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Old 04-30-2017, 10:48 PM   #1
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Default Distance to TSS Primer Design

I have what is probably a stupid question, but I'm really not sure what to do. How do people usually use distance to TSS when designing primers for ChIP-qPCR validation? I was planning on using UCSC genome browser, but I'm not sure whether distance to TSS factors in the 5'UTR exon when trying to pull the sequence for a gene. For example, one of the genes that came up in a ChIP-Seq I did was Nhe1, and the distance to TSS is -17. Is that -17 with respect to the atg (which would include the 5'utr sequence), or is it -17 in the 'Promoter/Upstream' sequence that you get if you check the box in the genomic sequence? They aren't the same for most of the genes that I've checked so far. Any help would be greatly appreciated.
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promoter analysis, qpcr primer, tss

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