Depends on the question you're asking- you can design primers to hit all splice variants, or if you're only interested in the activity of a particular isoform, you can target your primers to only amplify that variant. You have to decide that for yourself depending on your research question. PrimerBLAST (NCBI) is able to handle both.

Mostafa, I assume you are only concerned with whether the gene is expressed in the tissue/cells you are investigating? If so, then a primer pair that would detect all isoforms would be advisable.

You should not design primers for specific transcript variants as you may arrive at the wrong conclusion, unless you already know which transcript variant is preferentially expressed in your tissue/cells.

Best.

Thank you guys very much for your kind answers. So I should first either find out which isoform is preferably expressed in the tissue of interest or design a primer that recognize all the isoform. Right?

Hi Mostafa,

If your intention is to measure gene expression, I also agree with Ricardo.   Long or short is less relevant for this purpose.   RT-qPCR assays are typically designed such that the resulting amplicon spans an exon-exon junction to avoid genomic amplification.  To answer your question --To increase the odds that you will capture the isoform expressed in your study, you should pick the exon-exon boundary that is present in the most isoforms.

Also, LIfeTech has a custom Taqman assay tool which could assist you:

http://www.lifetechnologies.com/us/en/home/life-science/pcr/real-time-pcr/real-time-pcr-assays.html

Thank you, Jeffery

Yes, I d like to measure gene expression. I really appreciate your help. Thank you all for your great comments.

Bests

Mostafa