Human Gene CST2 (ENST00000304725.3) from GENCODE V44
  Description: Homo sapiens cystatin SA (CST2), mRNA. (from RefSeq NM_001322)
RefSeq Summary (NM_001322): The cystatin superfamily encompasses proteins that contain multiple cystatin-like sequences. Some of the members are active cysteine protease inhibitors, while others have lost or perhaps never acquired this inhibitory activity. There are three inhibitory families in the superfamily, including the type 1 cystatins (stefins), type 2 cystatins and the kininogens. The type 2 cystatin proteins are a class of cysteine proteinase inhibitors found in a variety of human fluids and secretions, where they appear to provide protective functions. The cystatin locus on chromosome 20 contains the majority of the type 2 cystatin genes and pseudogenes. This gene is located in the cystatin locus and encodes a secreted thiol protease inhibitor found at high levels in saliva, tears and seminal plasma. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000304725.3
Gencode Gene: ENSG00000170369.4
Transcript (Including UTRs)
   Position: hg38 chr20:23,823,769-23,826,729 Size: 2,961 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg38 chr20:23,824,020-23,826,660 Size: 2,641 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr20:23,823,769-23,826,729)mRNA (may differ from genome)Protein (141 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMGIneXtProtOMIM
PubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CYTT_HUMAN
DESCRIPTION: RecName: Full=Cystatin-SA; AltName: Full=Cystatin-2; AltName: Full=Cystatin-S5; Flags: Precursor;
FUNCTION: Thiol protease inhibitor.
SUBCELLULAR LOCATION: Secreted.
TISSUE SPECIFICITY: Expressed in submandibular and sublingual saliva but not in parotid saliva (at protein level). Expressed in submandibular gland and parotid gland.
MASS SPECTROMETRY: Mass=14336.9856; Mass_error=0.0158; Method=Electrospray; Range=21-141; Source=PubMed:20189825;
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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 0.68 RPKM in Prostate
Total median expression: 3.47 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 -19.6069-0.284 Picture PostScript Text
3' UTR -77.20251-0.308 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

Pfam Domains:
PF00031 - Cystatin domain

ModBase Predicted Comparative 3D Structure on P09228
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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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0002020 protease binding
GO:0004869 cysteine-type endopeptidase inhibitor activity
GO:0005515 protein binding
GO:0030414 peptidase inhibitor activity

Biological Process:
GO:0001580 detection of chemical stimulus involved in sensory perception of bitter taste
GO:0010466 negative regulation of peptidase activity
GO:2000117 negative regulation of cysteine-type endopeptidase activity

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space


-  Descriptions from all associated GenBank mRNAs
  BC062679 - Homo sapiens cystatin SA, mRNA (cDNA clone MGC:71924 IMAGE:30350087), complete cds.
JD124445 - Sequence 105469 from Patent EP1572962.
JD054595 - Sequence 35619 from Patent EP1572962.
JD508342 - Sequence 489366 from Patent EP1572962.
JD110412 - Sequence 91436 from Patent EP1572962.
JD248800 - Sequence 229824 from Patent EP1572962.
JD201068 - Sequence 182092 from Patent EP1572962.
JD370674 - Sequence 351698 from Patent EP1572962.
JD121755 - Sequence 102779 from Patent EP1572962.
JD531056 - Sequence 512080 from Patent EP1572962.
JD531057 - Sequence 512081 from Patent EP1572962.
CU687582 - Synthetic construct Homo sapiens gateway clone IMAGE:100023087 5' read CST2 mRNA.
HQ447594 - Synthetic construct Homo sapiens clone IMAGE:100070937; CCSB014833_01 cystatin SA (CST2) gene, encodes complete protein.
KJ890990 - Synthetic construct Homo sapiens clone ccsbBroadEn_00384 CST2 gene, encodes complete protein.

-  Other Names for This Gene
  Alternate Gene Symbols: CYTT_HUMAN, ENST00000304725.1, ENST00000304725.2, NM_001322, P09228, Q9UCQ7, uc002wtq.1, uc002wtq.2, uc002wtq.3
UCSC ID: ENST00000304725.3
RefSeq Accession: NM_001322
Protein: P09228 (aka CYTT_HUMAN)
CCDS: CCDS13161.1

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