The difference between spanning and flanking?

[sotellme]

What is the difference between Primers that span introns and primers that flank intron-exon border? Spanning intron does it mean that it covers the whole intron segment? Flanking the border does it also mean that it covers the whole border?


Any ideas would help alot!


Thanks.

 

[Moonbear]

Spanning means inclusive of the intron. To flank means to be on either side, but not inclusive of the sequence in between.

 

[ravenprp]

The difference between spanning and flanking refers to the location of the primers in relation to the intron-exon border. Spanning primers cover the entire intron segment, while flanking primers cover the border of the intron and exon. This means that spanning primers will amplify the entire intron, while flanking primers will only amplify the border region.

In terms of primer design, spanning primers are typically used when studying the expression of a specific gene, as they provide a more comprehensive view of the gene's structure. Flanking primers, on the other hand, are commonly used in genetic testing and sequencing to specifically target the intron-exon border and identify potential mutations or variations in that region.

It is important to note that spanning does not necessarily mean covering the entire intron sequence, as there may be other introns within the gene that are not targeted by the primer. Similarly, flanking does not always cover the entire border, as there may be other regions of the gene that are not included in the primer design.

In conclusion, the difference between spanning and flanking primers lies in the specific location they target within the gene, with spanning primers covering the entire intron segment and flanking primers targeting the border between introns and exons.