tra-3 Calpain-5 [Caenorhabditis elegans] - Gene

Summary

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Gene symbol: tra-3
Gene description: Calpain-5
Primary source: WormBase:WBGene00006606
Locus tag: CELE_LLC1.1
See related: AllianceGenome:WB:WBGene00006606
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 cysteine-type endopeptidase activity. Involved in female germ-line sex determination; feminization of hermaphrodite soma; and proteolysis. Predicted to be located in membrane. Predicted to be active in cytoplasm. Is expressed in several structures, including excretory cell; hypodermis; intestine; ventral nerve cord; and vulva. Human ortholog(s) of this gene implicated in neovascular inflammatory vitreoretinopathy. Orthologous to several human genes including CAPN5 (calpain 5). [provided by Alliance of Genome Resources, Apr 2022]
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Genomic context

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See tra-3 in Genome Data Viewer

Location:: chromosome: IV

Exon count:: 8

Sequence:: Chromosome: IV; NC_003282.8 (14436445..14444183, complement)

Chromosome IV - NC_003282.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003282.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

A single nucleotide polymorphism in tra-3 leads to mutation F96L in the encoded calpain-like protease. This mutation attenuates the ability of CB4856 to grow larger at low temperature.
Title: A Caenorhabditis elegans wild type defies the temperature-size rule owing to a single nucleotide polymorphism in tra-3.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

LLC1.1 (e-PCR)
- UniSTS:319519

Homology

Orthologs from OrthoDB

Gene Ontology Provided by WormBase

Function	Evidence Code	Pubs
enables calcium-dependent cysteine-type endopeptidase activity	IBA Inferred from Biological aspect of Ancestor more info
enables calcium-dependent cysteine-type endopeptidase activity	IEA Inferred from Electronic Annotation more info
enables calcium-dependent cysteine-type endopeptidase activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables cysteine-type endopeptidase activity	IDA Inferred from Direct Assay more info	PubMed
enables cysteine-type endopeptidase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables cysteine-type peptidase activity	IEA Inferred from Electronic Annotation more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables peptidase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in female germ-line sex determination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in feminization of hermaphrodite soma	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in hermaphrodite somatic sex determination	IGI Inferred from Genetic Interaction more info	PubMed
involved_in hermaphrodite somatic sex determination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in membrane protein intracellular domain proteolysis	IDA Inferred from Direct Assay more info	PubMed
involved_in programmed cell death	IEA Inferred from Electronic Annotation more info
involved_in protein autoprocessing	IDA Inferred from Direct Assay more info	PubMed
involved_in proteolysis	IBA Inferred from Biological aspect of Ancestor more info
involved_in proteolysis	IDA Inferred from Direct Assay more info	PubMed
involved_in proteolysis	IEA Inferred from Electronic Annotation more info
involved_in proteolysis	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in sex differentiation	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	TAS Traceable Author Statement more info	PubMed

General protein information

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Preferred Names: Calpain-5

NP_502751.1

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_003282.8 Reference assembly

Range

14436445..14444183 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_070350.7 → NP_502751.1 Calpain-5 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_502751.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q22036

Conserved Domains (3) summary

smart00230
Location:15 → 361

CysPc; Calpain-like thiol protease family

cd04046
Location:526 → 646

C2_Calpain; C2 domain present in Calpain proteins

cd00214
Location:362 → 511

Calpain_III; Calpain, subdomain III. Calpains are calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are ...