Promoter and Exons... - can my promoter be over 100,000 bp away? (Feb/05/2008 )

Hi everyone! I needed a bit of help understanding this.

5' Promoter______exon 1______intron 1_______exon 2______intron 2 3'

If my CDS is located at the 5' end of exon 2, can my promoter still interact with it? My promoter is over 100,000 bp away from the CDS and I just want to be sure with what I am doing. I have been told that my promoter should be immediately upstream of my CDS. Can anyone help?

Thanks a bunch!

The NCBI CDS is confusing, it could mean "coding sequence" or "cDNA sequence". You said your CDS is located at exon 2, so the 5 UTR of your mRNA is on exon 1. Usually promoter is immediate upstream of exon 1, not matter how far it is from the coding sequence.

well it could be like the haemoglobin promoters... they are a long way off. It uses this weird spooling mechanism to pull coding sequence close to the transcription factor sitting on the promoter.

I checked with Ensembl and the CDS corresponds to the coding sequence from NCBI. Since I am trying to clone the promoter to determine if my transcription factor regulates its expression, then my promoter will be immediately upstream of exon 1, correct? Even though the coding sequence for the gene is located at exon 2?

Yes you are right. This is true for most cases. To make sure you should also check sequence upstream of 1st exon to see if there is any CpG island, predicted promoters, TATA box, GC box etc.