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CAPN9 calpain 9 [ Homo sapiens (human) ]

Gene ID: 10753, updated on 10-Dec-2024

Summary

Official Symbol
CAPN9provided by HGNC
Official Full Name
calpain 9provided by HGNC
Primary source
HGNC:HGNC:1486
See related
Ensembl:ENSG00000135773 MIM:606401; AllianceGenome:HGNC:1486
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
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Genomic context

See CAPN9 in Genome Data Viewer
Location:
1q42.2
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (230747388..230801989)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (230127941..230182452)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (230883134..230937735)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene component of oligomeric golgi complex 2 Neighboring gene uncharacterized LOC107985358 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230844373-230845194 Neighboring gene Sharpr-MPRA regulatory region 2465 Neighboring gene angiotensinogen Neighboring gene VISTA enhancer hs2133 Neighboring gene uncharacterized LOC107985359 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:230914014-230914159 Neighboring gene NANOG hESC enhancer GRCh37_chr1:230919761-230920350 Neighboring gene uncharacterized LOC124904546 Neighboring gene uncharacterized LOC124904548 Neighboring gene RNA, 5S ribosomal pseudogene 79

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 Functions

What's a GeneRIF?

Phenotypes

EBI 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.
EBI GWAS 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 PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
enables calcium-dependent cysteine-type endopeptidase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
Process Evidence Code Pubs
involved_in digestion TAS
Traceable Author Statement
more info
PubMed 
involved_in proteolysis IBA
Inferred from Biological aspect of Ancestor
more info
 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
 

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_016855587.1
XP_024308281.1
XP_024308282.1
XP_047295763.1
XP_047295764.1
XP_054189902.1
XP_054189903.1
XP_054189904.1
XP_054189905.1
XP_054189906.1
XP_054189907.1
XP_054189908.1
XP_054189909.1

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_001319676.2NP_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, AL512328
    Consensus CDS
    CCDS81431.1
    UniProtKB/TrEMBL
    E7ESS6, Q6PIV8
    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
    B1APS1, B1AQI0, O14815, Q9NS74
    UniProtKB/TrEMBL
    B2R942
    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_016452.3NP_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, AL512328
    Consensus CDS
    CCDS31053.1
    UniProtKB/TrEMBL
    B2R942
    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: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    230747388..230801989
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011544017.2XP_011542319.1  calpain-9 isoform X1

    UniProtKB/TrEMBL
    B2R942
    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 ...
  2. XM_011544018.2XP_011542320.1  calpain-9 isoform X2

    UniProtKB/TrEMBL
    B2R942
    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 ...
  3. XM_017000098.2XP_016855587.1  calpain-9 isoform X3

    UniProtKB/TrEMBL
    B2R942
  4. XM_011544019.3XP_011542321.1  calpain-9 isoform X4

    UniProtKB/TrEMBL
    Q6PIV8
    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 ...
  5. XM_047439807.1XP_047295763.1  calpain-9 isoform X5

  6. XM_047439808.1XP_047295764.1  calpain-9 isoform X6

  7. XM_024452513.2XP_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_024452514.2XP_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_949127.2 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    230127941..230182452
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054333927.1XP_054189902.1  calpain-9 isoform X1

    UniProtKB/TrEMBL
    B2R942
  2. XM_054333928.1XP_054189903.1  calpain-9 isoform X2

    UniProtKB/TrEMBL
    B2R942
  3. XM_054333929.1XP_054189904.1  calpain-9 isoform X3

    UniProtKB/TrEMBL
    B2R942
  4. XM_054333931.1XP_054189906.1  calpain-9 isoform X4

    UniProtKB/TrEMBL
    Q6PIV8
  5. XM_054333932.1XP_054189907.1  calpain-9 isoform X5

  6. XM_054333930.1XP_054189905.1  calpain-9 isoform X8

    UniProtKB/TrEMBL
    B2R942
  7. XM_054333933.1XP_054189908.1  calpain-9 isoform X7

  8. XM_054333934.1XP_054189909.1  calpain-9 isoform X7

RNA

  1. XR_008485878.1 RNA Sequence