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CAPN13 calpain 13 [ Homo sapiens (human) ]

Gene ID: 92291, updated on 2-Nov-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
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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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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
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)

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

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