promoter location - (May/30/2005 )

I am planning to do MSP on a new gene. Th first exon is non-coding and 30kb apart from the second exon (coding exon). One promoter region as well as CpG island are found upstream of the second exon by PromoterInspector and Ensembl/MethPrimer respectively. I am confused why there is no promoter region upstream of the first exon as transcription should start at 5' of the genome?
Thank you for any suggestion and help.

how far upstream from the first exon have you looked?

Nick

Hi Nick

Thanks for your reply. I have looked 10kb upstream of the first exon. One promoter region (with a stretch of C and T) was identified by PromoterInspector but of course no CpG island was found.

Just add in one more info - there is no CpG island found (by MethPrimer) in the 10kb upstream first exon.
Thanks for any suggestion and help.

keentolearn,

not all genes have "known" promoters to date, there could be a cryptic promoter that has yet to be described. Similarly, not all genes contain 5' CpG islands and there are some examples of CpG islands found after the first exon which may well indeed be your case.

I would look at this CpG island just out of curiosity and see if it is controlling the transcription of your gene of interest!

Good luck!

nick

Hi

Thanks for the suggestion. How many set of primers is normally used for a promoter region/CpG island?

small amplicons are better (150-400),

for more infor check out http://www.protocol-online.org/forums/inde...pic=5371&hl=msp

good luck!

Nick