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This question already has an answer here:

Update: Initially my question (below) was appropriately marked as duplicate/overlapping with two other questions; This and this ; among them a specific part of an answer of the second duplicate/overlap ; appropriately answer my question.

The convention is that in indicating any sequence feature† in a protein-coding gene on double-stranded DNA, a single strand‡ is represented — the one from which the amino sequence could be read using the genetic code (conceptually, with T substituted for U). Like any other nucleic acid sequence§, it is always written in the 5ʹ to 3ʹ direction in the same manner as the mRNA transcribed from it, without this being explicitly stated.

But what it does not mention (but I'm still looking for); is whether there is a standard and universal documentation for this particular convention (IUPAC/ IUBMB/ ICBN/ ICZN/ anything such); because "conventions" are human-made rules, and without "declared, universally followed, and accessible" documentation; the conventions does not make a sense. It rather feels like a rumor or viral phenomenon. I visited the IUPAC and IUBMB website home pages but I could not locate the documentation from there. Also google keyword search did not found the helpful.

So I specify my question that I want to get the standard/ official source of this convention. I would be highly grateful if anyone kindly mention the source hyperlink.


My Initial Question

I'm stuck at a very basic convention on notation on reading Gene sequence. *Specially when a book (or question paper or anything) does not mention whether a nucleic acid (usually DNA), uses a single stranded DNA

The problem appears because similar region of the 2 opposite strands of a DNA can contain different gene, i.e.

enter image description here

(So it is possible that if we note a stretch from gene-1 with its complementary sequence, that complementary sequence could be confused with gene-2.)

In some cases, a sequence to a stretch of nucleic acid, indeed mean the sequence directly.

For example; In the wikipedia image about Reading Frame (Permalink) Wikipedia Image the 5'to 3'Left to Right indicates the sequence of the template strand directly whereas

But at the more and more "interior chapters" I've seen a rather complicated and indirect notation (although I could not found clear mention of a convention anywhere in books or web)... when they mean a sequence of a stretch of a gene (or a regulatory sequence), they writes the "nontemplate" or "sense-strand" sequence of the respective gene.

In the Wikipedia image on TATA Transcription Box (Permalink);

Wikipedia image TATABOX it must be a sequence from the nontemplate strand because if it was the template strand, the "Promoter" location on the "template" strand must be on 3' side otherwise RNA polymerase would not be able to synthesize the nontemplate strand mRNA strand from 5' to 3' time-order. But it would become impossible to infer for me if the given sequence lacked labelling for relative locations of promoters and structural genes.

Now my question is If an article provides me a single stranded "Gene Sequence"; How can I infer it is directly the sequence of the mentioned gene stretch or it is the complementary ("sense") strand of the gene? What is the convention about it?

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marked as duplicate by David, Community Jun 11 '18 at 9:47

This question has been asked before and already has an answer. If those answers do not fully address your question, please ask a new question.

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    $\begingroup$ I have cited this as a possible duplicate of the What direction is a sequence in databases written? but my answer to that covers just part of the question. I think the rest is covered in Terminology of the sequences of promoters in relation to DNA strands. If the poster doesn't agree, perhaps he can explain what is not covered. $\endgroup$ – David Jun 3 '18 at 14:26
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    $\begingroup$ You should post a new question if you have, well, a new question. $\endgroup$ – canadianer Aug 9 '18 at 10:23
  • $\begingroup$ Sure, Thanks for the advice. Would I need to revert my current edits? $\endgroup$ – Always Confused Aug 9 '18 at 10:25
  • $\begingroup$ @canadianer i am dwindling if new question may also overlap/duplicate. I've initially put a comment on said answer to add that document; but to also ask the same question to other visitors I kept the update here. $\endgroup$ – Always Confused Aug 9 '18 at 10:27
  • $\begingroup$ Okay I'm submitting a new separate question as @canadianer said. But if any user want to submit the addition into their existing post, they may please feel free to do proceed and mark the new question as duplicate. It is upon community. $\endgroup$ – Always Confused Aug 9 '18 at 11:46
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Assume that you are given the gene in the "forward direction"; the one where the starting ATG is on the left, that the sequence you are looking at is what the single stranded RNA will be.

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    $\begingroup$ Not clear... say of fig.1; gene 1 (lower strand) will be "forward" if I read it as 3'...CGTACCGGTTAA..5'. Would I tell it "Sequence of Gene1"? Or would I have to write its complementary strand as "sequence of gene 1"? $\endgroup$ – Always Confused May 3 '18 at 16:46
  • $\begingroup$ I see more than one ATG in my question. Which specific ATG you are telling about? $\endgroup$ – Always Confused May 3 '18 at 16:48
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    $\begingroup$ In the context of a gene, I mean the ATG that is the actual start of translation. In figure 1, it would just be wrong to call those reading frames if the sequence is the reverse complement of the real RNA. $\endgroup$ – swbarnes2 May 3 '18 at 17:15
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    $\begingroup$ In real life, no one is going to give you data in the form of figure 1. $\endgroup$ – swbarnes2 Jun 4 '18 at 16:12

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