Exon Junction Primer Design
Beacon Designer™ can design primers that span across exon-exon and exon-intron junctions. The exons and introns are identified by interpreting GenBank header annotations when sequences are fetched from NCBI. Alternatively, they can be specified from within the program using the "Locate Exon" function. When the exon junction primer design option is chosen, Beacon Designer locates one of the primers from the pair of primers, at the junction. The other primer from the pair is located in the gene or region of interest depending on the amplicon size and other design parameters selected. This function is especially useful for selectively amplifying cDNA from gDNA.
Exon Junction Primer Design functionality is also available in our product AlleleID.