primer design - (Nov/18/2010 )

I need to design primers for a particular domain in my gene. The gene has got several different types of domain but I would like to check the expression of one particular domain.

Is there a tool that can help locate the mRNA sequence of a particualr domain? e.g. where the domain starts and finishes in term of bp in mRNA?

You can try primer blast or blast in general. It detects putative domains.

Manually: Translate your mRNA - go to SMART EMBL to detect domains - align domains to your translated mRNA - design primers.
Tedious, I know. Maybe someone has a better idea?

rsm