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I've seen many textbook images of alleles on homologous chromosomes with the gene loci identified but how could this be visualised on linear DNA sequences with the bases written out? Is it that you would have one DNA strand with its nucleotides and then another adjacent DNA strand with nucleotides at the same locus but different in sequence? Any visual representations would be helpful

Edit: This picture below shows how alleles can be seen on the chromosomes but it's not clear about where the change in sequence would be on the nucleotide bases. The typical diagrams show the homologous pairs but they don't usually show the change of base sequences on a small scale.

Typical textbook illustration of alleles

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    $\begingroup$ Unclear exactly what you mean. An allele is a variant. It's like having 1st edition vs. second edition of a book, where a typo was fixed on page 32. In a cell of a diploid organism, you might have 2 1st editions, 2 2nd editions, or one of each. But each of them is just a long string of characters. But there isn't a "right" way to visualize this because it's too small to see, all of these are metaphors to help us understand what's happening at the single molecule level. $\endgroup$ Aug 25, 2023 at 21:32
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    $\begingroup$ An allele of a gene is a segment of DNA so its diagram will be like any DNA helix with a unique nucleotide sequence. A chromosome is a single molecule of double stranded DNA with histones. So two alleles will be two extremely similar DNA segments. Or as @MaximilianPress said two editions of a book. I guess you asked for a diagrammatic representation? $\endgroup$
    – Aurelius
    Aug 25, 2023 at 22:08
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    $\begingroup$ @MaximilianPress Could also be a truncated version that ends on page 100 out of 500 original pages, or arguably even one that doesn't exist at all. $\endgroup$
    – Bryan Krause
    Aug 25, 2023 at 22:10
  • $\begingroup$ I've posted an answer and I would be interested to know if it answers your question. However can I ask two things of you. 1. Please finish reading the Tour — we know you haven't because you don't have the badge for doing so, and it will help you learn how this site works. 2. When you ask a question related to something you have read, please post a link to it, or even a copy of a typical image in this case. And did you search for such pictures? I found the one I modified Googling for images related to Sickle Cell Allele. $\endgroup$
    – David
    Aug 28, 2023 at 18:30
  • $\begingroup$ Thanks for the response David, will do the tour now and see if I can attach said pictures I was referring to $\endgroup$ Aug 31, 2023 at 12:29

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I think I may understand the point of difficulty the poster is encountering, and have produced the diagram below (adapted from an internet source) in the hope that it may help.

Sickle cell allele

This diagram shows the allele for the mutation in β-haemoglobin that causes sickle disease. The key points are:

  • There are two copies of the chromosome in diploid cells, either of which may be normal or mutated.
  • Each chromosome contains double-stranded DNA, so the mutation affects both of the two complementary strands. Thus the stated expectation of the poster to see “one DNA strand with its nucleotides and then another adjacent DNA strand with nucleotides at the same locus but different in sequence” is incorrect.

Now this may be a slip of the typewriter fingers on the part of the poster, but it may also be confusion because of there being two copies of the same chromosome. Anyway, the diagram seems to me to give an example of what was requested. It can be amended if necessary

Of corse the allele may extend over more base pairs if the mutation is a deletion, but let’s walk before we try to run.

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  • $\begingroup$ This illustration could mislead some, as the left-hand part illustrates a chromosome form that is not typical in the life of a cell, but is a form that occurs during meiosis. That special form of chromosome has two chromatids with the chromatids having different alleles. (The normal form of chromosome has only one chromatid, and hence only one allele form.) $\endgroup$
    – mgkrebbs
    Aug 28, 2023 at 20:25
  • $\begingroup$ @mgkrebbs — Yes, that was a point of concern to me also, although I'm not an expert on chromosomes, just graphics. Is the replacement OK? The combination of 2D and 3D jars, but then, nobody is paying me for this. $\endgroup$
    – David
    Aug 29, 2023 at 19:54
  • $\begingroup$ Yes, that is a definite improvement, as it shows two homologous chromosomes as normally exist in a cell. $\endgroup$
    – mgkrebbs
    Aug 29, 2023 at 20:05
  • $\begingroup$ Hi David, thanks for your response - this is more what I was looking for with the visual representation as a lot of the textbook diagrams show a more zoomed out version of the chromosome which made it hard for me to visualise how the nucleotide bases looked. Just to clarify are alleles comparing the variation of genes on the different chromosome then? As opposed to an allele being the variation of genes on one chromosome on its own? $\endgroup$ Aug 31, 2023 at 13:47
  • $\begingroup$ For example is the change of sequence (on small scale terms) going to be on one antisense strand whereas the sense strand has the typical reference sequence? Or is it comparing the differences of sequences on the other homologue as opposed to a single change in sequence on one chromosome? Apologies for the long winded question. I'm just trying to visualise this for a short sequence (e.g. 10 bases) not a large scale one as usual. Also, I think what tripped me up with the textbook diagram is that I thought the chromosomes shown only had one singular strand instead of the double stranded form. $\endgroup$ Aug 31, 2023 at 13:48

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