Primer desing for transcript variant - (Aug/18/2008 )

I am designing primer for SYBR real time pcr to verify the microarray data.

The gene i am interested has three splice variants.

Shall i design it specific to one splice variant? If so, my forward and reverse primer will not able to span any intron.

I am not sure which splice variant should i look into either.

Any advice for this?

Thanks in advance.

Do your splice variants share the 5'UTR (and start site) or the 3'UTR regions? These could be a good place to make a common primer to detect all types.

I would also design primers to detect all splice variants as you find find something interesting.

Fully agree with AUssieUSA. First thing you better compare the sequences of different splicing transcripts, and find out unique sequence for each splicing variant, and design the primers for each one. You still could design primers that span introns.