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CAPN1 calpain 1 [ Homo sapiens (human) ]

Gene ID: 823, updated on 10-Dec-2024

Summary

Official Symbol
CAPN1provided by HGNC
Official Full Name
calpain 1provided by HGNC
Primary source
HGNC:HGNC:1476
See related
Ensembl:ENSG00000014216 MIM:114220; AllianceGenome:HGNC:1476
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; muCL; CANP1; SPG76; CANPL1; muCANP
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 the large subunit of the ubiquitous enzyme, calpain 1. Several transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Nov 2010]
Expression
Ubiquitous expression in esophagus (RPKM 94.2), skin (RPKM 48.8) and 24 other tissues See more
Orthologs
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Genomic context

See CAPN1 in Genome Data Viewer
Location:
11q13.1
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (65181373..65212006)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (65174678..65205290)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (64948844..64979477)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene hESC enhancers GRCh37_chr11:64949086-64949875 and GRCh37_chr11:64949876-64950664 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64950665-64951454 Neighboring gene phosphoglycerate mutase 1 pseudogene 8 Neighboring gene speedy/RINGO cell cycle regulator family member C Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:64952638-64953204 Neighboring gene CAPN1 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64953771-64954337 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64955709-64956255 Neighboring gene MPRA-validated peak1300 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64971432-64972419 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4949 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:64976880-64978079 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:64978770-64978973 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64980323-64981239 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64981240-64982155 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64984183-64984746 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64984747-64985310 Neighboring gene solute carrier family 22 member 20, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr11:64989237-64989466 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4951 Neighboring gene MPRA-validated peak1301 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:65011321-65011846 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3512 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:65028571-65029458 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:65029459-65030344 Neighboring gene DNA polymerase alpha 2, accessory subunit Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:65046741-65047940 Neighboring gene uncharacterized LOC105369344 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:65068776-65069313 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:65069314-65069850

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Autosomal recessive spastic paraplegia type 76
MedGen: C5567483 OMIM: 616907 GeneReviews: Not available
Compare labs

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Activation of the Ca(2+)-dependent protease, calpain, is involved in cytotoxic effects mediated by HIV-1 gp120 in neuroblastoma cultures PubMed
Tat tat Calpain-mediated cleavage of HIV-1 Tat occurs in the C-terminus of this viral protein, between amino acids 68 and 69. The cleavage of Tat by calpain 1 increases neurotoxic effect of this viral protein PubMed
tat HIV-1 Tat increases plasma membrane (PM) dopamine transporter (DAT) activity and calpain protease activity at the PM PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

General gene information

Clone Names

  • FLJ56829

Gene Ontology Provided by GOA

Component Evidence Code Pubs
part_of calpain complex  
located_in cornified envelope  
is_active_in cytoplasm  
located_in cytosol PubMed 
located_in cytosol  
located_in extracellular exosome PubMed 
located_in extracellular region  
located_in ficolin-1-rich granule lumen  
located_in focal adhesion PubMed 
located_in lysosome  
located_in membrane PubMed 
located_in mitochondrion  
located_in plasma membrane PubMed 
located_in plasma membrane  

General protein information

Preferred Names
calpain-1 catalytic subunit
Names
CANP 1
calcium-activated neutral proteinase 1
calpain 1, (mu/I) large subunit
calpain mu-type
calpain, large polypeptide L1
calpain-1 large subunit
cell proliferation-inducing gene 30 protein
cell proliferation-inducing protein 30
micromolar-calpain
NP_001185797.1
NP_001185798.1
NP_005177.2
XP_006718761.1
XP_011543594.1
XP_054226070.1
XP_054226071.1

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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.

Genomic

  1. NG_052817.1 RefSeqGene

    Range
    5714..35792
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001198868.2NP_001185797.1  calpain-1 catalytic subunit

    See identical proteins and their annotated locations for NP_001185797.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Variants 1, 2, and 3 all encode the same protein.
    Source sequence(s)
    AK315556, BC008751, X04366
    Consensus CDS
    CCDS44644.1
    UniProtKB/Swiss-Prot
    P07384, Q2TTR0, Q6DHV4
    UniProtKB/TrEMBL
    B2RDI5
    Related
    ENSP00000435272.1, ENST00000533820.5
    Conserved Domains (3) summary
    cd00214
    Location:364524
    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 ...
    pfam00648
    Location:56352
    Peptidase_C2; Calpain family cysteine protease
    cd16198
    Location:546714
    EFh_PEF_CAPN1; Penta-EF hand, calcium binding motifs, found in mu-type calpain (CAPN1)
  2. NM_001198869.2NP_001185798.1  calpain-1 catalytic subunit

    See identical proteins and their annotated locations for NP_001185798.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 all encode the same protein.
    Source sequence(s)
    AK301538, BC008751, BC075862
    Consensus CDS
    CCDS44644.1
    UniProtKB/Swiss-Prot
    P07384, Q2TTR0, Q6DHV4
    UniProtKB/TrEMBL
    B2RDI5
    Related
    ENSP00000434176.1, ENST00000524773.5
    Conserved Domains (3) summary
    cd00214
    Location:364524
    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 ...
    pfam00648
    Location:56352
    Peptidase_C2; Calpain family cysteine protease
    cd16198
    Location:546714
    EFh_PEF_CAPN1; Penta-EF hand, calcium binding motifs, found in mu-type calpain (CAPN1)
  3. NM_005186.4NP_005177.2  calpain-1 catalytic subunit

    See identical proteins and their annotated locations for NP_005177.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 all encode the same protein.
    Source sequence(s)
    BC008751, X04366
    Consensus CDS
    CCDS44644.1
    UniProtKB/Swiss-Prot
    P07384, Q2TTR0, Q6DHV4
    UniProtKB/TrEMBL
    B2RDI5
    Related
    ENSP00000279247.7, ENST00000279247.11
    Conserved Domains (3) summary
    cd00214
    Location:364524
    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 ...
    pfam00648
    Location:56352
    Peptidase_C2; Calpain family cysteine protease
    cd16198
    Location:546714
    EFh_PEF_CAPN1; Penta-EF hand, calcium binding motifs, found in mu-type calpain (CAPN1)

RNA

  1. NR_040008.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate 5' splice pattern, compared to variant 1. It is represented as non-coding due to the presence of an upstream ORF that is predicted to interfere with translation of the longest ORF; translation of the upstream ORF renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK315556, BC008751, BE018156, DC365116, X04366

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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    65181373..65212006
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006718698.3XP_006718761.1  calpain-1 catalytic subunit isoform X1

    See identical proteins and their annotated locations for XP_006718761.1

    UniProtKB/Swiss-Prot
    P07384, Q2TTR0, Q6DHV4
    UniProtKB/TrEMBL
    B2RDI5
    Conserved Domains (3) summary
    cd00214
    Location:364524
    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 ...
    pfam00648
    Location:56352
    Peptidase_C2; Calpain family cysteine protease
    cd16198
    Location:546714
    EFh_PEF_CAPN1; Penta-EF hand, calcium binding motifs, found in mu-type calpain (CAPN1)
  2. XM_011545292.2XP_011543594.1  calpain-1 catalytic subunit isoform X1

    See identical proteins and their annotated locations for XP_011543594.1

    UniProtKB/Swiss-Prot
    P07384, Q2TTR0, Q6DHV4
    UniProtKB/TrEMBL
    B2RDI5
    Related
    ENSP00000431984.1, ENST00000527323.5
    Conserved Domains (3) summary
    cd00214
    Location:364524
    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 ...
    pfam00648
    Location:56352
    Peptidase_C2; Calpain family cysteine protease
    cd16198
    Location:546714
    EFh_PEF_CAPN1; Penta-EF hand, calcium binding motifs, found in mu-type calpain (CAPN1)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    65174678..65205290
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054370095.1XP_054226070.1  calpain-1 catalytic subunit isoform X1

    UniProtKB/TrEMBL
    B2RDI5
  2. XM_054370096.1XP_054226071.1  calpain-1 catalytic subunit isoform X1

    UniProtKB/TrEMBL
    B2RDI5
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