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    CAPN13 calpain 13 [ Homo sapiens (human) ]

    Gene ID: 92291, updated on 28-Oct-2024

    Summary

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    Official Symbol
    CAPN13provided by HGNC
    Official Full Name
    calpain 13provided by HGNC
    Primary source
    HGNC:HGNC:16663
    See related
    Ensembl:ENSG00000162949 MIM:610228; AllianceGenome:HGNC:16663
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    The calpains, calcium-activated neutral proteases, are nonlysosomal, intracellular cysteine proteases. The mammalian calpains include ubiquitous, stomach-specific, and muscle-specific proteins. The ubiquitous enzymes consist of heterodimers with distinct large, catalytic subunits associated with a common small, regulatory subunit. This gene encodes a member of the calpain large subunit family. [provided by RefSeq, Jun 2012]
    Expression
    Biased expression in small intestine (RPKM 8.2), duodenum (RPKM 5.3) and 6 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CAPN13 in Genome Data Viewer
    Location:
    2p23.1
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (30722771..30807446, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (30767038..30851702, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (30945637..31030312, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1936 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:30633050-30633962 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15544 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:30666124-30666624 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:30669802-30670539 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:30670540-30671276 Neighboring gene lysocardiolipin acyltransferase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:30738762-30739262 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:30739263-30739763 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:30835819-30836816 Neighboring gene MPRA-validated peak3643 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15548 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:30874941-30875672 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:30875673-30876403 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11329 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:30943850-30944350 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:30944351-30944851 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:30988245-30988745 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:31020137-31020846 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:31020847-31021554 Neighboring gene uncharacterized LOC124905982 Neighboring gene uncharacterized LOC105374435 Neighboring gene uncharacterized LOC124907750

    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. Gene-environment interaction for hypertension among African American women across generations. Taylor JY, et al. Biol Res Nurs, 2010 Oct. PMID 20591971, Free PMC Article
    2. Inactivating mutations of tumor suppressor genes ABCA1 and CAPN13 in colorectal cancers. Mo HY, et al. Pathol Res Pract, 2020 May. PMID 32088085
    3. Identification and characterization of two novel calpain large subunit genes. Dear TN, et al. Gene, 2001 Aug 22. PMID 11675017
    4. Gene structure, chromosomal localization, and expression pattern of Capn12, a new member of the calpain large subunit gene family. Dear TN, et al. Genomics, 2000 Sep 1. PMID 10964513
    5. Meta-analysis of genome-wide association studies in African Americans provides insights into the genetic architecture of type 2 diabetes. Ng MC, et al. PLoS Genet, 2014 Aug. PMID 25102180, Free PMC Article

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Inactivating mutations of tumor suppressor genes ABCA1 and CAPN13 in colorectal cancers.
      Title: Inactivating mutations of tumor suppressor genes ABCA1 and CAPN13 in colorectal cancers.
    2. Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Gene-environment interaction for hypertension among African American women across generations.
    3. 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.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Meta-analysis of genome-wide association studies in african americans provides insights into the genetic architecture of type 2 diabetes.
    EBI GWAS Catalog

    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ23523

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium-dependent cysteine-type endopeptidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    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

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    Preferred Names
    calpain-13
    Names
    CANP 13
    calcium-activated neutral proteinase 13

    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_144575.3 → NP_653176.2  calpain-13

      See identical proteins and their annotated locations for NP_653176.2

      Status: VALIDATED

      Source sequence(s)
      AC092569, AK074418, BM127691, BX476842, BX640793, BX647678
      Consensus CDS
      CCDS46252.1
      UniProtKB/Swiss-Prot
      Q17RF0, Q580X1, Q6MZZ7, Q8TE80
      UniProtKB/TrEMBL
      A8K2N3
      Related
      ENSP00000295055.8, ENST00000295055.12
      Conserved Domains (3) summary
      cd16195
      Location:501 → 669
      EFh_PEF_CAPN13_14; Penta-EF hand, calcium binding motifs, found in calpain-13 (CAPN13), calpain-14 (CAPN14), and similar proteins
      pfam00648
      Location:35 → 331
      Peptidase_C2; Calpain family cysteine protease
      cl00165
      Location:347 → 474
      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 ...

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      30722771..30807446 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047446332.1 → XP_047302288.1  calpain-13 isoform X1

      UniProtKB/Swiss-Prot
      Q17RF0, Q580X1, Q6MZZ7, Q8TE80

    2. XM_011533161.4 → XP_011531463.1  calpain-13 isoform X1

      See identical proteins and their annotated locations for XP_011531463.1

      UniProtKB/Swiss-Prot
      Q17RF0, Q580X1, Q6MZZ7, Q8TE80
      UniProtKB/TrEMBL
      A8K2N3
      Conserved Domains (3) summary
      cd16195
      Location:501 → 669
      EFh_PEF_CAPN13_14; Penta-EF hand, calcium binding motifs, found in calpain-13 (CAPN13), calpain-14 (CAPN14), and similar proteins
      pfam00648
      Location:35 → 331
      Peptidase_C2; Calpain family cysteine protease
      cl00165
      Location:347 → 474
      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 ...

    3. XM_017005266.3 → XP_016860755.1  calpain-13 isoform X2

      UniProtKB/TrEMBL
      A8K2N3

    4. XM_011533159.4 → XP_011531461.1  calpain-13 isoform X1

      See identical proteins and their annotated locations for XP_011531461.1

      UniProtKB/Swiss-Prot
      Q17RF0, Q580X1, Q6MZZ7, Q8TE80
      UniProtKB/TrEMBL
      A8K2N3
      Conserved Domains (3) summary
      cd16195
      Location:501 → 669
      EFh_PEF_CAPN13_14; Penta-EF hand, calcium binding motifs, found in calpain-13 (CAPN13), calpain-14 (CAPN14), and similar proteins
      pfam00648
      Location:35 → 331
      Peptidase_C2; Calpain family cysteine protease
      cl00165
      Location:347 → 474
      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 ...

    5. XM_011533160.3 → XP_011531462.1  calpain-13 isoform X1

      See identical proteins and their annotated locations for XP_011531462.1

      UniProtKB/Swiss-Prot
      Q17RF0, Q580X1, Q6MZZ7, Q8TE80
      UniProtKB/TrEMBL
      A8K2N3
      Conserved Domains (3) summary
      cd16195
      Location:501 → 669
      EFh_PEF_CAPN13_14; Penta-EF hand, calcium binding motifs, found in calpain-13 (CAPN13), calpain-14 (CAPN14), and similar proteins
      pfam00648
      Location:35 → 331
      Peptidase_C2; Calpain family cysteine protease
      cl00165
      Location:347 → 474
      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 ...

    6. XM_011533163.3 → XP_011531465.1  calpain-13 isoform X3

      Related
      ENSP00000416191.2, ENST00000458085.6
      Conserved Domains (1) summary
      pfam00648
      Location:35 → 331
      Peptidase_C2; Calpain family cysteine protease

    RNA

    1. XR_939741.4 RNA Sequence

    2. XR_939742.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      30767038..30851702 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054344553.1 → XP_054200528.1  calpain-13 isoform X1

    2. XM_054344554.1 → XP_054200529.1  calpain-13 isoform X1

    3. XM_054344555.1 → XP_054200530.1  calpain-13 isoform X1

    4. XM_054344556.1 → XP_054200531.1  calpain-13 isoform X3

    RNA

    1. XR_008486602.1 RNA Sequence

    2. XR_008486603.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6MZZ7.2 GenPept UniProtKB/Swiss-Prot:Q6MZZ7

    Gene LinkOut

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

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