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33

There is still a lot to be learned about the roles introns play in biological processes, but there are a couple of things that have been pretty well established. Introns enable alternative splicing, which enables a single gene to encode multiple proteins that perform different functions under different conditions. For example, a signal the cell receives ...


20

The terms intron and exon were coined by Walter Gilbert in a renowned 'News and Views' article, Why Genes in Pieces, published in the journal Nature in 1978. Introns are the intragenic regions and exons are the regions which are expressed. This is the relevant passage in full: The notion of the cistron, the genetic unit of function that one thought ...


9

Yes. Ribonucleases (RNAses) break down the spliced RNA strands back into mononucleotides, and these building blocks can be reused. They will be broken down into nucleotide monophosphates, so they will have to be re-phosphorylated to triphosphates before they can be reused for transcription. Here are a couple of reasonable reviews of the mechanisms: ...


7

Not less efficient, but introns are under less selective pressure than exons. Exons actually encode the protein. A single bp insertion will ruin a mRNA encoding a protein by causing a frame shift in how the sequence is read. However the same is not true for introns. 1bp insertion even if the intron has function such as transcription or translation factor ...


6

Evolution - Douglas J. Futuyma, Chapter 19, p. 461 Michael Lynch and John Conery (2003) have pointed out that a variety of genomic features that appear to have little fitness advantage for organisms-introns, transposable elements, large tracts of noncoding DNA-may be more prevalent in species with small effective population sizes. They have ...


5

A few percent codes for RNA, like microRNA, long non coding RNA, shRNA ect. These RNA while not translated into protein do have a function. Some RNA are ribozymes, catalytically active in their own right, but they do work with proteins. An example of such complex is the ribosome, where the catalytic peptidyl transferase activity that links amino acids ...


5

One paper after this question was asked indicates that it might be both stronger purifying selection in exons and a higher basal mutation rate in introns, likely due to the different accessibility of the DNA. You are correct that introns play an important role in regulation (perhaps both timing and overall expression, in addition to the presence of ...


5

Prokaryotes can't have introns, because they have transcription coupled to translation. They don't have time/space for that, since intron splicing will stop the coupling. Eukaryotes evolved the nucleus, where splicing can be done. The ancestor of eukaryotes that developed the nucleus could afford more variability (because of introns) than species without it, ...


5

There are references in the literature to the phenomenon of "exon scrambling" which seems to be what you are asking about, but the prevailing view is that the evidence for this process, which comes from comparing EST sequences with genome sequences, can be explained by cloning artefacts occurring during EST characterisation. Certainly I agree that there is ...


4

Mitochondrial genomes differ greatly in size, coding potential and even whether they are circular or linear. Mammalian mitochondrial DNA is small (11–28 kbp) and intronless. However the mitochondria of certain other organisms range up to 1000 kbp in size. Certain sponges (demosponges) with large mitochondrial genomes contain type I introns and type II ...


4

I think that you are talking about trans-splicing. This does indeed happen. It is fairly common in protist organisms, though in humans it is quite rare. For more information about how this process works, including mechanisms in vertebrate organisms, see this paper. Here is one model from that last paper for how it works:


4

The only information you are missing is a way to identify the splice sites. There are many ways of doing what you need. The simplest, assuming you are sure of the origins of the mRNA, is to use a BLAST flavor, either plain BLASTn or, even better, BLAT, to compare your mRNA sequence to the genome of interest. BLAT really should be all you need if the mRNA ...


3

Quick answer: we don't really know. As WYSIWYG said, splice sites do have a sequence signature. The image below (taken from [1]) shows the consensus for human acceptor and donor sites: In the images above, the size of a nucleotide represents its frequency at that location. As you can see, there is a clear signal around the splice sites and this signal is ...


2

There are some signature sequence which mark intron-exon boundaries. Usually introns start with a GU and end with an AG. But this feature per-se is not sufficient for splicing; there are other cis-elements such as exon/intron splicing enhancers/silencers [ESE/ESS; ISE/ISS]. Refer this article. Also, there are protein regulators of splicing such as SR ...


2

You should ask this question over at biostars.org -- and could use a bit more clarity. Do you actually have RNA-seq data that you want to use to find the exon/splicing structure of an mRNA? First step would be to use a splicing-aware aligner. A few free ones are: STAR TopHat GSNAP Let us know why that wouldn't do what you want when you re-ask this ...


2

It is not unusual for RNA sequences to be reported with T instead of U; the writer is reporting the cDNA sequence instead of the RNA sequence. In RNA at the boundary of the minor intron, there is a uracil. In the following page, the writers follow the oft-used convention of describing RNA with T instead of U (writing the cDNA sequence). https://en....


2

There are two factors that involve the ability of enzymes to process RNA. 1) Structure see wikipedia 2) Binding affinitya Let's take a look at the splicing process: The active 'sites' (GU,A & AG) need to be in spatial proximity (point one), and the enzyme needs to be able to bind there, aka forming hydrogen bonds with the nucleotides, which is mostly ...


1

The thinnest blue line is intron, so not in your transcript. The medium thickness segment is untranslated exon, the thickest blue segment is translated.


1

Another use for a spliced out intronic piece of RNA is as noncoding RNA. Here's an example which include pre-mRNA also transcribing microRNAs. http://www.nature.com/nrm/journal/v10/n2/fig_tab/nrm2632_F1.html?foxtrotcallback=true


1

Nuclear genes for proteins destined for the mitochondrion can have introns… …to the extent that other nuclear genes for that organism have introns. For certain insects there is a database of such genes entitled MitoDrome, and if you click on D. melanogaster in the side panel on the home page of that site you get to a list of such genes for the eponymous ...


1

Well, as this question seems to be about helping the X- or M- generations get to grips with baby boomer terminology, let me explain how I remember what introns are. Before Gilbert coined the term (as @xusr explains) original reports of the research that established the mosaic nature of eukaryotic genes refered to in-tervening sequences. For example, ...


1

It's not clear what is 'several database searches with the sequences'. The most obvious solution is blasting your sequence so you can see which part can't be aligned and then blasting the rest. You can choose different implementations (megablast of blastn) and play with algorithm parameters because it may not work for you as-is. But it will work as-is if you'...


1

As Armatus said TF can remain bound without an effect. There are some alternative explanations: Promoters need not be always upstream to the Transcription Start Site (TSS). There are promoters called Downstream Promoter Elements that are actually downstream to TSS. There can be alternate TSS within the introns TF bound to intron may regulate elongation ...


1

Even in a quiescent state, DNA is bound to a lot of proteins. It is not a lone double-helix of DNA with an occasional protein attaching here or there. Rather, it is tightly wrapped around histones, which themselves have other proteins attaching and detaching constantly. Repair enzymes are always whizzing about and fixing the random damage that occurs in DNA ...


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