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

Summary

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Official Symbol: tra-3
Official Full Name: 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 several processes, including female germ-line sex determination; feminization of hermaphrodite soma; and protein autoprocessing. 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, Dec 2024]
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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.

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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

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

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 ...