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

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9.4 years ago

gaelgarcia ▴ 270

Hi all,

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!

PCR exons qPCR primers • 3.1k views

ADD COMMENT • link updated 2.2 years ago by Ram 44k • written 9.4 years ago by gaelgarcia ▴ 270

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I think you can do that with UCSC genome browser, it has a feature called in-silico PCR feature where you can input the primer sequence.

ADD REPLY • link 9.4 years ago by Michael 55k

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Thanks, Michael! That's exactly what I was looking for:

image: screenshot

ADD REPLY • link updated 2.2 years ago by Ram 44k • written 9.4 years ago by gaelgarcia ▴ 270

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