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Aliases for CAPN9 Gene

Aliases for CAPN9 Gene

  • Calpain 9 2 3
  • Digestive Tract-Specific Calpain 3 4
  • Novel Calpain Large Subunit-4 2 3
  • New Calpain 4 3 4
  • NCL-4 3 4
  • Calpain 9 (NCL-4) 2
  • Protein CG36 4
  • EC 63
  • EC 3.4.22.- 4
  • Calpain-9 3
  • EC 3.4.22 63
  • GC36 3
  • NCL4 4

External Ids for CAPN9 Gene

Previous GeneCards Identifiers for CAPN9 Gene

  • GC01P229360
  • GC01P226611
  • GC01P227356
  • GC01P227918
  • GC01P227189
  • GC01P228949
  • GC01P230883
  • GC01P201367

Summaries for CAPN9 Gene

Entrez Gene Summary for CAPN9 Gene

  • Calpains are ubiquitous, well-conserved family of calcium-dependent, cysteine proteases. The calpain proteins are heterodimers consisting of an invariant small subunit and variable large subunits. The large subunit possesses a cysteine protease domain, and both subunits possess calcium-binding domains. Calpains have been implicated in neurodegenerative processes, as their activation can be triggered by calcium influx and oxidative stress. The protein encoded by this gene is expressed predominantly in stomach and small intestine and may have specialized functions in the digestive tract. This gene is thought to be associated with gastric cancer. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for CAPN9 Gene

CAPN9 (Calpain 9) is a Protein Coding gene. Among its related pathways are ERK Signaling and Apoptosis Pathway. GO annotations related to this gene include calcium ion binding and calcium-dependent cysteine-type endopeptidase activity. An important paralog of this gene is CAPNS2.

UniProtKB/Swiss-Prot for CAPN9 Gene

  • Calcium-regulated non-lysosomal thiol-protease

Tocris Summary for CAPN9 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 CAPN9 Gene

No data available for PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CAPN9 Gene

Genomics for CAPN9 Gene

Regulatory Elements for CAPN9 Gene

Genomic Location for CAPN9 Gene

230,747,343 bp from pter
230,802,003 bp from pter
54,661 bases
Plus strand

Genomic View for CAPN9 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for CAPN9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CAPN9 Gene

Proteins for CAPN9 Gene

  • Protein details for CAPN9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • B1APS1
    • B1AQI0
    • Q9NS74

    Protein attributes for CAPN9 Gene

    690 amino acids
    Molecular mass:
    79097 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for CAPN9 Gene

    Alternative splice isoforms for CAPN9 Gene


neXtProt entry for CAPN9 Gene

Proteomics data for CAPN9 Gene at MOPED

Post-translational modifications for CAPN9 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CAPN9 Gene

Antibody Products

Domains for CAPN9 Gene

Gene Families for CAPN9 Gene

Suggested Antigen Peptide Sequences for CAPN9 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Contains 1 calpain catalytic domain.
  • Belongs to the peptidase C2 family.
  • Contains 1 calpain catalytic domain.
  • Contains 3 EF-hand domains.
  • Belongs to the peptidase C2 family.
genes like me logo Genes that share domains with CAPN9: view

Function for CAPN9 Gene

Molecular function for CAPN9 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
Broad endopeptidase specificity
UniProtKB/Swiss-Prot Function:
Calcium-regulated non-lysosomal thiol-protease
UniProtKB/Swiss-Prot Induction:
Down-regulated in gastric cancer tissue and in gastric cell lines of differentiated and poorly differentiated types

Enzyme Numbers (IUBMB) for CAPN9 Gene

Gene Ontology (GO) - Molecular Function for CAPN9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004198 calcium-dependent cysteine-type endopeptidase activity IBA --
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with CAPN9: view
genes like me logo Genes that share phenotypes with CAPN9: view

Animal Models for CAPN9 Gene

MGI Knock Outs for CAPN9:

miRNA for CAPN9 Gene

miRTarBase miRNAs that target CAPN9

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for CAPN9

In Situ Assay Products

Flow Cytometry Products

No data available for Transcription Factor Targeting and HOMER Transcription for CAPN9 Gene

Localization for CAPN9 Gene

Subcellular locations from

Jensen Localization Image for CAPN9 Gene COMPARTMENTS Subcellular localization image for CAPN9 gene
Compartment Confidence
cytosol 3
nucleus 2

Gene Ontology (GO) - Cellular Components for CAPN9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
GO:0005622 intracellular --
GO:0005737 cytoplasm IBA --
genes like me logo Genes that share ontologies with CAPN9: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for CAPN9 Gene

Pathways for CAPN9 Gene

genes like me logo Genes that share pathways with CAPN9: view

Pathways by source for CAPN9 Gene

Interacting Proteins for CAPN9 Gene

Gene Ontology (GO) - Biological Process for CAPN9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006508 proteolysis IBA --
GO:0007586 digestion IEA --
genes like me logo Genes that share ontologies with CAPN9: view

Compounds for CAPN9 Gene

(4) Tocris Compounds for CAPN9 Gene

Compound Action Cas Number
MDL 28170 Potent, selective calpain and cathepsin B inhibitor [88191-84-8]
MG 101 Calpain inhibitor; activates p53-dependent apoptosis [110044-82-1]
MG 132 Proteasome and calpain inhibitor. Inhibits NF-kappaB activation [133407-82-6]
PD 150606 Cell permeable calpain inhibitor [179528-45-1]

(1) HMDB Compounds for CAPN9 Gene

Compound Synonyms Cas Number PubMed IDs
  • Ca

(1) Novoseek inferred chemical compound relationships for CAPN9 Gene

Compound -log(P) Hits PubMed IDs
calcium 8.92 1
genes like me logo Genes that share compounds with CAPN9: view

Transcripts for CAPN9 Gene

Unigene Clusters for CAPN9 Gene

Calpain 9:
Representative Sequences:

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for CAPN9

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CAPN9 Gene

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

ExUns: 21a · 21b · 21c

Relevant External Links for CAPN9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CAPN9 Gene

mRNA expression in normal human tissues for CAPN9 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CAPN9 Gene

This gene is overexpressed in Stomach (14.5), Colon - Transverse (10.4), and Minor Salivary Gland (6.5).

Protein differential expression in normal tissues for CAPN9 Gene

This gene is overexpressed in Stomach (67.3).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for CAPN9 Gene

SOURCE GeneReport for Unigene cluster for CAPN9 Gene Hs.498021

mRNA Expression by UniProt/SwissProt for CAPN9 Gene

Tissue specificity: Expressed predominantly in stomach
genes like me logo Genes that share expressions with CAPN9: view

Expression partners for CAPN9 Gene

* - Elite partner

Primer Products

In Situ Assay Products

Orthologs for CAPN9 Gene

This gene was present in the common ancestor of animals.

Orthologs for CAPN9 Gene

Organism Taxonomy Gene Similarity Type Details
(Canis familiaris)
Mammalia CAPN9 35
  • 89.37 (n)
  • 91.88 (a)
CAPN9 36
  • 91 (a)
(Mus musculus)
Mammalia Capn9 35
  • 83.24 (n)
  • 85.8 (a)
Capn9 16
Capn9 36
  • 86 (a)
(Pan troglodytes)
Mammalia CAPN9 35
  • 99.66 (n)
  • 99.71 (a)
CAPN9 36
  • 100 (a)
(Rattus norvegicus)
Mammalia Capn9 35
  • 83.24 (n)
  • 85.8 (a)
(Monodelphis domestica)
Mammalia CAPN9 36
  • 80 (a)
(Ornithorhynchus anatinus)
Mammalia CAPN9 36
  • 73 (a)
(Gallus gallus)
Aves CAPN9 35
  • 75.75 (n)
  • 79.28 (a)
CAPN9 36
  • 79 (a)
(Anolis carolinensis)
Reptilia CAPN9 36
  • 77 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia capn9 35
  • 69.28 (n)
  • 70.43 (a)
Str.2459 35
(Danio rerio)
Actinopterygii capn9 35
capn9 35
  • 64.83 (n)
  • 62.79 (a)
capn9 36
  • 63 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2168 35
fruit fly
(Drosophila melanogaster)
Insecta CalpA 37
  • 51 (a)
CalpB 37
  • 44 (a)
CalpC 37
  • 31 (a)
CalpA 35
  • 54.57 (n)
  • 50.23 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012068 35
  • 55.08 (n)
  • 48.86 (a)
(Caenorhabditis elegans)
Secernentea clp-3 37
  • 39 (a)
clp-6 37
  • 42 (a)
clp-7 37
  • 47 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.4609 36
  • 46 (a)
Species with no ortholog for CAPN9:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • cow (Bos Taurus)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • 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)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)

Evolution for CAPN9 Gene

Gene Tree for CAPN9 (if available)
Gene Tree for CAPN9 (if available)

Paralogs for CAPN9 Gene

(14) SIMAP similar genes for CAPN9 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with CAPN9: view

Variants for CAPN9 Gene

Sequence variations from dbSNP and Humsavar for CAPN9 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type MAF
rs868143 -- 230,753,931(-) CAAGG(C/G)TAGCT intron-variant, upstream-variant-2KB
rs872504 -- 230,768,513(+) TGAAA(C/T)GGGAT intron-variant
rs872505 -- 230,768,522(+) ATCTT(C/T)CTATC intron-variant
rs1133038 -- 230,790,143(-) GCTGT(C/G)ACCTC synonymous-codon, reference, nc-transcript-variant
rs1316408 -- 230,749,967(+) TCTCC(A/G)AGATA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CAPN9 Gene

Variant ID Type Subtype PubMed ID
nsv832836 CNV Loss 17160897

Relevant External Links for CAPN9 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CAPN9 Gene

Disorders for CAPN9 Gene

(2) Novoseek inferred disease relationships for CAPN9 Gene

Disease -log(P) Hits PubMed IDs
gastric cancer 51.2 3
alzheimers disease 28 1

Relevant External Links for CAPN9

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with CAPN9: view

No data available for MalaCards , OMIM , UniProtKB/Swiss-Prot , University of Copenhagen DISEASES and Genatlas for CAPN9 Gene

Publications for CAPN9 Gene

  1. Isolation of two novel genes, down-regulated in gastric cancer. (PMID: 10835488) Yoshikawa Y. … Kato I. (Jpn. J. Cancer Res. 2000) 2 3 4 23
  2. The crystal structures of human calpains 1 and 9 imply diverse mechanisms of action and auto-inhibition. (PMID: 17157313) Davis T.L. … Dhe-Paganon S. (J. Mol. Biol. 2007) 3 4 23
  3. Molecular cloning and characterization of a novel tissue-specific calpain predominantly expressed in the digestive tract. (PMID: 9524069) Lee H.-J. … Suzuki K. (Biol. Chem. 1998) 2 3 4
  4. Characterization of a human digestive tract-specific calpain, nCL-4, expressed in the baculovirus system. (PMID: 9917325) Lee H.J. … Suzuki K. (Arch. Biochem. Biophys. 1999) 3 23
  5. The calpain family and human disease. (PMID: 11516996) Huang Y. … Wang K.K. (Trends Mol Med 2001) 3 23

Products for CAPN9 Gene

  • Addgene plasmids for CAPN9

Sources for CAPN9 Gene

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