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I am having trouble understanding the reference sequence for sars-cov-2, NC_045512.2

Three nucleotides equals one amino acid, right? But the nucleotide at position 13468 seems to be used twice, so the sequence starting at 13463 reads:

tta aac ggg ttt ... which translates to LNGF

However, according to the reference, the translation is LNRV, so it's read as tta aac cgg gtt etc - like the c is repeated.

The reference says "join(266..13468,13468..21555)" but how does this work and why?

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    $\begingroup$ en.wikipedia.org/wiki/… $\endgroup$ – reuns Apr 26 '20 at 23:23
  • $\begingroup$ And if you think that's wierd, the transcriptional phase can get even more so because of the error-prone RdRP: "For some nsNSV, like those of the Paramyxovirinae subfamily (e.g., measles, mumps, and Sendai virus) and Ebola filovirus, there is also a form of programmed transcriptional frameshifting (PTF). The most egregious example of this is parainfluenza virus type 3 (PIV3), where a stretch of 300-odd nucleotides in the middle of the P gene is translated in all 3 frames." rnajournal.cshlp.org/content/21/4/667.full $\endgroup$ – Fizz May 3 '20 at 13:27
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In the reference genome browser, it seems you are looking at the first Coding Sequence (CDS) line, YP_009724389.1, which shows the translation to LNRV...:

browser image

If you look lower down, you'll see a line for CDS YP_009725295.1, which shows translation to LNGF... as you expected.

So, these are two different interpretations of possible translations for this area of the genome. Why does the first have the weird peptide sequence? If you hover over the CDS line, the browser will pop up more information about it. For the top CDS, that includes this comment: "pp1ab; translated by -1 ribosomal frameshift". This suggests that someone believes that sometimes the ribosome translating the RNA glitches at that point and advances only 2 nucleotides instead of 3 after the "N" codon. This shifts the interpretation frame as if there were another C present.

If you search for "pp1ab", you'll see it's mentioned in the Feb. Nature article on the sequence.

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    $\begingroup$ it seems there is one wiki article per coronavirus secondary structure en.wikipedia.org/wiki/… $\endgroup$ – reuns Apr 26 '20 at 23:24

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