• It depends on what question you want answered but if the question is " are there any sequence changes of interest in this gene?" then you will have to sequence all of  the variants  because sometimes mutations are found only in some splice variants

 Dear Mohamoud,

Use the largest gene sequence.  If you are planning to carry out sequencing,I would suggest to use ENSEMBLE database. However, I wonder whether you found any variations in the sequence rather then their length? 

Thank you very much for your loyal cooperation my question is which variant is suitable for designing the primer to get a good PCR product?

Is there a protocol to choose a single variant in case of multi variant?

We need to know why you need the pcr product please. If it is just to prove that the gene exists in samples then choose a small amplimer in the part of the gene common to all of the isofoems but if you are looking for mutations in the gene then you will have to amplify all isoforms (most of which will be very similar) assuming , as Fawaz says that there is a significant size difference in the isoforms and that they are not differing just in a few changed bases

 Paul and Fawaz, thanks, i got it.