The calpains, calcium-activated neutral proteases, are nonlysosomal, intracellular cysteine proteases. The mammalian calpains include ubiquitous, stomach-specific, and muscle-specific proteins. The ubiquitous enzymes consist of heterodimers with distinct large, catalytic subunits associated with a common small, regulatory subunit. This gene encodes a member of the calpain large... See more...

Aliases for CAPN13 Gene

Aliases for CAPN13 Gene

  • Calpain 13 2 3 5
  • Calcium-Activated Neutral Proteinase 13 3 4
  • Calpain-13 3 4
  • CANP 13 3 4
  • EC 3.4.22.- 4
  • FLJ23523 2
  • CAPN13 5

External Ids for CAPN13 Gene

Previous GeneCards Identifiers for CAPN13 Gene

  • GC02M030860
  • GC02M031061
  • GC02M030938
  • GC00U916966
  • GC02M030857
  • GC02M030799
  • GC02M030683
  • GC02M030945

Summaries for CAPN13 Gene

Entrez Gene Summary for CAPN13 Gene

  • The calpains, calcium-activated neutral proteases, are nonlysosomal, intracellular cysteine proteases. The mammalian calpains include ubiquitous, stomach-specific, and muscle-specific proteins. The ubiquitous enzymes consist of heterodimers with distinct large, catalytic subunits associated with a common small, regulatory subunit. This gene encodes a member of the calpain large subunit family. [provided by RefSeq, Jun 2012]

GeneCards Summary for CAPN13 Gene

CAPN13 (Calpain 13) is a Protein Coding gene. Diseases associated with CAPN13 include Exudative Vitreoretinopathy 2, X-Linked and Coffin-Siris Syndrome 1. Among its related pathways are Degradation of the extracellular matrix and Apoptosis Pathway. Gene Ontology (GO) annotations related to this gene include calcium ion binding and calcium-dependent cysteine-type endopeptidase activity. An important paralog of this gene is CAPN14.

UniProtKB/Swiss-Prot Summary for CAPN13 Gene

Tocris Summary for CAPN13 Gene

  • Calpains are a group of calcium-sensitive cysteine proteases that are ubiquitously expressed in mammals. 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.

No data available for CIViC Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CAPN13 Gene

Genomics for CAPN13 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CAPN13 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02J030820 Enhancer 0.3 Ensembl 250.7 -0.2 -159 1 SPI1 CAPN13 piR-59136-011 lnc-LCLAT1-2 GALNT14
GH02J030756 Enhancer 1 Ensembl ENCODE 10.7 +64.0 64041 1.8 NCOR1 IKZF1 JUND REST ZNF217 ELF1 CTBP1 CUX1 TAL1 FOSL2 CAPN13 GALNT14 HSALNG0013992 HSALNG0013993 LCLAT1
GH02J030861 Enhancer 0.6 Ensembl 10.9 -41.7 -41655 0.6 ZNF654 YY1 REST ZNF592 TRIM22 CTCF RAD21 CUX1 SMC3 ZNF384 CAPN13 piR-59769-335 ENSG00000285984 GALNT14
GH02J030796 Enhancer 0.6 Ensembl ENCODE 11.3 +22.4 22441 3.4 SPI1 EZH2 MNT CAPN13 HSALNG0013993 piR-59136-011 LCLAT1
GH02J030846 Enhancer 0.6 Ensembl 10.7 -27.1 -27051 1.4 CTBP1 SMARCE1 ZNF8 PKNOX1 FOXA1 DPF2 ATF2 CREB1 FOS RFX1 piR-33605-222 CAPN13 CAPN14 LOC105374435 lnc-LCLAT1-2 GALNT14
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CAPN13 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CAPN13

Top Transcription factor binding sites by QIAGEN in the CAPN13 gene promoter:
  • ATF-2
  • c-Ets-1
  • E2F
  • E2F-1
  • HNF-1
  • HNF-1A
  • NF-1
  • POU2F1
  • POU2F1a
  • STAT5A

Genomic Locations for CAPN13 Gene

Latest Assembly
chr2:30,722,771-30,820,542
(GRCh38/hg38)
Size:
97,772 bases
Orientation:
Minus strand

Previous Assembly
chr2:30,945,637-31,030,312
(GRCh37/hg19 by Entrez Gene)
Size:
84,676 bases
Orientation:
Minus strand

chr2:30,945,637-31,043,408
(GRCh37/hg19 by Ensembl)
Size:
97,772 bases
Orientation:
Minus strand

Genomic View for CAPN13 Gene

Genes around CAPN13 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CAPN13 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CAPN13 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CAPN13 Gene

Proteins for CAPN13 Gene

  • Protein details for CAPN13 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6MZZ7-CAN13_HUMAN
    Recommended name:
    Calpain-13
    Protein Accession:
    Q6MZZ7
    Secondary Accessions:
    • Q17RF0
    • Q580X1
    • Q8TE80

    Protein attributes for CAPN13 Gene

    Size:
    669 amino acids
    Molecular mass:
    76696 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for CAPN13 Gene

    Alternative splice isoforms for CAPN13 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CAPN13 Gene

Post-translational modifications for CAPN13 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CAPN13 Gene

Domains & Families for CAPN13 Gene

Gene Families for CAPN13 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for CAPN13 Gene

Suggested Antigen Peptide Sequences for CAPN13 Gene

GenScript: Design optimal peptide antigens:
  • Calcium-activated neutral proteinase 13 (CAN13_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q6MZZ7

UniProtKB/Swiss-Prot:

CAN13_HUMAN :
  • Belongs to the peptidase C2 family.
Family:
  • Belongs to the peptidase C2 family.
genes like me logo Genes that share domains with CAPN13: view

Function for CAPN13 Gene

Molecular function for CAPN13 Gene

UniProtKB/Swiss-Prot Function:
Probable non-lysosomal thiol-protease.

Enzyme Numbers (IUBMB) for CAPN13 Gene

Phenotypes From GWAS Catalog for CAPN13 Gene

Gene Ontology (GO) - Molecular Function for CAPN13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004198 calcium-dependent cysteine-type endopeptidase activity IEA,IBA 21873635
GO:0005509 calcium ion binding IEA --
GO:0008233 peptidase activity IEA --
GO:0008234 cysteine-type peptidase activity IEA --
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with CAPN13: view
genes like me logo Genes that share phenotypes with CAPN13: view

Animal Models for research

  • Taconic Biosciences Mouse Models for CAPN13

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CAPN13

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CAPN13 Gene

Localization for CAPN13 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CAPN13 gene
Compartment Confidence
cytosol 3
nucleus 2
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for CAPN13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA 21873635
genes like me logo Genes that share ontologies with CAPN13: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for CAPN13 Gene

Pathways & Interactions for CAPN13 Gene

genes like me logo Genes that share pathways with CAPN13: view

Pathways by source for CAPN13 Gene

1 Tocris pathway for CAPN13 Gene

Gene Ontology (GO) - Biological Process for CAPN13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006508 proteolysis IEA,IBA 21873635
GO:0043066 negative regulation of apoptotic process IBA 21873635
genes like me logo Genes that share ontologies with CAPN13: view

No data available for SIGNOR curated interactions for CAPN13 Gene

Drugs & Compounds for CAPN13 Gene

(3) Drugs for CAPN13 Gene - From: HMDB and Tocris

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Nutra 6959
Calpeptin Pharma Ca2+-dependent protease,calpain inhibitor, Calpain and cathepsin L inhibitor 0
MDL 28170 Pharma Calpain and cathepsin B inhibitor, selective, Potent, selective calpain and cathepsin B inhibitor 0

(2) Tocris Compounds for CAPN13 Gene

Compound Action Cas Number
Calpeptin Calpain and cathepsin L inhibitor 117591-20-5
MDL 28170 Potent, selective calpain and cathepsin B inhibitor 88191-84-8
genes like me logo Genes that share compounds with CAPN13: view

Transcripts for CAPN13 Gene

mRNA/cDNA for CAPN13 Gene

1 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CAPN13

Alternative Splicing Database (ASD) splice patterns (SP) for CAPN13 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16a · 16b ^ 17 ^ 18a · 18b ^ 19 ^ 20 ^ 21 ^
SP1:
SP2:
SP3: -
SP4: -
SP5: - - -
SP6:

ExUns: 22 ^ 23
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:

Relevant External Links for CAPN13 Gene

GeneLoc Exon Structure for
CAPN13

Expression for CAPN13 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CAPN13 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CAPN13 Gene

This gene is overexpressed in Stomach (x13.2), Small Intestine - Terminal Ileum (x10.5), Colon - Transverse (x5.3), and Cervix - Endocervix (x5.2).

Protein differential expression in normal tissues from HIPED for CAPN13 Gene

This gene is overexpressed in Pancreatic juice (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CAPN13 Gene



Protein tissue co-expression partners for CAPN13 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CAPN13

SOURCE GeneReport for Unigene cluster for CAPN13 Gene:

Hs.660911

mRNA Expression by UniProt/SwissProt for CAPN13 Gene:

Q6MZZ7-CAN13_HUMAN
Tissue specificity: Weakly expressed in lung and testis. Weakly or not expressed in other tissues.

Evidence on tissue expression from TISSUES for CAPN13 Gene

  • Intestine(4.2)
genes like me logo Genes that share expression patterns with CAPN13: view

Primer products for research

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for CAPN13 Gene

Orthologs for CAPN13 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CAPN13 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia CAPN13 29 30
  • 96.75 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia CAPN13 29 30
  • 76.26 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Capn13 29 16 30
  • 75.85 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Capn13 29
  • 75.34 (n)
Cow
(Bos Taurus)
Mammalia CAPN13 29 30
  • 73.99 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia CAPN13 30
  • 53 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia CAPN13 30
  • 49 (a)
OneToOne
Chicken
(Gallus gallus)
Aves CAPN13 29 30
  • 55.22 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia CAPN13 30
  • 39 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia capn13 29
  • 53.3 (n)
Zebrafish
(Danio rerio)
Actinopterygii zgc:136872 30
  • 34 (a)
ManyToMany
si:ch211-202f3.3 30
  • 33 (a)
ManyToMany
si:ch211-202f3.4 30
  • 33 (a)
ManyToMany
zgc:162184 30
  • 32 (a)
ManyToMany
Species where no ortholog for CAPN13 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for CAPN13 Gene

ENSEMBL:
Gene Tree for CAPN13 (if available)
TreeFam:
Gene Tree for CAPN13 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CAPN13: view image
Alliance of Genome Resources:
Additional Orthologs for CAPN13

Paralogs for CAPN13 Gene

(7) SIMAP similar genes for CAPN13 Gene using alignment to 4 proteins:

  • CAN13_HUMAN
  • F5GYA7_HUMAN
  • F8W7Z8_HUMAN
  • H7C1Z4_HUMAN
genes like me logo Genes that share paralogs with CAPN13: view

Variants for CAPN13 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CAPN13 Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
rs17010210 -- p.His249Tyr
rs2276568 -- p.Ile596Thr
rs508405 -- p.Ala280Thr

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for CAPN13 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for CAPN13 Gene

Variant ID Type Subtype PubMed ID
esv275432 CNV loss 21479260
esv3011181 CNV deletion 24192839
esv3583707 CNV loss 25503493
esv9096 CNV gain 19470904
nsv456019 CNV loss 19166990
nsv520269 CNV gain 19592680
nsv581267 CNV loss 21841781
nsv833659 CNV gain 17160897
nsv961023 CNV duplication 23825009

Variation tolerance for CAPN13 Gene

Residual Variation Intolerance Score: 97.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.59; 78.08% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CAPN13 Gene

Human Gene Mutation Database (HGMD)
CAPN13
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CAPN13
Leiden Open Variation Database (LOVD)
CAPN13

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CAPN13 Gene

Disorders for CAPN13 Gene

MalaCards: The human disease database

(2) MalaCards diseases for CAPN13 Gene - From: COP

- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for CAPN13

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with CAPN13: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CAPN13 Gene

Publications for CAPN13 Gene

  1. Identification and characterization of two novel calpain large subunit genes. (PMID: 11675017) Dear TN … Boehm T (Gene 2001) 2 3 4
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 40
  3. Gene-environment interaction for hypertension among African American women across generations. (PMID: 20591971) Taylor JY … Kardia SL (Biological research for nursing 2010) 3 40
  4. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PMID: 15815621) Hillier LW … Wilson RK (Nature 2005) 3 4
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4

Products for CAPN13 Gene

Sources for CAPN13 Gene