Predict CpG island - (Mar/23/2005 )

I would like to predict whether the 5'region of a gene contains CpG islands..I pasted the ~10000nucleotide from the last nucleotide of the exon 1 to CpG island searcher . is it enough? should i include intron 1 and exon 2?


samantha

sounds good samantha, though it wouldn't hurt to included intron 1 and exon 2 as the island of some genes run into these regions.

Good luck!

Nick

Then how long of the 5'region do you guys usually use for CpG island prediction? and which regions do you usually use, or is there a common rule for the prediction, say we have to use intron 1+ exon 1+ exon 2 for prediction? Thanks

samantha

For methylation study, I only focus on the cpg islands that surround the transcriptional start site unless there are identified transcriptional regulatory elements further upstream.