Could anyone please clarify whether or not in computational studies one can treat the transcription start site (TSS) as being equivalent to the first exon?
Some seemingly contradictory quotes (and sources) that I've found on this issue:
"Promoter sequences are usually the sequence immediately upstream the transcription start site (TSS) or first exon." (SOURCE: http://www.protocol-online.org/forums/blog/4/entry-10-from-how-to-find-promoter-sequences/)
"The TSS is the first nucleotide of the UTR (at least I think so, I don't think there's any gene which immediately begins with ATG), so yes, UTRs can also be 'relaxed' and differ in length." (SOURCE: http://www.protocol-online.org/forums/index.php?app=forums&module=forums§ion=printtopic&client=printer&f=1&t=6050)
"No, the first codon of the first exon is the start codon "ATG" which also codes for methionine. This is called the translation start site. The transcription start site is where the RNA polymerase binds to in the 5' UTR upstream of the start codon. IMHO Maybe someone else can elaborate more. I dont want to give you the incorrect info." (SOURCE: http://seqanswers.com/forums/archive/index.php/t-12773.html)