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CAPN3 Gene

protein-coding   GIFtS: 68
GCID: GC15P042640

Calpain 3, (P94)


(Previous symbols: LGMD2, LGMD2A)
  See CAPN3-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Calpain 3, (P94)1 2     Calpain P94, Large [Catalytic] Subunit2
CANP32 3 5     Calpain, Large Polypeptide L32
LGMD21 2     calpain-32
LGMD2A1 2     Muscle-Specific Calcium-Activated Neutral Protease 3 Large Subunit2
Calcium-Activated Neutral Proteinase 32 3     p942
Calpain L32 3     NCL13
New Calpain 12 3     Calpain P943
CANPL32 3     CANP 33
nCL-12 3     Muscle-Specific Calcium-Activated Neutral Protease 33
EC 3.4.22.543 8     EC 3.4.228

External Ids:    HGNC: 14801   Entrez Gene: 8252   Ensembl: ENSG000000925297   OMIM: 1142405   UniProtKB: P208073   

Export aliases for CAPN3 gene to outside databases

Previous GC identifers: GC15P038019 GC15P035547 GC15P040144 GC15P040367 GC15P040283 GC15P040353 GC15P040427 GC15P019488


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for CAPN3 Gene:
Calpain, a heterodimer consisting of a large and a small subunit, is a major intracellular protease, although its
function has not been well established. This gene encodes a muscle-specific member of the calpain large subunit
family that specifically binds to titin. Mutations in this gene are associated with limb-girdle muscular
dystrophies type 2A. Alternate promoters and alternative splicing result in multiple transcript variants encoding
different isoforms and some variants are ubiquitously expressed. (provided by RefSeq, Jul 2008)

GeneCards Summary for CAPN3 Gene:
CAPN3 (calpain 3, (p94)) is a protein-coding gene. Diseases associated with CAPN3 include idiopathic eosinophilic myositis, and calpainopathy. GO annotations related to this gene include cysteine-type peptidase activity and calcium ion binding. An important paralog of this gene is CAPN6.

UniProtKB/Swiss-Prot: CAN3_HUMAN, P20807
Function: Calcium-regulated non-lysosomal thiol-protease

summary for CAPN3 Gene:
Calpains are a group of calcium-sensitive cysteine proteases that are ubiquitously expressed in mammals.
This family contains 14 members with mu-calpain (calpain 1) and m-calpain (calpain 2) being the most
well-characterized. Structurally, calpains contain two subunits; an 80 kDa catalytic subunit and a 28 kDa
regulatory subunit that functions as a chaperone to stabilize the 80 kDa structure. Calpains are regulated
by Ca2+ concentration, phosphorylation, calpastatin and probably by altering their subcellular localization
(limiting access to substrate). These endopeptidases have numerous functions including, but not limited to,
remodeling of cytoskeletal attachments to the plasma membrane during cell fusion and cell motility,
proteolytic modification of molecules in signal transduction pathways, degradation of enzymes controlling
progression through the cell cycle, regulation of gene expression, substrate degradation in some apoptotic
pathways, and an involvement in long-term potentiation. Perturbations in calpain activity have been
associated in pathophysiological processes contributing to type II diabetes (calpain 10), Alzheimer's
disease (calpain 1), gastric cancer (calpain 9) and muscular dystrophy (calpain 3).

Gene Wiki entry for CAPN3 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000015.9  NC_018926.2  NT_010194.18  
Regulatory elements:
   Regulatory transcription factor binding sites in the CAPN3 gene promoter:
         GR   Sox5   GATA-3   GR-beta   Nkx2-5   CUTL1   MIF-1   GR-alpha   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): CAPN3 promoter sequence
   Search Chromatin IP Primers for CAPN3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CAPN3


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 15q15.1   Ensembl cytogenetic band:  15q15.1   HGNC cytogenetic band: 15q15.1

CAPN3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CAPN3 gene location

GeneLoc information about chromosome 15         GeneLoc Exon Structure

GeneLoc location for GC15P042640:  view genomic region     (about GC identifiers)

Start:
42,640,301 bp from pter      End:
42,704,516 bp from pter
Size:
64,216 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: CAN3_HUMAN, P20807 (See protein sequence)
Recommended Name: Calpain-3  
Size: 821 amino acids; 94254 Da
Subunit: Interacts with TTN/titin. Interacts with CMYA5; this interaction, which results in CMYA5 proteolysis, may
protect CAPN3 from autolysis
1 PDB 3D structure from and Proteopedia for CAPN3:
1Y9V (3D)    
Secondary accessions: A6H8K6 Q7L4R0 Q9BQC8 Q9BTU4 Q9Y5S6 Q9Y5S7
Alternative splicing: 5 isoforms:  P20807-1   P20807-2   P20807-3   P20807-4   P20807-5   

Explore the universe of human proteins at neXtProt for CAPN3: NX_P20807

Explore proteomics data for CAPN3 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for CAPN3 (P20807) (see all 38)
     LSEEVEN  TFWTNPQ  IDFDSFI  YAGIFHF 


    See CAPN3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (6 alternative transcripts): 
    NP_000061.1  NP_077320.1  NP_775110.1  NP_775111.1  NP_775112.1  NP_775113.1  

    ENSEMBL proteins: 
     ENSP00000350181   ENSP00000183936   ENSP00000380349   ENSP00000380384   ENSP00000454379  
     ENSP00000456607   ENSP00000336840   ENSP00000455254   ENSP00000456575   ENSP00000380387  
     ENSP00000457878   ENSP00000457759   ENSP00000457898   ENSP00000456514   ENSP00000454937  
     ENSP00000348667   ENSP00000326281  

    CAPN3 Human Recombinant Protein Products:

    Browse Purified and Recombinant Proteins at EMD Millipore
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    OriGene Protein Over-expression Lysate for CAPN3
    OriGene Custom MassSpec
    OriGene Custom Protein Services for CAPN3
    GenScript Custom Purified and Recombinant Proteins Services for CAPN3
    Novus Biologicals CAPN3 Proteins
    Novus Biologicals CAPN3 Lysates
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for CAPN3

     
    Search eBioscience for Proteins for CAPN3 

     
    antibodies-online proteins for CAPN3 (4 products) 

     
    antibodies-online peptides for CAPN3

    CAPN3 Antibody Products:

    Browse EMD Millipore's Extensive Line of Mono- and Polyclonal Antibodies
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    ThermoFisher Antibody for CAPN3
    antibodies-online antibodies for CAPN3 (19 products) 

    CAPN3 Assay Products:

    Browse Kits and Assays available from EMD Millipore
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    Cloud-Clone Corp. ELISAs for CAPN3
    Cloud-Clone Corp. CLIAs for CAPN3
    Search eBioscience for ELISAs for CAPN3 
    antibodies-online kits for CAPN3 (15 products) 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    EFHAND: EF-hand domain containing

    Selected InterPro protein domains (see all 8):
     IPR011992 EF-hand-dom_pair
     IPR002048 EF_hand_dom
     IPR001300 Peptidase_C2_calpain_cat
     IPR018247 EF_Hand_1_Ca_BS
     IPR000169 Pept_cys_AS

    Graphical View of Domain Structure for InterPro Entry P20807

    ProtoNet protein and cluster: P20807

    1 Blocks protein domain: IPB001300 Calpain cysteine protease (C2) family signature

    UniProtKB/Swiss-Prot: CAN3_HUMAN, P20807
    Similarity: Belongs to the peptidase C2 family
    Similarity: Contains 1 calpain catalytic domain
    Similarity: Contains 4 EF-hand domains


    Find genes that share domains with CAPN3           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: CAN3_HUMAN, P20807
    Function: Calcium-regulated non-lysosomal thiol-protease
    Catalytic activity: Broad endopeptidase activity
    Enzyme regulation: Activated by micromolar concentrations of calcium and inhibited by calpastatin

         Genatlas biochemistry entry for CAPN3:
    calpain,large polypeptide L3,calcium dependent neutral cysteine proteinase,papain superfamily (subunit
    p94,muscle-specific,possessing a proteolytic activity against a potential substrat,fodrin)

         Enzyme Numbers (IUBMB): EC 3.4.22.541 2 EC 3.4.222

         Gene Ontology (GO): Selected molecular function terms (see all 12):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003824catalytic activity IDA9642272
    GO:0004198calcium-dependent cysteine-type endopeptidase activity TAS9642272
    GO:0004871signal transducer activity TAS7720071
    GO:0005509calcium ion binding ISS--
    GO:0005515protein binding IPI--
         
    Find genes that share ontologies with CAPN3           About GenesLikeMe


    Phenotypes:
         3 GenomeRNAi human phenotypes for CAPN3:
     Decreased focal adhesion (FA)   Decreased number of cells in m  Synthetic lethal with Ras 

         7 MGI mutant phenotypes (inferred from 4 alleles(MGI details for Capn3):
     cardiovascular system  growth/size/body  homeostasis/metabolism  muscle  no phenotypic analysis 
     normal  reproductive system 

    Find genes that share phenotypes with CAPN3           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Capn3tm1Jsb for CAPN3

       genOway: Develop your customized and physiologically relevant rodent model for CAPN3

    miRNA
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    Block miRNA regulation of human, mouse, rat CAPN3 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate CAPN3 (see all 14):
    hsa-miR-98 hsa-miR-4324 hsa-let-7d hsa-miR-202 hsa-let-7c hsa-let-7i hsa-let-7g hsa-let-7e
    SwitchGear 3'UTR luciferase reporter plasmidCAPN3 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for CAPN3
    Predesigned siRNA for gene silencing in human, mouse, rat CAPN3

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for CAPN3

    Clone
    Products:
         
    OriGene clones in human, mouse for CAPN3 (see all 43)
    OriGene ORF clones in mouse, rat for CAPN3
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 6): CAPN3 (NM_173088)
    Sino Biological Human cDNA Clone for CAPN3
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for CAPN3
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CAPN3

    Cell Line
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    GenScript Custom overexpressing Cell Line Services for CAPN3
    Browse ESI BIO Cell Lines and PureStem Progenitors for CAPN3 
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CAPN3


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    CAN3_HUMAN, P20807: Cytoplasm
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol4
    plasma membrane4
    cytoskeleton1
    endoplasmic reticulum1
    mitochondrion1
    peroxisome1

    Gene Ontology (GO): Selected cellular component terms (see all 9):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622intracellular TAS9642272
    GO:0005634nucleus IDA19386580
    GO:0005737cytoplasm IDA19386580
    GO:0005829cytosol ISS--
    GO:0005886plasma membrane ISS--

    Find genes that share ontologies with CAPN3           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for CAPN3 About   (see all 6)  
    See pathways by source

    SuperPathContained pathways About
    1DREAM Repression and Dynorphin Expression
    nNOS Signaling in Skeletal Muscle0.37
    Calpain Protease Regulates Cellular Mechanics0.31
    Caspase Cascade0.36
    2Integrin Pathway
    FAK1 Signaling0.67
    3ERK Signaling
    ERK Signaling0.61
    4Apoptosis Pathway
    Apoptosis Pathway0.45
    5Focal adhesion
    Integrin-mediated cell adhesion0.38

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    5 Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for CAPN3
        Caspase Cascade
    ERK Signaling
    Calpain Protease Regulates Cellular Mechanics
    FAK1 Signaling
    nNOS Signaling in Skeletal Muscle

    1 Tocris Bioscience Pathway for CAPN3
        Apoptosis Pathway

    2 BioSystems Pathways for CAPN3
        Integrin-mediated cell adhesion
    TNF-alpha/NF-kB Signaling Pathway



        Pathway & Disease-focused RT2 Profiler PCR Arrays including CAPN3: 
              Skeletal Muscle: Myogenesis & Myopathy in human mouse rat
              Necrosis in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for CAPN3

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for CAPN3 (P208071, 2, 3 ENSP000003803494) via UniProtKB, MINT, STRING, and/or I2D (see all 43)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    TTNQ8WZ421, 2, 3EBI-5655000,EBI-681210 MINT-7990374 I2D: score=3 
    DYSFO759233, ENSP000003868814I2D: score=1 STRING: ENSP00000386881
    FLNCQ143153, ENSP000003271454I2D: score=2 STRING: ENSP00000327145
    NECAB2Q7Z6G33, ENSP000003074494I2D: score=3 STRING: ENSP00000307449
    YWHAQP273483, ENSP000002380814I2D: score=2 STRING: ENSP00000238081
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 28):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001896autolysis IEA--
    GO:0006461protein complex assembly ISS--
    GO:0006508proteolysis IDA18310072
    GO:0006915apoptotic process TAS19386580
    GO:0007165signal transduction TAS7720071

    Find genes that share ontologies with CAPN3           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
    9 ApexBio Compounds for CAPN3     About this table
    CompoundAction CAS #
    Acetyl-Calpastatin (184-210) (human)Selective calpain inhibitor[123714-50-1]
    Calpain Inhibitor I, ALLNA cell-permeable inhibitor of calpain I, calpain II, cathepsin B, and cathepsin L. [110044-82-1]
    Calpain Inhibitor II, ALLMA cell-permeable inhibitor of calpain 1 and calpain 2[136632-32-1]
    CalpeptinPotent, cell-permeable inhibitor of calpain[117591-20-5]
    E-64Irriversible cysteine protease inhibitor[66701-25-5]
    MDL 28170Potent, selective inhibitor of calpain and cathepsin B[88191-84-8]
    MG-132Proteasome and calpain inhibitor[133407-82-6]
    PD 150606Selective, cell-permeable non-peptide calpain inhibitor[179528-45-1]
    Z-FA-FMKAn inhibitor of cysteine proteases, such as cathepsin B--

    Compounds for CAPN3 available from Tocris Bioscience    About this table
    CompoundAction CAS #
    Acetyl-Calpastatin (184-210) (human)Selective calpain inhibitor[123714-50-1]
    MDL 28170 Potent, selective calpain and cathepsin B inhibitor [88191-84-8]
    PD 150606Cell permeable calpain inhibitor[179528-45-1]
    MG 132Proteasome and calpain inhibitor. Inhibits NF-kappaB activation[133407-82-6]
    MG 101Calpain inhibitor; activates p53-dependent apoptosis[110044-82-1]

    1 HMDB Compound for CAPN3    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--

    3 Novoseek inferred chemical compound relationships for CAPN3 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    cysteine 52.3 13 15351423 (1), 18676612 (1), 10330145 (1), 16884488 (1) (see all 9)
    creatinine 21.7 2 16607617 (1), 15221789 (1)
    calcium 0 19 16107503 (4), 18676612 (4), 14755246 (1), 10330145 (1) (see all 6)



    Find genes that share compounds with CAPN3           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for CAPN3 gene (7 alternative transcripts): 
    NM_000070.2  NM_024344.1  NM_173087.1  NM_173088.1  NM_173089.1  NM_173090.1  NM_212465.2  

    Unigene Cluster for CAPN3:

    Calpain 3, (p94)
    Hs.143261  [show with all ESTs]
    Unigene Representative Sequence: NM_000070
    Selected Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 20):
    ENST00000357568 ENST00000349748(uc001zpp.1) ENST00000397163(uc001zpn.1 uc001zpo.1)
    ENST00000397200(uc001zpq.1) ENST00000569827 ENST00000567071 ENST00000337571(uc010bcv.1 uc001zpr.1 uc001zps.1 uc001zpt.1)
    ENST00000569136 ENST00000561817 ENST00000565173 ENST00000397204 ENST00000565559
    ENST00000565274 ENST00000564503 ENST00000466222 ENST00000562199 ENST00000567817
    ENST00000568153
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate CAPN3 (see all 14):
    hsa-miR-98 hsa-miR-4324 hsa-let-7d hsa-miR-202 hsa-let-7c hsa-let-7i hsa-let-7g hsa-let-7e
    SwitchGear 3'UTR luciferase reporter plasmidCAPN3 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat CAPN3
    Clone
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    GenScript: all cDNA clones in your preferred vector (see all 6): CAPN3 (NM_173088)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for CAPN3
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CAPN3
    Primer
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    OriGene qPCR primer pairs and template standards for CAPN3
    OriGene qSTAR qPCR primer pairs in human, mouse for CAPN3
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat CAPN3
      QuantiTect SYBR Green Assays in human, mouse, rat CAPN3
      QuantiFast Probe-based Assays in human, mouse, rat CAPN3

    Additional mRNA sequence: 

    AF127764.1 AF127765.3 AF147441.1 AK027249.1 AK293792.1 AK308103.1 BC003169.1 BC003521.1 
    BC004883.2 BC007810.2 BC067126.1 BC100782.1 BC100783.1 BC100784.2 BC107791.1 BC128605.1 
    BC146649.1 BC146672.1 BT007322.1 EU791850.1 EU791851.1 X85030.1 

    Selected DOTS entries (see all 31):

    DT.92446226  DT.92446229  DT.455419  DT.92446221  DT.100822091  DT.121036768  DT.92446223  DT.102837450 
    DT.121036532  DT.95296729  DT.92446212  DT.95251013  DT.121036817  DT.92446231  DT.102837448  DT.91658071 
    DT.100822103  DT.92446225  DT.91858525  DT.91785771  DT.95075842  DT.115273  DT.121036693  DT.100037626 

    Selected AceView cDNA sequences (see all 72):

    BQ425112 BQ427836 BM476314 BX474600 AJ346081 NM_173089 BQ878602 BI821506 
    AJ574026 CF552300 BF026120 BU189710 AA278326 BE897910 NM_212464 AK074037 
    BE220887 F20464 BC004883 BQ677982 BG033560 BE275944 BQ232655 AL044086 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for CAPN3 (see all 22)    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b · 7c · 7d ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^ 16 ^ 17 ^ 18 ^ 19 ^
    SP1:                                                                                                                                                            
    SP2:                                -           -     -     -     -     -     -                                                           -     -               
    SP3:                                                                                                                                                            
    SP4:                                -           -     -     -     -     -     -                                                           -                     
    SP5:                                                                                                                                                            

    ExUns: 20 ^ 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30 ^ 31a · 31b ^ 32a · 32b ^ 33 ^ 34 ^ 35 ^ 36 ^ 37a · 37b ^ 38 ^ 39 ^ 40 ^ 41 ^ 42 ^
    SP1:                                                                                      -           -                                                         
    SP2:                                            -                                                                                                               
    SP3:                                                                                      -           -                                                         
    SP4:                                                                                                                                                            
    SP5:                                                                                                                                                            

    ExUns: 43 ^ 44 ^ 45a · 45b · 45c ^ 46a · 46b ^ 47a · 47b ^ 48a · 48b · 48c ^ 49a · 49b ^ 50 ^ 51 ^ 52 ^ 53 ^ 54 ^ 55 ^ 56 ^ 57 ^ 58 ^ 59
    SP1:                                      -           -     -     -     -           -     -                                                         
    SP2:                                                                                                                                                
    SP3:                                      -                                                                                                         
    SP4:                                                                                                                                                
    SP5:                                                                                -     -                                                         


    ECgene alternative splicing isoforms for CAPN3

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

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    CAPN3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TGTATGGCTG
    CAPN3 Expression
    About this image


    CAPN3 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 5) fully expand
     
     Eye (Sensory Organs)    fully expand to see all 2 entries
             Retina
     
     Liver (Hepatobiliary System)
             Hepatocyte-like cells
     
     Brain (Nervous System)
             Cerebral Cortex
     
     Kidney (Urinary System)
     
     Skeletal Muscle (Muscoskeletal System)
    CAPN3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    CAPN3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.143261

    UniProtKB/Swiss-Prot: CAN3_HUMAN, P20807
    Tissue specificity: Isoform I is skeletal muscle specific

        Pathway & Disease-focused RT2 Profiler PCR Arrays including CAPN3: 
              Skeletal Muscle: Myogenesis & Myopathy in human mouse rat
              Necrosis in human mouse rat

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

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    This gene was present in the common ancestor of chordates.

    Orthologs for CAPN3 gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Capn31 , 5 calpain 31, 5 90.13(n)1
    93.42(a)1
      2 (60.31 cM)5
    123351  NM_007601.31  NP_031627.21 
     1204560195 
    chicken
    (Gallus gallus)
    Aves CAPN31 calpain 3, (p94) 75.68(n)
    78.77(a)
      423233  NM_001004405.1  NP_001004405.1 
    lizard
    (Anolis carolinensis)
    Reptilia CAPN36
    calpain 3, (p94)
    74(a)
    1 ↔ 1
    1(39928351-39961233)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia LOC1004975321 calpain-3-like 72.5(n)
    76.27(a)
      100497532  XM_002935335.2  XP_002935381.2 
    zebrafish
    (Danio rerio)
    Actinopterygii capn3a1 calpain 3a, (p94) 71.33(n)
    72.63(a)
      447832  NM_001004571.1  NP_001004571.1 


    ENSEMBL Gene Tree for CAPN3 (if available)
    TreeFam Gene Tree for CAPN3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for CAPN3 gene
    CAPN62  CAPN82  CAPN142  CAPNS12  CAPN132  CAPN12  CAPN52  CAPN92  
    CAPNS22  CAPN22  CAPN122  CAPN112  CAPN102  
    15 SIMAP similar genes for CAPN3 using alignment to 17 protein entries:     CAN3_HUMAN (see all proteins):
    CAPNS2    CAPN2    CAPNS1    CAPN9    CAPN1    CAPN8
    CAPN11    SRI    GCA    CAPN14    PDCD6    CAPN12
    CAPN5    CAPN6    CAPN13

    Find genes that share paralogs with CAPN3           About GenesLikeMe


    1 Pseudogenes.org Pseudogene for CAPN3
    PGOHUM00000262251


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for CAPN3 (see all 1528)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 15 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs358899561,2,,4
    C,FLimb-girdle muscular dystrophy 2A (LGMD2A)4 --22745573(+) GCCAAC/TGTACA 6 T M mis16Minor allele frequency- T:0.01NA WA 4750
    rs1416567191,2,,4
    CLimb-girdle muscular dystrophy 2A (LGMD2A)4 --22759521(+) ACCGGC/TGGAAG 7 R W mis1 us2k11Minor allele frequency- T:0.00NA 4548
    rs1998068791,2,,4
    CLimb-girdle muscular dystrophy 2A (LGMD2A)4 --22765994(+) CGTTTC/TGGACA 9 S L mis1 int11Minor allele frequency- T:0.00EU 1323
    VAR_0095724
    Limb-girdle muscular dystrophy 2A (LGMD2A)4--see VAR_0095722 W C mis40--------
    VAR_0095564
    Limb-girdle muscular dystrophy 2A (LGMD2A)4--see VAR_0095562 I L mis40--------
    VAR_0095554
    Limb-girdle muscular dystrophy 2A (LGMD2A)4--see VAR_0095552 C R mis40--------
    VAR_0095804
    Limb-girdle muscular dystrophy 2A (LGMD2A)4--see VAR_0095802 S G mis40--------
    VAR_0095714
    Limb-girdle muscular dystrophy 2A (LGMD2A)4--see VAR_0095712 Y N mis40--------
    VAR_0095974
    Limb-girdle muscular dystrophy 2A (LGMD2A)4--see VAR_0095972 F S mis40--------
    VAR_0095744
    Limb-girdle muscular dystrophy 2A (LGMD2A)4--see VAR_0095742 R W mis40--------

    HapMap Linkage Disequilibrium report for CAPN3 (42640301 - 42704516 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for CAPN3:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv832986CNV Loss17160897
    nsv904133CNV Gain21882294
    nsv832987CNV Gain17160897

    Human Gene Mutation Database (HGMD): CAPN3
    Locus Specific Mutation Databases (LSDB): CAPN3

    Site Specific Mutation Identification with PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

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    OMIM gene information: 114240   
    OMIM disorders: 253600  
    UniProtKB/Swiss-Prot: CAN3_HUMAN, P20807
  • Limb-girdle muscular dystrophy 2A (LGMD2A) [MIM:253600]: An autosomal recessive degenerative myopathy
    characterized by progressive symmetrical atrophy and weakness of the proximal limb muscles and elevated serum
    creatine kinase. The symptoms usually begin during the first two decades of life, and the disease gradually
    worsens, often resulting in loss of walking ability 10 or 20 years after onset. Note=The disease is caused by
    mutations affecting the gene represented in this entry

  • 7 diseases for CAPN3:    
    About MalaCards
    idiopathic eosinophilic myositis    calpainopathy    miyoshi myopathy    isolated hyperckemia
    dysferlinopathy    familial partial lipodystrophy    myositis

    2 diseases from the University of Copenhagen DISEASES database for CAPN3:
    Myopathy     Neuropathy

    Find genes that share disorders with CAPN3           About GenesLikeMe

    Selected Novoseek inferred disease relationships for CAPN3 gene (see all 24)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    lgmd2a 99 173 16971480 (5), 18563459 (4), 9642272 (4), 15221789 (4) (see all 58)
    muscular dystrophy limb-girdle 95.7 35 11053681 (3), 8537379 (2), 17596655 (2), 14981715 (1) (see all 23)
    lgmd2g 92.8 8 11665864 (3), 14959561 (1), 15316618 (1)
    limb girdle 90.8 15 15843148 (2), 15884399 (1), 15221789 (1), 16542520 (1) (see all 10)
    muscular dystrophy, limb-girdle, autosomal recessive 90.1 3 11245721 (1), 17979987 (1)
    lgmd2h 89.2 6 14959561 (1), 15316618 (1), 11665864 (1)
    muscular dystrophies 88.8 34 16115818 (5), 15843148 (2), 9309711 (2), 11829483 (2) (see all 22)
    lgmd2f 87.9 6 9266733 (1), 14959561 (1), 15316618 (1)
    lgmd2i 87.7 7 14959561 (1), 15689361 (1), 18337726 (1), 15316618 (1) (see all 5)
    lgmd2e 87.1 6 9266733 (1), 14959561 (1), 15316618 (1)

    GeneTests: CAPN3
    GeneReviews: CAPN3
    Genetic Association Database (GAD): CAPN3
    Human Genome Epidemiology (HuGE) Navigator: CAPN3 (6 documents)

    Export disorders for CAPN3 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for CAPN3 gene, integrated from 10 sources (see all 200):
    (articles sorted by number of sources associating them with CAPN3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Mutations in the proteolytic enzyme calpain 3 cause limb-girdle muscular dystrophy type 2A. (PubMed id 7720071)1, 2, 3 Richard I.... Beckmann J.S. (Cell 1995)
    2. Molecular cloning of a novel mammalian calcium-dependent protease distinct from both m- and mu-types. Specific expression of the mRNA in skeletal muscle. (PubMed id 2555341)1, 2, 3 Sorimachi H.... Suzuki K. (J. Biol. Chem. 1989)
    3. Molecular diagnosis in LGMD2A: mutation analysis or protein testing? (PubMed id 15221789)1, 4, 9 Fanin M....Angelini C. (Hum. Mutat. 2004)
    4. LGMD2A: genotype-phenotype correlations based on a large mutational survey on the calpain 3 gene. (PubMed id 15689361)1, 4, 9 SA!enz A....LA^pez de Munain A. (Brain 2005)
    5. A biochemical, genetic, and clinical survey of autosomal recessive limb girdle muscular dystrophies in Turkey. (PubMed id 9266733)1, 2, 9 Dincer P.... Topaloglu H. (Ann. Neurol. 1997)
    6. Prevalence of the 550delA mutation in calpainopathy (LGMD 2A) in Croatia. (PubMed id 14981715)1, 4, 9 Canki-Klain N....Feingold J. (Am. J. Med. Genet. A 2004)
    7. Calpainopathy -- a survey of mutations and polymorphisms. (PubMed id 10330340)1, 2, 9 Richard I.... Beckmann J.S. (Am. J. Hum. Genet. 1999)
    8. Biological, clinical and population relevance of 95 loci for blood lipids. (PubMed id 20686565)1, 4 Teslovich T.M....Kathiresan S. (Nature 2010)
    9. Interactions with M-band titin and calpain 3 link myospryn (CMYA5) to tibial and limb-girdle muscular dystrophies. (PubMed id 20634290)1, 2 Sarparanta J.... Udd B. (J. Biol. Chem. 2010)
    10. Genetic variants in apoptosis and immunoregulation-related genes are associated with risk of chronic lymphocytic leukemia. (PubMed id 19074885)1, 4 Enjuanes A....Campo E. (Cancer Res. 2008)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 825 HGNC: 1480 AceView: CAPN3 Ensembl:ENSG00000092529 euGenes: HUgn825
    ECgene: CAPN3 H-InvDB: CAPN3

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for CAPN3 Pharmacogenomics, SNPs, Pathways
    LEIDEN Muscular Dystrophy page for CAPN3 Scientfic Information about Duchenne and Duchenne-like muscular dystrophies.
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=CAPN3[genesymbol]
    NIEHS-SNPshttp://egp.gs.washington.edu/data/capn3/

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for CAPN3 gene:
    Search GeneIP for patents involving CAPN3

    GeneCards and IP:
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