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I have a problem in my bioinformatics class that I thought I was doing right, but someone else is getting a different answer. Here is the problem:

Given the following DNA sequence, 5'-GGATCGTGCCACCATCCACCATCGTTA-3', if two introns are in bases 3-9 and 15-22, what is the mRNA transcribed? Give the answer 5' to 3'. Note that the first base is base 1.

And here are the steps that I took:

  1. 5'-GG ATCGTGC CACCA TCCACCAT CGTTA-3' (remove the bolded)
  2. 5'-GGCACCACGTTA-3' (new string)
  3. take reverse complement
  4. swap T's with U's

Is this correct? Or where am I going wrong?

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If you look on ensembl.org, which real biologists use, the DNA sequence given for a gene, and the DNA sequence given for a transcript are the same, if the gene runs in the forward direction. They aren't rev-comped; people don't even substitute U's in the sequences. So just keep in mind that some of what you are doing is just to prove that you really know that RNA has U's, that there is a difference between template and coding strands...real biologists take that for granted –  swbarnes2 Feb 3 at 19:06
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up vote 4 down vote accepted

I think the only place you are going wrong is in getting confused about strands ("take reverse complement").

5'-GGATCGTGCCACCATCCACCATCGTTA-3'   << coding strand
3'-CCTAGCACGGTGGTAGGTGGTAGCAAT-5'   << template strand

The coding strand has the same sequence as the transcribed RNA (apart from T>U), so the primary transcript is:

5'-GGAUCGUGCCACCAUCCACCAUCGUUA

Then, positions of introns:

5'-GG AUCGUGC CACCA UCCACCAU CGUUA

and after splicing:

5'-GGCACCACGUUA
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Do you take the reverse complement after the splicing? It looks like we got the same result, I just took the reverse complement and flipped the T's to U's last –  Brett Feb 1 at 18:52
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You don't need to take the reverse complement - the 'top' strand of the DNA (i.e. the sequence in your question) is the same sequence as the RNA, because the RNA is made using the complementary strand as template. I included the 'bottom' strand for clarity. –  Alan Boyd Feb 1 at 19:03
    
I see, thank you. –  Brett Feb 1 at 21:23
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