Talk:Alternative splicing

nice work, people

Wonderful article. Thanks to all who have contributed. JMBurke1791 (talk) 22:44, 14 December 2010 (UTC)

thyroid hormone calcitonin?

In the discovery section it is mentioned "thyroid hormone calcitonin" as one of the first examples of alternative splicing found. but calcitonin is not a thyroid hormone. it is a hormone secreted by the parathyroid gland, which is a different thing. —Preceding unsigned comment added by 121.2.225.207 (talk) 15:01, 10 October 2009 (UTC)

transcripts diversity

I would start by stating something like this:

Alternative splicing is one of the main mechanisms that eukaryotic cells have evolved to generate a great diversity of functional transcripts from a fixed number of genes.

Its role has been particuarly studied and understood after the publication of the human genome and the subsequent debates about the number of genes in the human specie. It has become clear that many of the most complex organisms tend to have a smaller number of genes than expected, and that mechanisms like alternative splicing help to generate diversity.

What do you think? Dalloliogm 14:23, 10 October 2007 (UTC)

For the first sentence, more like

Alternative splicing is a mechanism that eukaryotic cells have evolved to generate a great diversity of functional messenger RNAs, encoding multiple functional proteins, from a fixed number of genes.

I think it's especially important to say that it generates diverse mRNAs, rather than transcripts. The transcript is the immediate product of transcription, and that's the same all the time -- after splicing you have a messenger RNA, and those are what are diverse because of alternative splicing. Agathman (talk) 00:41, 24 April 2009 (UTC)

I think you are confusing transcript with primary transcript. Narayanese (talk) 18:23, 24 April 2009 (UTC)

Okay, but I don't find that the use of the terms is really consistent in the literature. Perhaps the best usage would be "primary transcript" and "mRNA", thus avoiding the potential for confusion. Agathman (talk) 18:29, 24 April 2009 (UTC)

SR proteins

"The regulation and selection of splice sites is done by Serine/Arginine-residue proteins, or SR proteins."

Are you sure of this? I think there are other class of proteins involved, like hnRNPs.

Dalloliogm 14:23, 10 October 2007 (UTC)

Alternative promotor mechanism

This is not splicing mechanism. neffk 04:24, 29 August 2006 (UTC)

Alternative poly-A mechanism

I have not heard of this... RNA polymerase II and cleavage, polyadenylation specificity factor (CPSF), and cleavage stimulatory factor (CStF) terminate transcription 10-30 nt downstream of the AAUAAA transcription stop sequence. Poly-A tail is produced by PAP (poly-A polymerase). Unless scholarly research can be referenced, I think this should be removed. neffk 04:22, 29 August 2006 (UTC)

nonfunctional alternative splicing

The article contains no indication that alternatively spliced variants might be anything other than adaptive. It's an issue that's currently in need of emphasis in the field. Alternative splicing can clearly be regulated and adaptive, but essentially all of the diagrammed forms of alternative configurations for a transcript can also occur as a result of abberant transcript processing resulting from exon skipping, incorrect choice of cryptic splice sites, etc. For example, perhaps 1/3 to 1/2 (possibly more) of alternatively spliced variants in humans contain premature termination codons and are almost certainly nonfunctional. Unfortunately, a general belief perhaps uncharitably characterized by "if the cell produces it, it must be good" has led to coupling this mechanism to nonsense-mediated decay in proposals of a new form of gene regulation, when really the most parsimonious explanation is that NMD is just doing its job in removing these incorrectly processed transcripts. Dgscofield 02:51, 28 October 2006 (UTC)

clean-up

i tagged this article for clean-up since it is written in rather colloquial language, and since it lacks interesting details such as the explanation of trans- and cis regulatory elements, which influence the regulation of alternative splicing. Further, in this article many facts refer to splicing in general, which can be left out or should be included in the article "splicing (genetics)". —The preceding unsigned comment was added by Inside x (talk • contribs) 15:06, 27 April 2007 (UTC).

Intron Retention mode

However, the intron must be properly encoding for amino acids. The intron's code must be properly expressible, otherwise a stop codon or a shift in the reading frame will cause the protein to be non-functional.

This is not necessarly true: in fact, a retained intron can also occur in one of the Non Translated Regions (NTRs) on the upstream or the downstream of the transcript.

My beef with this is that if "the intron must be properly encoding for amino acids", does that not, by definition, make it an exon? Or is this trying to say that retained introns, such as those in the UTR's, must not interfere with the transcription machinery(stop codon etc)? Because it seems to imply that "coding introns" have to ...code properly. Geno-Supremo (talk) 16:32, 9 November 2008 (UTC)

First discovered in.. ?

I wonder who and when first discovered alt. splicing. --CopperKettle (talk) 00:35, 1 January 2009 (UTC)

Peer review

After ten years I think this is done.--Akrasia25 (talk) 23:02, 18 November 2019 (UTC)

22:07, 14 June 2023 (UTC)Genome42 (talk)§§== Biased article ==

This article is extremely biased in favor of abundant alternative splicing even though there is no evidence to support that concept. Some genes exhibit alternative splicing but whether more than 5% of human gene products are alternatively spliced is highly controversial. There's no explanation in the article of error-prone splicing and no mention of the fact that the vast majority of inappropriately-spliced transcripts have been rejected by genome annotators.

The article needs to make the distinction between true biologically relevant alternative splicing and transcripts than are produced in low abundance by splicing errors. Low abundance transcripts may or may not be examples of real alternative splicing and it's wrong to label them as alternative splicing examples without evidence that they produce a functional product. (That evidence is lacking for the vast majority of genes.)

This article does not measure up to the standard of Wikipedia because it ignores the views of some prominent scientists who oppose abundant alternative splicing and who object to many of the statements made in this article. (I am one of those scientists.) Genome42 (talk) 15:51, 19 May 2022 (UTC)

My earlier criticism has not been addressed. The most important issue in the field of alternative splicing is how many transcript variants are biologically functional and how many are merely due to splicing errors. This issue is addressed in the Sommer et al (2022) paper cited by 128.220.159.219 in the latest edit but the edit doesn't mention the most important part of the paper; namely, the difficulty in determining whether predicted protein isoforms are functional. The data in the Sommer et al. paper shows that a few percent of human genes may have been improperly annotated because they specified a primary protein product that may not be the correct version. In some cases, an unusual and non-conserved splice variant was used to make the original (probably false) prediction.

The recent edit (June 14, 2023) does not make a substantial contribution to the Wikipedia article and may even be misleading. This article needs massive cleanup and revision.Genome42 (talk) 22:07, 14 June 2023 (UTC)

my elective course assignment

Hello everyone , i am nour abu amer , from USKUDAR UNIVERSITY in ISTANBUL , i am doing this editing assignment because of my elective course "Gene environment and behavior" Nour abu amer (talk) 16:08, 11 January 2023 (UTC)