How to obatin intron sequence from cDNA sequence? - (Oct/03/2010 )
Is it difficult to get the intronic sequence based on known cDNA sequence? Since we don't know where is the intron.
I've read a paper where the authors designed 3 sets of primers to amplify 3 overlapping sequence of a gDNA, and combine the sequence to obtain the sequence of exon and intron. Is there any other way?
erm I think it is impossible to get the intron sequence from the cDNA sequence, as by definition, cDNA doesn't contain intron sequences!
However I suppose you could design primers based on the beginning and end or other regions of the cDNA, and use them to PCR up or sequence gDNA, which will give you the full sequence of the gene, introns and exons. I have not tried to PCR or sequence gDNA before however, and I believe there are other complications when using that sheer amount of DNA.
Or you could try BLASTing sections of the cDNA and seeing if they match any gDNA sequences. As I said however i don't know much about gDNA techniques!