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I am not a biologist therefore, it might seem as an elementary question. I retrieved rodent sequences from UTR database:

http://utrdb.ba.itb.cnr.it

And I know there are supposed to be four nucleotides namely: A,G,C, and T. However, on this database I get sequences that have 'n' nucleotide in several locations, 'm' and 'k' as well. What does these letters mean? I haven't been able to find anything regarding it. Does it mean these positions in UTR are undefined or they are some 'intermediate' nucleotides if there are any?

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These are IUPAC codes for so-called "degenerate" or ambiguous bases, alternatives to the usual A, T, C, and G nucleotides (for DNA). The N code represents any base, while M and K map to A or C, and G or T, respectively.

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  • $\begingroup$ Okay. Thanks. That makes much more sense to me now. $\endgroup$
    – John
    May 28, 2020 at 7:08

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