When you say variant, do you mean isoform, or sequence variant?

If you mean isoform: what is the goal of your experiment? For gene expression analysis in the first instance, I would try to design primers that bind to all of the isoforms if possible. Discriminating between isoforms usually comes later in the sequence of experiments.

If you mean sequence variant: what is your sample type? If you will be using samples from a large number of individual humans, then you should do your best to design primers away from known SNPs and other genetic variants so that the primers will work for the largest possible range of people. If you are using a specific cell line or an inbred model organism, this matters less, design against the reference sequence for that line/organism.

I C Renu

Hi,

First, you select the species variant, whether it's from Homosapien or another organism.

Based on that data, check the gene in NCBI later, and you start designing primers.

You may search the organism name and your field of study on google scholar. consider which variant is more applicable in more cited articles.

Hello Dear,

It is better to choose which one is more than like your sequence. First, you should blast 2 sequences and choose the most like among your sequence and that sequence