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CAPN9 calpain 9 [ Homo sapiens (human) ]

Gene ID: 10753, updated on 7-Dec-2018

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 current GRCh38.p12 (GCF_000001405.38) 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 IEA
Inferred from Electronic Annotation
more info
 
proteolysis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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, ENST00000271971.6
    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.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 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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