CAPN9 calpain 9 [Homo sapiens (human)] - Gene

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: mouse all
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Genomic context

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_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

these data provide a strong signature for tolerance of therapeutic strategies for fibrosis aimed at CAPN9 antagonism.
Title: Calpain 9 as a therapeutic target in TGFβ-induced mesenchymal transition and fibrosis.
Study shows that calpain-9 is a tumor suppressor that can be regarded as a potential prognosis indicator for clinical outcomes in gastric cancer.
Title: Decreased expression of Calpain-9 predicts unfavorable prognosis in patients with gastric cancer.
calpain-9 may play a role in breast cancer and that low expression is associated with poorer patient clinical outcome following endocrine therapy.
Title: Low calpain-9 is associated with adverse disease-specific survival following endocrine therapy in breast cancer.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Observational study of gene-disease association. (HuGE Navigator)
Title: A Large-scale genetic association study of esophageal adenocarcinoma risk.
We have solved the structures of human calpain 1 and calpain 9 protease cores ; both structures have clear implications for the function of non-catalytic domains of full-length calpains in the calcium-mediated activation of the enzyme.
Title: The crystal structures of human calpains 1 and 9 imply diverse mechanisms of action and auto-inhibition.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-148871 (e-PCR)
- UniSTS:176657

G15722 (e-PCR)
- UniSTS:43809

AL009462 (e-PCR)
- UniSTS:19505

SHGC-148285 (e-PCR)
- UniSTS:176299

D1S1656 (e-PCR), detects polymorphism
- UniSTS:58809

D1S3730 (e-PCR)
- UniSTS:31168

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 cellular_component	ND No biological Data available more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: calpain-9

Names: digestive tract-specific calpain; new calpain 4; novel calpain large subunit-4

NP_001306605.1

EC 3.4.22.-

NP_006606.1

EC 3.4.22.-

NP_057536.1

EC 3.4.22.-

XP_011542319.1

EC 3.4.22.-

XP_011542320.1

EC 3.4.22.-

XP_011542321.1

EC 3.4.22.-

XP_016855587.1

EC 3.4.22.-

XP_024308281.1

EC 3.4.22.-

XP_024308282.1

EC 3.4.22.-

XP_047295763.1

EC 3.4.22.-

XP_047295764.1

EC 3.4.22.-

XP_054189902.1

EC 3.4.22.-

XP_054189903.1

EC 3.4.22.-

XP_054189904.1

EC 3.4.22.-

XP_054189905.1

EC 3.4.22.-

XP_054189906.1

EC 3.4.22.-

XP_054189907.1

EC 3.4.22.-

XP_054189908.1

EC 3.4.22.-

XP_054189909.1

EC 3.4.22.-

NCBI Reference Sequences (RefSeq)

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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)

NM_001319676.2 → NP_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:503 → 558

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:43 → 272

Peptidase_C2; Calpain family cysteine protease

pfam01067
Location:286 → 428

Calpain_III; Calpain large subunit, domain III

pfam13499
Location:535 → 589

EF-hand_7; EF-hand domain pair

cl08302
Location:537 → 589

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 ...
NM_006615.3 → NP_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:514 → 657

PTZ00184; calmodulin; Provisional

cd00051
Location:566 → 621

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:43 → 335

Peptidase_C2; Calpain family cysteine protease

pfam01067
Location:349 → 491

Calpain_III; Calpain large subunit, domain III

cl08302
Location:600 → 652

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 ...
NM_016452.3 → NP_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:488 → 631

PTZ00184; calmodulin; Provisional

cd00051
Location:540 → 595

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:43 → 309

Peptidase_C2; Calpain family cysteine protease

pfam01067
Location:323 → 465

Calpain_III; Calpain large subunit, domain III

cl08302
Location:574 → 626

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

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

230747388..230801989

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

B2R942

Conserved Domains (5) summary

PTZ00184
Location:514 → 657

PTZ00184; calmodulin; Provisional

cd00051
Location:566 → 621

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:43 → 335

Peptidase_C2; Calpain family cysteine protease

pfam01067
Location:349 → 491

Calpain_III; Calpain large subunit, domain III

cl08302
Location:600 → 652

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 ...
XM_011544018.2 → XP_011542320.1 calpain-9 isoform X2

UniProtKB/TrEMBL

B2R942

Conserved Domains (5) summary

PTZ00184
Location:488 → 631

PTZ00184; calmodulin; Provisional

cd00051
Location:540 → 595

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:43 → 309

Peptidase_C2; Calpain family cysteine protease

pfam01067
Location:323 → 465

Calpain_III; Calpain large subunit, domain III

cl08302
Location:574 → 626

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 ...
XM_017000098.2 → XP_016855587.1 calpain-9 isoform X3

UniProtKB/TrEMBL

B2R942
XM_011544019.3 → XP_011542321.1 calpain-9 isoform X4

UniProtKB/TrEMBL

Q6PIV8

Conserved Domains (5) summary

PTZ00184
Location:451 → 594

PTZ00184; calmodulin; Provisional

cd00051
Location:503 → 558

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:43 → 272

Peptidase_C2; Calpain family cysteine protease

pfam01067
Location:286 → 428

Calpain_III; Calpain large subunit, domain III

cl08302
Location:537 → 589

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 ...
XM_047439807.1 → XP_047295763.1 calpain-9 isoform X5
XM_047439808.1 → XP_047295764.1 calpain-9 isoform X6
XM_024452513.2 → XP_024308281.1 calpain-9 isoform X7

Conserved Domains (4) summary

cd00214
Location:29 → 178

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:204 → 232

EFh_PEF; EF-hand motif [structural motif]

cl00051
Location:1 → 26

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:204 → 344

EFh_PEF; The penta-EF hand (PEF) family
XM_024452514.2 → XP_024308282.1 calpain-9 isoform X7

Conserved Domains (4) summary

cd00214
Location:29 → 178

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:204 → 232

EFh_PEF; EF-hand motif [structural motif]

cl00051
Location:1 → 26

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:204 → 344

EFh_PEF; The penta-EF hand (PEF) family