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    CAPN9 calpain 9 [ Homo sapiens (human) ]

    Gene ID: 10753, updated on 17-Jun-2019

    Summary

    Official Symbol
    CAPN9provided by HGNC
    Official Full Name
    calpain 9provided by HGNC
    Primary source
    HGNC:HGNC:1486
    See related
    Ensembl:ENSG00000135773 MIM:606401
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    GC36; nCL-4
    Summary
    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]
    Expression
    Biased expression in stomach (RPKM 15.1), colon (RPKM 3.9) and 3 other tissues See more
    Orthologs

    Genomic context

    See CAPN9 in Genome Data Viewer
    Location:
    1q42.2
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    109.20190607 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (230747289..230803356)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (230883089..230937749)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373166 Neighboring gene angiotensinogen Neighboring gene VISTA enhancer hs2133 Neighboring gene uncharacterized LOC107985359 Neighboring gene RNA, 5S ribosomal pseudogene 79 Neighboring gene chromosome 1 open reading frame 198 Neighboring gene VISTA enhancer hs1766

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Phenotypes

    NHGRI GWAS Catalog

    Description
    A genome-wide association study provides evidence for association of chromosome 8p23 (MYP10) and 10q21.1 (MYP15) with high myopia in the French Population.
    NHGRI GWA Catalog

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of calpain 9 (CAPN9) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from BioSystems

    • Degradation of the extracellular matrix, organism-specific biosystem (from REACTOME)
      Degradation of the extracellular matrix, organism-specific biosystemMatrix metalloproteinases (MMPs), previously referred to as matrixins because of their role in degradation of the extracellular matrix (ECM), are zinc and calcium dependent proteases belonging to the...
    • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
      Extracellular matrix organization, organism-specific biosystemThe extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin and associated-microfibrils, fibronectin and laminins embedded...
    • Integrin-mediated Cell Adhesion, organism-specific biosystem (from WikiPathways)
      Integrin-mediated Cell Adhesion, organism-specific biosystemIntegrins are receptors that mediate attachment between a cell and the tissues surrounding it, which may be other cells or the extracellular matrix (ECM). They also play a role in cell signaling and ...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    calcium-dependent cysteine-type endopeptidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Process Evidence Code Pubs
    digestion TAS
    Traceable Author Statement
    more info
    PubMed 
    proteolysis IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    sarcomere organization IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    cellular_component ND
    No biological Data available
    more info
     
    cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 

    General protein information

    Preferred Names
    calpain-9
    Names
    digestive tract-specific calpain
    new calpain 4
    novel calpain large subunit-4
    NP_001306605.1
    NP_006606.1
    NP_057536.1
    XP_011542319.1
    XP_011542320.1
    XP_011542321.1
    XP_011542322.1
    XP_016855587.1
    XP_016855588.1
    XP_024308281.1
    XP_024308282.1

    NCBI Reference Sequences (RefSeq)

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001319676.1NP_001306605.1  calpain-9 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks two alternate coding exons compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AB038463, AF022799, AK298024
      Consensus CDS
      CCDS81431.1
      UniProtKB/Swiss-Prot
      O14815
      UniProtKB/TrEMBL
      B4DNR4, E7ESS6
      Related
      ENSP00000355626.2, ENST00000366666.6
      Conserved Domains (5) summary
      cd00051
      Location:503558
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
      pfam00648
      Location:43272
      Peptidase_C2; Calpain family cysteine protease
      pfam01067
      Location:286428
      Calpain_III; Calpain large subunit, domain III
      pfam13499
      Location:535589
      EF-hand_7; EF-hand domain pair
      cl08302
      Location:537589
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
    2. NM_006615.3NP_006606.1  calpain-9 isoform 1

      See identical proteins and their annotated locations for NP_006606.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AF022799, AL512328, BC027993
      Consensus CDS
      CCDS1586.1
      UniProtKB/Swiss-Prot
      O14815
      UniProtKB/TrEMBL
      Q6PIV8
      Related
      ENSP00000271971.2, ENST00000271971.7
      Conserved Domains (5) summary
      PTZ00184
      Location:514657
      PTZ00184; calmodulin; Provisional
      cd00051
      Location:566621
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
      pfam00648
      Location:43335
      Peptidase_C2; Calpain family cysteine protease
      pfam01067
      Location:349491
      Calpain_III; Calpain large subunit, domain III
      cl08302
      Location:600652
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
    3. NM_016452.2NP_057536.1  calpain-9 isoform 2

      See identical proteins and their annotated locations for NP_057536.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AB038463, AF022799
      Consensus CDS
      CCDS31053.1
      UniProtKB/Swiss-Prot
      O14815
      Related
      ENSP00000346538.1, ENST00000354537.1
      Conserved Domains (5) summary
      PTZ00184
      Location:488631
      PTZ00184; calmodulin; Provisional
      cd00051
      Location:540595
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
      pfam00648
      Location:43309
      Peptidase_C2; Calpain family cysteine protease
      pfam01067
      Location:323465
      Calpain_III; Calpain large subunit, domain III
      cl08302
      Location:574626
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

      Range
      230747289..230803356
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011544019.2XP_011542321.1  calpain-9 isoform X4

      Conserved Domains (5) summary
      PTZ00184
      Location:451594
      PTZ00184; calmodulin; Provisional
      cd00051
      Location:503558
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
      pfam00648
      Location:43272
      Peptidase_C2; Calpain family cysteine protease
      pfam01067
      Location:286428
      Calpain_III; Calpain large subunit, domain III
      cl08302
      Location:537589
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
    2. XM_011544017.1XP_011542319.1  calpain-9 isoform X1

      Conserved Domains (5) summary
      PTZ00184
      Location:514657
      PTZ00184; calmodulin; Provisional
      cd00051
      Location:566621
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
      pfam00648
      Location:43335
      Peptidase_C2; Calpain family cysteine protease
      pfam01067
      Location:349491
      Calpain_III; Calpain large subunit, domain III
      cl08302
      Location:600652
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
    3. XM_011544018.1XP_011542320.1  calpain-9 isoform X2

      Conserved Domains (5) summary
      PTZ00184
      Location:488631
      PTZ00184; calmodulin; Provisional
      cd00051
      Location:540595
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
      pfam00648
      Location:43309
      Peptidase_C2; Calpain family cysteine protease
      pfam01067
      Location:323465
      Calpain_III; Calpain large subunit, domain III
      cl08302
      Location:574626
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
    4. XM_017000098.1XP_016855587.1  calpain-9 isoform X3

    5. XM_017000099.1XP_016855588.1  calpain-9 isoform X6

    6. XM_011544020.1XP_011542322.1  calpain-9 isoform X5

      Conserved Domains (5) summary
      PTZ00184
      Location:319462
      PTZ00184; calmodulin; Provisional
      cd00051
      Location:371426
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
      pfam01067
      Location:154296
      Calpain_III; Calpain large subunit, domain III
      cl00051
      Location:1140
      CysPc; Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction.
      cl08302
      Location:405457
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
    7. XM_024452513.1XP_024308281.1  calpain-9 isoform X7

      Conserved Domains (4) summary
      cd00214
      Location:29178
      Calpain_III; Calpain, subdomain III. Calpains are calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are ...
      cd15897
      Location:204232
      EFh_PEF; EF-hand motif [structural motif]
      cl00051
      Location:126
      CysPc; Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction.
      cl25352
      Location:204344
      EFh_PEF; The penta-EF hand (PEF) family
    8. XM_024452514.1XP_024308282.1  calpain-9 isoform X7

      Conserved Domains (4) summary
      cd00214
      Location:29178
      Calpain_III; Calpain, subdomain III. Calpains are calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are ...
      cd15897
      Location:204232
      EFh_PEF; EF-hand motif [structural motif]
      cl00051
      Location:126
      CysPc; Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction.
      cl25352
      Location:204344
      EFh_PEF; The penta-EF hand (PEF) family

    RNA

    1. XR_001736933.1 RNA Sequence

    2. XR_949127.1 RNA Sequence

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