Human Gene CAPN7 (ENST00000253693.7_4) from GENCODE V47lift37
  Description: calpain 7, transcript variant 14 (from RefSeq NR_164767.1)
Gencode Transcript: ENST00000253693.7_4
Gencode Gene: ENSG00000131375.10_9
Transcript (Including UTRs)
   Position: hg19 chr3:15,247,753-15,294,423 Size: 46,671 Total Exon Count: 21 Strand: +
Coding Region
   Position: hg19 chr3:15,248,003-15,292,767 Size: 44,765 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 (chr3:15,247,753-15,294,423)mRNA (may differ from genome)Protein (813 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CAN7_HUMAN
DESCRIPTION: RecName: Full=Calpain-7; EC=3.4.22.-; AltName: Full=PalB homolog; Short=PalBH;
FUNCTION: Calcium-regulated non-lysosomal thiol-protease (By similarity).
CATALYTIC ACTIVITY: Broad endopeptidase specificity.
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Ubiquitous.
SIMILARITY: Belongs to the peptidase C2 family.
SIMILARITY: Contains 1 calpain catalytic domain.

-  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: 14.77 RPKM in Ovary
Total median expression: 438.87 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 -129.20250-0.517 Picture PostScript Text
3' UTR -360.201656-0.218 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
IPR007330 - MIT
IPR001300 - Peptidase_C2_calpain_cat

Pfam Domains:
PF00648 - Calpain family cysteine protease
PF01067 - Calpain large subunit, domain III
PF04212 - MIT (microtubule interacting and transport) domain

SCOP Domains:
48452 - TPR-like
116846 - MIT domain
49758 - Calpain large subunit, middle domain (domain III)
54001 - Cysteine proteinases

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2QFE - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9Y6W3
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 orthologGenome BrowserGenome Browser
Gene DetailsGene Details  Gene DetailsGene Details
Gene SorterGene Sorter  Gene SorterGene Sorter
 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004175 endopeptidase activity
GO:0004198 calcium-dependent cysteine-type endopeptidase activity
GO:0005515 protein binding
GO:0008233 peptidase activity
GO:0008234 cysteine-type peptidase activity
GO:0016787 hydrolase activity
GO:0090541 MIT domain binding

Biological Process:
GO:0006508 proteolysis
GO:0010634 positive regulation of epithelial cell migration
GO:0097264 self proteolysis

Cellular Component:
GO:0005622 intracellular
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  LF384974 - JP 2014500723-A/192477: Polycomb-Associated Non-Coding RNAs.
AB028639 - Homo sapiens CAPN7 mRNA for PalBH, complete cds.
BC056202 - Homo sapiens calpain 7, mRNA (cDNA clone MGC:51000 IMAGE:5274889), complete cds.
AK314253 - Homo sapiens cDNA, FLJ94999, highly similar to Homo sapiens calpain 7 (CAPN7), mRNA.
JD469085 - Sequence 450109 from Patent EP1572962.
JD151384 - Sequence 132408 from Patent EP1572962.
CU691130 - Synthetic construct Homo sapiens gateway clone IMAGE:100020981 5' read CAPN7 mRNA.
JF432832 - Synthetic construct Homo sapiens clone IMAGE:100074151 calpain 7 (CAPN7) gene, encodes complete protein.
JD027174 - Sequence 8198 from Patent EP1572962.
AK093742 - Homo sapiens cDNA FLJ36423 fis, clone THYMU2011308.
JD049467 - Sequence 30491 from Patent EP1572962.
MA620551 - JP 2018138019-A/192477: Polycomb-Associated Non-Coding RNAs.

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

Protein Q9Y6W3 (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: CAN7_HUMAN, ENST00000253693.1, ENST00000253693.2, ENST00000253693.3, ENST00000253693.4, ENST00000253693.5, ENST00000253693.6, NR_164767, PALBH, Q9Y6W3, uc317fly.1, uc317fly.2
UCSC ID: ENST00000253693.7_4
RefSeq Accession: NM_014296.3
Protein: Q9Y6W3 (aka CAN7_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.