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

Gene ID: 5798, updated on 9-Dec-2018

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
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

Genomic context

See PTPRN in Genome Data Viewer
Location:
2q35
Exon count:
24
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 2 NC_000002.12 (219289623..219309573, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (220154345..220174295, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene tubulin alpha 4a Neighboring gene tubulin alpha 4b Neighboring gene DnaJ heat shock protein family (Hsp40) member B2 Neighboring gene microRNA 153-1 Neighboring gene regulated endocrine specific protein 18 Neighboring gene uncharacterized LOC107985835

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 FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Type I diabetes mellitus, organism-specific biosystem (from KEGG)
    Type I diabetes mellitus, organism-specific biosystemType I diabetes mellitus is a disease that results from autoimmune destruction of the insulin-producing beta-cells. Certain beta-cell proteins act as autoantigens after being processed by antigen-pre...
  • Type I diabetes mellitus, conserved biosystem (from KEGG)
    Type I diabetes mellitus, conserved biosystemType I diabetes mellitus is a disease that results from autoimmune destruction of the insulin-producing beta-cells. Certain beta-cell proteins act as autoantigens after being processed by antigen-pre...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ16131

Gene Ontology Provided by GOA

Function Evidence Code Pubs
GTPase binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
NOT protein tyrosine phosphatase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
spectrin binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription factor binding IDA
Inferred from Direct Assay
more info
PubMed 
ubiquitin-like protein ligase binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
cytokine-mediated signaling pathway IEA
Inferred from Electronic Annotation
more info
 
dense core granule maturation IGI
Inferred from Genetic Interaction
more info
PubMed 
insulin secretion IGI
Inferred from Genetic Interaction
more info
PubMed 
insulin secretion involved in cellular response to glucose stimulus ISS
Inferred from Sequence or Structural Similarity
more info
 
luteinization ISS
Inferred from Sequence or Structural Similarity
more info
 
peptidyl-tyrosine dephosphorylation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of type B pancreatic cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
response to cAMP IEA
Inferred from Electronic Annotation
more info
 
response to estrogen IEA
Inferred from Electronic Annotation
more info
 
response to insulin IEA
Inferred from Electronic Annotation
more info
 
response to reactive oxygen species IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
colocalizes_with Golgi apparatus ISS
Inferred from Sequence or Structural Similarity
more info
 
axon terminus ISS
Inferred from Sequence or Structural Similarity
more info
 
cell junction IEA
Inferred from Electronic Annotation
more info
 
colocalizes_with endosome ISS
Inferred from Sequence or Structural Similarity
more info
 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
neuronal cell body ISS
Inferred from Sequence or Structural Similarity
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
perikaryon IEA
Inferred from Electronic Annotation
more info
 
colocalizes_with plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
secretory granule ISS
Inferred from Sequence or Structural Similarity
more info
 
synapse ISS
Inferred from Sequence or Structural Similarity
more info
 
NOT colocalizes_with synaptic vesicle ISS
Inferred from Sequence or Structural Similarity
more info
 
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
XP_011509868.1
XP_016860098.1
XP_016860099.1
XP_016860100.1
XP_016860101.1

NCBI Reference Sequences (RefSeq)

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
    5001..24951
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001199763.1NP_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/Swiss-Prot
    Q16849
    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_001199764.1NP_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, DC352946
    Consensus CDS
    CCDS56167.1
    UniProtKB/Swiss-Prot
    Q16849
    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
    Q16849
    UniProtKB/TrEMBL
    Q96IA0
    Related
    ENSP00000295718.2, ENST00000295718.6
    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: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p12 Primary Assembly

    Range
    219289623..219309573 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017004612.2XP_016860101.1  receptor-type tyrosine-protein phosphatase-like N isoform X5

  2. XM_011511566.2XP_011509868.1  receptor-type tyrosine-protein phosphatase-like N isoform X4

    Conserved Domains (4) summary
    smart00194
    Location:636895
    PTPc; Protein tyrosine phosphatase, catalytic domain
    cd00047
    Location:663895
    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:472556
    Receptor_IA-2; Protein-tyrosine phosphatase receptor IA-2
    pfam14948
    Location:60138
    RESP18; RESP18 domain
  3. XM_017004610.2XP_016860099.1  receptor-type tyrosine-protein phosphatase-like N isoform X2

  4. XM_017004611.2XP_016860100.1  receptor-type tyrosine-protein phosphatase-like N isoform X3

  5. XM_017004609.2XP_016860098.1  receptor-type tyrosine-protein phosphatase-like N isoform X1

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