Human Gene CAST (uc010jbj.3) Description and Page Index
  Description: Homo sapiens calpastatin (CAST), transcript variant 2, mRNA.
RefSeq Summary (NM_173060): The protein encoded by this gene is an endogenous calpain (calcium-dependent cysteine protease) inhibitor. It consists of an N-terminal domain L and four repetitive calpain-inhibition domains (domains 1-4), and it is involved in the proteolysis of amyloid precursor protein. The calpain/calpastatin system is involved in numerous membrane fusion events, such as neural vesicle exocytosis and platelet and red-cell aggregation. The encoded protein is also thought to affect the expression levels of genes encoding structural or regulatory proteins. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jun 2010].
Transcript (Including UTRs)
   Position: hg19 chr5:96,076,970-96,110,385 Size: 33,416 Total Exon Count: 18 Strand: +
Coding Region
   Position: hg19 chr5:96,078,365-96,107,383 Size: 29,019 Coding Exon Count: 15 

Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:96,076,970-96,110,385)mRNA (may differ from genome)Protein (399 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMGIOMIM
PubMedStanford SOURCETreefamUniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CAST
CDC HuGE Published Literature: CAST
Positive Disease Associations: Alcohol dependence , blood pressure, arterial hypertension , Hodgkin Disease , Parkinson Disease , Psoriasis , Respiratory Function Tests
Related Studies:
  1. Alcohol dependence
    Treutlein ,et al. 2009, Genome-wide association study of alcohol dependence, Archives of general psychiatry 2009 66- 7 : 773-84. [PubMed 19581569]
  2. blood pressure, arterial hypertension
    Kokubo, Y. et al. 2006, Association of sixty-one non-synonymous polymorphisms in forty-one hypertension candidate genes with blood pressure variation and hypertension, Hypertens Res 2006 29(8) 611-9. [PubMed 17137217]
  3. Hodgkin Disease
    Kevin Y Urayama et al. Journal of the National Cancer Institute 2012, Genome-wide association study of classical Hodgkin lymphoma and Epstein-Barr virus status-defined subgroups., Journal of the National Cancer Institute. [PubMed 22286212]
    Overall, these results provide strong evidence that EBV status is an etiologically important classification of cHL and also suggest that some components of the pathological process are common to both EBV-positive and EBV-negative patients.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: CAST
Diseases sorted by gene-association score: peeling skin with leukonychia, acral punctate keratoses, cheilitis, and knuckle pads* (1270), cheilitis (31)
* = 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: 61.32 RPKM in Esophagus - Mucosa
Total median expression: 988.61 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 -54.57186-0.293 Picture PostScript Text
3' UTR -475.702065-0.230 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
IPR026998 - Calpastatin
IPR001259 - Prot_inh_calpain

Pfam Domains:
PF00748 - Calpain inhibitor

ModBase Predicted Comparative 3D Structure on Q86YM9
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 Details     
Gene Sorter     
      
      
      

-  Descriptions from all associated GenBank mRNAs
  AB208816 - Homo sapiens mRNA for calpastatin isoform a variant protein.
BC016066 - Homo sapiens calpastatin, mRNA (cDNA clone IMAGE:4861420), partial cds.
KX533486 - Homo sapiens calpastatin (CAST) mRNA, complete cds.
AK296919 - Homo sapiens cDNA FLJ56102 complete cds, highly similar to Homo sapiens calpastatin (CAST), transcript variant 8, mRNA.
AK299384 - Homo sapiens cDNA FLJ53909 complete cds, moderately similar to Calpastatin.
D16217 - Homo sapiens CAST mRNA for calpastatin, complete cds.
AL832349 - Homo sapiens mRNA; cDNA DKFZp451B196 (from clone DKFZp451B196).
AK303900 - Homo sapiens cDNA FLJ52045 complete cds, highly similar to Homo sapiens calpastatin (CAST), transcript variant 5, mRNA.
AK314290 - Homo sapiens cDNA, FLJ95046.
AK315146 - Homo sapiens cDNA, FLJ96117, highly similar to Homo sapiens calpastatin (CAST), transcript variant 4, mRNA.
AK299402 - Homo sapiens cDNA FLJ50632 complete cds, highly similar to Calpastatin.
AK298541 - Homo sapiens cDNA FLJ56123 complete cds, highly similar to Calpastatin.
AK300624 - Homo sapiens cDNA FLJ50686 complete cds, highly similar to Calpastatin.
AL832174 - Homo sapiens mRNA; cDNA DKFZp686K2216 (from clone DKFZp686K2216).
BX648397 - Homo sapiens mRNA; cDNA DKFZp686N07213 (from clone DKFZp686N07213).
AK303836 - Homo sapiens cDNA FLJ52193 complete cds, highly similar to Calpastatin.
AK297879 - Homo sapiens cDNA FLJ59277 complete cds, highly similar to Calpastatin.
M86258 - Homo sapiens calpastatin (CAST) mRNA, 5' end.
AB527289 - Synthetic construct DNA, clone: pF1KB9389, Homo sapiens CAST gene for calpastatin, without stop codon, in Flexi system.
AM393425 - Synthetic construct Homo sapiens clone IMAGE:100002556 for hypothetical protein (CAST gene).
AM393434 - Synthetic construct Homo sapiens clone IMAGE:100002280 for hypothetical protein (CAST gene).
E02261 - cDNA encoding Homo sapiens calpastatin.
DQ894668 - Synthetic construct Homo sapiens clone IMAGE:100009128; FLH177344.01L; RZPDo839G07123D calpastatin (CAST) gene, encodes complete protein.
BT009783 - Homo sapiens calpastatin mRNA, complete cds.
DQ891479 - Synthetic construct clone IMAGE:100004109; FLH177347.01X; RZPDo839G07124D calpastatin (CAST) gene, encodes complete protein.
AF327443 - Homo sapiens calpastatin mRNA, complete cds.
E02134 - cDNA encoding human carbastatin containing 4 functional units.
BC078149 - Homo sapiens calpastatin, mRNA (cDNA clone IMAGE:6070772), partial cds.
M33328 - Homo sapiens calpastatin (CAST) mRNA, partial cds.
U26724 - Homo sapiens calpastatin (BS-17) mRNA, complete cds.
MF577037 - Homo sapiens clone hcast 3-25 calpastatin (CAST) mRNA, partial cds.
MK585065 - Homo sapiens calpastatin (CAST) mRNA, complete cds.
U31345 - Human calpastatin mRNA, partial cds, short 3'UTR.
AY189741 - Homo sapiens calpastatin (CAST) mRNA, partial cds; alternatively spliced.
AK311585 - Homo sapiens cDNA, FLJ18627.
AK311598 - Homo sapiens cDNA, FLJ18640.
AK302206 - Homo sapiens cDNA FLJ55287 complete cds, highly similar to Calpastatin.
AK292289 - Homo sapiens cDNA FLJ77693 complete cds, highly similar to Homo sapiens calpastatin (CAST), transcript variant 3, mRNA.
AK292356 - Homo sapiens cDNA FLJ77737 complete cds, highly similar to Homo sapiens calpastatin (CAST), transcript variant 3, mRNA.
U58996 - Homo sapiens testis calpastatin mRNA, complete cds.
AK315673 - Homo sapiens cDNA, FLJ96767, highly similar to Homo sapiens calpastatin (CAST), transcript variant 3, mRNA.
U38525 - Human placental calpastatin mRNA, partial cds.
U31346 - Human calpastatin mRNA, partial cds, long 3'UTR.
S73329 - calpastatin=glycoprotein BS-17 component {3' region} [human, sperm, mRNA Partial, 758 nt].
D50827 - Homo sapiens mRNA for calpastatin, partial cds.
AF095891 - Homo sapiens calpastatin mRNA, partial cds and 3' UTR.
AK098137 - Homo sapiens cDNA FLJ40818 fis, clone TRACH2010698.
JD228770 - Sequence 209794 from Patent EP1572962.
JD283561 - Sequence 264585 from Patent EP1572962.
JD359775 - Sequence 340799 from Patent EP1572962.
JD097303 - Sequence 78327 from Patent EP1572962.
JD050595 - Sequence 31619 from Patent EP1572962.
JD098786 - Sequence 79810 from Patent EP1572962.
JD298904 - Sequence 279928 from Patent EP1572962.
JD268575 - Sequence 249599 from Patent EP1572962.
JD092885 - Sequence 73909 from Patent EP1572962.
JD373861 - Sequence 354885 from Patent EP1572962.
JD433115 - Sequence 414139 from Patent EP1572962.
JD420833 - Sequence 401857 from Patent EP1572962.
JD280615 - Sequence 261639 from Patent EP1572962.
JD301811 - Sequence 282835 from Patent EP1572962.
JD306093 - Sequence 287117 from Patent EP1572962.
JD547358 - Sequence 528382 from Patent EP1572962.
JD088016 - Sequence 69040 from Patent EP1572962.
JD482799 - Sequence 463823 from Patent EP1572962.
JD564877 - Sequence 545901 from Patent EP1572962.
JD524036 - Sequence 505060 from Patent EP1572962.
JD524037 - Sequence 505061 from Patent EP1572962.
JD303247 - Sequence 284271 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: AY189741, NM_173060, NP_775083, Q86YM9, Q86YM9_HUMAN
UCSC ID: uc010jbj.3
RefSeq Accession: NM_173060
Protein: Q86YM9

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AY189741.1
exon count: 18CDS single in 3' UTR: no RNA size: 3390
ORF size: 1200CDS single in intron: no Alignment % ID: 99.97
txCdsPredict score: 2589.50frame shift in genome: no % Coverage: 99.53
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.