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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 58
  • EC 3.4.22.- 4
  • Calpain-9 3
  • EC 3.4.22 58
  • 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, Somatic. Among its related pathways are Arrhythmogenic right ventricular cardiomyopathy (ARVC) 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 CAPN3.

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

Additional gene information for CAPN9 Gene

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

Genomics for CAPN9 Gene

Regulatory Elements for CAPN9 Gene

Enhancers for CAPN9 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01H230750 1.9 VISTA Ensembl ENCODE dbSUPER 19.2 +5.5 5503 5.2 ELF3 PKNOX1 FOXA2 ARID4B SIN3A ZNF76 KLF17 RAD21 ZSCAN9 ZBTB7B CAPN9 AGT COG2 GC01P230769
GH01H230768 0.9 ENCODE dbSUPER 30.4 +22.1 22093 1.2 RFX1 HLF SIN3A MNT DPF2 TEAD3 FOXA1 ZNF217 NFIL3 CTBP1 CAPN9 LOC101927604 C1orf198 COG2 GC01P230769
GH01H230758 1 ENCODE dbSUPER 19.8 +12.3 12273 2.5 CTCF ESRRA SAP130 TAL1 ARID4B EBF1 RAD21 ZKSCAN1 FOSL1 TCF12 CAPN9 AGT COG2 LOC101927604 GC01P230769
GH01H230820 1.4 Ensembl ENCODE dbSUPER 13 +77.4 77361 8.2 TBP PKNOX1 ZNF23 ZNF766 ZNF548 FOS CEBPB ZNF623 NR2F2 SREBF1 C1orf131 C1orf198 LOC101927604 CAPN9 COG2 ENSG00000244137 ENSG00000225656 RNA5SP79
GH01H230746 0.9 ENCODE dbSUPER 14.5 +0.4 421 1.9 TFAP4 KLF1 FOXA2 ZMYM3 KLF4 ZBTB40 RARA FOXA1 KLF9 FOS CAPN9 AGT GC01P230769
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CAPN9 on UCSC Golden Path with GeneCards custom track

Genomic Locations for CAPN9 Gene

Genomic Locations for CAPN9 Gene
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

Selected DME Specific Peptides for CAPN9 Gene


Post-translational modifications for CAPN9 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for CAPN9 Gene

Gene Families for CAPN9 Gene

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

Suggested Antigen Peptide Sequences for CAPN9 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the peptidase C2 family.
  • 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

Phenotypes From GWAS Catalog 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 --
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 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

Clone Products

  • Addgene plasmids for CAPN9

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CAPN9 Gene

Localization for CAPN9 Gene

Subcellular locations from

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 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 IEA --
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 and Subcellular locations from the Human Protein Atlas (HPA) 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

Gene Ontology (GO) - Biological Process for CAPN9 Gene

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

No data available for SIGNOR curated interactions for CAPN9 Gene

Drugs & Compounds for CAPN9 Gene

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

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Nutra 0

(1) Additional Compounds for CAPN9 Gene - From:

Name Synonyms Role CAS Number PubChem IDs PubMed IDs

(2) Tocris Compounds for CAPN9 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 CAPN9: view

Transcripts for CAPN9 Gene

Unigene Clusters for CAPN9 Gene

Calpain 9:
Representative Sequences:

Clone Products

  • Addgene plasmids for CAPN9

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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

Protein tissue co-expression partners for CAPN9 Gene

NURSA nuclear receptor signaling pathways regulating expression of CAPN9 Gene:


SOURCE GeneReport for Unigene cluster for CAPN9 Gene:


mRNA Expression by UniProt/SwissProt for CAPN9 Gene:

Tissue specificity: Expressed predominantly in stomach.

Evidence on tissue expression from TISSUES for CAPN9 Gene

  • Stomach(4.7)
genes like me logo Genes that share expression patterns with CAPN9: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for CAPN9 Gene

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 33 34
  • 99.66 (n)
(Canis familiaris)
Mammalia CAPN9 33 34
  • 89.37 (n)
(Mus musculus)
Mammalia Capn9 33 16 34
  • 83.24 (n)
(Rattus norvegicus)
Mammalia Capn9 33
  • 83.24 (n)
(Monodelphis domestica)
Mammalia CAPN9 34
  • 80 (a)
(Ornithorhynchus anatinus)
Mammalia CAPN9 34
  • 73 (a)
(Gallus gallus)
Aves CAPN9 33 34
  • 75.75 (n)
(Anolis carolinensis)
Reptilia CAPN9 34
  • 77 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia capn9 33
  • 69.28 (n)
Str.2459 33
(Danio rerio)
Actinopterygii capn9 33 33 34
  • 64.83 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2168 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012068 33
  • 55.08 (n)
fruit fly
(Drosophila melanogaster)
Insecta CalpA 35 33
  • 54.57 (n)
CalpB 35
  • 44 (a)
CalpC 35
  • 31 (a)
(Caenorhabditis elegans)
Secernentea clp-7 35
  • 47 (a)
clp-6 35
  • 42 (a)
clp-3 35
  • 39 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.4609 34
  • 46 (a)
Species where no ortholog for CAPN9 was found in the sources mined by GeneCards:
  • 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

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
rs1000038725 -- 230,788,722(+) CAGCC(C/G)TGGGC intron-variant
rs1000042529 -- 230,752,709(+) TATGT(C/T)CACTT intron-variant, utr-variant-5-prime
rs1000089052 -- 230,798,381(+) TTTAT(C/G)AAGTA intron-variant
rs1000121841 -- 230,797,917(+) TGGCC(A/G)GCTGA intron-variant
rs1000152877 -- 230,788,501(+) AATGA(C/T)TCTAT intron-variant

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

Variant ID Type Subtype PubMed ID
nsv832836 CNV loss 17160897
nsv549335 CNV gain 21841781
nsv1010882 CNV gain 25217958
nsv1000488 CNV gain 25217958
esv3589093 CNV gain 21293372

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

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

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: Novoseek

Disorder Aliases PubMed IDs
gastric cancer, somatic
  • gastric 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 (Japanese journal of cancer research : Gann 2000) 2 3 4 22 60
  2. The crystal structures of human calpains 1 and 9 imply diverse mechanisms of action and auto-inhibition. (PMID: 17157313) Davis TL … Dhe-Paganon S (Journal of molecular biology 2007) 3 4 22 60
  3. Molecular cloning and characterization of a novel tissue-specific calpain predominantly expressed in the digestive tract. (PMID: 9524069) Lee HJ … Suzuki K (Biological chemistry 1998) 2 3 4 60
  4. 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 45 60
  5. A Large-scale genetic association study of esophageal adenocarcinoma risk. (PMID: 20453000) Liu CY … Christiani DC (Carcinogenesis 2010) 3 45 60

Products for CAPN9 Gene

Sources for CAPN9 Gene

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