Talk:Allele

Who defined Allele ?

"...An allele is one member of a pair or series of different forms of a gene. Usually alleles are coding sequences, but sometimes the term is used to refer to a non-coding sequence..." Who is the individual that formally established this and where did he do this ? TongueSpeaker (talk) 12:00, 3 November 2008 (UTC)

Hey backspace! Whats up? I see you're still playing your silly word games, how fun! Anyway, allele was first used by Bateson and Saunders (1902) in this work: Bateson W. (1902). Mendel's Principles of Hereditary: A Defence. London: Cambridge University Press. Available at: www.esp.org/books/bateson/mendel/facsimile

Edith Saunders was a woman living in a man's word so she didn't get much credit (if any). Remember: its just a wordf describing a thing, just because you don't understand it doesn't mean that there is a gian conspiracy against you! --Woland (talk) 17:30, 3 November 2008 (UTC)

What about this allele is it that I don't understand because you defined it yet. Did Saunders for example know that a gene is an encoding/decoding mechanism, in what way will this influence the yet to be defined concept of "allele"? This author says the following about genes "....Physical evolution requires genes to work. Any rational scientists knows that there's not a smidgen of evidence there is a single gene, much less genes. Read Watson's and Crick's two original articles in Science magazine, and you'll discover they ask a number of "what if" questions, not of which have been answered. For example. When the two strands of DNA untwist to replicate, what prevents them from getting tangled up? The concepts of genes is one of the most irrational concept that ever existed...."http://time-blog.com/eye_on_science/2007/02/the_evolution_wars_visit_eye_o.html. How should we interpret the yet to be defined concept of an allele in the light of what he wrote.?TongueSpeaker (talk) 12:47, 4 November 2008 (UTC)

Two different meanings of allele

What I am missing from the page is that the fact that allele has actually two related meanings, and both are used in different communities. The first meaning is the one that is described here in detail, and is most commonly used, namely: the gene variant found or inferred at a particular locus. In this meaning, there can be hundreds of different alleles, as e.g in the case of the HLA locus. In this case it makes sense to talk about 'different alleles', and 'allele' uniquely identifies a particular variant (in fact, DNA sequence), in of course the context of a locus in a diploid organism. The article, incidentally, can be 'an' and 'the'.

The second meaning is becoming more prominent in our era of next generation sequencing and single-cell sequencing. Here, allele identifies which of the two homologous chromosomes is being talked about (again in the context of a particular locus in a diploid organism). In this usage, it does not make sense to talk about 'different alleles', since there always only two alleles: the maternal and paternal (even though often it is not known which is which). In this usage, 'allele' often occurs with 'other' or 'other allele' and always with 'the' as the article, never 'a'. E.g. https://en.wikipedia.org/wiki/Dominance_%28genetics%29 has: "The allele that masks the other is said to be dominant to the latter, and the allele that is masked is said to be recessive to the former." Here, we are not talking about the fact that there many different variants of a particular gene, but about the fact that the version in one chromosome dominates the version of the other.

Why the distinction is important is that people get confused by terms such as monoallelic mutation or biallelic expression. These terms are perfectly normal and perfectly understable with the second meaning, but make no sense when only knowing the first meaning (monoallelic mutation is a mutation observed in one of the two homologous chromosomes in a particular locus, rendering the locus heterozygous; biallelic expression is when transcription takes place at both copies of a locus).

Personally I think in many cases when people use the word 'allele', they had better use the term 'gene variant', which is even understandable to the uninitiated. I vaguely recall that in Matt Ridley's book 'Genome', there is a line that says roughly: "genes do not cause disease, alleles do!", reflecting the first meaning. I think this sentence becomes both much clearer and much more precise if it read "genes do not cause disease, (broken) gene variants do!" :-)

What do people think? Plijnzaad (talk) 08:00, 13 May 2016 (UTC)

PS: citation needed? "humans are diploid organisms and have two alleles at each genetic locus, with one allele inherited from each parent", see Note in http://varnomen.hgvs.org/recommendations/DNA/variant/alleles/ — Preceding unsigned comment added by Plijnzaad (talk • contribs) 08:17, 13 May 2016 (UTC)

An allele does not necessarily function as a gene, but is simply a variation at a locus.

Non-gene DNA loci are important to the phenotype,

Agreed, and that is important (we could/should include examples on promoters and enhancers), but that is a different matter, in the sense that here you are equating 'allele' with 'gene variant', which I agree should be broadened to 'sequence variant' (both terms occur frequently in current scientific literature). And I am arguing that main page should point out the difference in meaning/usage of the term 'allele' (and personally I think that the first meaning has become outdated). Plijnzaad (talk) 23:31, 19 May 2016 (UTC)

so talking about those alleles is important, and DNA fingerprinting relies on hypervariable DNA in non-coding regions, and those variations are referred to as alleles. Also, a locus may be large or small, from single-nucleotide polymorphism alleles (possibly several within one gene), to larger loci that have some particular function that turn out to contain a group of tightly linked genes. An allele difference may be an inversion or a deletion. I therefore disagree that "gene variant" is a better phrase.

Copy-number variation is becoming an extremely important topic in human disease research, such as for developmental control (e.g., schizophrenia) and for cancer-suppression mechanisms, so I think it is important to try to keep that in mind and to avoid making blanket statements about a single gene with two alleles at each locus.

I am not, but in the hugely important case of diploid organisms it's certainly something to explain in a bit more detail. Surely you aren't implying that the (diploid) case where in one locus you have sequence variant 'V' on the paternal chromosome and a duplicated sequence variant 'v v' on the maternal, should be called triallelic? (I have never seen it used that way). These cases are too complex to be described as 'alleles', and here things are much clearer by using the term 'variant', and this is exactly what's happening in literature: sequence variants are defined and used separately from the chromosome they 'live on', and 'allele' is more and more only used when having to distinguish between which of the paternal/maternal chromosome (or both, or neither, or 'the other') is being talked about, not which variant. Plijnzaad (talk) 23:31, 19 May 2016 (UTC)

For that reason, I'd say that the Dominance (genetics) page has a hole in it, because a recessive allele can be masked by an allele at another locus.

Another problem is that although humans are diploid, many organisms are not, so to make this page only about diploids would be a great disservice to wikipedia's treatment of biology.

I am not suggesting that of course.Plijnzaad (talk) 23:33, 19 May 2016 (UTC)

So for your other meaning of allele, I think people are abbreviating "the other allele of the pair" by saying "the other allele". I think they are saying "biallelic expression" because the term "biparental" has other meanings (though it is used in this way in discussing imprinting), but I don't think there is really a fundamental problem with the meaning of allele. Sminthopsis84 (talk) 13:31, 13 May 2016 (UTC)

Test

"... if the "red" allele is dominant to the "white" allele, in a heterozygous flower (with one red and one white allele), the petals will be white."

My genetics is very rusty, but surely the petals in this case will be red?

I think you're right. Fixed. Evercat 22:25 30 Jun 2003 (UTC)

uhmm... isn't the flower supposed to be pink? Because I tought that the flower Mendel is talking about has two dominant alleles. like this

  P   GG + gg
  F1  Gg

• Read the text: "if the red allele is dominant..." If it is dominant, that means the heterozygote is red. In the absence of dominance, the flower would indeed be pink. If both the red and white alleles would be dominant (i.e., co-dominant), you would be able to see the phenotypes associated with both alleles simultaneously: a flower with red and whit patches or stripes or something like that. --Crusio (talk) 15:51, 29 March 2010 (UTC)

'The petals will definitely be red '

Pronunciation

As a newcomer to Wikipedia I wonder if it would be appropriate to note that the word rhymes with 'heel' and not 'ukelele'.

IPA is typically used to this end. —Casey J. Morris 21:12, July 21, 2005 (UTC)

mechanism for dominance?

How does the ribosomes, etc. recognise which is a dominant gene, which is a recessive one, or which sequences trigger it to be recessive or dominant in the first place? Do we know? -- Natalinasmpf 08:31, 28 Mar 2005 (UTC)

It doesn't. If both dominant and recessive alleles are present, both are transcribed and translated by the ribosome. "Dominant" and "recessive" are a result of the different properties of the fully-formed proteins themselves. There's various mechanisms whereby this can happen, depending on what the gene is. Graft 03:43, 29 Mar 2005 (UTC)

If one allele has no start codon it will not even be transcribed into RNA. The resulting "no protein allele" will be the same phenotype as "malformed protein allele" to the casual observer.--35.11.210.84 21:28, 2 August 2005 (UTC)

This is wrong - if it has no start codon, it will make it to RNA, but the RNA will not be translated into protein. If the promoter or some enhancer element, etc., is damaged, THEN the RNA will not be transcribed. You are correct that this will result in a "null" phenotype (assuming no other intact copy of the gene is present on the other chromosome). However, a "malformed" (truncated) protein may end up having a phenotype after all, depending on where it truncates. Graft 13:04, 11 August 2005 (UTC)

"As a newcomer to Wikipedia I wonder if it would be appropriate to note that the word rhymes with 'heel' and not 'ukelele'" YES! this is my Daughters name and everery one alway pronounces it "Ah-Lay-Lee" When its pronounced "Ah-Lee-uhl". Thanks for pointing this out...

It is incorrect to say that one allele is dominant over another. It is the phenotype that is dominant. In the flower example, it is the character red that is dominant over white. In humans, for instance, being pigmented is dominant over being albino, meaning that heterozygotes are pigmented and are not intermediate in phenotype between the two homozygotes. However, if one goes to the molecular level, the underlying enzyme defect concerns tyrosinase. When one looks at the inheritance of the character "tyrosinase activity", there is no dominance, the heterozygote being completely intermediate between the two homozygotes. This is an improper use of nomenclature that unfortunately even can be found in many genetics texts. --Crusio 20:09, 11 October 2007 (UTC)

Some Examples

An Allel would be the like the controller of game systems the comand the genes where to go.I don't have an example off the top of my head, but the defintion in the first sentence of the article points out that some definitions of Allele include variation at non-gene sequences. I double checked the fact with the NHGRI (http://www.genome.gov/glossary.cfm?key=allele see the real player voice over). I would suggest perhaps something about variation in promotor regions as was described so ably by Graft above. My defintion of an Allele is the captian of the genes telling them where to go.

What is the reasoning behind using capital I and i to stand for the different blood types and what is the reasoning for i to always match up with blood type O? —Preceding unsigned comment added by 206.176.81.1 (talk) 16:10, 20 February 2009 (UTC)

The capital I is used for the dominant genes, while the lower case i is used for recessive. That's why blood type O is so rare. 18:49, 28 September 2009

• Actualy, O is the most frequent blood type, despite being recessive to A and B. --Crusio (talk) 00:01, 29 September 2009 (UTC)

Unidentical copies?

I would like to ask about the following sentence:

"An organism in which the two copies of the gene are identical"

Can COPIES be unidentical? Is the term appropriate and correct?

This is appropriate and correct: COPY here is used in the sense of 'instance' (as in 'a copy of a magazine', although unlike in this example, there are always only exactly two instances in diploid organisms: one that was maternally inherited, the other paternally). Plijnzaad (talk) 07:03, 13 May 2016 (UTC)

Introduction - Parenthetic sentence

Should one start a paragraph with a sentence enclosed in parentheses? I have never seen this before. 06:58, 11 September 2007 (UTC)

2 Equations ?

There are two equations for the frequency of two alleles of a given gene (see Hardy-Weinberg principle).

Equation 1: $p+q=1$,

Equation 2: $p^{2}+2pq+q^{2}=1$

This sounds very silly since Equation 1 clearly implies that equation 2 is also true. Does it make sense to say that the frequency of 2 alleles is predicted by 2 equations? Why not 3 with the third being $p^{3}+3p^{2}q+3pq^{2}+q^{3}=1$?

This is indeed a very muddled section. It mixes the frequency of certain alleles ($p$ and $q$) with the alleles themselves. The main article on the Hardy-weinberg equilibrium is clearer and perhaps this whole paragraph should be deleted and redirect to that article. --Crusio 20:11, 11 October 2007 (UTC)

I don't see how this can be true:

$p^{2}+2pq+2pr+q^{2}+2qr+r^{2}=1-(p^{2}+q^{2}+r^{2})=1$

Because

If $1-(p^{2}+q^{2}+r^{2})=1$ then $(p^{2}+q^{2}+r^{2})=0$

If $(p^{2}+q^{2}+r^{2})=0$ then $p=0,q=0,r=0$

If $p=0,q=0,r=0$ then $(p^{2}+2pq+2pr+q^{2}+2qr+r^{2})=0$

Am I missing something? 76.121.251.78 (talk) 01:54, 11 August 2009 (UTC)

Types

This section is still rather muddled after I did some cleanup. I propose to delete it, thre is already a link to dominance and recessive in the opening paragraph. --Crusio (talk) 10:26, 9 March 2008 (UTC)

I'm not sure about complete deletion but at the very least I think everything after the first paragraph in that section should be removed.--Woland (talk) 12:29, 10 March 2008 (UTC)

Disputed tag

• I have placed a "disputed" tag on the article because, although many scientists speak about "dominant" or "recessive alleles", technically speaking, only traits are dominant/recessive. On the DNA level, all alleles of all genes act in an additive way without any dominance being present. An allele may be dominant/recessive for one trait, but not for another. An example is the albino allele, c. The albino trait is recessive as Cc individuals are pigmented. However, if you look at the underlying enzyme defect, Cc individuals are intermediate between CC and cc ones for tyrosinase activity. So for the character "tyrosinase activity" dominance is absent, but for the character "pigmentation" albino is recessive to pigmented. --Crusio (talk) 12:41, 27 August 2009 (UTC)

--I don't think this warrents the tag as this appears to be pretty minor and almost seems to be about semantics, so have now removed the tag. When I saw the tag I assumed there was a major error. It would probably be better to add this to the article. Any other comments? 194.83.139.177 (talk) 11:38, 23 September 2009 (UTC)

• The above means that the definitions currently given in the article are wrong. What else justifies a "disputed" tag? I am reverting this. --Crusio (talk) 11:42, 23 September 2009 (UTC)

• You are mistaken on two levels; one, the tag is not for such a small dispute, and two, you are wrong about your claim that the phenotype is what is recessive. An organism has only one phenotype. Provide a source that makes this distinction. Abductive (reasoning) 10:45, 5 October 2009 (UTC)
• Here in a book with Lewontin as a coauthor, they use the terms in the usual manner [1]. Abductive (reasoning) 10:54, 5 October 2009 (UTC)
• Here is Hartl's take on it [2]. Abductive (reasoning) 11:02, 5 October 2009 (UTC)

• Unfortunately, this incorrect usage has become a shorthand, like people studying KO mice, who find no difference with controls saying "my mouse has no phenotype". Google it, you'll find plenty of reputable geneticists who have said this. That doesn't make it correct, though (see DOI 10.1034/j.1601-183X.2002.10201.x). I have currently no time to continue this discussion. Just one citation: Gregor Mendal stated (as cited by Reeve, Encyclopedia of Genetics, p. 63): "The dominant character can have ..." No need to continue. Mendel defined dominance, without knowing anything about genes of alleles. He talked about characters (what we now call phenotypes). And look at my albino example above. Whether C or c is dominant or not, depends on what character you investigate. --Crusio (talk) 12:00, 5 October 2009 (UTC)

• I suggest this be explained in a footnote to avoid breaking up the flow. The article is rather wanting in many respects. Abductive (reasoning) 12:49, 5 October 2009 (UTC)

• Absolutely! :-) --Crusio (talk) 13:22, 5 October 2009 (UTC)

Good call Abductive, sometimes it is best not to interrupt the flow, however right you may be, as genetics is a very complicated field wherein the data collected from experiments is not exactly as precise as measuring temperature, it is much closer to recording peoples description of the weather often including emotional interpretation. Mendel himself was only doing pre-cursor work to science on genetics. Now days scientists can order restriction enzymes to cut strands after a specific sequence of a single strand, they can custom order any sequence they want. Genetics and gene expression is a science that may never be fully understood, but we are rapidly approaching our limit. Scientists like Mendel and Darwin were instrumental in the progress, but even they were only correct as to the jist of the events. Citing Gregor Mendel doesn't give proof to scientific correctness, it gives a historical account, but it just happens to be one of the "close" shot arrows that caused the tree of knowledge to bleed a littleDirtclustit (talk) 05:06, 20 September 2013 (UTC)

Most organisms probably not diploid

I think the article should read most animals, or perhaps most multicellular organisms, but not most organisms, as most archaea and bacteria are not diploid, and they are arguably the most well represented (depending of course on your definition of species). 71.209.2.169 (talk) 19:26, 31 December 2010 (UTC)

The mess I created.

I'm sorry for all the unnecessary edits. I don't usually need so many edits just to revert to a previous version... But during the editing my internet connection was unstable, and I clicked on save page and nothing happened, I did something else, and suddenly the edit was saved even though I was not finished with it, and furthermore I suspect I sometimes got a "cache-version" of the page, which is why I thought things needed to be fixed that didn't need to be fixed. However, 60.240.109.108's edit was clearly improductive (removing text and instead writing that something was wrong), but also EagerToddler39's edit was incorrect, because the footnote was not unused. However, I did not realize did until I copied EagerToddler39's edit and discovered that there was a problem in the ref-section.
Anyway, the article is back to a previous version now. Lova Falk talk 10:02, 9 September 2012 (UTC)

That sort of thing happens to all of us. The important thing is that you fixed it! Sminthopsis84 (talk) 12:40, 9 September 2012 (UTC)

Thank you! :) Lova Falk talk 13:45, 9 September 2012 (UTC)

Tell me about it! I sooo know what you mean, I get cached versions of many sites on my home computers and if I log in anywhere it's guaranteed to be cached. The internet ain't a friendly place when you seriously upset both sides of any bitter division. I don't recommend doing so when the fence separates those who would knowingly lie to get folks to believe that God exists and the those who knowingly lie to get folks to believe that God doesn't exist. The hard cores of the religious right and the angry Atheists/IT people can be vicious. Luckily though that is exactly what makes the normally difficult tight rope walk across the top of the fence so darn easyDirtclustit (talk) 05:17, 20 September 2013 (UTC)

Latin Greek and "Genetics"

The term used by Greeks, way back when, was in regards to generation (like the generations distinguished by terms like ""grandparent", "parent" and "child" . It is related to the term "genetics" but I think a distinction should be made between "generations" and "genetics" as noting phenotypic inheritance from parents is not to have knowledge of genetics. The difference between having actual knowledge of the two subjects "generation" and "genetics" can be night and day, as in knowledge of generations but not genetics by today's understanding of the life and the world it inhabits is akin to knowing a story but not being able to tell what IS real and what is not. There is a difference between the actual occurrence in the present and the story of it retold as history. Their is a difference between being affected by the occurrence happening to You, and the effect of listening to a person's story that you yourself did not experience and not being able to tell the difference is to not be able to distinguish what Is real from what is not. The etymology of a word is NOT synonymous with intimate knowledge of the topic. There was no ancient Greek word or even root for "genetics" even though the words relation is obvious.

Not being conscious of your thoughts and word choice in encyclopedic writing is detrimental mistake to make, and will lead to unfathomable levels of confusion and misery, EVEN IS EVERY SINGLE WORD WRITTEN IS TRUE. Similar topics or words that describe a topic, when the words come from languages which serve different purposes cannot be used interchangeably.

As for as Understanding Everything, using words like "genetics" in terms of Ancient Greek knowledge of "generations" brings about complete misunderstanding of fundamental core knowledge, it fosters confusion. It's the difference between between two understanding the books like the Bible wherein the first book is titled Genesis and the understanding of it with the first book titled Genus

This is not knocking Greeks, to be fair Latin terms from the etymology of "genetics" are just as unrelated as the night and day difference between "generations" and "genetics"

Both languages have terms to describe the topic "genetics" and they could tell stories about genetics, but they did not have the vocabulary because they did not understand genetics. It could be said that neither had knowledge of it's existence. So to employ sentences like...oh I stand corrected, as the article now has that wording omitted without admitting to it under the historical records. Yeah wikipedia Gods.Dirtclustit (talk) 01:47, 20 September 2013 (UTC)

Relationships?

I remember from all those CSI: Crime Scene Investigation episodes I watched, that the number of matching alleles determine the biological relationship between two persons. Call me a dumb-bunny (I don't mind), but I don't understand how that relationship thing works and the articles seem not to mention that aspect of allele-ism. Thank you for your time, Wordreader (talk) 00:08, 29 March 2014 (UTC)

My main memory of those programs is that they'd get things wrong sometimes, such as saying that siblings must have 50% alleles in common, when full-sibs would actually share anywhere between 0 and 100%, though 50% on average. Genealogical DNA test, which is listed under "See also" should have the material you need. Sminthopsis84 (talk) 01:04, 29 March 2014 (UTC)

Proposed merge with Allele frequency - no consensus

Substantial conceptual overlap, but Allele frequency strays into textbook, demonstrative territory. Having one centralized article is better than having multiple parallel strands of a topic, in my opinion, and neither articles are long enough to warrant a size-related split. --Animalparty-- (talk) 19:08, 27 June 2014 (UTC)

• I object because allele frequency is an explicitly searched basic biostatistical concept. --M2k1 (talk) 11:44, 10 March 2015 (UTC)

• Both should remain distinct for clarity and ease of access. --Lukedehart

Okay, I can go with this, oppose based on above arguments, I'll remove the tags, ♫ SqueakBox talk contribs 21:14, 20 July 2015 (UTC)

Relationship to SNPs

Should we explicitly say one allele can include many SNPs - eg as used in CYP3A7*1C Allele Associated With Poor Outcomes in CLL, Breast, and Lung Cancer ? - Rod57 (talk) 16:08, 27 March 2016 (UTC)

Assessment comment

The comment(s) below were originally left at Talk:Allele/Comments, and are posted here for posterity. Following several discussions in past years, these subpages are now deprecated. The comments may be irrelevant or outdated; if so, please feel free to remove this section.

Rated "high" as high school/SAT biology content. This article needs an explanation what an allele is from a molecular biology perspective. The current explanation is extremely insufficient. - tameeria 23:14, 18 February 2007 (UTC) grammar: "classical genetics recognizes three alleles... that determines compatibility" -- should be "determine" not "determines" (noun-verb agreement)

Last edited at 15:03, 25 October 2011 (UTC). Substituted at 07:23, 29 April 2016 (UTC)