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PTPRB protein tyrosine phosphatase, receptor type B [ Homo sapiens (human) ]

Gene ID: 5787, updated on 8-Dec-2018

Summary

Official Symbol
PTPRBprovided by HGNC
Official Full Name
protein tyrosine phosphatase, receptor type Bprovided by HGNC
Primary source
HGNC:HGNC:9665
See related
Ensembl:ENSG00000127329 MIM:176882
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
PTPB; HPTPB; VEPTP; HPTP-BETA; R-PTP-BETA
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 contains an extracellular domain, a single transmembrane segment and one intracytoplasmic catalytic domain, thus belongs to receptor type PTP. The extracellular region of this PTP is composed of multiple fibronectin type_III repeats, which was shown to interact with neuronal receptor and cell adhesion molecules, such as contactin and tenascin C. This protein was also found to interact with sodium channels, and thus may regulate sodium channels by altering tyrosine phosphorylation status. The functions of the interaction partners of this protein implicate the roles of this PTP in cell adhesion, neurite growth, and neuronal differentiation. Alternate transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2011]
Expression
Broad expression in lung (RPKM 16.0), spleen (RPKM 13.5) and 22 other tissues See more
Orthologs

Genomic context

See PTPRB in Genome Data Viewer
Location:
12q15
Exon count:
37
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 12 NC_000012.12 (70515871..70637440, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (70910630..71031220, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369827 Neighboring gene RNA, U4 small nuclear 65, pseudogene Neighboring gene uncharacterized LOC105369828 Neighboring gene protein tyrosine phosphatase, receptor type R Neighboring gene fumarylacetoacetate hydrolase domain containing 2 pseudogene 1 Neighboring gene tetraspanin 8

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?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association study of peripheral neuropathy with D-drug-containing regimens in AIDS Clinical Trials Group protocol 384.
NHGRI GWA 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
Tat tat HIV-1 Tat C treated human brain microvascular endothelial cells result in downregulation and dissociation of VE-PTP and SHP2 from VE-cadherin PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Adherens junction, organism-specific biosystem (from KEGG)
    Adherens junction, organism-specific biosystemCell-cell adherens junctions (AJs), the most common type of intercellular adhesions, are important for maintaining tissue architecture and cell polarity and can limit cell movement and proliferation....
  • Adherens junction, conserved biosystem (from KEGG)
    Adherens junction, conserved biosystemCell-cell adherens junctions (AJs), the most common type of intercellular adhesions, are important for maintaining tissue architecture and cell polarity and can limit cell movement and proliferation....
  • Ectoderm Differentiation, organism-specific biosystem (from WikiPathways)
    Ectoderm Differentiation, organism-specific biosystemModel depicting ectoderm specification based on the literature and highly enriched gene expression profiles via comparison across dozens of independent induced and embryonic pluripotent stem cell lin...
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Innate Immune System, organism-specific biosystem (from REACTOME)
    Innate Immune System, organism-specific biosystemInnate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
  • Neutrophil degranulation, organism-specific biosystem (from REACTOME)
    Neutrophil degranulation, organism-specific biosystemNeutrophils are the most abundant leukocytes (white blood cells), indispensable in defending the body against invading microorganisms. In response to infection, neutrophils leave the circulation and ...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ44133, MGC59935, MGC142023, DKFZp686E2262, DKFZp686H15164

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
transmembrane receptor protein tyrosine phosphatase activity TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
angiogenesis IEA
Inferred from Electronic Annotation
more info
 
dephosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
neutrophil degranulation TAS
Traceable Author Statement
more info
 
peptidyl-tyrosine dephosphorylation IEA
Inferred from Electronic Annotation
more info
 
phosphate-containing compound metabolic process TAS
Traceable Author Statement
more info
PubMed 
protein dephosphorylation TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
integral component of plasma membrane TAS
Traceable Author Statement
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 
receptor complex IDA
Inferred from Direct Assay
more info
PubMed 
specific granule membrane TAS
Traceable Author Statement
more info
 
tertiary granule membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
receptor-type tyrosine-protein phosphatase beta
Names
VE-PTP
protein tyrosine phosphatase, receptor type, beta polypeptide
vascular endothelial protein tyrosine phosphatase
NP_001103224.1
NP_001193900.1
NP_001193901.1
NP_001317133.1
NP_002828.3
XP_006719591.1
XP_006719592.1
XP_011536916.1
XP_016875213.1

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_029940.2 RefSeqGene

    Range
    5001..126570
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001109754.3NP_001103224.1  receptor-type tyrosine-protein phosphatase beta isoform a

    See identical proteins and their annotated locations for NP_001103224.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AC025569, AI688145, BC051329, BC101679, BC143360, BQ710210, DN999550
    Consensus CDS
    CCDS44943.1
    UniProtKB/Swiss-Prot
    P23467
    UniProtKB/TrEMBL
    Q86VA4
    Related
    ENSP00000334928.6, ENST00000334414.10
    Conserved Domains (5) summary
    smart00194
    Location:19202178
    PTPc; Protein tyrosine phosphatase, catalytic domain
    cd00047
    Location:19472178
    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:507582
    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 ...
    cd00161
    Location:2294
    RICIN; Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ...
    pfam00041
    Location:14801562
    fn3; Fibronectin type III domain
  2. NM_001206971.2NP_001193900.1  receptor-type tyrosine-protein phosphatase beta isoform c precursor

    See identical proteins and their annotated locations for NP_001193900.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and coding region compared to variant 1. The resulting isoform (c) is shorter and has a distinct N-terminus compared to isoform a.
    Source sequence(s)
    AC025569, AC083809, AI688145, BC143360, BQ710210, X54131
    Consensus CDS
    CCDS55845.1
    UniProtKB/Swiss-Prot
    P23467
    Related
    ENSP00000447302.1, ENST00000550857.5
    Conserved Domains (4) summary
    smart00194
    Location:16121870
    PTPc; Protein tyrosine phosphatase, catalytic domain
    cd00047
    Location:16391870
    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:289364
    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:11721254
    fn3; Fibronectin type III domain
  3. NM_001206972.2NP_001193901.1  receptor-type tyrosine-protein phosphatase beta isoform d precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and coding region compared to variant 1. The resulting isoform (d) is shorter and has a distinct N-terminus compared to isoform a.
    Source sequence(s)
    AC025569, AC083809, AI688145, BC101679, BC143356, BC143360, BQ710210, X54131
    Consensus CDS
    CCDS55846.1
    UniProtKB/Swiss-Prot
    P23467
    Related
    ENSP00000438927.1, ENST00000538708.5
    Conserved Domains (4) summary
    smart00194
    Location:16121870
    PTPc; Protein tyrosine phosphatase, catalytic domain
    cd00047
    Location:16391870
    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:289364
    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:11721254
    fn3; Fibronectin type III domain
  4. NM_001330204.1NP_001317133.1  receptor-type tyrosine-protein phosphatase beta isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks an alternate in-frame exon in the 3' coding region compared to variant 1. The resulting isoform (e) is shorter but has the same N- and C-termini compared to isoform a.
    Source sequence(s)
    AC025569, AI688145, AK097371, BC051329, BC101679, BC143360, BQ710210, CR749546, DN999550
    Consensus CDS
    CCDS81713.1
    UniProtKB/Swiss-Prot
    P23467
    UniProtKB/TrEMBL
    F8VU56, Q68D73, Q86VA4
    Related
    ENSP00000448058.1, ENST00000550358.5
  5. NM_002837.5NP_002828.3  receptor-type tyrosine-protein phosphatase beta isoform b precursor

    See identical proteins and their annotated locations for NP_002828.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding region compared to variant 1. The resulting isoform (b) is shorter and has a distinct N-terminus compared to isoform a.
    Source sequence(s)
    AC025569, AC083809, AI688145, BC101679, BC143360, BQ710210, X54131
    Consensus CDS
    CCDS44944.1
    UniProtKB/Swiss-Prot
    P23467
    Related
    ENSP00000261266.5, ENST00000261266.9
    Conserved Domains (4) summary
    smart00194
    Location:17021960
    PTPc; Protein tyrosine phosphatase, catalytic domain
    cd00047
    Location:17291960
    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:289364
    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:12621344
    fn3; Fibronectin type III 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_000012.12 Reference GRCh38.p12 Primary Assembly

    Range
    70515871..70637440 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011538614.1XP_011536916.1  receptor-type tyrosine-protein phosphatase beta isoform X2

    Conserved Domains (5) summary
    smart00194
    Location:18322090
    PTPc; Protein tyrosine phosphatase, catalytic domain
    cd00047
    Location:18592090
    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:507582
    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 ...
    cd00161
    Location:2294
    RICIN; Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ...
    pfam00041
    Location:13921474
    fn3; Fibronectin type III domain
  2. XM_006719528.1XP_006719591.1  receptor-type tyrosine-protein phosphatase beta isoform X1

    Conserved Domains (5) summary
    smart00194
    Location:19202178
    PTPc; Protein tyrosine phosphatase, catalytic domain
    cd00047
    Location:19472178
    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:507582
    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 ...
    cd00161
    Location:2294
    RICIN; Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ...
    pfam00041
    Location:14801562
    fn3; Fibronectin type III domain
  3. XM_006719529.4XP_006719592.1  receptor-type tyrosine-protein phosphatase beta isoform X3

    Conserved Domains (4) summary
    smart00194
    Location:17021960
    PTPc; Protein tyrosine phosphatase, catalytic domain
    cd00047
    Location:17291960
    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:289364
    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:12621344
    fn3; Fibronectin type III domain
  4. XM_017019724.1XP_016875213.1  receptor-type tyrosine-protein phosphatase beta isoform X4

RNA

  1. XR_944651.1 RNA Sequence

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