I need to design primers to detect the changes of gene expression from soybean tissues in a qRT-PCR assay. However, the genes I want to detect are predicted genes in NCBI and there are more than one transcript variants for one gene, with starting by XM, rather than NM. 

So, I want to know how can I design the primers based on many transcript variants? By using the homologous sequence? Or it is scarcely possible to design primers according to the PREDICTED genes with many transcript variants.

Thanks for your attention.

 

Depends on what you need. One way is to design primers on conserved stretches.