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I feel like this might be a really silly question and I've been going back and forth for awhile and I think confusing myself- so sorry if this is dumb.

I am using Seqmonk to visualize genes in an assembly (but I suspect the issue would be the same in any visualization software). I am trying to identify promoters of specific genes to determine if they are differentially methylated. Genes on the forward strand (highlighted in red), the promoter would inherently be upstream- in this case to the left (i.e. if my start site was 5000 and the end site 6000, I would assume I could find my promoter to the left of the start site between 3000 and 5000 bases.

My confusion is what happens with genes that are on the reverse strand (in blue here). Start site and end site could be the same (5000 and 6000- as end sites are always bigger than the start site). Does this mean that in the software, the promoter is expected to be on the right hand side (i.e. bases 6000-8000)? This has been my going thought but now I wonder if having bases that seem downstream (because they're bigger) makes sense, even though it really does because downstream on the forward strand would be upstream on the reverse strand. Or if I need to always do 3000-5000 bases as the promoter, regardless of the the strand of origin.

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  • $\begingroup$ If I'm looking at a gene on the reverse strand, where would I find the promoter. $\endgroup$
    – user18170
    Commented Sep 13, 2023 at 17:02
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    $\begingroup$ If you intended to post an image, we are not able to see it. Not clear what red and blue are. $\endgroup$ Commented Sep 13, 2023 at 17:37

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Have a look at this UCSC browser shot. UCSC browser shot of WDR92 showing promoter histone marks to the right of the transcribed unit on human chromosome 2

Looking at the WDR92 transcript, note that it is transcribed right to left. This would indicate that the promoter is on the right. Indeed, we see a variety of promoter histone marks on the right of the gene, but not on the left.

In other words, yes, for genes on the reverse strand, the larger coordinate will be at the beginning of the gene, and the promoter will include a larger coordinate than the rightmost transcribed base.

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  • $\begingroup$ THANK YOU. This is what I thought but I suddenly got wrapped up in my head. Super helpful. $\endgroup$
    – user18170
    Commented Sep 13, 2023 at 19:13
  • $\begingroup$ @user18170 No problem. consider upvoting/accepting the answer if you found it helpful, in case others find this in the future. $\endgroup$ Commented Sep 13, 2023 at 22:28

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