Re: [jbovlaste] SNP, RFLP, allele

[Austin Thomas <amt2839@gmail.com>]

I think your definition of a RFLP is a bit off.  It is just a restriction fragment and depending on the restriction enzyme or enzymes used the fragment lengths vary.  Restriction sites can vary based on differing sequences therefore homologous regions can yield different fragment lengths. These can be statistically associated with particular alleles of genes and therefore associated with with particular phenotypes (diseases) but it actually doesn't have a direct link to it.  The lengths do not differ (necessarily) between alleles in a RFLP, only the restriction sites (and these could stretch across multiple genes or be within a single allele). (I have done RFLP analysis so I hope I know what I am talking about)

You also keep using allele improperly.  An SNP is not an allele, it might possibly define an allele but allele does not refer specifically to single base pairs, at least not in any context that I am aware of.  An allele can be non-coding though like is usually the case with VNTRs in which diffirent repeats are reffered to as different alleles.  When talking about a coding sequence Allele refers to the entire protein encoding sequence.  Allele is often used to refer to multiple protein encoding genes that all effect one phenotype although I am not sure that all molecular geneticists would agree with that usage but traditionally it was accepted.

Personally I think ginpanra could work but note that these are homologues not identical strands, alleles are different sequences.

On Mon, Jan 21, 2013 at 12:03 AM, Pierre Abbat <phma@bezitopo.org> wrote:

On Sunday, January 20, 2013 21:33:36 Eitan Postavsky wrote:
> SNP: If you don't mind my suggesting an entirely different veljvo, I think
> the key word is {panra}. An SNP is a terpanra be lo jgina bei lo jgina,
> y'see?

So is a RFLP, if I understand you right. And neither has to be in a gene.

> RFLP: Are you referring to the difference between homologous DNA molecules
> or the laboratory technique? Oh well, I don't understand either.

I'm referring to a site on a chromosome where different alleles differ in the
distance between consecutive occurrences of some sequence. It could be a
variable-length repetition; it could be a SNP where one of the alleles is in
the sequence.

> Allele: ginpanra. It's two jgina that panra each other, not differing in
> their terjgina. I'm aware that you're thinking of an allele as a particular
> sequence of base pairs that implements a given terjgina, but ginpanra works
> too, doesn't it?

Let's take a concrete example: OPN1LW. I was looking that up because I have
some mutation of it. OPN1LW codes for the protein which combines with
something to make it see red. It has seven SNPs (one is listed as "deleted"),
each of which may cause some change to the protein. There are three phenotypes
in men and four in women (it's on X): normal red vision, tetrachromacy (only
in women), protanopia, and protanomalopia. There are three alleles
distinguishable without looking at the SNPs: normal, missense causing
protanomalopia, and nonsense causing protanopia. I can't tell which SNP is
which from SNPedia, because it says "protan", and I don't know whether it
means protanopia, protanomalopia, or both.

la'o .gin. OPN1LW .gin. jgina lo remna lo jei je ka viska lo xunre

Let's denote the three alleles by R, R', and r. I'd like to say:

la'o zoi. R' .zoi <allele> la'o .gin. OPN1LW lo ka frica viska lo xunre

or with x2 and x3 exchanged.

Pierre
--
gau do li'i co'e kei do

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