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

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; AllianceGenome:HGNC:9665
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: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 12q15

Exon count:: 37

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (70515870..70637429, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (70495299..70616833, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (70909650..71031209, complement)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

Project title: HPA RNA-seq normal tissues 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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Novel rare mutation in a conserved site of PTPRB causes human hypoplastic left heart syndrome.
Title: Novel rare mutation in a conserved site of PTPRB causes human hypoplastic left heart syndrome.
The variants in PTPRB, TRAF3IP3, and DISC1 genes were associated with Graves' disease in the Chinese population.
Title: The variants in PTPRB, TRAF3IP3, and DISC1 genes were associated with Graves' disease in the Chinese population.
PSMD11, PTPRM and PTPRB as novel biomarkers of pancreatic cancer progression.
Title: PSMD11, PTPRM and PTPRB as novel biomarkers of pancreatic cancer progression.
Exploring the effect of inhibitor AKB-9778 on VE-PTP by molecular docking and molecular dynamics simulation.
Title: Exploring the effect of inhibitor AKB-9778 on VE-PTP by molecular docking and molecular dynamics simulation.
The search for substrates of VE-PTP revealed that proteins relevant for the regulation of endothelial junctions and of cell adhesion are over-represented among the potential targets of VE-PTP, supporting the concept that VEPTP is an important regulator of vascular integrity and junctional signaling.
Title: Vascular Endothelial Receptor Tyrosine Phosphatase: Identification of Novel Substrates Related to Junctions and a Ternary Complex with EPHB4 and TIE2.
PTPRB overexpression decreased vimentin expression and promoted E-cadherin expression, consistent with promotion of EMT, while PTPRB knockdown had the opposite effect.
Title: PTPRB promotes metastasis of colorectal carcinoma via inducing epithelial-mesenchymal transition.
Study found PTPRB negatively correlated with miR-624 expression in osteosarcoma (OS) tissues. PTPRB was confirmed as a downstream target of miR-624.
Title: miR-624-5p promoted tumorigenesis and metastasis by suppressing hippo signaling through targeting PTPRB in osteosarcoma cells.
Collagen regulates the ability of endothelial progenitor cells to protect hypoxic myocardium through a mechanism involving miR-377/VE-PTP axis.
Title: Collagen regulates the ability of endothelial progenitor cells to protect hypoxic myocardium through a mechanism involving miR-377/VE-PTP axis.
PTPRB was down-regulated in non-small-cell lung cancer patients and was associated with patient overall survival.
Title: Protein tyrosine phosphatase PTPRB regulates Src phosphorylation and tumour progression in NSCLC.
STIM1-induced Ca(2+) signaling activates Pyk2 to inhibit the interaction of VE-PTP and VE-cadherin and hence increase endothelial permeability.
Title: Pyk2 phosphorylation of VE-PTP downstream of STIM1-induced Ca(2+) entry regulates disassembly of adherens junctions.

Submit: New GeneRIF Correction See all GeneRIFs (23)

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study of peripheral neuropathy with D-drug-containing regimens in AIDS Clinical Trials Group protocol 384. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

Go to the top of the page Help

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

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

RH92659 (e-PCR)
- UniSTS:92963

SGC33710 (e-PCR)
- UniSTS:47666

G17666 (e-PCR)
- UniSTS:43338

RH80030 (e-PCR)
- UniSTS:87680

D12S1722 (e-PCR), detects polymorphism
- UniSTS:4482

D12S1493 (e-PCR)
- UniSTS:153994

D12S1043 (e-PCR)
- UniSTS:34443

SHGC-150877 (e-PCR)
- UniSTS:173465

SHGC-144132 (e-PCR)
- UniSTS:172190

RH44716 (e-PCR)
- UniSTS:63391

A008P13 (e-PCR)
- UniSTS:79530

RH121587 (e-PCR)
- UniSTS:134359

PTPRB_7863 (e-PCR)
- UniSTS:466410

SHGC-31640 (e-PCR)
- UniSTS:60918

Clone Names

FLJ44133, MGC59935, MGC142023, DKFZp686E2262, DKFZp686H15164

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables cadherin binding	IBA Inferred from Biological aspect of Ancestor more info
enables cadherin binding	IPI Inferred from Physical Interaction more info	PubMed
enables histone H2AXY142 phosphatase activity	IEA Inferred from Electronic Annotation more info
enables non-membrane spanning protein tyrosine phosphatase activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein tyrosine phosphatase activity, metal-dependent	IEA Inferred from Electronic Annotation more info
enables transmembrane receptor protein tyrosine phosphatase activity	TAS Traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in angiogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in dephosphorylation	IDA Inferred from Direct Assay more info	PubMed
involved_in glial cell migration	IEA Inferred from Electronic Annotation more info
involved_in osteoblast differentiation	IDA Inferred from Direct Assay more info	PubMed
involved_in phosphate-containing compound metabolic process	TAS Traceable Author Statement more info	PubMed
involved_in protein dephosphorylation	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
is_active_in plasma membrane	IC Inferred by Curator more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info
part_of receptor complex	IBA Inferred from Biological aspect of Ancestor more info
part_of receptor complex	IDA Inferred from Direct Assay more info	PubMed
located_in specific granule membrane	TAS Traceable Author Statement more info
located_in tertiary granule membrane	TAS Traceable Author Statement more info

General protein information

Go to the top of the page Help

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

EC 3.1.3.48

NP_001193900.1

EC 3.1.3.48

NP_001193901.1

EC 3.1.3.48

NP_001317133.1

EC 3.1.3.48

NP_002828.3

EC 3.1.3.48

XP_006719591.1

EC 3.1.3.48

XP_006719592.1

EC 3.1.3.48

XP_011536916.1

EC 3.1.3.48

XP_016875213.1

EC 3.1.3.48

XP_054228695.1

EC 3.1.3.48

XP_054228696.1

EC 3.1.3.48

XP_054228697.1

EC 3.1.3.48

XP_054228698.1

EC 3.1.3.48

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

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

NG_029940.2 RefSeqGene

Range

5012..126571

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001109754.4 → NP_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/TrEMBL

Q6MZF6

Related

ENSP00000334928.6, ENST00000334414.11

Conserved Domains (5) summary

smart00194
Location:1920 → 2178

PTPc; Protein tyrosine phosphatase, catalytic domain

cd00047
Location:1947 → 2178

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:507 → 582

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:22 → 94

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:1480 → 1562

fn3; Fibronectin type III domain
NM_001206971.3 → NP_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/TrEMBL

Q6MZF6

Related

ENSP00000447302.1, ENST00000550857.5

Conserved Domains (4) summary

smart00194
Location:1612 → 1870

PTPc; Protein tyrosine phosphatase, catalytic domain

cd00047
Location:1639 → 1870

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:289 → 364

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:1172 → 1254

fn3; Fibronectin type III domain
NM_001206972.3 → NP_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/TrEMBL

Q6MZF6

Related

ENSP00000438927.1, ENST00000538708.5

Conserved Domains (4) summary

smart00194
Location:1612 → 1870

PTPc; Protein tyrosine phosphatase, catalytic domain

cd00047
Location:1639 → 1870

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:289 → 364

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:1172 → 1254

fn3; Fibronectin type III domain
NM_001330204.2 → NP_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/TrEMBL

F8VU56, Q6MZF6

Related

ENSP00000448058.1, ENST00000550358.5
NM_002837.6 → NP_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

B7ZKS8, B7ZKT0, C9JX87, F5H3G6, P23467, Q14D85, Q3MIV7

UniProtKB/TrEMBL

Q6MZF6

Related

ENSP00000261266.5, ENST00000261266.9

Conserved Domains (4) summary

smart00194
Location:1702 → 1960

PTPc; Protein tyrosine phosphatase, catalytic domain

cd00047
Location:1729 → 1960

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:289 → 364

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:1262 → 1344

fn3; Fibronectin type III 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

NC_000012.12 Reference GRCh38.p14 Primary Assembly

Range

70515870..70637429 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011538614.2 → XP_011536916.1 receptor-type tyrosine-protein phosphatase beta isoform X2

UniProtKB/TrEMBL

Q6MZF6

Conserved Domains (5) summary

smart00194
Location:1832 → 2090

PTPc; Protein tyrosine phosphatase, catalytic domain

cd00047
Location:1859 → 2090

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:507 → 582

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:22 → 94

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:1392 → 1474

fn3; Fibronectin type III domain
XM_006719528.2 → XP_006719591.1 receptor-type tyrosine-protein phosphatase beta isoform X1

UniProtKB/TrEMBL

Q6MZF6

Conserved Domains (5) summary

smart00194
Location:1920 → 2178

PTPc; Protein tyrosine phosphatase, catalytic domain

cd00047
Location:1947 → 2178

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:507 → 582

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:22 → 94

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:1480 → 1562

fn3; Fibronectin type III domain
XM_006719529.5 → XP_006719592.1 receptor-type tyrosine-protein phosphatase beta isoform X3

UniProtKB/TrEMBL

Q6MZF6

Conserved Domains (4) summary

smart00194
Location:1702 → 1960

PTPc; Protein tyrosine phosphatase, catalytic domain

cd00047
Location:1729 → 1960

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:289 → 364

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:1262 → 1344

fn3; Fibronectin type III domain
XM_017019724.1 → XP_016875213.1 receptor-type tyrosine-protein phosphatase beta isoform X4

RNA

XR_944651.2 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060936.1 Alternate T2T-CHM13v2.0

Range

70495299..70616833 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054372721.1 → XP_054228696.1 receptor-type tyrosine-protein phosphatase beta isoform X2
XM_054372720.1 → XP_054228695.1 receptor-type tyrosine-protein phosphatase beta isoform X1
XM_054372722.1 → XP_054228697.1 receptor-type tyrosine-protein phosphatase beta isoform X3
XM_054372723.1 → XP_054228698.1 receptor-type tyrosine-protein phosphatase beta isoform X4