Human Gene CAPN13 (ENST00000295055.12_7) from GENCODE V47lift37
  Description: calpain 13 (from RefSeq NM_144575.3)
Gencode Transcript: ENST00000295055.12_7
Gencode Gene: ENSG00000162949.16_12
Transcript (Including UTRs)
   Position: hg19 chr2:30,945,637-31,030,312 Size: 84,676 Total Exon Count: 23 Strand: -
Coding Region
   Position: hg19 chr2:30,953,626-31,010,191 Size: 56,566 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 (chr2:30,945,637-31,030,312)mRNA (may differ from genome)Protein (669 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MGIOMIMPubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CAN13_HUMAN
DESCRIPTION: RecName: Full=Calpain-13; EC=3.4.22.-; AltName: Full=Calcium-activated neutral proteinase 13; Short=CANP 13;
FUNCTION: Probable non-lysosomal thiol-protease (By similarity).
TISSUE SPECIFICITY: Weakly expressed in lung and testis. Weakly or not expressed in other tissues.
SIMILARITY: Belongs to the peptidase C2 family.
SIMILARITY: Contains 1 calpain catalytic domain.
SIMILARITY: Contains 2 EF-hand domains.
CAUTION: It is unlikely that this protein binds calcium as none of the 2 EF-hand domains seem to contain a canonical calcium-binding site.

-  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

+  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: 17.85 RPKM in Small Intestine - Terminal Ileum
Total median expression: 51.85 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 -46.20177-0.261 Picture PostScript Text
3' UTR -167.40496-0.337 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
IPR011992 - EF-hand-like_dom
IPR001300 - Peptidase_C2_calpain_cat

Pfam Domains:
PF00648 - Calpain family cysteine protease
PF01067 - Calpain large subunit, domain III

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
2I7A - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q6MZZ7
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:0004198 calcium-dependent cysteine-type endopeptidase activity
GO:0005509 calcium ion binding
GO:0008233 peptidase activity
GO:0008234 cysteine-type peptidase activity
GO:0016787 hydrolase activity

Biological Process:
GO:0006508 proteolysis

Cellular Component:
GO:0005622 intracellular
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  AK027176 - Homo sapiens cDNA: FLJ23523 fis, clone LNG05548.
BX647678 - Homo sapiens mRNA; cDNA DKFZp779O203 (from clone DKFZp779O203).
BX640793 - Homo sapiens mRNA; cDNA DKFZp686L13193 (from clone DKFZp686L13193).
BC117345 - Homo sapiens calpain 13, mRNA (cDNA clone MGC:150954 IMAGE:40125896), complete cds.
BC117347 - Homo sapiens calpain 13, mRNA (cDNA clone MGC:150956 IMAGE:40125898), complete cds.
AK290298 - Homo sapiens cDNA FLJ76080 complete cds, highly similar to Homo sapiens calpain 13 (CAPN13), mRNA.
AK026692 - Homo sapiens cDNA: FLJ23039 fis, clone LNG02242.
HQ258338 - Synthetic construct Homo sapiens clone IMAGE:100072647 calpain 13 (CAPN13) (CAPN13) gene, encodes complete protein.
KJ899939 - Synthetic construct Homo sapiens clone ccsbBroadEn_09333 CAPN13 gene, encodes complete protein.
KJ899940 - Synthetic construct Homo sapiens clone ccsbBroadEn_09334 CAPN13 gene, encodes complete protein.
KR711626 - Synthetic construct Homo sapiens clone CCSBHm_00027879 CAPN13 (CAPN13) mRNA, encodes complete protein.
AK074418 - Homo sapiens cDNA FLJ23838 fis, clone KAT02256.
JD530484 - Sequence 511508 from Patent EP1572962.
JD393918 - Sequence 374942 from Patent EP1572962.
JD473823 - Sequence 454847 from Patent EP1572962.
JD137566 - Sequence 118590 from Patent EP1572962.
JD435273 - Sequence 416297 from Patent EP1572962.
AK308037 - Homo sapiens cDNA, FLJ97985.
JD270966 - Sequence 251990 from Patent EP1572962.
JD170079 - Sequence 151103 from Patent EP1572962.
JD525790 - Sequence 506814 from Patent EP1572962.
JD375371 - Sequence 356395 from Patent EP1572962.
JD394897 - Sequence 375921 from Patent EP1572962.
JD458925 - Sequence 439949 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q6MZZ7 (Reactome details) participates in the following event(s):

R-HSA-8848658 CAPN:4xCa2+:CAPNS cleave cytoskeletal proteins
R-HSA-1474228 Degradation of the extracellular matrix
R-HSA-1474244 Extracellular matrix organization

-  Other Names for This Gene
  Alternate Gene Symbols: CAN13_HUMAN, ENST00000295055.1, ENST00000295055.10, ENST00000295055.11, ENST00000295055.2, ENST00000295055.3, ENST00000295055.4, ENST00000295055.5, ENST00000295055.6, ENST00000295055.7, ENST00000295055.8, ENST00000295055.9, NM_144575, Q17RF0, Q580X1, Q6MZZ7, Q8TE80, uc317ljk.1, uc317ljk.2
UCSC ID: ENST00000295055.12_7
RefSeq Accession: NM_144575.3
Protein: Q6MZZ7 (aka CAN13_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.