When you generate RNAi oligo designs, the target sequence is screened against the species-specific database that you selected to BLAST search in Step 3 of the design parameters. Areas of homology identified by the BLAST search are "masked" in the target sequence to ensure that the designs are highly specific.
The unique regions and masked regions of the target sequence are shown in the sequence diagram on the BLAST Results page. Only designs in the unique regions are selected by the Designer.
Note: Each BLAST search is performed against a nonredundant version of the UniGene database that is updated regularly. The database contains representative gene sequences for the selected species. The databases used in this search contain one representation of each gene and do not include splice variants.
The table below the diagram lists each homologous region in the sequence, the corresponding database sequence that it matches, and the percentage similarity.
The Query Start and Query Stop columns show the begin and end of each homologous region of the target sequence. The Subject column lists the accession number of the gene sequence identified as matching the target sequence region. The Subject Start and Subject Stop columns show the begin and end of the homologous gene sequence region. The % Identity column shows the percentage similarity of the sequences.
Click on the accession number in the Subject column to access the database record of the homologous sequence using the Entrez search engine.
Use the Back button in your browser to return to the design results page.