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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 3.4.22.- 4
  • Calpain-9 3
  • 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 Focal Adhesion and Integrin 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 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

GeneHancer (GH) Regulatory Elements for CAPN9 Gene

Promoters and enhancers for CAPN9 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J230746 Promoter/Enhancer 1.3 EPDnew ENCODE dbSUPER 664.5 +0.4 421 1.9 KLF1 TFAP4 FOXA2 ZMYM3 KLF4 ZBTB40 RARA FOXA1 SMAD4 KDM1A CAPN9 AGT GC01P230769 ENSG00000244137
GH01J230749 Enhancer 0.7 Ensembl dbSUPER 656.2 +1.8 1767 0.2 NR2F1 IKZF1 ATF7 MEF2B PRDM2 CAPN9 GC01P230769 ENSG00000244137
GH01J230750 Enhancer 1.7 VISTA Ensembl ENCODE dbSUPER 19.2 +5.5 5502 5.2 PKNOX1 CLOCK FOXA2 ARID4B SIN3A ZBTB7B GLIS2 FOS SP3 PPARG CAPN9 AGT COG2 GC01P230769 ENSG00000244137
GH01J230768 Enhancer 0.9 ENCODE dbSUPER 30.4 +22.1 22092 1.2 USF1 SIN3A ZNF507 TEAD3 CTBP1 GATA3 FOS RFX1 HLF DACH1 GC01P230769 CAPN9 LOC101927604 C1orf198 COG2 ENSG00000244137
GH01J230758 Enhancer 0.9 ENCODE dbSUPER 19.8 +12.3 12273 2.5 CTCF TFAP4 ESRRA SAP130 TEAD4 TAL1 ARID4B EBF1 ZNF48 RBPJ CAPN9 AGT COG2 LOC101927604 GC01P230769 ENSG00000244137
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CAPN9 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CAPN9 gene promoter:
  • PPAR-gamma2
  • PPAR-gamma1
  • Roaz
  • AML1a
  • deltaCREB

Genomic Locations for CAPN9 Gene

Genomic Locations for CAPN9 Gene
54,670 bases
Plus strand
54,620 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

Post-translational modifications for CAPN9 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CAPN9 Gene

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 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:

Animal Model Products

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

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

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

mRNA/cDNA for CAPN9 Gene

(11) REFSEQ mRNAs :
(6) Additional mRNA sequences :
(17) Selected AceView cDNA sequences:
(4) Ensembl transcripts including schematic representations, and UCSC links where relevant :

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 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 34 33
  • 99.66 (n)
(Canis familiaris)
Mammalia CAPN9 34 33
  • 89.37 (n)
(Mus musculus)
Mammalia Capn9 16 34 33
  • 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 34 33
  • 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 34 33 33
  • 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)
Evolutionary constrained regions (ECRs) for CAPN9: view image

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 Variation AA Info Type
rs1000038725 -- 230,788,722(+) C/G genic_downstream_transcript_variant, intron_variant
rs1000042529 -- 230,752,709(+) C/T 5_prime_UTR_variant, intron_variant
rs1000089052 -- 230,798,381(+) C/G genic_downstream_transcript_variant, intron_variant
rs1000121841 -- 230,797,917(+) G/A genic_downstream_transcript_variant, intron_variant
rs1000152877 -- 230,788,501(+) C/T genic_downstream_transcript_variant, intron_variant

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

Variant ID Type Subtype PubMed ID
esv3589093 CNV gain 21293372
nsv1000488 CNV gain 25217958
nsv1010882 CNV gain 25217958
nsv549335 CNV gain 21841781
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)

Additional Variant Information for CAPN9 Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for CAPN9 Gene

Additional Disease Information for CAPN9

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for CAPN9 Gene.

No data available for MalaCards , 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 58
  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 58
  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 58
  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 44 58
  5. A Large-scale genetic association study of esophageal adenocarcinoma risk. (PMID: 20453000) Liu CY … Christiani DC (Carcinogenesis 2010) 3 44 58

Products for CAPN9 Gene

Sources for CAPN9 Gene

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