Dear All,
I know that my question is simple but I have a problem with understanding the transcript database. In big simplification I don’t understand the strand orientation. I read that one strand is + while the other is - and it means that forward (+) strand is coding, and reverse (-) is a template. So if my gene of interest is on reverse strand, is that mean that in this case - strand is coding ? When I search a database (like for example ensembl) I have a transcript written in 5->3 direction. So can I use it to find the right primers ? Or should I have reverse complement ?
Thank you.
This is an oversimplification IMO. There is no global coding/template strand.
If your gene of interest is on the reverse strand, that is the coding strand for that gene. You'd design primers based on the transcript sequence, so once you get to a transcript, don't worry about which strand it is in. Just base your primer on the sequence.