    PTPN20A for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/61 NCBI SNPs in PTPN20A are shown (see all 61    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 10 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs2021988051,2
    C,--46553823(+) TGTGT-/GAGAGTG 10 -- int10--------
    rs1882088121,2
    --46562102(+) TTGAGA/TTGGAG 10 -- int10--------
    rs1932764051,2
    --46562878(+) ATCCCC/TGATGA 10 -- int10--------
    rs1389057681,2
    C--46578019(+) ATGAGC/TGGAGG 10 -- int10--------
    rs614456121,2
    C--46581272(+) GCCTCG/AGCCTC 10 -- int11Minor allele frequency- A:0.00WA 2
    rs28910591,2
    C--46581339(-) CTATTG/AATTAC 10 -- int11Minor allele frequency- A:0.00NA 2
    rs1854741601,2
    --46581465(+) TAGAAC/TATTGT 10 -- int10--------
    rs1880056931,2
    --46581491(+) AAATAC/TTGGGA 10 -- int10--------
    rs607006901,2
    C--46581517(+) AAAAA-/ACAAAA 10 -- int10--------
    rs1913924421,2
    --46584016(+) GATTAA/GCAGCT 10 -- int10--------

    HapMap Linkage Disequilibrium report for PTPN20A (46549955 - 46641045 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 21 variations for PTPN20A
         15/20 CNVs (see all 20): 9150 8652 48536 3798 65654 4691 34456 48538 48539 30486 65652 3799 48537 8651 31728
         1 Indel: 33523

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    PTPN20A for disorders           About MalaCards

    PTPN20A for disorders           About GeneDecksing

    OMIM gene information: 610630    OMIM disorders: --


    Export disorders for PTPN20A gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for PTPN20A gene integrated from 9 sources:
    (articles sorted by number of sources associating them with PTPN20A)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Protein tyrosine phosphatase hPTPN20a is targeted to sites of actin polymerization. (PubMed id 15790311)1, 2 Fodero-Tavoletti M.T.... Tiganis T. (2005)
    2. The DNA sequence and comparative analysis of human chromosome 10. (PubMed id 15164054)2 Deloukas P.... Rogers J. (2004)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 653129 HGNC: 23422 Ensembl:ENSG00000204179 euGenes: HUgn653129 ECgene: PTPN20A
    H-InvDB: PTPN20A

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for PTPN20A Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for PTPN20A gene:
    Search GeneIP for patents involving PTPN20A

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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