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PTPN23 protein tyrosine phosphatase non-receptor type 23 [ Homo sapiens (human) ]

Gene ID: 25930, updated on 24-Nov-2020

Summary

Official Symbol
PTPN23provided by HGNC
Official Full Name
protein tyrosine phosphatase non-receptor type 23provided by HGNC
Primary source
HGNC:HGNC:14406
See related
Ensembl:ENSG00000076201 MIM:606584
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
HDPTP; HD-PTP; NEDBASS; PTP-TD14
Summary
This gene encodes a member of the non-receptor type protein-tyrosine phosphatase family. The encoded protein may be involved in the regulation of small nuclear ribonucleo protein assembly and pre-mRNA splicing by modifying the survival motor neuron (SMN) complex. The encoded protein additionally plays a role in ciliogenesis and is part of endosomal sorting complex required for transport (ESCRT) pathways. This gene may serve a tumor suppressor function. [provided by RefSeq, Jul 2016]
Expression
Ubiquitous expression in spleen (RPKM 10.2), brain (RPKM 9.8) and 25 other tissues See more
Orthologs

Genomic context

See PTPN23 in Genome Data Viewer
Location:
3p21.31
Exon count:
25
Annotation release Status Assembly Chr Location
109.20201120 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (47381001..47413435)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (47422383..47454931)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene kinesin family member 9 Neighboring gene small nucleolar RNA, C/D box 13 pseudogene 3 Neighboring gene small nucleolar RNA, C/D box 13J Neighboring gene kelch like family member 18 Neighboring gene SREBF chaperone Neighboring gene uncharacterized LOC105377073 Neighboring gene bolA family member 2 pseudogene 2 Neighboring gene elongator acetyltransferase complex subunit 6

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?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Pr55(Gag) gag The isolated Bro1 domains of HD-PTP and rhophilin both bind to HIV-1 NC and share the capacity to stimulate VLP production by a minimal HIV-1 Gag molecule PubMed
Tat tat HIV-1 Tat upregulates the tyrosine phosphatase HD-PTP mRNA in a human endothelial cell line, however Tat-induction of HD-PTP mRNA parallels only with a slight increase of the protein PubMed
nucleocapsid gag The isolated Bro1 domains of HD-PTP and rhophilin both bind to HIV-1 NC and share the capacity to stimulate VLP production by a minimal HIV-1 Gag molecule PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA1471, DKFZp564F0923

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein kinase binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein tyrosine phosphatase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
ciliary basal body IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IEA
Inferred from Electronic Annotation
more info
 
early endosome IDA
Inferred from Direct Assay
more info
PubMed 
endosome IDA
Inferred from Direct Assay
more info
PubMed 
extracellular exosome HDA PubMed 
nuclear body IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
tyrosine-protein phosphatase non-receptor type 23
Names
his domain-containing protein tyrosine phosphatase
protein tyrosine phosphatase TD14
NP_001291411.1
NP_056281.1
XP_005265088.2

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_051056.1 RefSeqGene

    Range
    5040..37454
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001304482.2NP_001291411.1  tyrosine-protein phosphatase non-receptor type 23 isoform 2

    See identical proteins and their annotated locations for NP_001291411.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon in its 5' UTR and uses a downstream start codon compared to variant 1. It encodes isoform 2 which has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AF290614, AK299906, BU173747
    UniProtKB/Swiss-Prot
    Q9H3S7
    UniProtKB/TrEMBL
    B4DST5
    Conserved Domains (5) summary
    cd09234
    Location:236574
    V_HD-PTP_like; Protein-interacting V-domain of mammalian His-Domain type N23 protein tyrosine phosphatase and related domains
    cd00047
    Location:10941323
    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 ...
    pfam00102
    Location:10941324
    Y_phosphatase; Protein-tyrosine phosphatase
    pfam13949
    Location:291575
    ALIX_LYPXL_bnd; ALIX V-shaped domain binding to HIV
    cl14649
    Location:1231
    BRO1_Alix_like; Protein-interacting Bro1-like domain of mammalian Alix and related domains
  2. NM_015466.4NP_056281.1  tyrosine-protein phosphatase non-receptor type 23 isoform 1

    See identical proteins and their annotated locations for NP_056281.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AB040904, AF290614, BU173747
    Consensus CDS
    CCDS2754.1
    UniProtKB/Swiss-Prot
    Q9H3S7
    Related
    ENSP00000265562.4, ENST00000265562.5
    Conserved Domains (5) summary
    cd09234
    Location:362700
    V_HD-PTP_like; Protein-interacting V-domain of mammalian His-Domain type N23 protein tyrosine phosphatase and related domains
    cd09239
    Location:2357
    BRO1_HD-PTP_like; Protein-interacting, N-terminal, Bro1-like domain of mammalian His-Domain type N23 protein tyrosine phosphatase and related domains
    cd00047
    Location:12201449
    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 ...
    pfam00102
    Location:12201450
    Y_phosphatase; Protein-tyrosine phosphatase
    pfam13949
    Location:417701
    ALIX_LYPXL_bnd; ALIX V-shaped domain binding to HIV

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20201120

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    47381001..47413435
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005265031.2XP_005265088.2  tyrosine-protein phosphatase non-receptor type 23 isoform X1

    Conserved Domains (5) summary
    cd09234
    Location:352690
    V_HD-PTP_like; Protein-interacting V-domain of mammalian His-Domain type N23 protein tyrosine phosphatase and related domains
    cd09239
    Location:2347
    BRO1_HD-PTP_like; Protein-interacting, N-terminal, Bro1-like domain of mammalian His-Domain type N23 protein tyrosine phosphatase and related domains
    cd00047
    Location:12101439
    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 ...
    pfam00102
    Location:12101440
    Y_phosphatase; Protein-tyrosine phosphatase
    pfam13949
    Location:407691
    ALIX_LYPXL_bnd; ALIX V-shaped domain binding to HIV
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