Capn3 calpain 3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Capn3provided by RGD
Official Full Name: calpain 3provided by RGD
Primary source: RGD:2269
See related: EnsemblRapid:ENSRNOG00000008609 AllianceGenome:RGD:2269
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: p94; Lp82; Lp84; Lp85
Summary: Enables several functions, including calcium-dependent cysteine-type endopeptidase activity; enzyme binding activity; and titin binding activity. Involved in several processes, including response to calcium ion; response to muscle activity; and sodium-dependent self proteolysis. Located in T-tubule and Z disc. Biomarker of hepatocellular carcinoma. Human ortholog(s) of this gene implicated in autosomal dominant limb-girdle muscular dystrophy; autosomal recessive limb-girdle muscular dystrophy type 2A; and muscular dystrophy. Orthologous to human CAPN3 (calpain 3). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Restricted expression toward (RPKM 401.2) See more
Orthologs: human mouse all
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Genomic context

Location:: 3q35

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	3	NC_086021.1 (127860002..127913677)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	3	NC_051338.1 (107407518..107457858)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	3	NC_005102.4 (112227486..112278408)

Chromosome 3 - NC_086021.1 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?

Identification of Phosphorylated Calpain 3 in Rat Brain Mitochondria under mPTP Opening.
Title: Identification of Phosphorylated Calpain 3 in Rat Brain Mitochondria under mPTP Opening.
MEF2A is a transcriptional regulator for Capn3 gene expression.
Title: MEF2A regulates Calpain 3 expression in L6 myoblasts.
the expression pattern of the active CAPN3 protein is linked to muscle atrophy and regeneration following denervation
Title: Calpain 3 Expression Pattern during Gastrocnemius Muscle Atrophy and Regeneration Following Sciatic Nerve Injury in Rats.
roles for Na(+) dependence of p94
Title: Skeletal muscle-specific calpain is an intracellular Na+-dependent protease.
calpain-3 is not responsible for Ca(2+)-induced disruption of EC coupling, but that mu-calpain is a plausible candidate
Title: Involvement of calpains in Ca2+-induced disruption of excitation-contraction coupling in mammalian skeletal muscle fibers.
calpain-3 remains quiescent with normal exercise but is activated following eccentric (stretching) contractions, when resting [Ca(2+)] is elevated
Title: Endogenous calpain-3 activation is primarily governed by small increases in resting cytoplasmic [Ca2+] and is not dependent on stretch.
All calpain-3 is bound tightly within a fibre, whereas most mu-calpain ( approximately 0.2 microm) is initially freely diffusible in the cytoplasm at resting [Ca(2+)] but binds within seconds at high [Ca(2+)].
Title: Ca2+ activation of diffusible and bound pools of mu-calpain in rat skeletal muscle.
Calpain 3 is specifically expressed in a subset of astrocytes and may be involved in astrocyte plasticity and/or motility.
Title: Calpain 3 is expressed in astrocytes of rat and Microcebus brain.
the time- and concentration-dependent changes in [Ca2+]i that occurred during concentric exercise fall near but below the level necessary to cause autolysis of calpains in vivo
Title: mu-Calpain and calpain-3 are not autolyzed with exhaustive exercise in humans.
Calpain-3 has a differential role in the early and late stages of skeletal muscle regeneration in a calcineurin-dependent manner in rats.
Title: Expression of tropism-related genes in regenerating skeletal muscle of rats treated with cyclosporin-A.

Submit: New GeneRIF Correction See all GeneRIFs (13)

General gene information

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Markers

RH94578 (e-PCR)
- UniSTS:119826

Capn3 (e-PCR), detects polymorphism
- UniSTS:507941

RH130533 (e-PCR)
- UniSTS:213817

D3Rat261 (e-PCR), detects polymorphism
- UniSTS:227646

GDB:595526 (e-PCR)
- UniSTS:158024

Capn3 (e-PCR), detects polymorphism
- UniSTS:141224

CANP3SKM (e-PCR)
- UniSTS:253914

RH130699 (e-PCR)
- UniSTS:213983

SKM-CALPOV (e-PCR)
- UniSTS:251621

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables calcium ion binding	ISO Inferred from Sequence Orthology more info
enables calcium ion binding	ISS Inferred from Sequence or Structural Similarity more info
enables calcium ion binding	TAS Traceable Author Statement more info	PubMed
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	ISO Inferred from Sequence Orthology more info
enables calcium-dependent cysteine-type endopeptidase activity	TAS Traceable Author Statement more info	PubMed
enables catalytic activity	ISO Inferred from Sequence Orthology more info
enables catalytic activity	ISS Inferred from Sequence or Structural Similarity more info
enables enzyme binding	IPI Inferred from Physical Interaction more info	PubMed
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables ligase regulator activity	IEA Inferred from Electronic Annotation more info
enables ligase regulator activity	ISO Inferred from Sequence Orthology more info
enables ligase regulator activity	ISS Inferred from Sequence or Structural Similarity more info
enables molecular adaptor activity	IEA Inferred from Electronic Annotation more info
enables molecular adaptor activity	ISO Inferred from Sequence Orthology more info
enables molecular adaptor activity	ISS Inferred from Sequence or Structural Similarity more info
enables peptidase activity	IDA Inferred from Direct Assay more info	PubMed
enables peptidase activity	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables signaling receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables sodium ion binding	IEA Inferred from Electronic Annotation more info
enables sodium ion binding	ISO Inferred from Sequence Orthology more info
enables sodium ion binding	ISS Inferred from Sequence or Structural Similarity more info
enables structural constituent of muscle	IEA Inferred from Electronic Annotation more info
enables structural constituent of muscle	ISO Inferred from Sequence Orthology more info
enables structural constituent of muscle	ISS Inferred from Sequence or Structural Similarity more info
enables titin binding	IDA Inferred from Direct Assay more info	PubMed
enables titin binding	IEA Inferred from Electronic Annotation more info
enables titin binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in G1 to G0 transition involved in cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in G1 to G0 transition involved in cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in calcium-dependent self proteolysis	IEA Inferred from Electronic Annotation more info
involved_in calcium-dependent self proteolysis	ISO Inferred from Sequence Orthology more info
involved_in calcium-dependent self proteolysis	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to calcium ion	IEA Inferred from Electronic Annotation more info
involved_in cellular response to calcium ion	ISO Inferred from Sequence Orthology more info
involved_in cellular response to calcium ion	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to salt stress	IEA Inferred from Electronic Annotation more info
involved_in cellular response to salt stress	ISO Inferred from Sequence Orthology more info
involved_in cellular response to salt stress	ISS Inferred from Sequence or Structural Similarity more info
involved_in muscle structure development	ISO Inferred from Sequence Orthology more info
involved_in muscle structure development	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within myofibril assembly	ISO Inferred from Sequence Orthology more info
involved_in myofibril assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of apoptotic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of apoptotic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of protein sumoylation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of protein sumoylation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of protein sumoylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of NF-kappaB transcription factor activity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of NF-kappaB transcription factor activity	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of proteolysis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of proteolysis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of proteolysis	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of release of sequestered calcium ion into cytosol	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of release of sequestered calcium ion into cytosol	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of release of sequestered calcium ion into cytosol	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of satellite cell activation involved in skeletal muscle regeneration	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of satellite cell activation involved in skeletal muscle regeneration	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of satellite cell activation involved in skeletal muscle regeneration	ISS Inferred from Sequence or Structural Similarity more info
involved_in programmed cell death	IEA Inferred from Electronic Annotation more info
involved_in programmed cell death	ISO Inferred from Sequence Orthology more info
involved_in protein catabolic process	IEA Inferred from Electronic Annotation more info
involved_in protein catabolic process	ISO Inferred from Sequence Orthology more info
involved_in protein catabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein destabilization	IEA Inferred from Electronic Annotation more info
involved_in protein destabilization	ISO Inferred from Sequence Orthology more info
involved_in protein localization to membrane	IEA Inferred from Electronic Annotation more info
involved_in protein localization to membrane	ISO Inferred from Sequence Orthology more info
involved_in protein localization to membrane	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein-containing complex assembly	IEA Inferred from Electronic Annotation more info
involved_in protein-containing complex assembly	ISO Inferred from Sequence Orthology more info
involved_in protein-containing complex assembly	ISS Inferred from Sequence or Structural Similarity more info
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
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 proteolysis	TAS Traceable Author Statement more info	PubMed
involved_in regulation of canonical NF-kappaB signal transduction	IEA Inferred from Electronic Annotation more info
involved_in regulation of canonical NF-kappaB signal transduction	ISO Inferred from Sequence Orthology more info
involved_in regulation of canonical NF-kappaB signal transduction	ISS Inferred from Sequence or Structural Similarity 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 regulation of myoblast differentiation	IEA Inferred from Electronic Annotation more info
involved_in regulation of myoblast differentiation	ISO Inferred from Sequence Orthology more info
involved_in response to calcium ion	IDA Inferred from Direct Assay more info	PubMed
involved_in response to muscle activity	IDA Inferred from Direct Assay more info	PubMed
involved_in response to xenobiotic stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in sarcomere organization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within sarcomere organization	ISO Inferred from Sequence Orthology more info
involved_in sarcomere organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in self proteolysis	IDA Inferred from Direct Assay more info	PubMed
involved_in self proteolysis	ISO Inferred from Sequence Orthology more info
involved_in sodium-dependent self proteolysis	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in T-tubule	IDA Inferred from Direct Assay more info	PubMed
located_in Z disc	IDA Inferred from Direct Assay more info	PubMed
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 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
located_in myofibril	IDA Inferred from Direct Assay more info	PubMed
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleolus	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleus	ISO Inferred from Sequence Orthology 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 plasma membrane	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
part_of protein-containing complex	IEA Inferred from Electronic Annotation more info
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info
part_of protein-containing complex	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: calpain-3

Names: CANP 3; calcium-activated neutral proteinase 3; calpain L3; calpain p94; muscle-specific calcium-activated neutral protease 3

NP_058813.2

EC 3.4.22.54

XP_006234791.1

EC 3.4.22.54

XP_008760303.1

EC 3.4.22.54

XP_038960349.1

EC 3.4.22.54

XP_038960350.1

EC 3.4.22.54

XP_063139267.1

EC 3.4.22.54

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_017117.2 → NP_058813.2 calpain-3

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000003

UniProtKB/Swiss-Prot

P16259

UniProtKB/TrEMBL

A0A8I5ZRY1

Related

ENSRNOP00000069651.3, ENSRNOT00000079079.3

Conserved Domains (4) summary

cd16190
Location:653 → 821

EFh_PEF_CAPN3; Calcium-activated neutral

pfam00648
Location:77 → 415

Peptidase_C2; Calpain family cysteine protease

pfam01067
Location:436 → 574

Calpain_III; Calpain large subunit, domain III

pfam16648
Location:583 → 653

Calpain_u2; Unstructured region on Calpain-3

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_086021.1 Reference GRCr8

Range

127860002..127913677

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063283197.1 → XP_063139267.1 calpain-3 isoform X1
XM_039104421.2 → XP_038960349.1 calpain-3 isoform X3

UniProtKB/TrEMBL

A0A8I5ZMW7, F1LSQ2

Conserved Domains (3) summary

cd16190
Location:561 → 729

EFh_PEF_CAPN3; Calcium-activated neutral

pfam00648
Location:77 → 367

Peptidase_C2; Calpain family cysteine protease

pfam01067
Location:388 → 526

Calpain_III; Calpain large subunit, domain III
XM_008762081.4 → XP_008760303.1 calpain-3 isoform X2

UniProtKB/TrEMBL

F1LSQ2

Conserved Domains (5) summary

cd00051
Location:653 → 707

EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

pfam00648
Location:77 → 415

Peptidase_C2; Calpain family cysteine protease

pfam01067
Location:429 → 579

Calpain_III; Calpain large subunit, domain III

pfam13499
Location:684 → 740

EF-hand_7; EF-hand domain pair

cl08302
Location:684 → 773

EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
XM_006234729.5 → XP_006234791.1 calpain-3 isoform X4

See identical proteins and their annotated locations for XP_006234791.1

UniProtKB/TrEMBL

O70482, Q9QZF9

Related

ENSRNOP00000075081.1, ENSRNOT00000082876.3

Conserved Domains (3) summary

cd16190
Location:589 → 757

EFh_PEF_CAPN3; Calcium-activated neutral

pfam00648
Location:51 → 395

Peptidase_C2; Calpain family cysteine protease

pfam01067
Location:416 → 554

Calpain_III; Calpain large subunit, domain III
XM_039104422.2 → XP_038960350.1 calpain-3 isoform X5

UniProtKB/TrEMBL

A0A0G2K0L5, O08702

Conserved Domains (3) summary

cd16190
Location:541 → 709

EFh_PEF_CAPN3; Calcium-activated neutral

pfam00648
Location:51 → 347

Peptidase_C2; Calpain family cysteine protease

pfam01067
Location:368 → 506

Calpain_III; Calpain large subunit, domain III