Things I have repeatedly read, but have trouble understanding why they work that way:
1)Go to ensemble, look up gene, export sequence ~ first 1000 bp, blast this to make sure you have right region. I dont understand how getting the first 1000 bp will ALWAYS give you the promoter? Then they say put the sequence into primer design program (methylprimer express), and just "assume"? where the CpG islands pop up are..thats where your promoter is? (lets say you have 2 cpg islands..how do you know where the promoter is? is it one of the cpg islands, or does it span both...?)
2) + / - strand... i understand that one is sense (+) the other is (-) antisense strand..but why is it important to incorporate this when you are looking for promoter sequences?
Thanks for your help! (my gene is AXIN2) if anyone wants to show me with screenshots...that would be HIGHLY appreciated!
