Human Gene CAPNS1 (ENST00000587718.5) from GENCODE V44
  Description: calpain small subunit 1 (from HGNC CAPNS1)
RefSeq Summary (NM_001749): This gene is a member of the calpain small subunit family. Calpains are calcium-dependent cysteine proteinases that are widely distributed in mammalian cells. Calpains operate as heterodimers, comprising a specific large catalytic subunit (calpain 1 subunit in Calpain I, and calpain 2 subunit in Calpain II), and a common small regulatory subunit encoded by this gene. This encoded protein is essential for the stability and function of both calpain heterodimers, whose proteolytic activities influence various cellular functions including apoptosis, proliferation, migration, adhesion, and autophagy. Calpains have been implicated in neurodegenerative processes, such as myotonic dystrophy. A pseudogene of this gene has been defined on chromosome 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014].
Gencode Transcript: ENST00000587718.5
Gencode Gene: ENSG00000126247.11
Transcript (Including UTRs)
   Position: hg38 chr19:36,140,108-36,150,349 Size: 10,242 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg38 chr19:36,141,012-36,149,825 Size: 8,814 Coding Exon Count: 9 

Page IndexSequence and LinksPrimersMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureOther SpeciesmRNA DescriptionsPathwaysOther Names
Methods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:36,140,108-36,150,349)mRNA (may differ from genome)Protein (322 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGencodeGeneCardsHGNC
LynxMalacardsMGIPubMedUniProtKBWikipedia

-  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: CAPNS1
Diseases sorted by gene-association score: chronic neutrophilic leukemia (2)

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 160.43 RPKM in Esophagus - Mucosa
Total median expression: 4638.68 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 -22.1065-0.340 Picture PostScript Text
3' UTR -161.00524-0.307 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.

-  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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Descriptions from all associated GenBank mRNAs
  AK289606 - Homo sapiens cDNA FLJ75451 complete cds, highly similar to Homo sapiens calpain, small subunit 1 (CAPNS1), mRNA.
X04106 - Human mRNA for calcium dependent protease (small subunit).
DI441761 - KR 1020140091683-A/5: METHODS AND COMPOSITIONS FOR NEUROPROTECTION.
HI635181 - Sequence 41028 from Patent EP2242854.
HI635182 - Sequence 41029 from Patent EP2242854.
HV708930 - JP 2012506450-A/28: Methods for treating eye disorders.
HV708931 - JP 2012506450-A/29: Methods for treating eye disorders.
HW061190 - JP 2012529430-A/65: METHODS FOR TREATING CHRONIC KIDNEY DISEASE.
HW061191 - JP 2012529430-A/66: METHODS FOR TREATING CHRONIC KIDNEY DISEASE.
HW819140 - JP 2015501634-A/5: METHODS AND COMPOSITIONS FOR NEUROPROTECTION.
JA394579 - Sequence 1 from Patent WO2011066475.
JA394580 - Sequence 2 from Patent WO2011066475.
JA482169 - Sequence 152 from Patent WO2011072091.
JA482170 - Sequence 153 from Patent WO2011072091.
JB251998 - Sequence 65 from Patent EP2440214.
JB251999 - Sequence 66 from Patent EP2440214.
JB747464 - Sequence 5 from Patent WO2013067076.
JE980461 - Sequence 152 from Patent EP2862929.
JE980462 - Sequence 153 from Patent EP2862929.
LF384242 - JP 2014500723-A/191745: Polycomb-Associated Non-Coding RNAs.
LP764897 - Sequence 65 from Patent EP3276004.
LP764898 - Sequence 66 from Patent EP3276004.
MA619819 - JP 2018138019-A/191745: Polycomb-Associated Non-Coding RNAs.
BC018931 - Homo sapiens calpain, small subunit 1, mRNA (cDNA clone MGC:14442 IMAGE:4303926), complete cds.
JB747465 - Sequence 6 from Patent WO2013067076.
JD140460 - Sequence 121484 from Patent EP1572962.
BC007779 - Homo sapiens calpain, small subunit 1, mRNA (cDNA clone MGC:12745 IMAGE:4301394), complete cds.
BC011903 - Homo sapiens calpain, small subunit 1, mRNA (cDNA clone MGC:20290 IMAGE:4120579), complete cds.
GQ901017 - Homo sapiens clone HEL-T-129 epididymis secretory sperm binding protein mRNA, complete cds.
BC000592 - Homo sapiens calpain, small subunit 1, mRNA (cDNA clone MGC:1790 IMAGE:3347146), complete cds.
JD306600 - Sequence 287624 from Patent EP1572962.
BC064998 - Homo sapiens calpain, small subunit 1, mRNA (cDNA clone MGC:75186 IMAGE:5785274), complete cds.
BC017308 - Homo sapiens calpain, small subunit 1, mRNA (cDNA clone MGC:29672 IMAGE:5089022), complete cds.
BC023643 - Homo sapiens calpain, small subunit 1, mRNA (cDNA clone MGC:29704 IMAGE:5017512), complete cds.
AY007141 - Homo sapiens clone CDABP0068 mRNA sequence.
BC021933 - Homo sapiens calpain, small subunit 1, mRNA (cDNA clone MGC:32094 IMAGE:4872635), complete cds.
JD325080 - Sequence 306104 from Patent EP1572962.
CU680106 - Synthetic construct Homo sapiens gateway clone IMAGE:100018913 5' read CAPNS1 mRNA.
KJ905160 - Synthetic construct Homo sapiens clone ccsbBroadEn_14567 CAPNS1 gene, encodes complete protein.
KJ905704 - Synthetic construct Homo sapiens clone ccsbBroadEn_15374 CAPNS1 gene, encodes complete protein.
KJ905705 - Synthetic construct Homo sapiens clone ccsbBroadEn_15375 CAPNS1 gene, encodes complete protein.
BT009775 - Homo sapiens calpain, small subunit 1 mRNA, complete cds.
LF367312 - JP 2014500723-A/174815: Polycomb-Associated Non-Coding RNAs.
MA602889 - JP 2018138019-A/174815: Polycomb-Associated Non-Coding RNAs.
JD020880 - Sequence 1904 from Patent EP1572962.
JD030726 - Sequence 11750 from Patent EP1572962.
DQ590872 - Homo sapiens piRNA piR-57984, complete sequence.
JD264288 - Sequence 245312 from Patent EP1572962.
JD320639 - Sequence 301663 from Patent EP1572962.
JD096929 - Sequence 77953 from Patent EP1572962.
JD239719 - Sequence 220743 from Patent EP1572962.
JD503709 - Sequence 484733 from Patent EP1572962.
JD185830 - Sequence 166854 from Patent EP1572962.
JD251599 - Sequence 232623 from Patent EP1572962.
JD178717 - Sequence 159741 from Patent EP1572962.
JD400781 - Sequence 381805 from Patent EP1572962.
JD321216 - Sequence 302240 from Patent EP1572962.
JD382257 - Sequence 363281 from Patent EP1572962.
JD190022 - Sequence 171046 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_ucalpainPathway - uCalpain and friends in Cell spread
h_integrinPathway - Integrin Signaling Pathway
h_mCalpainPathway - mCalpain and friends in Cell motility
h_p35alzheimersPathway - Deregulation of CDK5 in Alzheimers Disease
h_mef2dPathway - Role of MEF2D in T-cell Apoptosis

-  Other Names for This Gene
  Alternate Gene Symbols: A0A0C4DGQ5, BC011903, ENST00000587718.1, ENST00000587718.2, ENST00000587718.3, ENST00000587718.4, uc002odi.1, uc002odi.2
UCSC ID: ENST00000587718.5
RefSeq Accession: NM_001749

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