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    PTPRN protein tyrosine phosphatase receptor type N [ Homo sapiens (human) ]

    Gene ID: 5798, updated on 27-Nov-2024

    Summary

    Official Symbol
    PTPRNprovided by HGNC
    Official Full Name
    protein tyrosine phosphatase receptor type Nprovided by HGNC
    Primary source
    HGNC:HGNC:9676
    See related
    Ensembl:ENSG00000054356 MIM:601773; AllianceGenome:HGNC:9676
    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
    IA2; IA-2; ICA512; R-PTP-N; IA-2/PTP
    Summary
    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 possesses an extracellular region, a single transmembrane region, and a single catalytic domain, and thus represents a receptor-type PTP. This PTP was found to be an autoantigen that is reactive with insulin-dependent diabetes mellitus (IDDM) patient sera, and thus may be a potential target of autoimmunity in diabetes mellitus. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Dec 2010]
    Expression
    Biased expression in brain (RPKM 53.0), adrenal (RPKM 12.2) and 2 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See PTPRN in Genome Data Viewer
    Location:
    2q35
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (219289623..219309401, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (219774379..219794153, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (220154345..220174123, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17146 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17147 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12351 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17148 Neighboring gene tubulin alpha 4a Neighboring gene tubulin alpha 4b Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:220142208-220142912 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12352 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:220150891-220151858 Neighboring gene DnaJ heat shock protein family (Hsp40) member B2 Neighboring gene Sharpr-MPRA regulatory region 13803 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17149 Neighboring gene microRNA 153-1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:220199445-220200644 Neighboring gene regulated endocrine specific protein 18 Neighboring gene uncharacterized LOC107985835 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17150

    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?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ16131

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    NOT enables protein tyrosine phosphatase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables spectrin binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables transcription factor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables ubiquitin-like protein ligase binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in axon terminus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in endosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in neuronal cell body ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in perikaryon IEA
    Inferred from Electronic Annotation
    more info
     
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    is_active_in secretory granule IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in secretory granule ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    is_active_in synapse IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in synapse ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    NOT located_in synaptic vesicle ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in transport vesicle membrane IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    receptor-type tyrosine-protein phosphatase-like N
    Names
    ICA 512
    PTP IA-2
    insulinoma-associated tyrosine-phosphatase-like protein
    islet cell antigen 2
    islet cell antigen 512
    islet cell autoantigen 3
    protein tyrosine phosphatase-like N
    NP_001186692.1
    NP_001186693.1
    NP_002837.1

    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_029546.1 RefSeqGene

      Range
      5173..24951
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001199763.2NP_001186692.1  receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor

      See identical proteins and their annotated locations for NP_001186692.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AC114803, BC070053, DC344431
      Consensus CDS
      CCDS56168.1
      UniProtKB/TrEMBL
      A8K604
      Related
      ENSP00000386638.3, ENST00000409251.7
      Conserved Domains (4) summary
      smart00194
      Location:680939
      PTPc; Protein tyrosine phosphatase, catalytic domain
      cd00047
      Location:707939
      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 ...
      pfam11548
      Location:476528
      Receptor_IA-2; Protein-tyrosine phosphatase receptor IA-2
      pfam14948
      Location:60138
      RESP18; RESP18 domain
    2. NM_001199764.2NP_001186693.1  receptor-type tyrosine-protein phosphatase-like N isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and has multiple coding region differences, compared to variant 1. These differences causes translation initiation at a downstream AUG and results an isoform (3) with a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AC114803, AK296335, BC070053
      Consensus CDS
      CCDS56167.1
      UniProtKB/TrEMBL
      Q96IA0
      Related
      ENSP00000392598.2, ENST00000423636.6
      Conserved Domains (4) summary
      smart00194
      Location:619878
      PTPc; Protein tyrosine phosphatase, catalytic domain
      cd00047
      Location:646878
      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 ...
      pfam11548
      Location:382467
      Receptor_IA-2; Protein-tyrosine phosphatase receptor IA-2
      pfam14948
      Location:148
      RESP18; RESP18 domain
    3. NM_002846.4NP_002837.1  receptor-type tyrosine-protein phosphatase-like N isoform 1 precursor

      See identical proteins and their annotated locations for NP_002837.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      BC007713, L18983, X62899
      Consensus CDS
      CCDS2440.1
      UniProtKB/Swiss-Prot
      B4DK12, F5GZS3, Q08319, Q16849, Q53QD6, Q6NSL1
      UniProtKB/TrEMBL
      A0A4Y5WWT4
      Related
      ENSP00000295718.2, ENST00000295718.7
      Conserved Domains (4) summary
      smart00194
      Location:709968
      PTPc; Protein tyrosine phosphatase, catalytic domain
      cd00047
      Location:736968
      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 ...
      pfam11548
      Location:472557
      Receptor_IA-2; Protein-tyrosine phosphatase receptor IA-2
      pfam14948
      Location:60138
      RESP18; RESP18 domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      219289623..219309401 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      219774379..219794153 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)