ptp-3 Protein-tyrosine-phosphatase;Tyrosine-protein phosphatase Lar-like;protein-tyrosine-phosphatase [Caenorhabditis elegans] - Gene

Summary

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Official Symbol: ptp-3
Official Full Name: Protein-tyrosine-phosphatase;Tyrosine-protein phosphatase Lar-like;protein-tyrosine-phosphatase
Primary source: WormBase:WBGene00004215
Locus tag: CELE_C09D8.1
See related: AllianceGenome:WB:WBGene00004215
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Caenorhabditis elegans (strain: Bristol N2)
Lineage: Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
Summary: Enables protein tyrosine phosphatase activity. Involved in several processes, including embryonic morphogenesis; nervous system development; and neuroblast migration. Located in adherens junction and synapse. Is expressed in body wall musculature; embryonic cell; hypodermis; and nervous system. Human ortholog(s) of this gene implicated in coronary artery disease; diabetes mellitus; hyperinsulinism; hypertension; and type 2 diabetes mellitus. Orthologous to several human genes including PTPRD (protein tyrosine phosphatase receptor type D) and PTPRF (protein tyrosine phosphatase receptor type F). [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See ptp-3 in Genome Data Viewer

Location:: chromosome: II

Exon count:: 34

Sequence:: Chromosome: II; NC_003280.10 (10975539..11012247)

Chromosome II - NC_003280.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003280.10

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Vitamin B12 Regulates Glial Migration and Synapse Formation through Isoform-Specific Control of PTP-3/LAR PRTP Expression.
Title: Vitamin B12 Regulates Glial Migration and Synapse Formation through Isoform-Specific Control of PTP-3/LAR PRTP Expression.
loss of the cell adhesion molecule (CAM) CDH-4/Fat-like cadherin causes dendrites to be ordered randomly, despite remaining bundled. Loss of the CAMs PTP-3/LAR or SAX-7/L1CAM causes dendrites to adopt an altered order, which becomes increasingly random as animals grow.
Title: Ordered arrangement of dendrites within a C. elegans sensory nerve bundle.
These data are suggestive of ptp-3 as a potential negative regulator of several kinase families, such as the mitogen activated kinases (MAPKs), and multiple tyrosine kinases including FER, MET, and NTRK2.
Title: Unbiased identification of substrates of protein tyrosine phosphatase ptp-3 in C. elegans.
an inherent left-right asymmetry in the Q neuroblasts with regard to UNC-40, PTP-3, and MIG-21 function that results in posterior vs. anterior migration of neuroblasts
Title: Transmembrane proteins UNC-40/DCC, PTP-3/LAR, and MIG-21 control anterior-posterior neuroblast migration with left-right functional asymmetry in Caenorhabditis elegans.
Long isoform PTP-3A acts as a molecular link between the extracellular matrix and alpha-liprin during synaptogenesis; the short isoform PTP-3B is extrasynaptic.
Title: The two isoforms of the Caenorhabditis elegans leukocyte-common antigen related receptor tyrosine phosphatase PTP-3 function independently in axon guidance and synapse formation.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

C09D8.1 (e-PCR)
- UniSTS:309022

C09D8.2 (e-PCR)
- UniSTS:307234

Homology

Orthologs from OrthoDB

Gene Ontology Provided by WormBase

Function	Evidence Code	Pubs
enables phosphatase activity	IEA Inferred from Electronic Annotation more info
enables phosphoprotein phosphatase activity	IEA Inferred from Electronic Annotation more info
enables protein tyrosine phosphatase activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein tyrosine phosphatase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein tyrosine phosphatase activity	IEA Inferred from Electronic Annotation more info
enables protein tyrosine phosphatase activity	ISS Inferred from Sequence or Structural Similarity more info
enables transmembrane receptor protein tyrosine phosphatase activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed

Process	Evidence Code	Pubs
involved_in embryonic body morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in epidermis development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in gastrulation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in motor neuron axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nervous system development	IBA Inferred from Biological aspect of Ancestor more info
involved_in nervous system development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuroblast migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuron migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein dephosphorylation	IEA Inferred from Electronic Annotation more info
involved_in protein dephosphorylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein localization to synapse	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in signal transduction	IBA Inferred from Biological aspect of Ancestor more info
involved_in synapse assembly	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in adherens junction	IDA Inferred from Direct Assay more info	PubMed
located_in adherens junction	IEA Inferred from Electronic Annotation more info
located_in adherens junction	IMP Inferred from Mutant Phenotype more info	PubMed
located_in anchoring junction	IEA Inferred from Electronic Annotation more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in synapse	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: Protein-tyrosine-phosphatase;Tyrosine-protein phosphatase Lar-like;protein-tyrosine-phosphatase

NP_001021942.1

Confirmed by transcript evidence

NP_001021943.1

Confirmed by transcript evidence

NP_001021944.1

Confirmed by transcript evidence

NP_001254270.1

Confirmed by transcript evidence

NP_001263670.1

Confirmed by transcript evidence

NP_001263671.1

Confirmed by transcript evidence

NP_001263672.1

Confirmed by transcript evidence

NP_001263673.1

Confirmed by transcript evidence

NP_001263674.1

Confirmed by transcript evidence

NP_001364658.1

Confirmed by transcript evidence

NP_001364823.1

Confirmed by transcript evidence

NP_001364824.1

Confirmed by transcript evidence

NP_001391073.1

Confirmed by transcript evidence

NP_001391074.1

Confirmed by transcript evidence

NCBI Reference Sequences (RefSeq)

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Genome Annotation

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

Reference assembly

Genomic

NC_003280.10 Reference assembly

Range

10975539..11012247

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001026771.3 → NP_001021942.1 Tyrosine-protein phosphatase Lar-like [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001021942.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q09434, Q17859, Q20137, Q9BMN7, Q9BMN8

Conserved Domains (7) summary

smart00194
Location:1626 → 1881

PTPc; Protein tyrosine phosphatase, catalytic domain

smart00410
Location:157 → 243

IG_like; Immunoglobulin like

cd00047
Location:1652 → 1881

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:750 → 850

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 ...

pfam07679
Location:49 → 140

I-set; Immunoglobulin I-set domain

pfam00041
Location:1057 → 1145

fn3; Fibronectin type III domain

cl11960
Location:265 → 333

Ig; Immunoglobulin domain
NM_001377858.3 → NP_001364824.1 protein-tyrosine-phosphatase [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/Swiss-Prot

Q09434, Q17859, Q20137, Q9BMN7, Q9BMN8

UniProtKB/TrEMBL

V6CJV7

Conserved Domains (7) summary

cd00063
Location:664 → 764

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 ...

cd14553
Location:1562 → 1799

R-PTPc-LAR-1; catalytic domain of LAR family receptor-type tyrosine-protein phosphatases, repeat 1

pfam00041
Location:971 → 1059

fn3; Fibronectin type III domain

pfam13927
Location:49 → 126

Ig_3; Immunoglobulin domain

cd00096
Location:267 → 275

Ig; Ig strand B [structural motif]

cl11960
Location:265 → 336

Ig; Immunoglobulin domain

cl28904
Location:1847 → 2084

PTP_DSP_cys; cys-based protein tyrosine phosphatase and dual-specificity phosphatase superfamily
NM_001276741.3 → NP_001263670.1 protein-tyrosine-phosphatase [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001263670.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q09434, Q17859, Q20137, Q9BMN7, Q9BMN8

UniProtKB/TrEMBL

L8E6W1

Conserved Domains (7) summary

smart00194
Location:1650 → 1905

PTPc; Protein tyrosine phosphatase, catalytic domain

smart00410
Location:157 → 243

IG_like; Immunoglobulin like

cd00047
Location:1676 → 1905

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:774 → 874

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 ...

pfam07679
Location:49 → 140

I-set; Immunoglobulin I-set domain

pfam00041
Location:1081 → 1169

fn3; Fibronectin type III domain

cl11960
Location:265 → 333

Ig; Immunoglobulin domain
NM_001377859.2 → NP_001364823.1 protein-tyrosine-phosphatase [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/Swiss-Prot

Q09434, Q17859, Q20137, Q9BMN7, Q9BMN8

UniProtKB/TrEMBL

V6CIQ1

Conserved Domains (7) summary

cd00063
Location:640 → 740

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 ...

cd14553
Location:1538 → 1775

R-PTPc-LAR-1; catalytic domain of LAR family receptor-type tyrosine-protein phosphatases, repeat 1

pfam00041
Location:947 → 1035

fn3; Fibronectin type III domain

pfam13927
Location:49 → 126

Ig_3; Immunoglobulin domain

cd00096
Location:267 → 275

Ig; Ig strand B [structural motif]

cl11960
Location:265 → 336

Ig; Immunoglobulin domain

cl28904
Location:1823 → 2060

PTP_DSP_cys; cys-based protein tyrosine phosphatase and dual-specificity phosphatase superfamily
NM_001276742.3 → NP_001263671.1 protein-tyrosine-phosphatase [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001263671.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q09434, Q17859, Q20137, Q9BMN7, Q9BMN8

UniProtKB/TrEMBL

L8E6H9

Conserved Domains (7) summary

smart00194
Location:1694 → 1949

PTPc; Protein tyrosine phosphatase, catalytic domain

smart00410
Location:201 → 287

IG_like; Immunoglobulin like

cd00047
Location:1720 → 1949

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:818 → 918

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 ...

pfam07679
Location:93 → 184

I-set; Immunoglobulin I-set domain

pfam00041
Location:1125 → 1213

fn3; Fibronectin type III domain

cl11960
Location:309 → 377

Ig; Immunoglobulin domain
NM_001276743.3 → NP_001263672.1 protein-tyrosine-phosphatase [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001263672.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q09434, Q17859, Q20137, Q9BMN7, Q9BMN8

UniProtKB/TrEMBL

L8E7X5

Conserved Domains (7) summary

smart00194
Location:1670 → 1925

PTPc; Protein tyrosine phosphatase, catalytic domain

smart00410
Location:201 → 287

IG_like; Immunoglobulin like

cd00047
Location:1696 → 1925

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:794 → 894

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 ...

pfam07679
Location:93 → 184

I-set; Immunoglobulin I-set domain

pfam00041
Location:1101 → 1189

fn3; Fibronectin type III domain

cl11960
Location:309 → 377

Ig; Immunoglobulin domain
NM_001267341.4 → NP_001254270.1 protein-tyrosine-phosphatase [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001254270.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q09434, Q17859, Q20137, Q9BMN7, Q9BMN8

UniProtKB/TrEMBL

G5EE54

Conserved Domains (6) summary

smart00194
Location:1431 → 1686

PTPc; Protein tyrosine phosphatase, catalytic domain

smart00410
Location:63 → 139

IG_like; Immunoglobulin like

cd00047
Location:1457 → 1686

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:555 → 655

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:862 → 950

fn3; Fibronectin type III domain

cl11960
Location:70 → 138

Ig; Immunoglobulin domain
NM_001404237.1 → NP_001391073.1 protein-tyrosine-phosphatase [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/Swiss-Prot

Q09434, Q17859, Q20137, Q9BMN7, Q9BMN8

UniProtKB/TrEMBL

A0A5S9MM89
NM_001377860.2 → NP_001364658.1 protein-tyrosine-phosphatase [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/Swiss-Prot

Q09434, Q17859, Q20137, Q9BMN7, Q9BMN8

UniProtKB/TrEMBL

G5EDC5

Conserved Domains (6) summary

cd00063
Location:579 → 679

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 ...

cd14553
Location:1477 → 1714

R-PTPc-LAR-1; catalytic domain of LAR family receptor-type tyrosine-protein phosphatases, repeat 1

pfam00041
Location:461 → 567

fn3; Fibronectin type III domain

cd00096
Location:72 → 80

Ig; Ig strand B [structural motif]

cl11960
Location:70 → 141

Ig; Immunoglobulin domain

cl28904
Location:1762 → 1999

PTP_DSP_cys; cys-based protein tyrosine phosphatase and dual-specificity phosphatase superfamily
NM_001404238.1 → NP_001391074.1 protein-tyrosine-phosphatase [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/Swiss-Prot

Q09434, Q17859, Q20137, Q9BMN7, Q9BMN8

UniProtKB/TrEMBL

A0A5S9MN58
NM_001026772.6 → NP_001021943.1 Tyrosine-protein phosphatase Lar-like [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001021943.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q9BMN8

Conserved Domains (4) summary

smart00194
Location:913 → 1168

PTPc; Protein tyrosine phosphatase, catalytic domain

cd00047
Location:939 → 1168

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:37 → 137

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:344 → 432

fn3; Fibronectin type III domain
NM_001026773.6 → NP_001021944.1 protein-tyrosine-phosphatase [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001021944.1

Status: REVIEWED

UniProtKB/TrEMBL

Q8I120

Conserved Domains (4) summary

smart00194
Location:662 → 917

PTPc; Protein tyrosine phosphatase, catalytic domain

cd00047
Location:688 → 917

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:198 → 276

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:93 → 181

fn3; Fibronectin type III domain
NM_001276744.4 → NP_001263673.1 protein-tyrosine-phosphatase [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001263673.1

Status: REVIEWED

UniProtKB/TrEMBL

L8E6Z3

Conserved Domains (4) summary

smart00194
Location:693 → 948

PTPc; Protein tyrosine phosphatase, catalytic domain

cd00047
Location:719 → 948

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:229 → 307

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:124 → 212

fn3; Fibronectin type III domain
NM_001276745.3 → NP_001263674.1 Protein-tyrosine-phosphatase [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001263674.1

Status: REVIEWED

UniProtKB/TrEMBL

L8E6L2

Conserved Domains (3) summary

smart00194
Location:529 → 784

PTPc; Protein tyrosine phosphatase, catalytic domain

cd00047
Location:555 → 784

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:65 → 143

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 ...