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    PTPRO protein tyrosine phosphatase receptor type O [ Homo sapiens (human) ]

    Gene ID: 5800, updated on 29-Jan-2024

    Summary

    Official Symbol
    PTPROprovided by HGNC
    Official Full Name
    protein tyrosine phosphatase receptor type Oprovided by HGNC
    Primary source
    HGNC:HGNC:9678
    See related
    Ensembl:ENSG00000151490 MIM:600579; AllianceGenome:HGNC:9678
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NPHS6; PTPU2; GLEPP1; PTP-OC; PTP-U2; PTPROT; R-PTP-O
    Summary
    This gene encodes a member of the R3 subtype family of receptor-type protein tyrosine phosphatases. These proteins are localized to the apical surface of polarized cells and may have tissue-specific functions through activation of Src family kinases. This gene contains two distinct promoters, and alternatively spliced transcript variants encoding multiple isoforms have been observed. The encoded proteins may have multiple isoform-specific and tissue-specific functions, including the regulation of osteoclast production and activity, inhibition of cell proliferation and facilitation of apoptosis. This gene is a candidate tumor suppressor, and decreased expression of this gene has been observed in several types of cancer. [provided by RefSeq, May 2011]
    Expression
    Biased expression in kidney (RPKM 3.7), brain (RPKM 2.7) and 11 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See PTPRO in Genome Data Viewer
    Location:
    12p12.3; 12p13-p12
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (15322508..15598331)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (15199775..15475561)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (15475442..15751265)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene RAS like estrogen regulated growth inhibitor Neighboring gene uncharacterized LOC124902886 Neighboring gene uncharacterized LOC105369673 Neighboring gene methyltransferase like 8 pseudogene 1 Neighboring gene ribosomal protein S2 pseudogene 42 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:15678492-15679691 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6067 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:15687897-15689096 Neighboring gene uncharacterized LOC105369672 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6068 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6069 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6070 Neighboring gene HNF4 motif-containing MPRA enhancer 23 Neighboring gene EGFR pathway substrate 8, signaling adaptor Neighboring gene RNA, U6 small nuclear 251, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4278 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4279 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4280 Neighboring gene mitochondrial ribosomal protein S7 pseudogene 2

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Nephrotic syndrome, type 6 Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide study identifies PTPRO and WDR72 and FOXQ1-SUMO1P1 interaction associated with neurocognitive function.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env HIV-1 gp120 induces CD4 association with lymphocyte surface molecules CD3, CD11a, CD27, CD45RA, CD45RB, CD45RO, CD49d, CD38, CD26, CD59, CD95 and class I MHC molecules PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables Wnt-protein binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables Wnt-protein binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables cadherin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables cadherin binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables phosphatase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein homodimerization activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables protein tyrosine phosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein tyrosine phosphatase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein tyrosine phosphatase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables protein tyrosine phosphatase activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables transmembrane receptor protein tyrosine phosphatase activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in axon guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in axon guidance ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cell morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in glomerulus development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in lamellipodium assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in monocyte chemotaxis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of canonical Wnt signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in negative regulation of canonical Wnt signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of cell-substrate adhesion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of glomerular filtration ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of neuron projection development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of retinal ganglion cell axon guidance ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in peptidyl-tyrosine dephosphorylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in podocyte differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in podocyte differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in protein dephosphorylation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in protein dephosphorylation TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in regulation of glomerular filtration IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of glomerular filtration ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of synapse organization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in slit diaphragm assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in slit diaphragm assembly NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in GABA-ergic synapse IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in apical plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in axon ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in dendritic spine ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in extracellular exosome HDA PubMed 
    is_active_in glutamatergic synapse IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in growth cone ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in lamellipodium ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in lateral plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in neuron projection ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in plasma membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in postsynaptic density membrane IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    receptor-type tyrosine-protein phosphatase O
    Names
    PTP phi
    PTPase U2
    glomerular epithelial protein 1
    osteoclastic transmembrane protein-tyrosine phosphatase
    phosphotyrosine phosphatase U2
    protein tyrosine phosphatase PTP-U2
    NP_002839.1
    NP_109592.1
    NP_109593.1
    NP_109594.1
    NP_109595.1
    NP_109596.1
    XP_016875214.1
    XP_054228699.1
    XP_054228700.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_031857.1 RefSeqGene

      Range
      5252..281075
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_002848.4NP_002839.1  receptor-type tyrosine-protein phosphatase O isoform b precursor

      See identical proteins and their annotated locations for NP_002839.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an exon in the coding region but maintains the reading frame, compared to variant 1. The encoded isoform (b) is shorter than isoform a.
      Source sequence(s)
      AC007542, DR000351, U20489
      Consensus CDS
      CCDS8674.1
      UniProtKB/TrEMBL
      A8K169
      Related
      ENSP00000343434.2, ENST00000348962.7
      Conserved Domains (4) summary
      smart00194
      Location:9091164
      PTPc; Protein tyrosine phosphatase, catalytic domain
      cd00047
      Location:9371165
      PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...
      cd00063
      Location:434526
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam00041
      Location:725805
      fn3; Fibronectin type III domain
    2. NM_030667.3NP_109592.1  receptor-type tyrosine-protein phosphatase O isoform a precursor

      See identical proteins and their annotated locations for NP_109592.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AC007542, BC126201, DR000351
      Consensus CDS
      CCDS8675.1
      UniProtKB/Swiss-Prot
      A0AV39, Q13101, Q16827, Q8IYG3, Q9UBF0, Q9UBT5
      UniProtKB/TrEMBL
      A8K169
      Related
      ENSP00000281171.4, ENST00000281171.9
      Conserved Domains (3) summary
      cd00047
      Location:9651193
      PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...
      cd00063
      Location:530630
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam00041
      Location:435521
      fn3; Fibronectin type III domain
    3. NM_030668.3NP_109593.1  receptor-type tyrosine-protein phosphatase O isoform d

      See identical proteins and their annotated locations for NP_109593.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and has multiple differences in the coding region but maintains the reading frame, compared to variant 1. Variants 4 and 6 encode the same isoform (d), which is shorter than isoform a.
      Source sequence(s)
      AC007542, AF187044
      Consensus CDS
      CCDS53754.1
      UniProtKB/TrEMBL
      A0A6I8PRG8
      Related
      ENSP00000437571.1, ENST00000542557.5
      Conserved Domains (1) summary
      cd14614
      Location:112356
      R-PTPc-O; catalytic domain of receptor-type tyrosine-protein phosphatase O
    4. NM_030669.3NP_109594.1  receptor-type tyrosine-protein phosphatase O isoform c

      See identical proteins and their annotated locations for NP_109594.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. Variants 3 and 5 encode the same isoform (c), which has a shorter N-terminus compared to isoform a.
      Source sequence(s)
      AC007542, AF187043
      Consensus CDS
      CCDS44837.1
      UniProtKB/TrEMBL
      A0A6I8PRG8
      Related
      ENSP00000501494.1, ENST00000674388.1
      Conserved Domains (1) summary
      cd00047
      Location:154382
      PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...
    5. NM_030670.3NP_109595.1  receptor-type tyrosine-protein phosphatase O isoform d

      See identical proteins and their annotated locations for NP_109595.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR and 3' UTR, and has multiple differences in the coding region but maintains the reading frame, compared to variant 1. Variants 4 and 6 encode the same isoform (d), which is shorter than isoform a.
      Source sequence(s)
      AC007542, AF187042
      Consensus CDS
      CCDS53754.1
      UniProtKB/TrEMBL
      A0A6I8PRG8
      Related
      ENSP00000439234.1, ENST00000544244.5
      Conserved Domains (1) summary
      cd14614
      Location:112356
      R-PTPc-O; catalytic domain of receptor-type tyrosine-protein phosphatase O
    6. NM_030671.3NP_109596.1  receptor-type tyrosine-protein phosphatase O isoform c

      See identical proteins and their annotated locations for NP_109596.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR and 3' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. Variants 3 and 5 encode the same isoform (c), which has a shorter N-terminus compared to isoform a.
      Source sequence(s)
      AC007542, AF152378
      Consensus CDS
      CCDS44837.1
      UniProtKB/TrEMBL
      A0A6I8PRG8
      Related
      ENSP00000393449.2, ENST00000445537.6
      Conserved Domains (1) summary
      cd00047
      Location:154382
      PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      15322508..15598331
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017019725.3XP_016875214.1  receptor-type tyrosine-protein phosphatase O isoform X1

    RNA

    1. XR_931316.4 RNA Sequence

    2. XR_007063106.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      15199775..15475561
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054372724.1XP_054228699.1  receptor-type tyrosine-protein phosphatase O isoform X1

    2. XM_054372725.1XP_054228700.1  receptor-type tyrosine-protein phosphatase O isoform X2

      UniProtKB/TrEMBL
      A0A6I8PRG8

    RNA

    1. XR_008488649.1 RNA Sequence

    2. XR_008488650.1 RNA Sequence