Mouse Gene Csta1 (ENSMUST00000096090.2) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus cystatin A1 (Csta1), mRNA. (from RefSeq NM_001033239)
Gencode Transcript: ENSMUST00000096090.2
Gencode Gene: ENSMUSG00000034362.7
Transcript (Including UTRs)
   Position: mm10 chr16:36,119,946-36,131,241 Size: 11,296 Total Exon Count: 3 Strand: -
Coding Region
   Position: mm10 chr16:36,122,244-36,131,050 Size: 8,807 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2019-09-19

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:36,119,946-36,131,241)mRNA (may differ from genome)Protein (97 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGeneCardsMGIPubMed
ReactomeSOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: CYTA_MOUSE
DESCRIPTION: RecName: Full=Cystatin-A; AltName: Full=Stefin-A;
FUNCTION: This is an intracellular thiol proteinase inhibitor (By similarity).
SUBCELLULAR LOCATION: Cytoplasm (By similarity).
SIMILARITY: Belongs to the cystatin family.

-  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


-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -42.30191-0.221 Picture PostScript Text
3' UTR -545.102298-0.237 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
IPR000010 - Prot_inh_cystat
IPR018073 - Prot_inh_cystat_CS
IPR001713 - Prot_inh_stefinA

Pfam Domains:
PF00031 - Cystatin domain

SCOP Domains:
54403 - Cystatin/monellin

ModBase Predicted Comparative 3D Structure on P56567
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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.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
GenBankRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0002020 protease binding
GO:0004866 endopeptidase inhibitor activity
GO:0004869 cysteine-type endopeptidase inhibitor activity
GO:0005198 structural molecule activity
GO:0030414 peptidase inhibitor activity
GO:0030674 protein binding, bridging

Biological Process:
GO:0010466 negative regulation of peptidase activity
GO:0010951 negative regulation of endopeptidase activity

Cellular Component:
GO:0001533 cornified envelope
GO:0005615 extracellular space
GO:0005622 intracellular
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  AK137702 - Mus musculus adult female vagina cDNA, RIKEN full-length enriched library, clone:9930101J17 product:Stefin homolog, full insert sequence.
BC139156 - Mus musculus cystatin A, mRNA (cDNA clone MGC:170783 IMAGE:8862178), complete cds.
BC139157 - Mus musculus cystatin A, mRNA (cDNA clone MGC:170784 IMAGE:8862179), complete cds.

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

Protein P56567 (Reactome details) participates in the following event(s):

R-MMU-6810937 Lamellar bodies bind the early cornified envelope
R-MMU-6814387 CASP14 cleaves filaggrin
R-MMU-6809371 Formation of the cornified envelope
R-MMU-6805567 Keratinization
R-MMU-1266738 Developmental Biology

-  Other Names for This Gene
  Alternate Gene Symbols: Csta, CYTA_MOUSE, NM_001033239, P56567, Q3UV05, uc007zcf.1, uc007zcf.2
UCSC ID: uc007zcf.2
RefSeq Accession: NM_001033239
Protein: P56567 (aka CYTA_MOUSE)
CCDS: CCDS37327.1

-  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.