Talk:Intron

Evolutionary

"Evolutionary kibble"? I think you mean evolutionary "kipple", as per Philip K. Dick.204.209.121.10 18:55, 5 March 2007 (UTC)

This is cited as a piece of evidence in support of evolution. By whom?

By just about every book ever written on the subject, which you'd

know if you ever care to read one. --LDC

LDC, no need to be rude to him. We clearly do not have a strong understanding on the significance of introns. It was just recently (relatively) that they were discovered. Prior to their discovery it was claimed that the human genome contained over 150,000 active genes. Just in 2004 the NHGRI stated that there was only 20,000 some active genes. Down from the 35,000 that was believed after the Human Genome Project and that figure was down from the 150,000 that was believed prior to the Human Genome Project. This all happening very recently. I accept evolution and common descent, primarily as a philosophical view on reality.... but you are being disingenuous to claim that our understanding of introns can be used as positive evidence for evolution. It's brash claims like the one you have just made that makes the rest of us in this field look inept. Again, the role of introns is not close to being even partially understood. --RobertShapiro(fan)

So, Great Master of intron science, please cite at least one if you know every book written on the subject...

come one – am I right that you just copied this from a secondary source...

Cf. dead code in most larger software systems...

Where he copied it from is of no improtance. This is established truth. The textbook Biology by Neil A. Campbell and Jane B. Reece states that introns may be spliced out in differnent ways to combine different exons from one gene. This mRNA will code for different proteins with new and possibly novel functions. These new proteins may allow one organism to survive better than another organism of the same species. It will live on to pass on its genetic information while others will not. If that is not evolution than I don't know what is.--Swimmer678 04:11, 15 November 2006 (UTC)

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"Junk DNA" is not a well-defined term, of course, but I would hesitate to say that it is synonymous with intron DNA. A lot of noncoding DNA that is never transcribed into RNA in the first place exists, and I believe that it is usually also considered to be "junk" DNA when factoids about how 90% or whatever of human DNA is junk are bandied about. Bryan Derksen

Good point. That should be stated within the article. There are in fact many types of non-junk DNA that are in fact vital to gene regulation and expression. So the statement you mention should read that "90% of all DNA does not code for any proteins". We might even want to have a separate article on this.

I wasn't trying to imply that the two terms were directly synonymous through the merge -- its just that the article at Junk DNA was mostly about Intron DNA. There is no reason not to have a separate article about the use of the term "junk DNA" while having intron keep to the technical facts. --maveric149

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The diagram a the top is neither informative nor accurate – wouldn't the one beneath it be just as good?

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Group I and group II introns are mentioned. What about pre-mRNA introns? They are the ones that your figure shows. What about mentioning how introns are spliced out?

Also, there are plenty of references showing that introns are not "junk DNA", on the contrary some contain regulatory elements necessary for expression. I think this should be made clear.

I think that is made very clear in the third paragraph of the article. --Mike Lin 17:49, 18 February 2006 (UTC)

"Introns are sections of DNA that will be spliced out after transcription" – sounds ambiguous, as if the pieces of DNA will be spliced out. RNA is mentioned later but in my opinion somebody not familiar with terminology might be confusedVicki Doronina 18:01, 13 January 2007 (UTC)

Just curious, but could we change the first sentence to something like "introns are transcribed but non translated regions of dna" and contrast them to exons? Seems like it would be less ambiguous than the current wording.

Group II introns in prokaryotic mRNA

The Intron article says that in prokaryotes, introns only occur in tRNA and rRNA. The group II intron article, however, says they occur in mRNA. I realize that this is not necessarily a contradiction, but could someone please clarify it? --aciel (talk) 18:40, 27 November 2007 (UTC)

more introns in "higher" organisms?

The article has a paragraph about how "higher" organisms (whatever that means) have many introns, while some "less advanced" (?) organisms have few introns. Does anyone have any data to suggest that mammals have more introns than other ophistokonts, and that the average land plant has more introns than protists like algae or dinoflagellates? Of course there is a vague connection between organism size and total genome size, but I don't think there is a connection for intron number or density. Ostreoccoccus for example, despite being perhaps the smallest eukaryote, with a relatively compact genome, has a very high intron density. The smallest known eukaryotic genome (nucleomorph) of chloroachnion has an average intron density despite its tininess. Whether or not one subscribes to an introns early or late hypothesis, it is clear that there is an extremely diverse pattern of intron distribution and density that defies a simple explanation of higher organsisms = many introns, lower organisms = few introns Spamburgler (talk) 10:23, 7 August 2008 (UTC)

I don't really know what "higher organism" mean (though it tends to include fungi...) and I doubt the typical reader does, so that word should hopefully be gone from the article. Perhaps it should say that bacteria and some excavates have fewer introns than other organisms? Narayanese (talk) 14:57, 7 August 2008 (UTC)

Btw, your removal of mentions of lower and higher organisms in another article was rather messy, with skewed content as a result. Better to read the ref where such exist so that the new version still follows it, or delete whole sentences. Narayanese (talk) 15:03, 7 August 2008 (UTC)

Sure, I am happy to change it to read better if I have left it reading poorly – which one(s) are you referring to specifically?Spamburgler (talk) 01:28, 8 August 2008 (UTC)

Heh, I'm a little fond of complaining sometimes... was referring to RNA splicing, but I fixed it (I didn't do too well prose-wise though).Narayanese (talk) 04:58, 8 August 2008 (UTC)

"Genes of higher organisms, such as mammals and flowering plants, have numerous introns, which can be much longer than the nearby exons. Some less advanced organisms, such as fungus Saccharomyces cerevisiae, and protists, have very few introns." This is wrong on many levels.

• "which can be much longer than the nearby exons" You're trying to imply exons use to be as long as introns, or even longer?
• "higher organisms ... Some less advanced organisms, such as fungus Saccharomyces cerevisiae" And since when weren't fungi higher organisms?
• "protists, have very few introns" No, they don't.
• " less advanced organisms ... protists" POV-pushing.
• Oh, and didn't you read the bit about controversial statements needing a reference for inclusion? And apologies if I get a little uncivil, but those 2 sentences should be gone from the article.

Narayanese (talk) 05:22, 11 August 2008 (UTC)

I see that English is not your native language. That probably explains the confusion.

• The phrase "which can be much longer" means that in some instances the introns are longer than the exons. It has no time value: it implies nothing about what existed previously.
• Loose categorizations of organisms as being "higher" and "lower" in their evolutionary complexity is an English idiom that will have meaning to any biology student above the age of fifteen. It may sound silly to you, but it is not mere speciesism. (The fungus in question is a single-celled yeast, not a mushroom or other more complex fungus.)
• Some protists have very few introns. This sentence does not make a sweeping claim that all protists have very few introns. It is correct as written.

I hope that this helps clear up the confusion for you. WhatamIdoing (talk) 07:24, 11 August 2008 (UTC)

No, didn't really help, I had no problem reading. Now go find a source that says more "advanced" organsims have more introns. Narayanese (talk) 17:10, 11 August 2008 (UTC)

PMID 10563578, which says that yeasts -- a classic example of a "lower" eukaryote (their words) -- usually have no more than one intron per gene, whereas "higher" (again, their word) are multi-exonic. Happy now? WhatamIdoing (talk) 18:39, 11 August 2008 (UTC)

That makes them no different from other fungi: fungi have few introns (PMID: 17949488). And why would flowering plants have more introns than other plants? Green algae certainly have no lack of introns (PMID: 18495022) While excavates have rather few introns (PMID: 16638131), the same is not true for rhizaria (PMID: 17618828) or chromalveolates (PMID: 18296415). Narayanese (talk) 22:38, 11 August 2008 (UTC)

Flowering plants are listed as examples of a "higher" plant. Fungi are listed as an examples of "lower" organisms. You have just conceded that the statement is factually correct: most flowering plants typically have more introns than fungi.

Why flowering plants have more introns than some other organisms is something you will have to ask the deity of your choice. Why is not a question that can be answered by the natural sciences, which concerns itself with the less cosmologically fraught questions of whether and how. WhatamIdoing (talk) 23:04, 11 August 2008 (UTC)

I guess part of the problem here is the use of the non-scientific concept of "higher" and "lower". These are old fashioned terms that may indeed be familiar to 15 year olds, but in fact do not impart meaningful scientific information, other than an erroneous impression of directed evolution, or a religous based view of biology with humans "higher" on the scale. "Higher" is sometimes used to convey multicellularity, or even in some cases size of organism, or in others size of genome. The terms might also imply number of genes – although presumably not in the last 10 years. Alternatively, the term could be used to mean organisms belonging to phyla with slowly evolving gene sequences. In a scientific context the term was sometimes applied to "crown eukaroytes" a grouping that is now generally recognised as not reflecting any genuine phyletic relationship. Clearly, many of these meanings are mutually inconsistent, and we cannot apply the terms here without unecessary ambiguity. The references to yeast/funghi /land plants/green algae/animals highlight the danger of using such ambiguous language. Clearly yeast is closely related to multicellular funghi and animals, and more distantly related to angiosperms, gymnosperms, green algae and other Plantae. The observation (not sure if it is true) that multicellular funghi generally have more introns than S. cerevisiae, and that angiosperms have more than most funghi demonstrates, while some other plantae have much few introns, demonstrates that intron density can be greatly variable within phylogenetic groups. It may follow some interesting trends, but the reduction of this trend to a nonsensical "higher and lower" does it no justice.

Several points of interest are worthy of discussion, and which are unclear in my mind;

1. That some deep branching phyla (eg excavata?) have few introns (may be true, but certainly lots of exceptions, and lots of reversions within recent branching groups)

2. That multicellular organisms have more introns per gene than unicellular organisms (may be true – though probably not enough sampling to know yet).

Does anyone have any knowledge of these specific questions? Spamburgler (talk) 07:09, 13 August 2008 (UTC)

"Higher" and "lower" are certainly references to an old-fashioned conception of the Tree of life: more complex organism are "higher" than simpler organisms. Furthermore, replacing those words with "more complex" and "less complex" doesn't actually improve things. It's like replacing Mental retardation with Congenital cognitive disability -- it sounds nicer to the modern ear, but the words have the same meaning. Given that we're making sweeping generalizations, though, the vagueness is not inappropriate.

I don't know whether your first statement is true. The second statement is generally true, although there are some notable exceptions. It's probably also worth mentioning that introns are related to exon size. WhatamIdoing (talk) 21:10, 13 August 2008 (UTC)

The terms more complex/less complex will lead to an as misleading generalisation as higher organism/lesser organism, even though it's not as ambiguous. As for Spamburgler's questions: With so few sequenced organisms it's hard to tell, although I guess the answer is yes to both, though the big variation (eg 18x more introns per gene in fission yeast than budding yeast) means you couln't really use the info about a group's intron density. Narayanese (talk) 21:40, 14 August 2008 (UTC)

But I could add something about how larger eukaryotes (body size, generation time) tend to have more introns than small ones, though it will have to be weakly worded. Narayanese (talk) 15:46, 15 August 2008 (UTC)

Wow guys, this is really quite sad. Not only are you in an arguement over semantics, but you're dragging it out to the point where this one segment is taking up about a fourth of the talk page. While it's true that a lot of these are generalizations with exceptions that seem to make them irrefutably untrue, every rule has it's exceptions. One or two examples that go against a generalized trend are not enough to break the trend down. That being said, you guys need to get over yourselves here. if you want to talk genetics, how about this: 75% of our genes are shared with worms, 98% with chimps, and about half with bananas. Why don't you contemplate why, with all those similarities, humans are the only species as of yet capable of fighting over wether someone is right, or right in a slightly different way. have fun with that, my argue-mental friends. —Preceding unsigned comment added by 71.227.217.60 (talk) 22:05, 8 December 2009 (UTC)

Intron vs Noncoding DNA

Hi wikipedians, what is the key difference between introns and noncoding DNA... merge? --Vojtech.dostal (talk) 07:32, 25 August 2008 (UTC)

Certainly not! Non-coding DNA includes intergenic regions and untranslated regions of mRNA. Narayanese (talk) 17:34, 25 August 2008 (UTC)

Also, introns are not always non-coding... WKoets (talk) 16:02, 21 September 2009 (UTC)

Definition of Introns

I don't think this is elsewhere discussed on this page, but there's a small but imprtant inaccuracy in the definition of an intron, where it states: "(Introns are) DNA regions in a gene that are not translated into proteins." While this is true, I'm not sure it's very accurate, and I suggest that it be modified to something like "(introns are) DNA regions which are removed by the joining of the two flanking exonic sequences, and thus are not represented in the mature RNA product" A bit clumsy i know, but I've got to have dinner... Thoughts? if there are no objections, I'll re-write the above and put it in... Geno-Supremo (talk) 20:11, 11 November 2008 (UTC)

The existing statement is accurate as it stands; your complaint seems to be primarily about its precision. The relevant guideline here is WP:MTAA, specifically "Put the most accessible parts of the article up front." So in technical articles like this one, the leads (should) contain general statements that can be grasped by non-technical people. Then we can follow up with the precise details. WhatamIdoing (talk) 17:45, 12 November 2008 (UTC)

What about this wording:

An intron is a section of a gene that is not found in the mature RNA formed by the gene. The intron is found in the precursor RNA, but is removed (spliced out of the RNA) during the formation of the mature RNA. The sequences at each side of the intron (the exons) are joined together during the splicing of the intron. Introns are found as non-coding sections of precursor messenger RNAs (pre-mRNA), but also in other RNAs such as long noncoding RNAs. Once the introns have been spliced out of a pre-mRNA, typically by the spliceosome in the cell nucleus, the resulting mRNA sequence is ready to be translated into a protein. The word intron derives from "intragenic regions", and an alternative term is intervening sequence (IVS),

The current lead is indeed not accurate, introns are also found in UTRs are noncoding RNAs (are all introns non-coding btw?). Narayanese (talk) 21:49, 12 November 2008 (UTC)

Introns are defined as non-coding. When you're dealing with a piece of RNA that has several alternative splicing arrangements, then which bits are considered the introns depends on how it gets spliced.

I don't think that, say, a poly-A tail, although a UTR, is normally considered an intron. Even if it is, then it's still a part that is not translated into a protein, which means that the first sentence is actually accurate. WhatamIdoing (talk) 03:13, 13 November 2008 (UTC)

Introns are not noncoding by definition, they are what is removed by splicing – if any part of the RNA is translated is not relavant. But yes, poly(A) tails have nothing to do with introns. Narayanese (talk) 17:36, 13 November 2008 (UTC)

Here are a few actual definitions from actual (medical) dictionaries:

• "is not expressed (as protein) in protein synthesis" [1]
• "does not code information for protein synthesis" [2]
• "noncoding sequence of DNA within a gene" [3]

I think I can fairly say that introns are defined (in part) as being non-coding.

The first sentence of this article says that introns are "DNA regions in a gene that are not translated into proteins". Do you think this is wrong (e.g., that introns are not in a gene, or that they are actually translated into proteins), or merely incomplete? WhatamIdoing (talk) 01:54, 14 November 2008 (UTC)

Your sources are not up to date. Read the sources in our Wikipedia article, or this nice review, and you'll see that many noncoding RNAs do have introns. Narayanese (talk) 18:04, 14 November 2008 (UTC)

Here is a free one if it helps, although it only mentions the splicing of noncoding RNAs in passing. Narayanese (talk) 18:32, 14 November 2008 (UTC)

Did you read the first one? The bit about "By customary usage, the term is extended to the corresponding regions in the primary transcript of mRNA prior to maturation..." -- which I interpret as meaning that the "RNA introns" aren't really truly introns, but that we apply the name to them for convenience. WhatamIdoing (talk) 18:38, 14 November 2008 (UTC)

Hello fellow Wikipedians,

Getting back at the above discussion: I really do think the first bit of the article should be changed. An intron doesn't code for the protein that the surrounding exons code for BUT it might code for a maturase (a protein needed for splicing). I can add citation but it is also mentioned in the article under 'Classification'. I will think about a decent sentencence (I am not a native English speaker) and post it here for you to comment on. WKoets (talk) 16:00, 21 September 2009 (UTC)

Something like... 'Most genes in eukaryotes, as well as some prokaryote genes, are interrupted by sequences that are not translated into the protein the gene codes for. These intervening sequences are called introns.' or 'An intron is a DNA region within a gene that is not translated into that gene's protein.' Well, something like this but then in decent English. WKoets (talk) 16:15, 21 September 2009 (UTC)

Genes don't code for proteins (well a few do, but it's not the norm) Narayanese (talk) 20:01, 21 September 2009 (UTC)

(edit: I shouldn't have repeated myself)

I must be missing something here. Genes don't code for proteins? Just what does, then? Some other protein? I thought that idea went out of fashion half a century ago. And what does the gene code for? A bunch of carbohydrates? More genes, that also never get translated into proteins?

Did you mean that DNA doesn't usually get translated directly into proteins (e.g., without the intervening stages of translation into RNA)? I don't think that's what WKoets meant. WhatamIdoing (talk) 00:59, 22 September 2009 (UTC)

Genes that don't code for protein are called pseudogenes as far as I know. Again, what I mean is that an intron isn't necessarily non-coding nor functionless and I think it's time the rest of the world grasped that idea as well! WKoets (talk) 09:50, 22 September 2009 (UTC)

References

Out of Date

Introns may also contain "old code", or sections of a gene that were once translated into a protein, but have since become inactive. It was generally assumed that the sequence of any given intron is Junk DNA with no biological function. More recently, however, this is being disputed.

I don't think this is strong enough. That at least some introns are functional and adaptive as opposed to relics is now the mainstream view amongst geneticists.

For proof, a few recent journals:

• Nelson, G.; Freedman, B.; Bowden, D.; Langefeld, C.; An, P.; Hicks, P.; Bostrom, M.; Johnson, R.; Kopp, J.; Winkler, C. A. (2010). "Dense mapping of MYH9 localizes the strongest kidney disease associations to the region of introns 13 to 15". Human Molecular Genetics. 19 (9): 1805–1815. doi:10.1093/hmg/ddq039. PMC 2850614. PMID 20124285.
• Lin, C.; Mount, S.; Jarmołowski, A.; Makałowski, W. (2010). "Evolutionary dynamics of U12-type spliceosomal introns". BMC Evolutionary Biology. 10: 47. doi:10.1186/1471-2148-10-47. PMC 2831892. PMID 20163699.{{cite journal}}: CS1 maint: unflagged free DOI (link)

Besides, the journal cited for the more recently ... this is being disputed was published almost 15 years ago. Jebus989^★ 15:25, 25 April 2010 (UTC)

Simple illustration

About Intron#Simple_illustration_of_an_intron_and_RNA_splicing: This seems a little too "instructional textbook" rather than "encyclopedia article" to me. What do other people think? WhatamIdoing (talk) 19:55, 7 March 2011 (UTC)

I agree that this section has a weird style Richard☺Decal (talk) 09:24, 11 April 2011 (UTC)

I too find this rather... Childish. 81.164.243.42 (talk) 13:28, 26 June 2011 (UTC)

I completely disagree. This the first time all night that wikipedia has helped me understand something quickly and easily. Keep it. I don't care if it doesn't fit the style guide, it does its job well. 64.223.122.74 (talk) 03:53, 28 September 2011 (UTC)

I came here to say this. Keep this section and start making Wikipedia more like this. There's no point in making text physically accessible to people if the text still doesn't make the concepts "click" as this section did for me. 50.0.7.143 (talk) 03:03, 22 March 2012 (UTC)

The section needs to stay. If a little simple, it's an elegant way of conveying the point. I also think that all of Wikipedia should attempt to incorporate this type of teaching tool. Since nucleic acids cannot be seen, many users have difficulty conceptualizing their structure and function. It's similar to the plumbing analogy commonly used to teach people about voltage and current.Kmcgregor123456 (talk) 17:25, 3 December 2013 (UTC)

Shouldn't it be moved to RNA_splicing? Klortho (talk) 14:06, 24 February 2012 (UTC)

It's good to have an illustration here but this one is inaccurate. A UTR is part of an exon. Compare this illustration with the one in the Exon article (https://en.wikipedia.org/wiki/File:Gene_structure.svg) Mutundis (talk) 23:34, 1 September 2015 (UTC)

This is my attempt at a better illustration IMHO:

Pre-mRNA to mRNA MH

— Preceding unsigned comment added by Mutundis (talk • contribs) 01:19, 2 September 2015 (UTC)

Popular culture?

Is it worth mentioning that some authors (such as Greg Bear) have fictionally hypothesised that introns are used to store memories in cells? — Preceding unsigned comment added by 92.24.51.92 (talk) 12:13, 27 August 2013 (UTC)

Biological functions and evolution

What is the reasoning behind the following statement?: "Since eukaryotes arose from a common ancestor (Common descent), there must have been extensive gain or loss of introns during evolutionary time.[23][24] This process is thought to be subject to selection, with a tendency towards intron gain in larger species due to their smaller population sizes, and the converse in smaller (particularly unicellular) species.[25]" ZFT (talk) 19:29, 26 February 2015 (UTC)

Introns are well known in bacterial and archaeal genes, but occur more rarely than in most eukaryotic genomes.[citation needed] A particularly extreme case is the Drosophila dhc7 gene containing a ≥3.6 Mb intron, which takes roughly three days to transcribe.[9][10]

This is ambiguous. The reference to cases found "more rarely" is then followed by what appears to be an example of "a particularly extreme case", but this turns out to be an example, not of the rarely found cases, but of a genome with particularly abundant introns referred to earlier. Myles325a (talk) 05:27, 7 December 2015 (UTC)

an ambiguity

Introns are well known in bacterial and archaeal genes, but occur more rarely than in most eukaryotic genomes.[citation needed] A particularly extreme case is the Drosophila dhc7 gene containing a ≥3.6 Mb intron, which takes roughly three days to transcribe.[9][10]

This is ambiguous. The reference to cases found "more rarely" is then followed by what appears to be an example of "a particularly extreme case", but this turns out to be an example, not of the rarely found cases, but of a genome with particularly abundant introns referred to earlier. Myles325a (talk) 05:27, 7 December 2015 (UTC)

Assessment comment

The comment(s) below were originally left at Talk:Intron/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, part of gene structure. - tameeria 23:56, 18 February 2007 (UTC)

Last edited at 23:56, 18 February 2007 (UTC). Substituted at 19:02, 29 April 2016 (UTC)

Textbook references

The article contains references to 14 and 15 year old textbooks. Are references to textbooks really necessary? A good Wikipedia article should be at least as authoritative as a textbook. (I say this as a textbook author.) I suggest replacing textbook references with references to recent reviews in primary literature. Genome42 (talk) 15:00, 19 May 2022 (UTC)

Introduction

The introduction is confusing because the first part only refers to introns in protein-coding genes. It also contains references to 14 and 15 year old textbooks and other references that are inappropriate.

I propose editing the introduction to make it more accurate and more relevant.Genome42 (talk) 15:03, 19 May 2022 (UTC)

Junk DNA

A good case can be made that introns are mostly junk DNA but that case isn't made in the article. That needs to be fixed.

I have proposed creating a separate Wikipedia entry on Junk DNA and I am actively working on it. The proposal is being discussed in the Talk section on the Noncoding DNA page. Please add your views on this proposal, which I think is long overdue.Genome42 (talk) 15:35, 19 May 2022 (UTC)

On the accuracy of splicing

I'm working on a new section with the tentative title "On the accuracy of splicing." The goal is to present the evidence showing that splicing is quite error-prone and that cells are expected to contain large numbers of incorrectly spliced transcripts due to mistakes in splicing. This is important because these splicing artifacts are easily detected by modern techniques and their sequences are entered into the transcript databases. Most of them are recognized and ignored by genome annotators but a significant number have made it into the standard reference genome. This leads to considerable confusion about alternative splicing because it is often assumed, without evidence, that these transcripts are biologically relevant leading to rather extraordinary claims about the prevalence of alternative splicing. Those false (IMHO) claims are prominently mentioned in this article but the counter-arguments also have to be addressed in order to provide balance.

Here's a blog post that I published two years ago. It discusses the problem and the pervasive bias in the scientific literature.

https://sandwalk.blogspot.com/2020/04/alternative-splicing-function-vs-noise.html

Genome42 (talk) 14:09, 21 May 2022 (UTC)

I added a section on splicing accuracy. Now we need to work on showing that there is considerable controversy over the number of human genes that have produce multiple biologically functional products by alternative splicing. Genome42 (talk) 20:55, 27 May 2022 (UTC)