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Possible # alleles at locus of 3 base-pairs (diploid)?

  1. Feb 14, 2016 #1
    How many possible alleles are at a locus consisting of 3 base-pairs in a diploid?

    ugh, I am so confused...
    So, I guess a locus is just a spot for a gene, so the gene is also considered to consist of 3 bases.
    Gene: _ _ _
    Each "_" could be either an A,T,C, or G.
    So there are 4 possibilities per "_"
    So, there are 4 x 4 x 4 = 64 different possible alleles of a gene on one chromosome...?
    Since there are 2 chromosomes in a diploid organism, there are 64 x 2 = 128 different possible alleles at a locus...? :(

    ugh, I am sure I am WAY off...
    Please help me, somebody! )':
  2. jcsd
  3. Feb 14, 2016 #2
    Hi Lo.Lee.Ta:

    I am not an expert, but I think I can offer some help you can use to search for more information.

    The usage of "locus" I know is, with respect to the start of a chromosome, the sequence number of (1) a single base or (2) a triplet. There may be other definitions that I don't know. For your example, I think it refers to (2) the triplet.

    The usage of "allele" that I know refers to (1) the particular sequence of bases in a (a) triplet or (b) gene, or (2) (a) to what the triplet codes for (amino acid, start, stop, etc.) or (b) the effect (phenotype) of the whole gene as it might change with different bases. That is, if two different triplets are codes for the same thing, the second usage would call them the same allele. There may be other definitions that I don't know. I am guessing that for your example, the first meaning (1a) is the one you want to use.

    My guess is that your calculation of 64 is correct. Counting the possibilities on both strands doesn't make sense because all of those bases in the second strand are constrained by what is in the first strand.

    Hope this helps.

  4. Feb 15, 2016 #3


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    Just thinking aloud, it seemed to me there can only be as many different alleles at a locus as there are amino acids i.e. 20.
    Then I thought maybe we should say 21, since a stop triplet replacing an amino acid codon gives mutation.
    I even thought: they say triplet not codon - so perhaps there could be two adjacent codons in which you could ring changes - a more complicated calculation.
    But then I thought after all we should say 2 - the triplet is either functional or it isn't (first approximation) - and when you talk of alleles you're mostly talking at genetic phenotypic level.
    I think if this is a quiz type question I think this last is what I would say. If instead it is a reasoning question, well you decide and write your reasons.
    Slight trap question in my opinion.
    Last edited: Feb 15, 2016
  5. Feb 15, 2016 #4
    Hi epenguin:

    My interpretation is that no trap was intended. The use of ambiguous terms is the difficulty, and that was probably due to carelessness.

    Using allele in the (1a) sense makes the count 64. Using allele in the (2a) sense makes the count 21.

  6. Feb 15, 2016 #5


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    An allele is simply a generic variant, and the definition does not specify that the variation must have any phenotypic effect. In fact, applications such as DNA fingerprinting purposefully look at alleles that have no known functional consequences (many of these alleles are at non-coding loci, so it would not make sense to think about the amino acid sequence encoded by the allele).
  7. Feb 16, 2016 #6


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    Ah yes I'll go along with that. Not always but a lot of the time you'll be talking about only two, but those two could be any of 64.

    I had some suspicions and looked it up. Apparently the word, not that old, comes from a shortening of 'allelomorph' = 'other form'. No doubt the word has a root in common with 'alternative'. I think it really does carry background psychological or historical load of 'one or the other of two'. So the common usage may have involved and expanded a bit. Looking it up in dictionaries and other sources you do often see them mention two forms with 'or more' as rather an afterthought. So you are right but I was not too wrong! :oldbiggrin:
    Last edited: Feb 16, 2016
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