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PTPRD Gene

protein-coding   GIFtS: 67
GCID: GC09M008307

Protein Tyrosine Phosphatase, Receptor Type, D

  See PTPRD-related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Protein Tyrosine Phosphatase, Receptor Type, D1 2     HPTPDELTA2
R-PTP-delta2 3     RPTPDELTA2
EC 3.1.3.483 8     Protein Tyrosine Phosphatase, Receptor Type, Delta Polypeptide2
HPTP2 5     Receptor-Type Tyrosine-Protein Phosphatase Delta2
PTPD2 5     Protein-Tyrosine Phosphatase Delta3
HPTPD2     

External Ids:    HGNC: 96681   Entrez Gene: 57892   Ensembl: ENSG000001537077   OMIM: 6015985   UniProtKB: P234683   

Export aliases for PTPRD gene to outside databases

Previous GC identifers: GC09M008470 GC09M008298


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for PTPRD Gene:
The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to
be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation,
mitotic cycle, and oncogenic transformation. This PTP contains an extracellular region, a single transmembrane
segment and two tandem intracytoplasmic catalytic domains, and thus represents a receptor-type PTP. The
extracellular region of this protein is composed of three Ig-like and eight fibronectin type III-like domains.
Studies of the similar genes in chicken and fly suggest the role of this PTP is in promoting neurite growth, and
regulating neurons axon guidance. Multiple alternatively spliced transcript variants of this gene have been
reported. A related pseudogene has been identified on chromosome 5. (provided by RefSeq, Jan 2010)

GeneCards Summary for PTPRD Gene:
PTPRD (protein tyrosine phosphatase, receptor type, D) is a protein-coding gene. Diseases associated with PTPRD include familial melanoma. GO annotations related to this gene include transmembrane receptor protein tyrosine phosphatase activity and receptor binding. An important paralog of this gene is PTPRK.

Gene Wiki entry for PTPRD Gene


(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000009.11  NT_008413.19  NC_018920.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the PTPRD gene promoter:
         HOXA9B   HOXA9   POU3F2 (N-Oct-5a)   POU3F2 (N-Oct-5b)   POU3F2   Meis-1b   AREB6   MEF-2A   aMEF-2   Meis-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPTPRD promoter sequence
   Search Chromatin IP Primers for PTPRD

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PTPRD


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

Entrez Gene cytogenetic band: 9p23-p24.3   Ensembl cytogenetic band:  9p23   HGNC cytogenetic band: 9p24.1-p23

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

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09M008307:  view genomic region     (about GC identifiers)

Start:
8,314,246 bp from pter      End:
10,612,723 bp from pter
Size:
2,298,478 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: PTPRD_HUMAN, P23468 (See protein sequence)
Recommended Name: Receptor-type tyrosine-protein phosphatase delta precursor  
Size: 1912 amino acids; 214760 Da
Subunit: Interacts with IL1RAPL1 (via extracellular region); interaction is required for IL1RAPL1-mediated synapse
formation (By similarity). Interacts with PPFIA1, PPFIA2 and PPFIA3
4 PDB 3D structures from and Proteopedia for PTPRD:
1X5Z (3D)        2DLH (3D)        2YD6 (3D)        2YD7 (3D)    
Secondary accessions: B1ALA0 Q3KPJ0 Q3KPJ1 Q3KPJ2
Alternative splicing: 6 isoforms:  P23468-1   P23468-2   P23468-3   P23468-4   P23468-5   P23468-6   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for PTPRD: NX_P23468

Explore proteomics data for PTPRD at MOPED

Post-translational modifications: 

  • A cleavage occurs, separating the extracellular domain from the transmembrane segment. This process called
    'ectodomain shedding' is thought to be involved in receptor desensitization, signal transduction and/or membrane
    localization1
  • Glycosylation2 at Asn254, Asn299, Asn724, Asn832
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for PTPRD (P23468) (see all 57)
     AVGSPMP  KCHQYWP  WPDHGVP  ATVVMMT 


    See PTPRD Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (6 alternative transcripts): 
    NP_001035802.1  NP_001164496.1  NP_002830.1  NP_569075.2  NP_569076.2  NP_569077.2  

    ENSEMBL proteins: 
     ENSP00000370593   ENSP00000417093   ENSP00000380731   ENSP00000417661   ENSP00000417890  
     ENSP00000348812   ENSP00000353187   ENSP00000351293   ENSP00000347373   ENSP00000380741  
     ENSP00000380735   ENSP00000440515   ENSP00000438164  

    PTPRD Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for PTPRD

     
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    Cloud-Clone Corp. ELISAs for PTPRD
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    Search eBioscience for ELISAs for PTPRD 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    FN3: Fibronectin type III domain containing
    ISET: Immunoglobulin superfamily / I-set domain containing
    PTPR: Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like

    IUPHAR Guide to PHARMACOLOGY protein family classification: Type D
    Receptor tyrosine phosphatases (RTP)

    Selected InterPro protein domains (see all 8):
     IPR003598 Ig_sub2
     IPR003961 Fibronectin_type3
     IPR013098 Ig_I-set
     IPR016130 Tyr_Pase_AS
     IPR013783 Ig-like_fold

    Graphical View of Domain Structure for InterPro Entry P23468

    ProtoNet protein and cluster: P23468

    4 Blocks protein domains:
    IPB000242 Protein tyrosine phosphatase signature
    IPB003598 Immunoglobulin C-2 type
    IPB003962 Fibronectin type III repeat signature
    IPB013098 Immunoglobulin I-set


    UniProtKB/Swiss-Prot: PTPRD_HUMAN, P23468
    Similarity: Belongs to the protein-tyrosine phosphatase family. Receptor class 2A subfamily
    Similarity: Contains 8 fibronectin type-III domains
    Similarity: Contains 3 Ig-like C2-type (immunoglobulin-like) domains
    Similarity: Contains 2 tyrosine-protein phosphatase domains


    Find genes that share domains with PTPRD           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: PTPRD_HUMAN, P23468
    Catalytic activity: Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate

         Genatlas biochemistry entry for PTPRD:
    protein tyrosine phosphatase,receptor-type II,delta polypeptide

         Enzyme Number (IUBMB): EC 3.1.3.481 2

         Gene Ontology (GO): Selected molecular function terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004725protein tyrosine phosphatase activity ----
    GO:0005001transmembrane receptor protein tyrosine phosphatase activity TAS7896816
    GO:0005102receptor binding ISS--
    GO:0005515protein binding IPI12570871
    GO:0016791phosphatase activity ----
         
    Find genes that share ontologies with PTPRD           About GenesLikeMe


    Phenotypes:
         6 GenomeRNAi human phenotypes for PTPRD:
     Apoptosis resistance  Decreased focal adhesion (FA)   G0/1 arrest  Increased S DNA content 
     Increased cell death in breast  Synthetic lethal with paclitax 

         9 MGI mutant phenotypes (inferred from 1 allele(MGI details for Ptprd):
     adipose tissue  behavior/neurological  growth/size/body  integument  mortality/aging 
     muscle  nervous system  respiratory system  skeleton 

    Find genes that share phenotypes with PTPRD           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Ptprdtm1Yiw for PTPRD

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for PTPRD
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for PTPRD
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for PTPRD

    miRNA
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    miRTarBase miRNAs that target PTPRD:
    hsa-mir-200c-3p (MIRT021067), hsa-mir-200b-3p (MIRT024123), hsa-mir-429 (MIRT016634), hsa-mir-1 (MIRT023978), hsa-mir-200a-3p (MIRT020345), hsa-mir-141-3p (MIRT021661)

    Block miRNA regulation of human, mouse, rat PTPRD using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate PTPRD (see all 185):
    hsa-miR-411* hsa-miR-579 hsa-miR-520f hsa-miR-106a hsa-miR-3653 hsa-miR-519a hsa-miR-502-3p hsa-miR-130b
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for PTPRD
    Predesigned siRNA for gene silencing in human, mouse, rat PTPRD

    Gene Editing
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    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for PTPRD
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat PTPRD
    Addgene plasmids for PTPRD 

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PTPRD


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    PTPRD_HUMAN, P23468: Membrane; Single-pass type I membrane protein
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane4
    cytoskeleton2
    extracellular2
    nucleus2
    cytosol1
    endoplasmic reticulum1
    golgi apparatus1
    mitochondrion1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005887integral component of plasma membrane TAS7896816

    Find genes that share ontologies with PTPRD           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, 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 Apr 2014 via Entrez Gene).
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    SuperPaths for PTPRD About    
    See pathways by source

    SuperPathContained pathways About
    1PAK Pathway
    Epithelial Adherens Junctions0.36

    1 Downloadable PowerPoint Slide of GeneGlobe Pathway Central Maps for PTPRD
        Epithelial Adherens Junctions


        Pathway & Disease-focused RT2 Profiler PCR Array including PTPRD: 
              Protein Phosphatases in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for PTPRD

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for PTPRD (P234681, 2, 3 ENSP000003488124) via UniProtKB, MINT, STRING, and/or I2D (see all 38)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ABL2P426843, ENSP000003565954I2D: score=2 STRING: ENSP00000356595
    PTPRSQ133323, ENSP000003499324I2D: score=2 STRING: ENSP00000349932
    MDM2Q009873, ENSP000004172814I2D: score=1 STRING: ENSP00000417281
    PPFIA3O751453, ENSP000003356144I2D: score=1 STRING: ENSP00000335614
    PTPREP234693, ENSP000002546674I2D: score=1 STRING: ENSP00000254667
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 9):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006470protein dephosphorylation TAS7896816
    GO:0006796phosphate-containing compound metabolic process NAS7896816
    GO:0007157heterophilic cell-cell adhesion ISS--
    GO:0007185transmembrane receptor protein tyrosine phosphatase signaling pathway TAS7896816
    GO:0016311dephosphorylation ----

    Find genes that share ontologies with PTPRD           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for PTPRD

    2 HMDB Compounds for PTPRD    About this table
    CompoundSynonyms CAS #PubMed Ids
    PhosphateNFB Orthophosphate (see all 13)14265-44-2--
    WaterDihydrogen oxide (see all 2)7732-18-5--

    1 Novoseek inferred chemical compound relationship for PTPRD gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    tyrosine 58.3 14 20139422 (2), 19478061 (1), 19514512 (1), 12570871 (1) (see all 12)



    Find genes that share compounds with PTPRD           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for PTPRD gene (6 alternative transcripts): 
    NM_001040712.2  NM_001171025.1  NM_002839.3  NM_130391.3  NM_130392.3  NM_130393.3  

    Unigene Cluster for PTPRD:

    Protein tyrosine phosphatase, receptor type, D
    Hs.446083  [show with all ESTs]
    Unigene Representative Sequence: NM_002839
    16 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000381196(uc003zkr.3 uc003zkk.3) ENST00000486161 ENST00000397606
    ENST00000477552 ENST00000471274 ENST00000488774 ENST00000463477(uc003zkt.1)
    ENST00000481079 ENST00000356435 ENST00000360074 ENST00000358503 ENST00000355233(uc003zkp.3 uc003zkq.3)
    ENST00000397617(uc003zks.3) ENST00000397611(uc022bdj.1) ENST00000537002
    ENST00000540109
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    Selected qRT-PCR Assays for microRNAs that regulate PTPRD (see all 185):
    hsa-miR-411* hsa-miR-579 hsa-miR-520f hsa-miR-106a hsa-miR-3653 hsa-miR-519a hsa-miR-502-3p hsa-miR-130b
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      QuantiFast Probe-based Assays in human, mouse, rat PTPRD

    Additional mRNA sequence: 

    AB208869.1 AB211400.1 AK296392.1 AL049338.1 BC028038.1 BC037801.2 BC045786.1 BC106713.1 
    BC106714.1 BC106715.2 BC106716.1 L38929.1 X54133.1 

    17 DOTS entries:

    DT.92054951  DT.414820  DT.100776675  DT.452325  DT.100776674  DT.95141758  DT.100023323  DT.86846541 
    DT.95161036  DT.95137056  DT.95160154  DT.121147994  DT.305347  DT.40191285  DT.87014093  DT.91713816 
    DT.75114037 

    2 AceView cDNA sequences:

    AW000884 AW362468 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for PTPRD    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^ 16a · 16b ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^
    SP1:                                                              -     -     -     -     -     -                                                               
    SP2:                                                                                            -                                               -               
    SP3:                                                                                                                                                            

    ExUns: 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30 ^ 31 ^ 32 ^ 33a · 33b
    SP1:                                                                  
    SP2:                                                                  
    SP3:                                                                  


    ECgene alternative splicing isoforms for PTPRD

    (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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    PTPRD expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GAAGGATTTT
    PTPRD Expression
    About this image


    PTPRD expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 9) fully expand
     
     Brain (Nervous System)    fully expand to see all 5 entries
             Cerebral Cortex
     
     Neural Tube (Nervous System)    fully expand to see all 3 entries
             Metencephalon
     
     Testis (Reproductive System)    fully expand to see all 2 entries
             Testicular Interstitial Cells Testis Interstitium
     
     Ovary (Reproductive System)    fully expand to see all 2 entries
             Pre-Granulosa Cells Primordial Follicle
     
     Kidney (Urinary System)
             Metanephros
    PTPRD Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PTPRD Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.446083
        Pathway & Disease-focused RT2 Profiler PCR Array including PTPRD: 
              Protein Phosphatases in human mouse rat

    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for PTPRD
    Pre-validated RT2 qPCR Primer Assay in human, mouse / rat PTPRD
    QuantiTect SYBR Green Assays in human, mouse, rat PTPRD
    QuantiFast Probe-based Assays in human, mouse, rat PTPRD
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PTPRD

    (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)
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    This gene was present in the common ancestor of eukaryotes.

    Orthologs for PTPRD gene from Selected species (see all 17)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ptprd5 protein tyrosine phosphatase, receptor type, D   --   4 (36.94 cM) 75941238 
    chicken
    (Gallus gallus)
    Aves PTPRD1 protein tyrosine phosphatase, receptor type, D 85.11(n)
    94.55(a)
      431602  XM_004949082.1  XP_004949139.1 
    lizard
    (Anolis carolinensis)
    Reptilia PTPRD6
    protein tyrosine phosphatase, receptor type, D
    90(a)
    1 ↔ 1
    2(53646412-54006603)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.210312 Xenopus laevis receptor protein tyrosine phosphatase more 83.25(n)    AF197944.1 
    zebrafish
    (Danio rerio)
    Actinopterygii ptprdb1 protein tyrosine phosphatase, receptor type, D, b 64.64(n)
    67.82(a)
      100073332  NM_001166048.1  NP_001159520.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Lar1 , 3 protein amino acid dephosphorylation
    protein tyrosine more3
    Leukocyte-antigen-related-like1
    40(a)
    (best of 2)3
    53.04(n)1
    51.29(a)1
      352591  NM_001273666.11  NP_001260595.11 
    worm
    (Caenorhabditis elegans)
    Secernentea F25H5.73
    ptp-31
    Protein-tyrosine phosphatase3
    ptp-31
    35(a)
    (best of 3)3
    59.52(n)1
    59.17(a)1
      I(9163621-9165470)3
    131869771  NM_001026773.31  NP_001021944.11 
    wheat
    (Triticum aestivum)
    Liliopsida Ta.11882 Triticum aestivum clone wlm24.pk0001.a4fis, full insert more 76.33(n)    BT009319.1 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PTPRD gene
    PTPRK2  PTPRC2  PTPRA2  PTPRG2  PTPRS2  PTPRU2  PTPRM2  PTPRF2  
    PTPRZ12  PTPRT2  PTPRE2  
    Selected SIMAP similar genes for PTPRD using alignment to 10 protein entries:     PTPRD_HUMAN (see all proteins) (see all similar genes):
    BPTP-2    DKFZp686B1310    PTPRF    PTPRS    PTPsigma    PTPRK
    DKFZp313F1310    DKFZp781C1038    PTPRR    PTPRA    PTPN12    PTPN5
    LAR    DKFZp686K0257    ROBO3    PTPRE    DKFZp566K0524    L1CAM

    Find genes that share paralogs with PTPRD           About GenesLikeMe


    1 Pseudogenes.org Pseudogene for PTPRD
    PGOHUM00000235366


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for PTPRD (see all 64222)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0356474
    A colorectal cancer sample4--see VAR_0356472 V A mis40--------
    VAR_0356464
    A colorectal cancer sample4--see VAR_0356462 L P mis40--------
    VAR_0356454
    A colorectal cancer sample4--see VAR_0356452 R Q mis40--------
    rs1500634461,2
    Cuntested18317921(+) GGCACG/AATAGG 12 /R /C mis11Minor allele frequency- A:0.00NA 4552
    rs1504955631,2
    --8313796(+) TCATAC/TTGAAT 6 -- ds50010--------
    rs1115158611,2
    C--8313816(+) AATAAC/TGCAAA 6 -- ds50012Minor allele frequency- T:0.13CSA WA 120
    rs1824144001,2
    --8313855(+) AGGTAG/TGAATA 6 -- ds50010--------
    rs771013271,2
    C--8313965(+) TTCTAC/TATAGT 6 -- ds50010--------
    rs1876686101,2
    --8314009(+) TCTGAA/TATGAA 6 -- ds50010--------
    rs38398871,2
    C--8314070(-) AAGCA-/AACA  
            
    GAGAC
    6 -- ds50010--------

    HapMap Linkage Disequilibrium report for PTPRD (8314246 - 8564246 bp, first 250kb of PTPRD)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for PTPRD (see all 284):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2661630CNV Deletion23128226
    esv2663894CNV Deletion23128226
    esv1585677CNV Deletion17803354
    esv2738192CNV Deletion23290073
    esv1010369CNV Deletion20482838
    esv1932426CNV Deletion18987734
    nsv820396CNV Deletion20802225
    esv2667750CNV Deletion23128226
    nsv821534CNV Deletion20802225
    esv2114231CNV Deletion18987734

    Human Gene Mutation Database (HGMD): PTPRD
    4 Site Specific Mutation Identification with PCR Assays for PTPRD:
    Cosmic IdAA Change
    125678p.L1036P
    142723p.P1690S
    48721p.L1036Q
    142724p.P1690L
    1 Copy Number PCR Panel containing PTPRD:
    Kinases & Phosphatases
    SeqTarget long-range PCR primers for resequencing PTPRD
    DNA2.0 Custom Variant and Variant Library Synthesis for PTPRD

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 601598    OMIM disorders: --

    1 disease for PTPRD:    
    About MalaCards
    familial melanoma

    4 diseases from the University of Copenhagen DISEASES database for PTPRD:
    Diabetes mellitus     Cancer     Hypersensitivity reaction type II disease     Plague

    Find genes that share disorders with PTPRD           About GenesLikeMe

    3 Novoseek inferred disease relationships for PTPRD gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    cancer lung 24.4 1 17420988 (1)
    tumors 10.8 3 19131950 (1), 19755842 (1), 18050303 (1)
    metastasis 0 1 12570871 (1)

    Genetic Association Database (GAD): PTPRD
    Human Genome Epidemiology (HuGE) Navigator: PTPRD (19 documents)

    Export disorders for PTPRD 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 PTPRD gene, integrated from 10 sources (see all 80):
    (articles sorted by number of sources associating them with PTPRD)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Molecular characterization of the human transmembrane protein- tyrosine phosphatase delta. Evidence for tissue-specific expression of alternative human transmembrane protein-tyrosine phosphatase delta isoforms. (PubMed id 7896816)1, 2, 3, 9 Pulido R.... Streuli M. (J. Biol. Chem. 1995)
    2. The polymorphisms of protein-tyrosine phosphatase receptor-type delta gene and its association with pediatric asthma in the Taiwanese population. (PubMed id 18414509)1, 4, 9 Shyur S.D....Wu L.S. (Eur. J. Hum. Genet. 2008)
    3. PTPRD (protein tyrosine phosphatase receptor type delta) is associated with restless legs syndrome. (PubMed id 18660810)1, 4, 9 Schormair B....Winkelmann J. (Nat. Genet. 2008)
    4. A genome-wide association study identifies susceptibility variants for type 2 diabetes in Han Chinese. (PubMed id 20174558)1, 4, 9 Tsai F.J....Wu J.Y. (PLoS Genet. 2010)
    5. The tyrosine phosphatase PTPRD is a tumor suppressor that is frequently inactivated and mutated in glioblastoma and other human cancers. (PubMed id 19478061)1, 4, 9 Veeriah S....Chan T.A. (Proc. Natl. Acad. Sci. U.S.A. 2009)
    6. Genome-wide association study identifies novel restless legs syndrome susceptibility loci on 2p14 and 16q12.1. (PubMed id 21779176)1, 4 Winkelmann J....Meitinger T. (PLoS Genet. 2011)
    7. Genome-wide association and meta-analysis in populations from Starr County, Texas, and Mexico City identify type 2 diabetes susceptibility loci and enrichment for expression quantitative trait loci in top signals. (PubMed id 21647700)1, 4 Below J.E....Hanis C.L. (Diabetologia 2011)
    8. Common genetic variation and susceptibility to partial epilepsies: a genome-wide association study. (PubMed id 20522523)1, 4 KasperaviciAte D....Sisodiya S.M. (Brain 2010)
    9. Novel association strategy with copy number variation for identifying new risk Loci of human diseases. (PubMed id 20808825)1, 4 Chen X....Kong X. (PLoS ONE 2010)
    10. Human variation in alcohol response is influenced by variation in neuronal signaling genes. (PubMed id 20201926)1, 4 Joslyn G....White R.L. (Alcohol. Clin. Exp. Res. 2010)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 5789 HGNC: 9668 AceView: PTPRD.1 Ensembl:ENSG00000153707 euGenes: HUgn5789
    ECgene: PTPRD H-InvDB: PTPRD

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for PTPRD Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for PTPRD Genetics and Cytogenetics in Oncology and Haematology

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

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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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