Hi,

Using DEXSeq I have identified a set of retina specific exons, for humans. I now retrieved the cdna sequences for these exons and I would like to perform a motif analysis using motif-based sequence analysis tools to identify splicing motifs that regulate the retina-specific splicing in humans. To identify motifs for these exons I would need to expand the dna sequences downstream or upstream of the sequence. How much basepairs should I need to expand downstream/upstream in order to identify motif binding sites, is there a common practice for this? I have not really been successful in finding papers about this subject.

Thanks in advance