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It seems that the promoter regions are written from the 5' to 3' direction. My lecture notes, for example, give the -35 and -10 promoter regions sequences like so:

Promoter region

Wikipedia seems to agree, on their article about promoters.

However, RNA polymerase transcribes in the 3' to 5', as in it reads the template strand in the 3' to 5' direction. In that case, why aren't the promoter regions written also in the 3' to 5' direction?

Meaning, instead of the -10 sequence being 5'-TATAAT-3', why is it not 3'-ATATTA-5', in agreement with the direction of transcription?

My intuitive guess is that the $\sigma$ factor recognises the promoter region in a 5' to 3' directionality. But I cannot find any information to back up this guess. Additionally, if this is true, how could it have been determined (experimentally)? Furthermore, whatever the answer is, does it also apply to transcription in eukaryotes?

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    $\begingroup$ Possible duplicate of What direction is a sequence in databases written? $\endgroup$ – David Apr 29 '18 at 21:15
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    $\begingroup$ Come on. You can't have people driving on the left in one town, and driving on the right in the next. It's bad enough when us Brits go on the Continent. There's no mystery, we just read all gene features on the same strand. $\endgroup$ – David Apr 29 '18 at 21:18
  • $\begingroup$ @David Fair enough, I'll take it as a consequence of convention. Thanks! $\endgroup$ – ning Apr 30 '18 at 11:19
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DNA sequence by convention is written starting at the 5' position so the directionality is assumed without explicitly writing the 5' and 3'. As for why its not the template strand sequence. I would say that's also a convention for simplicity because you only need to write one sequence if you want to discuss genes and regulatory elements.

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