clr-1 Receptor-type tyrosine-protein phosphatase;protein-tyrosine-phosphatase [Caenorhabditis elegans] - Gene

Summary

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Official Symbol: clr-1
Official Full Name: Receptor-type tyrosine-protein phosphatase;protein-tyrosine-phosphatase
Primary source: WormBase:WBGene00000548
Locus tag: CELE_F56D1.4
See related: AllianceGenome:WB:WBGene00000548
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 transmembrane receptor protein tyrosine phosphatase activity. Involved in several processes, including negative regulation of fibroblast growth factor receptor signaling pathway; netrin-activated signaling pathway; and positive regulation of synapse assembly. Located in plasma membrane and postsynapse. Is expressed in several structures, including AVA; body wall musculature; muscle cell; preanal ganglion; and somatic gonad. Human ortholog(s) of this gene implicated in multiple sclerosis; primary immunodeficiency disease; and severe combined immunodeficiency. Orthologous to human PTPRC (protein tyrosine phosphatase receptor type C); PTPRG (protein tyrosine phosphatase receptor type G); and PTPRZ1 (protein tyrosine phosphatase receptor type Z1). [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See clr-1 in Genome Data Viewer

Location:: chromosome: II

Exon count:: 20

Sequence:: Chromosome: II; NC_003280.10 (5466358..5473816)

Chromosome II - NC_003280.10

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?

Data show that the receptor protein tyrosine phosphatase (RPTP) clr-1 is necessary for synaptic partner recognition (SPR) between the PHB sensory neurons and the AVA interneurons.
Title: The receptor protein tyrosine phosphatase CLR-1 is required for synaptic partner recognition.
CLR-1 acts in C. elegans skin cells to promote sensory dendrite outgrowth
Title: Receptor tyrosine phosphatase CLR-1 acts in skin cells to promote sensory dendrite outgrowth.

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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

F56D1.4 (e-PCR)
- UniSTS:311866

Homology

Orthologs from OrthoDB

Gene Ontology Provided by WormBase

Function	Evidence Code	Pubs
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	IEA Inferred from Electronic Annotation more info
enables transmembrane receptor protein tyrosine phosphatase activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in chemosensory behavior	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of fibroblast growth factor receptor signaling pathway	IGI Inferred from Genetic Interaction more info	PubMed
involved_in nervous system development	IEA Inferred from Electronic Annotation more info
involved_in netrin-activated signaling pathway	IGI Inferred from Genetic Interaction more info	PubMed
involved_in neuron projection development	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of synapse assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein dephosphorylation	IEA Inferred from Electronic Annotation more info
involved_in sensory perception of chemical stimulus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in signal transduction	IBA Inferred from Biological aspect of Ancestor more info
involved_in synaptic signaling	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in postsynapse	IDA Inferred from Direct Assay more info	PubMed
located_in synapse	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: Receptor-type tyrosine-protein phosphatase;protein-tyrosine-phosphatase

NP_001022208.1

Confirmed by transcript evidence

NP_001022209.1

Confirmed by transcript evidence

NP_001129817.1

Confirmed by transcript evidence

NP_001334206.1

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

5466358..5473816

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001136345.4 → NP_001129817.1 Receptor-type tyrosine-protein phosphatase [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001129817.1

Status: REVIEWED

UniProtKB/Swiss-Prot

H2KZM6

Conserved Domains (4) summary

smart00194
Location:790 → 1069

PTPc; Protein tyrosine phosphatase, catalytic domain

smart00410
Location:173 → 256

IG_like; Immunoglobulin like

cd00047
Location:816 → 1069

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:366 → 486

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 ...
NM_001027037.4 → NP_001022208.1 Receptor-type tyrosine-protein phosphatase [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001022208.1

Status: REVIEWED

UniProtKB/Swiss-Prot

B2MZB0, H2KZM6, H2KZM7, H2KZM8, O76282, Q9TZZ1

Conserved Domains (4) summary

smart00194
Location:792 → 1071

PTPc; Protein tyrosine phosphatase, catalytic domain

smart00410
Location:175 → 258

IG_like; Immunoglobulin like

cd00047
Location:818 → 1071

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:368 → 488

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 ...
NM_001027038.3 → NP_001022209.1 Receptor-type tyrosine-protein phosphatase [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001022209.1

Status: REVIEWED

UniProtKB/Swiss-Prot

H2KZM6

Conserved Domains (4) summary

smart00194
Location:827 → 1106

PTPc; Protein tyrosine phosphatase, catalytic domain

smart00410
Location:175 → 258

IG_like; Immunoglobulin like

cd00047
Location:853 → 1106

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:403 → 523

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 ...
NM_001347284.3 → NP_001334206.1 protein-tyrosine-phosphatase [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/TrEMBL

A0A1I6CMB8