Human Gene CAPN2 (ENST00000295006.6_4) from GENCODE V47lift37
  Description: calpain 2, transcript variant 1 (from RefSeq NM_001748.5)
Gencode Transcript: ENST00000295006.6_4
Gencode Gene: ENSG00000162909.18_7
Transcript (Including UTRs)
   Position: hg19 chr1:223,900,241-223,963,720 Size: 63,480 Total Exon Count: 21 Strand: +
Coding Region
   Position: hg19 chr1:223,900,343-223,962,559 Size: 62,217 Coding Exon Count: 21 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:223,900,241-223,963,720)mRNA (may differ from genome)Protein (700 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CAN2_HUMAN
DESCRIPTION: RecName: Full=Calpain-2 catalytic subunit; EC=3.4.22.53; AltName: Full=Calcium-activated neutral proteinase 2; Short=CANP 2; AltName: Full=Calpain M-type; AltName: Full=Calpain large polypeptide L2; AltName: Full=Calpain-2 large subunit; AltName: Full=Millimolar-calpain; Short=M-calpain; Flags: Precursor;
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 7 calcium ions (By similarity).
ENZYME REGULATION: Activated by 200-1000 micromolar concentrations of calcium and inhibited by calpastatin.
SUBUNIT: Forms a heterodimer with a small (regulatory) subunit (CAPNS1).
INTERACTION: P04632:CAPNS1; NbExp=2; IntAct=EBI-1028956, EBI-711828;
SUBCELLULAR LOCATION: Cytoplasm. Cell membrane. Note=Translocates to the plasma membrane upon Ca(2+) binding.
TISSUE SPECIFICITY: Ubiquitous.
SIMILARITY: Belongs to the peptidase C2 family.
SIMILARITY: Contains 1 calpain catalytic domain.
SIMILARITY: Contains 3 EF-hand domains.
SEQUENCE CAUTION: Sequence=AAH07686.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=AAH11828.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence;
WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/capn2/";

-  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


-  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: 68.48 RPKM in Minor Salivary Gland
Total median expression: 1542.27 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 -43.40102-0.425 Picture PostScript Text
3' UTR -270.501161-0.233 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)
75005 - Arabinanase/levansucrase/invertase
54001 - Cysteine proteinases

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1KFU - X-ray MuPIT 1KFX - X-ray MuPIT 2NQA - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P17655
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    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004198 calcium-dependent cysteine-type endopeptidase activity
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0008092 cytoskeletal protein binding
GO:0008233 peptidase activity
GO:0008234 cysteine-type peptidase activity
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
GO:0046982 protein heterodimerization activity

Biological Process:
GO:0001666 response to hypoxia
GO:0001824 blastocyst development
GO:0006508 proteolysis
GO:0007520 myoblast fusion
GO:0016540 protein autoprocessing
GO:0051493 regulation of cytoskeleton organization
GO:0051603 proteolysis involved in cellular protein catabolic process
GO:0071230 cellular response to amino acid stimulus

Cellular Component:
GO:0000785 chromatin
GO:0005622 intracellular
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005783 endoplasmic reticulum
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005925 focal adhesion
GO:0016020 membrane
GO:0030425 dendrite
GO:0030864 cortical actin cytoskeleton
GO:0031143 pseudopodium
GO:0045121 membrane raft
GO:0070062 extracellular exosome
GO:0097038 perinuclear endoplasmic reticulum


-  Descriptions from all associated GenBank mRNAs
  AK316211 - Homo sapiens cDNA, FLJ79110 complete cds, highly similar to Calpain-2 catalytic subunit precursor (EC 3.4.22.53).
AK297800 - Homo sapiens cDNA FLJ58517 complete cds, highly similar to Calpain-2 catalytic subunit precursor (EC 3.4.22.53).
LF383668 - JP 2014500723-A/191171: Polycomb-Associated Non-Coding RNAs.
BC007686 - Homo sapiens calpain 2, (m/II) large subunit, mRNA (cDNA clone IMAGE:3637421), partial cds.
BC011828 - Homo sapiens calpain 2, (m/II) large subunit, mRNA (cDNA clone IMAGE:3833113), partial cds.
M23254 - Human Ca2-activated neutral protease large subunit (CANP) mRNA, complete cds.
AK303952 - Homo sapiens cDNA FLJ58224 complete cds, highly similar to Calpain-2 catalytic subunit precursor (EC 3.4.22.53).
AF261089 - Homo sapiens calpain large polypeptide L2 mRNA, complete cds.
AK315179 - Homo sapiens cDNA, FLJ96158, highly similar to Homo sapiens calpain 2, (m/II) large subunit (CAPN2), mRNA.
BC021303 - Homo sapiens calpain 2, (m/II) large subunit, mRNA (cDNA clone MGC:29448 IMAGE:5090865), complete cds.
JD375955 - Sequence 356979 from Patent EP1572962.
AB209855 - Homo sapiens mRNA for Calpain 2, large [catalytic] subunit precursor variant protein.
JD079989 - Sequence 61013 from Patent EP1572962.
CU676918 - Synthetic construct Homo sapiens gateway clone IMAGE:100023408 5' read CAPN2 mRNA.
KJ896539 - Synthetic construct Homo sapiens clone ccsbBroadEn_05933 CAPN2 gene, encodes complete protein.
AB385111 - Synthetic construct DNA, clone: pF1KB5513, Homo sapiens CAPN2 gene for calpain-2 catalytic subunit, complete cds, without stop codon, in Flexi system.
DQ893312 - Synthetic construct clone IMAGE:100005942; FLH196034.01X; RZPDo839C05154D calpain 2, (m/II) large subunit (CAPN2) gene, encodes complete protein.
DQ893620 - Synthetic construct clone IMAGE:100006250; FLH183753.01X; RZPDo839G03142D calpain 2, (m/II) large subunit (CAPN2) gene, encodes complete protein.
EU176804 - Synthetic construct Homo sapiens clone IMAGE:100011556; FLH196033.01L; RZPDo839B07256D calpain 2, (m/II) large subunit (CAPN2) gene, encodes complete protein.
AK124751 - Homo sapiens cDNA FLJ42761 fis, clone BRAWH3002574, highly similar to Calpain 2, large [catalytic] subunit precursor (EC 3.4.22.17).
AK097247 - Homo sapiens cDNA FLJ39928 fis, clone SPLEN2021273, highly similar to Calpain-2 catalytic subunit precursor (EC 3.4.22.53).
AK023851 - Homo sapiens cDNA FLJ13789 fis, clone SKNMC1000050, moderately similar to CALPAIN 2, LARGE [CATALYTIC] SUBUNIT (EC 3.4.22.17).
AK056838 - Homo sapiens cDNA FLJ32276 fis, clone PROST2000105, moderately similar to CALPAIN 2, LARGE [CATALYTIC] SUBUNIT (EC 3.4.22.17).
AK055046 - Homo sapiens cDNA FLJ30484 fis, clone BRAWH2000071.
JD434118 - Sequence 415142 from Patent EP1572962.
JD302759 - Sequence 283783 from Patent EP1572962.
JD526522 - Sequence 507546 from Patent EP1572962.
JD268762 - Sequence 249786 from Patent EP1572962.
JD088478 - Sequence 69502 from Patent EP1572962.
JD285247 - Sequence 266271 from Patent EP1572962.
JD120232 - Sequence 101256 from Patent EP1572962.
JD178107 - Sequence 159131 from Patent EP1572962.
JD491151 - Sequence 472175 from Patent EP1572962.
JD363550 - Sequence 344574 from Patent EP1572962.
JD321431 - Sequence 302455 from Patent EP1572962.
JD087554 - Sequence 68578 from Patent EP1572962.
JD287262 - Sequence 268286 from Patent EP1572962.
JD354530 - Sequence 335554 from Patent EP1572962.
JD195605 - Sequence 176629 from Patent EP1572962.
JD534084 - Sequence 515108 from Patent EP1572962.
MA619245 - JP 2018138019-A/191171: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_mCalpainPathway - mCalpain and friends in Cell motility
h_mef2dPathway - Role of MEF2D in T-cell Apoptosis

Reactome (by CSHL, EBI, and GO)

Protein P17655 (Reactome details) participates in the following event(s):

R-HSA-8863008 Calpain activation
R-HSA-8868134 CAST binds Ca2+ bound calpain
R-HSA-8863012 Calpain cleaves p35 to p25
R-HSA-8848658 CAPN:4xCa2+:CAPNS cleave cytoskeletal proteins
R-HSA-8862803 Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models
R-HSA-8863678 Neurodegenerative Diseases
R-HSA-1643685 Disease
R-HSA-1474228 Degradation of the extracellular matrix
R-HSA-1474244 Extracellular matrix organization

-  Other Names for This Gene
  Alternate Gene Symbols: A6NDG7, B7ZA96, CAN2_HUMAN, CANPL2, E7ES58, ENST00000295006.1, ENST00000295006.2, ENST00000295006.3, ENST00000295006.4, ENST00000295006.5, NM_001748, P17655, Q16738, Q6PJT3, Q8WU26, Q9HBB1, uc317liz.1, uc317liz.2
UCSC ID: ENST00000295006.6_4
RefSeq Accession: NM_001748.5
Protein: P17655 (aka CAN2_HUMAN)

-  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.