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

    Gene ID: 826, updated on 2-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
    mouse all
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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 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)

    Genotypes

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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