I am trying to Identify several specific genes in Transcriptome data in order to prove their present (and expression). but the problem is that ,in BLAST, all of my genes of interest are belong to the same family (MADS box family) , so share same domain. and that's why they all match to same transcripts (For example 7 genes match to 15 Transcripts, not much difference in e-value and identity )
I also done the Reciprocal Blast and for all of these 15 transcripts the first hit is same. I am so confused right now.
I wonder How can I differentiate these genes?
Which sequence is which gene?