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CpG island and promoter - (Jul/22/2007 )

Hi every one
i have few questions which surely be very simple for you people bu i am really confused about.
1. Dose the promoter sequence always exist within the 1000pbs 5' of the gene? if no how far it can be? The gene i am looking for has no CpG Island in the region 1000pbs upstream 5' end but there is a CpG island at position about 3000bps upstream? is it in the promoter sequence or outside?
2. where is the transcriptional start point usually located as i was thinking that it is the same point as ATG in the first exon? Does it change for a gene having variants?
Thanx in Advance
w

-w007-

not all promoters are associated with a CpG island. Theoretically, promoters are within the proximity of the transcription initiation site. However, as you are not sure what the transcriptional start site is, the 3000 bp upstream CpG island may be the one you're looking for, only to find out it is not 3000 bp upstream but at the exact transcriptional start site. If your gene is human or mouse, you can check the DBTSS (database for transcriptional start sites) to find out, well, the transcriptional start site.
And yes, some genes can have multiple TSS, but the DBTSS may also help you with this. Otherwise, you can check the BLAT Genome Browser at UCSC for a better 'guess' where your gene starts.

-dpo-

The DBTSS can be found at http://dbtss.hgc.jp/.

K.

-kr├╝melmonster-

QUOTE (w007 @ Jul 22 2007, 11:36 PM)
Hi every one
i have few questions which surely be very simple for you people bu i am really confused about.
1. Dose the promoter sequence always exist within the 1000pbs 5' of the gene? if no how far it can be? The gene i am looking for has no CpG Island in the region 1000pbs upstream 5' end but there is a CpG island at position about 3000bps upstream? is it in the promoter sequence or outside?
2. where is the transcriptional start point usually located as i was thinking that it is the same point as ATG in the first exon? Does it change for a gene having variants?
Thanx in Advance
w


The TSS is often not going to be at the first ATG in the first exon since there is usually a 5' untranslated region (UTR) upstream of the first ATG.

-KPDE-