intron spanning primers for non model organisms
Posted 13 April 2011 - 04:30 PM
I'm trying to design some primers that span introns. However, most of the sequences for my organism (brassica oleracea) are based on Arabidopsis and Refseq are not available. As an example i've been using actin (AF044573.1) with success using these primers, sense: GGTAACATTGTGCTCAGTGGTGGAA antisense: CCTGGACCTGCCTCATCATACTCA. But my went i tried with PAL (HM623311.1) using, sense: TGGATGAGGTGAAGAGGATGGTTGA antisense: CCTGTGCGTTAGATGATCGGTGAA i've got a bigger product than expected (800 bp). So, my question is, if i should try to design primers with Arabidopsis sequences for the same genes or try to do some alignmentand from the consensus make my primers?
Any help will be appreciated,
Posted 19 April 2011 - 08:20 PM
Posted 30 April 2011 - 05:38 AM
I'm a little loss here.