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    CAPN8 calpain 8 [ Homo sapiens (human) ]

    Gene ID: 388743, updated on 10-Dec-2024

    Summary

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    Official Symbol
    CAPN8provided by HGNC
    Official Full Name
    calpain 8provided by HGNC
    Primary source
    HGNC:HGNC:1485
    See related
    Ensembl:ENSG00000203697 MIM:618777; AllianceGenome:HGNC:1485
    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
    Also known as
    nCL-2
    Summary
    Predicted to enable calcium-dependent cysteine-type endopeptidase activity and identical protein binding activity. Predicted to be involved in proteolysis. Predicted to act upstream of or within calcium-dependent self proteolysis. Predicted to be located in Golgi apparatus. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Dec 2024]
    Annotation information
    Note: This gene aligns across a gap in the GRCh38 reference genome assembly, and therefore, the 5' end of this gene was annotated on NT_167186.2 and the 3' end was annotated on NT_004487.20 in NCBI's Homo sapiens Annotation Release 106. [17 Jun 2014]
    Annotation category: suggests misassembly
    Expression
    Biased expression in stomach (RPKM 65.0), lung (RPKM 7.1) and 2 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CAPN8 in Genome Data Viewer
    Location:
    1q41
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (223541616..223665701, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (222780346..222855423, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (223714979..223853403, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:223567321-223567822 Neighboring gene coiled-coil domain containing 185 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:223660470-223660970 Neighboring gene uncharacterized LOC105373034 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2589 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2590 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:223815955-223817154 Neighboring gene SNRPE pseudogene 10 Neighboring gene uncharacterized LOC105373281 Neighboring gene RNA, U6 small nuclear 1248, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:223888788-223889634 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:223894361-223895560 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:223895561-223896060 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2591 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:223899927-223900878 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_5382 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:223906461-223907308 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:223915193-223915853 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:223919231-223919826 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:223921601-223922461 Neighboring gene uncharacterized LOC105373046 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:223926031-223926546 Neighboring gene calpain 2

    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. A novel tissue-specific calpain species expressed predominantly in the stomach comprises two alternative splicing products with and without Ca(2+)-binding domain. Sorimachi H, et al. J Biol Chem, 1993 Sep 15. PMID 7690035
    2. Both the conserved and the unique gene structure of stomach-specific calpains reveal processes of calpain gene evolution. Hata S, et al. J Mol Evol, 2001 Sep. PMID 11523006
    3. The CAPN2/CAPN8 Locus on Chromosome 1q Is Associated with Variation in Serum Alpha-Carotene Concentrations. D'Adamo CR, et al. J Nutrigenet Nutrigenomics, 2016. PMID 28002826, Free PMC Article
    4. The calpain family and human disease. Huang Y, et al. Trends Mol Med, 2001 Aug. PMID 11516996
    5. Stomach-specific calpain, nCL-2/calpain 8, is active without calpain regulatory subunit and oligomerizes through C2-like domains. Hata S, et al. J Biol Chem, 2007 Sep 21. PMID 17646163

    See all (17) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    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

    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 proteolysis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    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-8
    Names
    new calpain 2
    stomach-specific M-type calpain
    NP_001137434.1
    XP_016856754.1
    XP_016856755.1
    XP_016856756.1
    XP_016856757.1
    XP_054192504.1
    XP_054192505.1
    XP_054192506.1
    XP_054192507.1

    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_001143962.2 → NP_001137434.1  calpain-8

      See identical proteins and their annotated locations for NP_001137434.1

      Status: VALIDATED

      Source sequence(s)
      BC157893, BG187068, BM739137, BM843240, DA874912, FO681503
      Consensus CDS
      CCDS73038.1
      UniProtKB/Swiss-Prot
      A6NHC0, B2RXL2
      Related
      ENSP00000355837.6, ENST00000366872.10
      Conserved Domains (4) summary
      PTZ00183
      Location:618 → 692
      PTZ00183; centrin; Provisional
      cd00051
      Location:580 → 635
      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:46 → 342
      Peptidase_C2; Calpain family cysteine protease
      pfam01067
      Location:356 → 509
      Calpain_III; Calpain large subunit, domain III

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      223541616..223665701 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017001265.2 → XP_016856754.1  calpain-8 isoform X1

    2. XM_017001266.2 → XP_016856755.1  calpain-8 isoform X2

    3. XM_017001267.3 → XP_016856756.1  calpain-8 isoform X3

    4. XM_017001268.2 → XP_016856757.1  calpain-8 isoform X4

      UniProtKB/TrEMBL
      B1B154
      Related
      ENSP00000355838.2, ENST00000366873.6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      222780346..222855423 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054336529.1 → XP_054192504.1  calpain-8 isoform X1

    2. XM_054336530.1 → XP_054192505.1  calpain-8 isoform X2

    3. XM_054336531.1 → XP_054192506.1  calpain-8 isoform X3

    4. XM_054336532.1 → XP_054192507.1  calpain-8 isoform X4

      UniProtKB/TrEMBL
      B1B154
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A6NHC0.3 GenPept UniProtKB/Swiss-Prot:A6NHC0

    Gene LinkOut

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