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Aliases for CAPN9 Gene

Aliases for CAPN9 Gene

  • Calpain 9 2 3 5
  • 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
  • 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. Diseases associated with CAPN9 include gastric cancer. Among its related pathways are Degradation of the extracellular matrix and Integrin 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 CAPN14.

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. 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.

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

230,747,334 bp from pter
230,802,003 bp from pter
54,670 bases
Plus strand

Genomic View for CAPN9 Gene

Genes around CAPN9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CAPN9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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

Domains & Families 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 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:

Animal Model Products

miRNA for CAPN9 Gene

miRTarBase miRNAs that target CAPN9

No data available for Human Phenotype Ontology , Transcription Factor Targets 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: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 & Interactions 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


No data available for SIGNOR curated interactions for CAPN9 Gene

Drugs & Compounds for CAPN9 Gene

(2) Drugs for CAPN9 Gene - From: Novoseek, HMDB, and Tocris

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Nutra 0
MDL 28170 Pharma Calpain and cathepsin B inhibitor, selective, Potent, selective calpain and cathepsin B inhibitor 0

(4) Additional Compounds for CAPN9 Gene - From: Tocris

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Acetyl-Calpastatin (184-210) (human)
MG 132
PD 150606
genes like me logo Genes that share compounds with CAPN9: view

Transcripts for CAPN9 Gene

Unigene Clusters for CAPN9 Gene

Calpain 9:
Representative Sequences:

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 (x14.5), Colon - Transverse (x10.4), and Minor Salivary Gland (x6.5).

Protein differential expression in normal tissues from HIPED for CAPN9 Gene

This gene is overexpressed in Stomach (67.3).

Integrated Proteomics: protein expression in normal tissues and cell lines 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 expression patterns with CAPN9: view

Protein tissue co-expression partners for CAPN9 Gene

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
(Pan troglodytes)
Mammalia CAPN9 36
  • 100 (a)
CAPN9 35
  • 99.66 (n)
  • 99.71 (a)
(Canis familiaris)
Mammalia CAPN9 35
  • 89.37 (n)
  • 91.88 (a)
CAPN9 36
  • 91 (a)
(Mus musculus)
Mammalia Capn9 16
Capn9 36
  • 86 (a)
Capn9 35
  • 83.24 (n)
  • 85.8 (a)
(Monodelphis domestica)
Mammalia CAPN9 36
  • 80 (a)
(Ornithorhynchus anatinus)
Mammalia CAPN9 36
  • 73 (a)
(Rattus norvegicus)
Mammalia Capn9 35
  • 83.24 (n)
  • 85.8 (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
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2168 35
(Danio rerio)
Actinopterygii capn9 35
capn9 35
  • 64.83 (n)
  • 62.79 (a)
capn9 36
  • 63 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012068 35
  • 55.08 (n)
  • 48.86 (a)
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)
(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
rs12562749 - 230,759,533(+) AGCCG(C/T)CATCG intron-variant, nc-transcript-variant, reference, missense, utr-variant-5-prime
rs28359608 - 230,759,594(+) CAAAG(A/C)TTTGG intron-variant, nc-transcript-variant, reference, missense, utr-variant-5-prime
rs28359632 - 230,762,740(+) CTGCC(A/G)ACCAC nc-transcript-variant, reference, missense, utr-variant-5-prime
rs28359644 - 230,767,705(+) CTTCA(C/T)TGATG nc-transcript-variant, reference, missense
rs28359647 - 230,769,189(+) GAAGT(A/G)CTGCA nc-transcript-variant, reference, missense

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

Variant ID Type Subtype PubMed ID
nsv832836 CNV Loss 17160897

Variation tolerance for CAPN9 Gene

Residual Variation Intolerance Score: 96.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 13.26; 95.28% of all genes are more intolerant (likely to be disease-causing)

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

MalaCards: The human disease database

(1) MalaCards diseases for CAPN9 Gene - From: GeneCards

Disorder Aliases PubMed IDs
gastric cancer
  • stomach cancer
- elite association - COSMIC cancer census association via MalaCards
Search CAPN9 in MalaCards View complete list of genes associated with diseases

Relevant External Links for CAPN9

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with CAPN9: view

No data available for UniProtKB/Swiss-Prot 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 67
  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 23
  3. The calpain family and human disease. (PMID: 11516996) Huang Y. … Wang K.K. (Trends Mol Med 2001) 3 23
  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. 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

Products for CAPN9 Gene

Sources for CAPN9 Gene

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