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CAPNS1 calpain small subunit 1 [ Homo sapiens (human) ]

Gene ID: 826, updated on 27-Nov-2024

Summary

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Official Symbol
CAPNS1provided by HGNC
Official Full Name
calpain small subunit 1provided by HGNC
Primary source
HGNC:HGNC:1481
See related
Ensembl:ENSG00000126247 MIM:114170; AllianceGenome:HGNC:1481
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
CANP; CDPS; CSS1; PPH6; CANPS; CAPN4; CALPAIN4
Summary
This gene is a member of the calpain small subunit family. Calpains are calcium-dependent cysteine proteinases that are widely distributed in mammalian cells. Calpains operate as heterodimers, comprising a specific large catalytic subunit (calpain 1 subunit in Calpain I, and calpain 2 subunit in Calpain II), and a common small regulatory subunit encoded by this gene. This encoded protein is essential for the stability and function of both calpain heterodimers, whose proteolytic activities influence various cellular functions including apoptosis, proliferation, migration, adhesion, and autophagy. Calpains have been implicated in neurodegenerative processes, such as myotonic dystrophy. A pseudogene of this gene has been defined on chromosome 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]
Expression
Ubiquitous expression in esophagus (RPKM 128.4), heart (RPKM 97.8) and 25 other tissues See more
Orthologs
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Genomic context

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See CAPNS1 in Genome Data Viewer
Location:
19q13.12
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (36140066..36150353)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (38685882..38696171)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (36630968..36641255)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10547 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14516 Neighboring gene uncharacterized LOC105372385 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14517 Neighboring gene tubulin folding cofactor B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14518 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14519 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:36646245-36646976 Neighboring gene cytochrome c oxidase subunit 7A1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:36678024-36678563 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:36678564-36679102 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:36683570-36684070 Neighboring gene zinc finger protein 565 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:36684071-36684571 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14520 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14521 Neighboring gene zinc finger protein 146 Neighboring gene uncharacterized LOC107985304 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:36724474-36724976 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:36724977-36725478

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Capn4 mRNA level is correlated with tumour progression and clinical outcome in clear cell renal cell carcinoma. Zhuang Q, et al. J Int Med Res, 2014 Apr. PMID 24514433
  2. Calpain restrains the stem cells compartment in breast cancer. Raimondi M, et al. Cell Cycle, 2016. PMID 26771715, Free PMC Article
  3. Overexpression of Capns1 Predicts Poor Prognosis and Correlates with Tumor Progression in Renal Cell Carcinoma. Zhuang Q, et al. Urol Int, 2021. PMID 33887737
  4. Gene organization of the small subunit of human calcium-activated neutral protease. Miyake S, et al. Nucleic Acids Res, 1986 Nov 25. PMID 3024120, Free PMC Article
  5. Capn4 contributes to tumour growth and metastasis of hepatocellular carcinoma by activation of the FAK-Src signalling pathways. Dai Z, et al. J Pathol, 2014 Nov. PMID 24962955

See all (121) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Identification of Crucial Genes and Key Functions in Type 2 Diabetic Hearts by Bioinformatic Analysis.
    Title: Identification of Crucial Genes and Key Functions in Type 2 Diabetic Hearts by Bioinformatic Analysis.
  2. Overexpression of Capns1 Predicts Poor Prognosis and Correlates with Tumor Progression in Renal Cell Carcinoma.
    Title: Overexpression of Capns1 Predicts Poor Prognosis and Correlates with Tumor Progression in Renal Cell Carcinoma.
  3. Circular RNA ABCB10 promotes cell proliferation and invasion, but inhibits apoptosis via regulating the microRNA1271mediated Capn4/Wnt/betacatenin signaling pathway in epithelial ovarian cancer.
    Title: Circular RNA ABCB10 promotes cell proliferation and invasion, but inhibits apoptosis via regulating the microRNA‑1271‑mediated Capn4/Wnt/β‑catenin signaling pathway in epithelial ovarian cancer.
  4. Capn4 contributes to tumor invasion and metastasis in gastric cancer via activation of the Wnt/beta-catenin/MMP9 signalling pathways.
    Title: Capn4 contributes to tumor invasion and metastasis in gastric cancer via activation of the Wnt/β-catenin/MMP9 signalling pathways.
  5. Capn4 coordination with LMP1 enhances NPC migration.
    Title: Capn4 is induced by and required for Epstein-Barr virus latent membrane protein 1 promotion of nasopharyngeal carcinoma metastasis through ERK/AP-1 signaling.
  6. our results show that enhanced Capn4 expression activates the Wnt/beta-catenin signaling pathway, resulting in increased ZEB1 expression and the promotion of esophageal squamous cell carcinoma (ESCC) cell metastasis.
    Title: Capn4 promotes esophageal squamous cell carcinoma metastasis by regulating ZEB1 through the Wnt/β-catenin signaling pathway.
  7. Collectively, these data suggested the tumor suppressive role of miR-337-3p in ccRCC. MiR-337-3p suppressed cell proliferation and metastasis in lear cell renal cell carcinoma partially via targeting Capn4.
    Title: MiR-337-3p suppresses the proliferation and metastasis of clear cell renal cell carcinoma cells via modulating Capn4.
  8. Suppression of Capn4 by miR-520b inhibits the growth and invasion of prostate cancer cells associated with downregulated Wnt/beta-catenin signaling.
    Title: Capn4 expression is modulated by microRNA-520b and exerts an oncogenic role in prostate cancer cells by promoting Wnt/β-catenin signaling.
  9. Low calpain 4 expression is associated with ovarian cancer.
    Title: Calpain system protein expression and activity in ovarian cancer.
  10. that Capn4 promotes cell proliferation by increasing MAPK7 expression
    Title: Capn4 promotes colorectal cancer cell proliferation by increasing MAPK7 through activation of the Wnt/β-Catenin pathway.
Submit: New GeneRIF Correction See all GeneRIFs (33)

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

Associated conditions

Description Tests
Pulmonary hypertension, primary, 6
MedGen: CN377269 OMIM: 620777 GeneReviews: Not available
not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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 IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in positive regulation of cell population proliferation TAS
Traceable Author Statement
more info
 PubMed 
involved_in proteolysis NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in regulation of macroautophagy NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of calpain complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of calpain complex IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of calpain complex ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in extracellular exosome HDA PubMed 
located_in membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
calpain small subunit 1
Names
CANP small subunit
calcium-activated neutral proteinase small subunit
calcium-dependent protease small subunit 1
calcium-dependent protease, small subunit
calpain 4, small subunit (30K)
calpain regulatory subunit
calpain, small polypeptide
epididymis secretory sperm binding protein
NP_001003962.1
NP_001289561.1
NP_001289562.1
NP_001740.1
XP_005259352.1
XP_005259353.1
XP_011525661.1
XP_054178264.1
XP_054178265.1
XP_054178266.1
XP_054178267.1

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)

  1. NM_001003962.3 → NP_001003962.1  calpain small subunit 1 isoform 1

    See identical proteins and their annotated locations for NP_001003962.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    AK289606, BC000592, BQ891655
    Consensus CDS
    CCDS12489.1
    UniProtKB/Swiss-Prot
    A8K0P1, P04632, Q8WTX3, Q96EW0
    UniProtKB/TrEMBL
    K7ELJ7
    Related
    ENSP00000465575.1, ENST00000590874.5
    Conserved Domains (2) summary
    cd00051
    Location:144 → 194
    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 ...
    cl08302
    Location:175 → 230
    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_001302632.2 → NP_001289561.1  calpain small subunit 1 isoform 1

    See identical proteins and their annotated locations for NP_001289561.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    AD001527, AK289606, BC064998
    Consensus CDS
    CCDS12489.1
    UniProtKB/Swiss-Prot
    A8K0P1, P04632, Q8WTX3, Q96EW0
    UniProtKB/TrEMBL
    K7ELJ7
    Related
    ENSP00000464849.1, ENST00000588815.5
    Conserved Domains (2) summary
    cd00051
    Location:144 → 194
    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 ...
    cl08302
    Location:175 → 230
    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_001302633.2 → NP_001289562.1  calpain small subunit 1 isoform 2

    See identical proteins and their annotated locations for NP_001289562.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks two 5' exons and uses an alternate 5' terminal exon which results in the use of a downstream in-frame start codon, compared to variant 1. It encodes isoform 2 which has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AD001527, AK289606, BC000592, BQ891655, CN349928, HY003903
    UniProtKB/Swiss-Prot
    P04632
    Conserved Domains (1) summary
    cd16188
    Location:1 → 156
    EFh_PEF_CPNS1_2; Penta-EF hand, calcium binding motifs, found in calcium-dependent protease small subunit CAPNS1 and CAPNS2

  4. NM_001749.4 → NP_001740.1  calpain small subunit 1 isoform 1

    See identical proteins and their annotated locations for NP_001740.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1). Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    AK289606, BC000592, BQ891655
    Consensus CDS
    CCDS12489.1
    UniProtKB/Swiss-Prot
    A8K0P1, P04632, Q8WTX3, Q96EW0
    UniProtKB/TrEMBL
    K7ELJ7
    Related
    ENSP00000246533.2, ENST00000246533.8
    Conserved Domains (2) summary
    cd00051
    Location:144 → 194
    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 ...
    cl08302
    Location:175 → 230
    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    36140066..36150353
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005259295.2 → XP_005259352.1  calpain small subunit 1 isoform X1

    See identical proteins and their annotated locations for XP_005259352.1

    UniProtKB/TrEMBL
    A0A0C4DGQ5, K7ELJ7
    Related
    ENSP00000468041.1, ENST00000587718.5
    Conserved Domains (1) summary
    cd16188
    Location:100 → 260
    EFh_PEF_CPNS1_2; Penta-EF hand, calcium binding motifs, found in calcium-dependent protease small subunit CAPNS1 and CAPNS2

  2. XM_005259296.2 → XP_005259353.1  calpain small subunit 1 isoform X1

    See identical proteins and their annotated locations for XP_005259353.1

    UniProtKB/TrEMBL
    A0A0C4DGQ5, K7ELJ7
    Conserved Domains (1) summary
    cd16188
    Location:100 → 260
    EFh_PEF_CPNS1_2; Penta-EF hand, calcium binding motifs, found in calcium-dependent protease small subunit CAPNS1 and CAPNS2

  3. XM_011527359.2 → XP_011525661.1  calpain small subunit 1 isoform X2

    UniProtKB/TrEMBL
    K7EIV0
    Related
    ENSP00000464903.2, ENST00000586851.5
    Conserved Domains (2) summary
    cd00051
    Location:76 → 126
    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 ...
    cl08302
    Location:107 → 162
    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 ...

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    38685882..38696171
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054322289.1 → XP_054178264.1  calpain small subunit 1 isoform X1

    UniProtKB/TrEMBL
    A0A0C4DGQ5

  2. XM_054322290.1 → XP_054178265.1  calpain small subunit 1 isoform X1

    UniProtKB/TrEMBL
    A0A0C4DGQ5

  3. XM_054322292.1 → XP_054178267.1  calpain small subunit 1 isoform X2

  4. XM_054322291.1 → XP_054178266.1  calpain small subunit 1 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P04632.1 GenPept UniProtKB/Swiss-Prot:P04632

Gene LinkOut

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