Someone gives you a short DNA sequence that comes from the middle of a gene.


From this sequence, determine the following:

  1. Is the promoter located to the left or right as the sequence is written?

  2. Is the sense strand the top or bottom strand?

  3. What amino acids are encoded by this gene fragment?

The only thing I have been able to come up with, is that since this is from the middle of a DNA sequence I need to choose a frame with no stop codons.

  • 1
    $\begingroup$ The two segments you provide are not complementary to each other. Is this a typo or a part of the actual question? $\endgroup$ – stochastic13 Feb 19 '14 at 8:05
  • $\begingroup$ I've edited the sequence to repair the 5' and 3' ends of the bottom strand, which are now as was shown in the original version of the question. $\endgroup$ – Alan Boyd Feb 19 '14 at 9:28
  • $\begingroup$ Gene doesnt essentially mean protein coding $\endgroup$ – WYSIWYG Feb 19 '14 at 10:58




AGA TTG ACT AAT CG <<< this is the ORF



If the sequence comes from the middle of a gene we assume it should encode an open reading frame. For this sequence only 1/6 frames does not include a stop codon (shown above in italics). So in standard format, with promoter to the left we can write the ds sequence as:



Since this is homework I'll leave the rest to you.

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  • $\begingroup$ Since the ORF has no stop codons, does that mean it is the template strand? $\endgroup$ – itsSLO Feb 19 '14 at 8:08
  • $\begingroup$ The open reading frame is the strand of DNA with the same sequence as the mRNA (with T>U). RNA polymerase makes that RNA using the other DNA strand, which is the template strand. If the dsDNA sequence is written in the conventional way with promoter to the left then the top strand is the coding strand and the bottom strand (running 3'>5') is the template strand. $\endgroup$ – Alan Boyd Feb 19 '14 at 9:25
  • $\begingroup$ Don't we want the template strand to have no stop codons? Cause when we are reading the template strand making the mRNA we don't want to encounter a stop codon. $\endgroup$ – itsSLO Feb 19 '14 at 9:56
  • $\begingroup$ For example if we use 3'TCTAACTGATTAGC as the template strand when the polymerase reaches TGA, it would stop right? $\endgroup$ – itsSLO Feb 19 '14 at 9:57
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    $\begingroup$ @itsSLO I would like to tell you a couple of things. 1. Stop codons do not stop transcription of mRNA, it will stop only the translation of mRNA. 2. Here, we are taking the sequence with no stop codons only because the question says that the sequence taken is from the middle of a gene. So, if we take a sequence with a stop codon the mRNA from rest of the part of the gene will not be translated. $\endgroup$ – biogirl Feb 19 '14 at 12:30

On the sequence alone, you can answer neither of these questions because:

  • from the sequence alone you don't know anything about the gene or the promoter.
  • the same is true for the orientation
  • and the codons, since you don't know if the code is in frame or not. If one base is cut-off from the original sequence, your codons shift, and don't show the original code. The sequence has 14 nucleotides which will not ressolve into a short amino acid sequence.

You can probably identify the gene using BLAST and then see, where the sequence is located and answer the questions. I tried to blast the sequence, but it is too short to give a definitive answer.

So the first thing, you need to do is identify the sequence (gene and the organism where it comes from), then you can do the rest of the work.

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  • $\begingroup$ Yeah this was all that was given for the problem. Nothing else.I was thinking you can determine the frame by choosing one without any stop codons. $\endgroup$ – itsSLO Feb 19 '14 at 8:06
  • $\begingroup$ Thats right. Alan showed what can be done, but the rest is problematic. $\endgroup$ – Chris Feb 19 '14 at 8:38

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