Human Gene CAPN1 (ENST00000279247.11_5) from GENCODE V47lift37
  Description: calpain 1, transcript variant 4 (from RefSeq NR_040008.2)
Gencode Transcript: ENST00000279247.11_5
Gencode Gene: ENSG00000014216.16_17
Transcript (Including UTRs)
   Position: hg19 chr11:64,949,399-64,979,477 Size: 30,079 Total Exon Count: 22 Strand: +
Coding Region
   Position: hg19 chr11:64,950,173-64,978,757 Size: 28,585 Coding Exon Count: 21 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:64,949,399-64,979,477)mRNA (may differ from genome)Protein (714 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MalacardsMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CAN1_HUMAN
DESCRIPTION: RecName: Full=Calpain-1 catalytic subunit; EC=3.4.22.52; AltName: Full=Calcium-activated neutral proteinase 1; Short=CANP 1; AltName: Full=Calpain mu-type; AltName: Full=Calpain-1 large subunit; AltName: Full=Cell proliferation-inducing gene 30 protein; AltName: Full=Micromolar-calpain; Short=muCANP;
FUNCTION: Calcium-regulated non-lysosomal thiol-protease which catalyze limited proteolysis of substrates involved in cytoskeletal remodeling and signal transduction.
CATALYTIC ACTIVITY: Broad endopeptidase specificity.
COFACTOR: Binds 4 calcium ions.
ENZYME REGULATION: Activated by micromolar concentrations of calcium and inhibited by calpastatin.
SUBUNIT: Forms a heterodimer with a small (regulatory) subunit (CAPNS1).
INTERACTION: P40763:STAT3; NbExp=2; IntAct=EBI-1542113, EBI-518675;
SUBCELLULAR LOCATION: Cytoplasm. Cell membrane. Note=Translocates to the plasma membrane upon Ca(2+) binding.
TISSUE SPECIFICITY: Ubiquitous.
PTM: Undergoes calcium-induced successive autoproteolytic cleavages that generate a membrane-bound 78 kDa active form and an intracellular 75 kDa active form. Calpastatin reduces with high efficiency the transition from 78 kDa to 75 kDa calpain forms.
SIMILARITY: Belongs to the peptidase C2 family.
SIMILARITY: Contains 1 calpain catalytic domain.
SIMILARITY: Contains 4 EF-hand domains.
WEB RESOURCE: Name=CaBP; Note=Calpain; URL="http://structbio.vanderbilt.edu/cabp_database/general/prot_pages/calpain.html";
WEB RESOURCE: Name=Calpains homepage; URL="http://ag.arizona.edu/calpains/";
WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/capn1/";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: CAPN1
Diseases sorted by gene-association score: spastic paraplegia 76, autosomal recessive* (1237), spastic paraplegia 76* (529), spasticity (9)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 155.15 RPKM in Esophagus - Mucosa
Total median expression: 2002.83 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -27.5087-0.316 Picture PostScript Text
3' UTR -289.40720-0.402 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR022684 - Calpain_cysteine_protease
IPR022682 - Calpain_domain_III
IPR022683 - Calpain_III
IPR011992 - EF-hand-like_dom
IPR018247 - EF_Hand_1_Ca_BS
IPR018249 - EF_HAND_2
IPR002048 - EF_hand_Ca-bd
IPR000169 - Pept_cys_AS
IPR001300 - Peptidase_C2_calpain_cat

Pfam Domains:
PF00648 - Calpain family cysteine protease
PF01067 - Calpain large subunit, domain III
PF13833 - EF-hand domain pair

SCOP Domains:
47473 - EF-hand
49758 - Calpain large subunit, middle domain (domain III)
54001 - Cysteine proteinases

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1ZCM - X-ray MuPIT 2ARY - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P07384
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004175 endopeptidase activity
GO:0004198 calcium-dependent cysteine-type endopeptidase activity
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0008233 peptidase activity
GO:0008234 cysteine-type peptidase activity
GO:0016787 hydrolase activity
GO:0046872 metal ion binding

Biological Process:
GO:0006508 proteolysis
GO:0008284 positive regulation of cell proliferation
GO:0016241 regulation of macroautophagy
GO:0032801 receptor catabolic process
GO:0043312 neutrophil degranulation
GO:0050790 regulation of catalytic activity
GO:0060056 mammary gland involution
GO:0070268 cornification
GO:0097264 self proteolysis
GO:2000310 regulation of N-methyl-D-aspartate selective glutamate receptor activity

Cellular Component:
GO:0005576 extracellular region
GO:0005622 intracellular
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005764 lysosome
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005925 focal adhesion
GO:0016020 membrane
GO:0070062 extracellular exosome
GO:1904813 ficolin-1-rich granule lumen


-  Descriptions from all associated GenBank mRNAs
  LF211183 - JP 2014500723-A/18686: Polycomb-Associated Non-Coding RNAs.
AK315556 - Homo sapiens cDNA, FLJ96627, highly similar to Homo sapiens calpain 1, (mu/I) large subunit (CAPN1), mRNA.
BC075862 - Homo sapiens calpain 1, (mu/I) large subunit, mRNA (cDNA clone MGC:90445 IMAGE:5223130), complete cds.
AK311001 - Homo sapiens cDNA, FLJ18043.
JA482179 - Sequence 162 from Patent WO2011072091.
JE980471 - Sequence 162 from Patent EP2862929.
X04366 - Human mRNA for calcium activated neutral protease large subunit (muCANP, calpain, EC 3.4.22.17).
BC008751 - Homo sapiens calpain 1, (mu/I) large subunit, mRNA (cDNA clone MGC:3082 IMAGE:3347480), complete cds.
JD261380 - Sequence 242404 from Patent EP1572962.
AK301538 - Homo sapiens cDNA FLJ53224 complete cds, highly similar to Calpain-1 catalytic subunit (EC 3.4.22.52).
JD408000 - Sequence 389024 from Patent EP1572962.
BC017200 - Homo sapiens calpain 1, (mu/I) large subunit, mRNA (cDNA clone MGC:3970 IMAGE:3629894), complete cds.
JD124567 - Sequence 105591 from Patent EP1572962.
AY550975 - Homo sapiens cell proliferation-inducing protein 30 mRNA, complete cds.
CU677859 - Synthetic construct Homo sapiens gateway clone IMAGE:100017464 5' read CAPN1 mRNA.
CU679087 - Synthetic construct Homo sapiens gateway clone IMAGE:100017779 5' read CAPN1 mRNA.
AB384822 - Synthetic construct DNA, clone: pF1KB3567, Homo sapiens CAPN1 gene for calpain-1 catalytic subunit, complete cds, without stop codon, in Flexi system.
DQ892905 - Synthetic construct clone IMAGE:100005535; FLH195800.01X; RZPDo839G05152D calpain 1, (mu/I) large subunit (CAPN1) gene, encodes complete protein.
DQ896600 - Synthetic construct Homo sapiens clone IMAGE:100011060; FLH195796.01L; RZPDo839G05151D calpain 1, (mu/I) large subunit (CAPN1) gene, encodes complete protein.
KJ905703 - Synthetic construct Homo sapiens clone ccsbBroadEn_15373 CAPN1 gene, encodes complete protein.
KJ890820 - Synthetic construct Homo sapiens clone ccsbBroadEn_00214 CAPN1 gene, encodes complete protein.
LF344456 - JP 2014500723-A/151959: Polycomb-Associated Non-Coding RNAs.
AK097277 - Homo sapiens cDNA FLJ39958 fis, clone SPLEN2025039, highly similar to CALPAIN 1, LARGE [CATALYTIC] SUBUNIT (EC 3.4.22.17).
AK025380 - Homo sapiens cDNA: FLJ21727 fis, clone COLF1107, highly similar to HSCANPR Human mRNA for calcium activated neutral protease large subunit.
BC015091 - Homo sapiens calpain 1, (mu/I) large subunit, mRNA (cDNA clone IMAGE:4054775), partial cds.
JD387824 - Sequence 368848 from Patent EP1572962.
JD227090 - Sequence 208114 from Patent EP1572962.
JD102542 - Sequence 83566 from Patent EP1572962.
JD282798 - Sequence 263822 from Patent EP1572962.
JD361369 - Sequence 342393 from Patent EP1572962.
JD020475 - Sequence 1499 from Patent EP1572962.
JD330020 - Sequence 311044 from Patent EP1572962.
JD101275 - Sequence 82299 from Patent EP1572962.
JD033508 - Sequence 14532 from Patent EP1572962.
JD481325 - Sequence 462349 from Patent EP1572962.
JD191334 - Sequence 172358 from Patent EP1572962.
JD227361 - Sequence 208385 from Patent EP1572962.
JD192740 - Sequence 173764 from Patent EP1572962.
JD174352 - Sequence 155376 from Patent EP1572962.
JD488972 - Sequence 469996 from Patent EP1572962.
JD101290 - Sequence 82314 from Patent EP1572962.
MA580033 - JP 2018138019-A/151959: Polycomb-Associated Non-Coding RNAs.
MA446760 - JP 2018138019-A/18686: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_p35alzheimersPathway - Deregulation of CDK5 in Alzheimers Disease
h_integrinPathway - Integrin Signaling Pathway
h_mCalpainPathway - mCalpain and friends in Cell motility
h_ucalpainPathway - uCalpain and friends in Cell spread

Reactome (by CSHL, EBI, and GO)

Protein P07384 (Reactome details) participates in the following event(s):

R-HSA-6800434 Exocytosis of ficolin-rich granule lumen proteins
R-HSA-8863008 Calpain activation
R-HSA-8868134 CAST binds Ca2+ bound calpain
R-HSA-2534260 E-cadherin degradation by caspase-3 and calpain-1
R-HSA-8934819 Cytoplasmic proteases cleave Profilaggrin producing Filaggrin
R-HSA-8863012 Calpain cleaves p35 to p25
R-HSA-8848658 CAPN:4xCa2+:CAPNS cleave cytoskeletal proteins
R-HSA-6798695 Neutrophil degranulation
R-HSA-8862803 Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models
R-HSA-168249 Innate Immune System
R-HSA-1474228 Degradation of the extracellular matrix
R-HSA-6809371 Formation of the cornified envelope
R-HSA-8863678 Neurodegenerative Diseases
R-HSA-168256 Immune System
R-HSA-1474244 Extracellular matrix organization
R-HSA-6805567 Keratinization
R-HSA-1643685 Disease
R-HSA-1266738 Developmental Biology

-  Other Names for This Gene
  Alternate Gene Symbols: CAN1_HUMAN, CANPL1, CAPN1 , ENST00000279247.1, ENST00000279247.10, ENST00000279247.2, ENST00000279247.3, ENST00000279247.4, ENST00000279247.5, ENST00000279247.6, ENST00000279247.7, ENST00000279247.8, ENST00000279247.9, NR_040008, P07384, PIG30 , Q2TTR0, Q6DHV4, uc317jrp.1, uc317jrp.2
UCSC ID: ENST00000279247.11_5
RefSeq Accession: NM_005186.4
Protein: P07384 (aka CAN1_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene CAPN1:
ataxias (Hereditary Ataxia Overview)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.