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I am going to perform some RT-qPCR tests to validate an experiment. 

I'm currently in the process of ordering primers, and I would like to get them from the Harvard Primer Bank since these have been validated before. 

However, I would like to get primer pairs that span an exon junction (i.e., one primer on one exon, the other primer on another exon.)

Currently, I have to do a lot of steps to figure this out, since the Primer Bank only gives the positions of the primers on the CDS, and not on the entire mRNA molecule.

Does anyone have a quick way to check on which exons the primers belong?

Thank you!

Is there a good site or software to see if a primer pair spans an exon junction?

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If there is a such a site, I have never encountered it. Since you say you have the genomic coordinates for each primer it seems to me like all you need is a list of the genomic coordinates of every transcribed exon in the human genome. Assuming that is correct then you are in luck because such lists do exist in the form of a GFF3 file. You should be able to obtain a comprehensive annotated GFF3 file of the human genome from the EnsEMBL website. It is possible that the UCSC browser has a similar file (except in their '.bed' format) but I am less familiar with the contents of that site.

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