Hello,
I am trying to do Methlation specific PCR and for that I have to design primers for it but when I search my gene of interest in ensembl, it shows two adjacent promoters, part of one of this promoter inside of the 1st exon of the gene (5' UTR). Both prmoter has CpG islands so which one should I choose for the designing primers? Any suggestion? There is no MSP primer desing for this gene in pubmed before.
Thanks
Hi Suleyman,
why not trying to analyse both promoters, since they can be used in specific conditions?have you analyzed their factor specific binding sequences? but nevertheless, I advice you to design your own primers, since a few proportion of the published ones are really quiet reliable. if you're not used in designing primers, almost try them in "in silico PCR" in the UCSC tools.
fred
Hi Suleyman,
Yes, CpG islands in the promoter or overlapping the TSS may both be important for gene expression, so it’s hard to predict which would be the most important one. It may be better to design primers to both regions. You can also search in the UCSC genome browser and in the regulation section click to show the CpG islands. There are also methylation tracks derived from experimental data that can be added to visualize methylation reported from some cells and tissues. You can use the MethPrimer program to design your MSP primers.
Good luck!
Blanca
If both promoters reside in the same CpG island, you can design primers to cover the entire island.
Try design the primers in Methyl Primer Express, her software show more details for considerates in the primers!
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