clp-1 Calpain clp-1 [Caenorhabditis elegans] - Gene

Summary

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Official Symbol: clp-1
Official Full Name: Calpain clp-1
Primary source: WormBase:WBGene00000542
Locus tag: CELE_C06G4.2
See related: AllianceGenome:WB:WBGene00000542
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: Predicted to enable calcium-dependent cysteine-type endopeptidase activity. Involved in several processes, including cellular response to calcium ion; muscle cell cellular homeostasis; and positive regulation of sarcomere organization. Located in M band. Is expressed in several structures, including body wall musculature; egg-laying apparatus; intestine; nervous system; and pharynx. Used to study Duchenne muscular dystrophy and hereditary spastic paraplegia. Human ortholog(s) of this gene implicated in autosomal dominant limb-girdle muscular dystrophy; autosomal recessive limb-girdle muscular dystrophy type 2A; hereditary spastic paraplegia 76; muscular dystrophy; and stomach cancer. Orthologous to several human genes including CAPN3 (calpain 3) and CAPN9 (calpain 9). [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See clp-1 in Genome Data Viewer

Location:: chromosome: III

Exon count:: 16

Sequence:: Chromosome: III; NC_003281.10 (7981074..7986328)

Chromosome III - NC_003281.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003281.10

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

this study reports crystal structures of Clp1 from Caenorhabditis elegans (ceClp1) in a number of nucleotide- and RNA-bound states along the reaction pathway.
Title: RNA specificity and regulation of catalysis in the eukaryotic polynucleotide kinase Clp1.
our analyses highlight the roles of calcium dysregulation and CLP-1 in muscle myopathies and suggest that the atypical calpains could retain conserved
Title: The atypical calpains: evolutionary analyses and roles in Caenorhabditis elegans cellular degeneration.

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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

C06G4.3 (e-PCR)
- UniSTS:315436

STS3-26 (e-PCR)
- UniSTS:242075

C06G4.2 (e-PCR)
- UniSTS:308976

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 cysteine-type peptidase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cellular response to calcium ion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mitochondrion organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in muscle cell cellular homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in necroptotic process	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of sarcomere organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in proteolysis	IBA Inferred from Biological aspect of Ancestor more info
involved_in proteolysis	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in M band	IDA Inferred from Direct Assay more info	PubMed
located_in M band	IEA Inferred from Electronic Annotation more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in sarcomere	IDA Inferred from Direct Assay more info	PubMed
located_in sarcomere	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: Calpain clp-1

NP_001367450.1

Confirmed by transcript evidence

NP_001367451.1

Confirmed by transcript evidence

NP_498740.2

Confirmed by transcript evidence

NP_498741.3

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_003281.10 Reference assembly

Range

7981074..7986328

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_066340.7 → NP_498741.3 Calpain clp-1 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_498741.3

Status: REVIEWED

UniProtKB/Swiss-Prot

P34308, P34309, Q5DX51, Q5DX52

Conserved Domains (2) summary

pfam00648
Location:317 → 609

Peptidase_C2; Calpain family cysteine protease

pfam01067
Location:631 → 772

Calpain_III; Calpain large subunit, domain III
NM_066339.7 → NP_498740.2 Calpain clp-1 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_498740.2

Status: REVIEWED

UniProtKB/Swiss-Prot

P34308

Conserved Domains (2) summary

pfam00648
Location:271 → 563

Peptidase_C2; Calpain family cysteine protease

pfam01067
Location:585 → 729

Calpain_III; Calpain large subunit, domain III
NM_001379817.1 → NP_001367450.1 Calpain clp-1 [Caenorhabditis elegans]

Status: REVIEWED
NM_001379816.3 → NP_001367451.1 Calpain clp-1 [Caenorhabditis elegans]

Status: REVIEWED

Conserved Domains (2) summary

smart00720
Location:610 → 757

calpain_III; calpain_III domain

pfam00648
Location:296 → 588

Peptidase_C2; Calpain family cysteine protease