Capn1 calpain 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Capn1provided by RGD
Official Full Name: calpain 1provided by RGD
Primary source: RGD:2267
See related: EnsemblRapid:ENSRNOG00000020935 AllianceGenome:RGD:2267
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: CANP 1; muCANP
Summary: Enables several functions, including calcium ion binding activity; calcium-dependent cysteine-type endopeptidase activity; and cytoskeletal protein binding activity. Involved in several processes, including negative regulation of non-canonical NF-kappaB signal transduction; positive regulation of cardiac muscle cell apoptotic process; and positive regulation of leukocyte tethering or rolling. Is active in glutamatergic synapse; postsynaptic density; and presynapse. Biomarker of acute kidney failure; aortic atherosclerosis; epilepsy; sciatic neuropathy; and traumatic brain injury. Human ortholog(s) of this gene implicated in hereditary spastic paraplegia 76. Orthologous to human CAPN1 (calpain 1). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Kidney (RPKM 134.4), Spleen (RPKM 107.5) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q43

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (212705219..212736134, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (203275912..203300848, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (221346081..221370965, complement)

Chromosome 1 - NC_086019.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Knockdown of calpain1 in lumbar motoneurons reduces spasticity after spinal cord injury in adult rats.
Title: Knockdown of calpain1 in lumbar motoneurons reduces spasticity after spinal cord injury in adult rats.
Hydrogen-rich saline alleviates cardiomyocyte apoptosis by reducing expression of calpain1 via miR-124-3p.
Title: Hydrogen-rich saline alleviates cardiomyocyte apoptosis by reducing expression of calpain1 via miR-124-3p.
MAPK8 and CAPN1 as potential biomarkers of intervertebral disc degeneration overlapping immune infiltration, autophagy, and ceRNA.
Title: MAPK8 and CAPN1 as potential biomarkers of intervertebral disc degeneration overlapping immune infiltration, autophagy, and ceRNA.
Exercise improves the body function and protects the neuronal injury in Parkinson's disease rats by activating calpain 1 and kallikrein 6.
Title: Exercise improves the body function and protects the neuronal injury in Parkinson's disease rats by activating calpain 1 and kallikrein 6.
Inhibition of Calpain Attenuates Degeneration of Substantia Nigra Neurons in the Rotenone Rat Model of Parkinson's Disease.
Title: Inhibition of Calpain Attenuates Degeneration of Substantia Nigra Neurons in the Rotenone Rat Model of Parkinson's Disease.
LXR activation ameliorates high glucose stress-induced aberrant mitochondrial dynamics via downregulation of Calpain1 expression in H9c2 cardiomyoblasts.
Title: LXR activation ameliorates high glucose stress-induced aberrant mitochondrial dynamics via downregulation of Calpain1 expression in H9c2 cardiomyoblasts.
elevated ammonia level may induce neuronal dysfunction via abnormal calcium influx and calpain-dependent CRMP-2 cleavage
Title: Ammonia induces calpain-dependent cleavage of CRMP-2 during neurite degeneration in primary cultured neurons.
In sum, by up- and down-regulating the persistent sodium current and KCC2, the calpain-mediated proteolysis of voltage-gated sodium (Nav) channels and KCC2 drives the hyperexcitability of motoneurons which leads to spasticity after spasticity after spinal cord injury.
Title: Calpain fosters the hyperexcitability of motoneurons after spinal cord injury and leads to spasticity.
The data support a link between Parkin phosphorylation and its cleavage by calpain.
Title: Mitochondrial and calcium perturbations in rat CNS neurons induce calpain-cleavage of Parkin: Phosphatase inhibition stabilizes pSer(65)Parkin reducing its calpain-cleavage.
Study found that the number of spontaneous seizures detected prior to sample collection was correlated with altered calpain activity and expression.
Title: Calpain activation and neuronal death during early epileptogenesis.

Submit: New GeneRIF Correction See all GeneRIFs (86)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

MARC_2595-2596:1027009134:1 (e-PCR)
- UniSTS:268910

MARC_4751-4752:996679637:1 (e-PCR)
- UniSTS:269428

D1Got194 (e-PCR)
- UniSTS:114297

RH128571 (e-PCR)
- UniSTS:211879

AU048692 (e-PCR)
- UniSTS:145142

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables calcium ion binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables calcium ion binding	ISO Inferred from Sequence Orthology more info
enables calcium-dependent cysteine-type endopeptidase activity	IBA Inferred from Biological aspect of Ancestor more info
enables calcium-dependent cysteine-type endopeptidase activity	IDA Inferred from Direct Assay more info	PubMed
enables calcium-dependent cysteine-type endopeptidase activity	IEA Inferred from Electronic Annotation more info
enables calcium-dependent cysteine-type endopeptidase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables calcium-dependent cysteine-type endopeptidase activity	ISO Inferred from Sequence Orthology more info
enables cytoskeletal protein binding	IDA Inferred from Direct Assay more info	PubMed
enables enzyme binding	IPI Inferred from Physical Interaction more info	PubMed
enables peptidase activity	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cellular response to hydrogen peroxide	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mammary gland involution	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within mammary gland involution	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of actin filament polymerization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of non-canonical NF-kappaB signal transduction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cardiac muscle cell apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of leukocyte tethering or rolling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of vascular permeability	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein autoprocessing	IDA Inferred from Direct Assay more info	PubMed
involved_in protein catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein catabolic process at postsynapse	EXP Inferred from Experiment more info	PubMed
involved_in protein catabolic process at postsynapse	IDA Inferred from Direct Assay more info	PubMed
involved_in protein catabolic process at postsynapse	IEP Inferred from Expression Pattern more info	PubMed
involved_in protein catabolic process at postsynapse	IMP Inferred from Mutant Phenotype 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
acts_upstream_of_or_within proteolysis	ISO Inferred from Sequence Orthology more info
involved_in proteolysis	ISO Inferred from Sequence Orthology more info
involved_in receptor catabolic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within receptor catabolic process	ISO Inferred from Sequence Orthology more info
involved_in regulation of catalytic activity	ISO Inferred from Sequence Orthology more info
involved_in regulation of catalytic activity	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to angiotensin	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to arsenic-containing substance	IEP Inferred from Expression Pattern more info	PubMed
involved_in self proteolysis	IEA Inferred from Electronic Annotation more info
involved_in self proteolysis	ISO Inferred from Sequence Orthology more info
involved_in self proteolysis	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in cornified envelope	IEA Inferred from Electronic Annotation more info
is_active_in cornified envelope	ISO Inferred from Sequence Orthology more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISS Inferred from Sequence or Structural Similarity more info
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in glutamatergic synapse	IMP Inferred from Mutant Phenotype more info	PubMed
located_in lysosome	IEA Inferred from Electronic Annotation more info
located_in lysosome	ISO Inferred from Sequence Orthology more info
located_in membrane	ISO Inferred from Sequence Orthology more info
located_in mitochondrion	IEA Inferred from Electronic Annotation more info
located_in mitochondrion	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
is_active_in postsynapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in postsynapse	IMP Inferred from Mutant Phenotype more info	PubMed
is_active_in postsynaptic density	IDA Inferred from Direct Assay more info	PubMed
is_active_in presynapse	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: calpain-1 catalytic subunit

Names: calcium-activated neutral proteinase 1; calpain 1, (mu/I) large subunit; calpain mu-type; calpain-1 large subunit; micromolar-calpain

XP_063138814.1

EC 3.4.22.52

XP_063138816.1

EC 3.4.22.52

XP_063138817.1

EC 3.4.22.52

XP_063138818.1

EC 3.4.22.52

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_019152.3 → NP_062025.2 calpain-1 catalytic subunit

Status: VALIDATED

Source sequence(s)

JAXUCZ010000001

UniProtKB/Swiss-Prot

P97571

Related

ENSRNOP00000112486.1, ENSRNOT00000156162.1

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086019.1 Reference GRCr8

Range

212705219..212736134 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063282744.1 → XP_063138814.1 calpain-1 catalytic subunit isoform X1

UniProtKB/Swiss-Prot

P97571
XM_063282746.1 → XP_063138816.1 calpain-1 catalytic subunit isoform X1

UniProtKB/Swiss-Prot

P97571
XM_063282747.1 → XP_063138817.1 calpain-1 catalytic subunit isoform X1

UniProtKB/Swiss-Prot

P97571
XM_063282748.1 → XP_063138818.1 calpain-1 catalytic subunit isoform X2

UniProtKB/Swiss-Prot

P97571