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19

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 ...


12

I don't have any literature to back this up but I doubt that it occurs (at least frequently). For example, imagine a simple three exon gene. Upon splicing exon 1 to exon 3, exon 2 would be excised as part of the intron lariat and subsequently degraded. So in order for exon 2 to be spliced to exon three you would need to either have splicing between exon ...


11

After performing a quick literature search, I am, as with GWW, unable to provide any literature against this occurring, although this paper by Black (2005) states that exons in multi-exon pre-mRNAs are always maintained in order. Black DL. 2005. A simple answer for a splicing conundrum. Proceedings of the National Academy of Sciences of the United States ...


9

Perhaps this question is whether the regions between genes sometimes known as 'junk DNA' has any function. In the human genome, out of ~5 billion bases there are something like 20-30,000 genes which take up perhaps 10s of millions of base pairs, depending on how you count it. 1% of all human DNA is the common figure. It is sometimes asked as if ...


8

Depends on what you mean by "non-coding". There are structural elements in telomeres & centromeres -- although the DNA there does not code for proteins, it contributes to the three dimensional structure of the chromosome. "Non-Coding" DNA can also act as a binding substrate for many proteins: transcription factors, enhancers, histone proteins; and ...


8

I think the above values (500-750 kb) are wrong. http://www.bioinfo.de/isb/2004040032/ shows that most introns are less than about 10 kb (and personal experience in Drosophila confirms that - I've rarely seen an intron bigger than about 5 kb). There are some very large ones, but since it's nearly impossible to detect the splicing reaction, particularly if ...


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 ...


6

If you examine the human genome ~99% of the introns are under 500 kb. I would assume that a limit between 250 kb - 500 kb is reasonable for gene prediction. You may incorrectly predict the proper structure of a small number of genes that have these very large introns but this should be a small number. Furthermore, most popular sequence aligners tend to set ...


6

By programmable, I suppose you mean that it contains information or can be altered in response to some input or stimulus. The answer is "no" for both. Well, sort of. Does noncoding DNA contain information? By definition, no. There are probably many regions of the genome that appear to have no information, only later to be found to contain introns, ...


6

I am very suprised nobody mentioned the field of DNA-computing. It is proofen by Leonard Adleman and Richard Lipton that you can compute with DNA molecules. In the article of Adleman they present an experiment to solve an instance of the Traveling-Salesman-Problem. Because this problem is in NP one can say that the DNA is turing-complete. Article of ...


4

Nature has done pretty well in the subject of formal computation. So much that we are still trying to keep its pace. As about your question, it depends on your definition of "non-coding DNA". In general, DNA together with the machinery in charge of its maintenance is Turing-complete in several senses. Take a look, for example, to the existence of mobile ...


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

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, ...


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 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 ...


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 ...


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 ...


1

Let me answer your question by splitting it into two parts: Can DNA be used as an programmable medium (=band) for Turing machine? The answer is YES. Starting from the breaking paper by Shapiro et al. in Nature, followed by another great article by Parker, there are many scientific publications about how to use DNA for computing. Unfortunately, these ...



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