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Saturday, April 9, 2011

inTRON Legacy... the problem of snRNPs (the smurfs of cell biology)

A recent study highlights the importance of spliceosome components by showing that a rare genetic disease is caused by a mutation in a
snRNP.  The spliceosome is a machine made of several snRNPs.  These molecular scissors cut precisely the right location on the DNA to remove an intron and promote the ligation of exons.  Prokaryotes appear to do just fine without introns. 

 So what is the purpose of introns?  What overall function do they provide for eukaryotes?  Why use such a complex splicing operation for a function which appears to do nothing more than rejoin exon regions?   How do evolutionary biologists propose that snRNPs and spliceosomes evolved? Is this good design or is this entire process wasteful and therefore not good evidence for design in nature?

44 comments:

  1. 1:The purpose of introns: Introns are apart of the process where RNA is made. rDNA separates to where the introns and exons are next to each other and strands of RNA is made. The rDNA polymerases line up and get longer.
    2:Introns overall function is that they sequence themselves in a certain order, so that they can make rRNA, which contributes to transcription as well. However, because introns are so key in the beginning of DNA/RNA making, they can also mutate which causes some serious problems within the body. Some introns also function as the control sequence in the process of making Chromosome X inactivation. Chromosome X is necessary to determine the male/female sex structures. This is excerpt that I found in a medical journal onlne: “The Sxl gene is the master regulator in the sex determination pathway of some organisms and functions by regulating how the introns are cut out of mRNA. It produces a functional protein only in females that culminates in the development of female structures. The Sxl gene is also critical for dosage compensation by blocking mle and msl genes, which make a protein that increases certain X chromosome proteins.36 Sxl functions by blocking removal of the introns in females, preventing females from producing functional msl-2 protein. The msl-2 gene is also controlled by removal of an intron in males, but not in females.37 Males lack an Sxl gene, and therefore process the msl-2 transcript properly. The two sets of proteins are coded by the same set of genes; the sex differences are largely due to different patterns of RNA splicing.”
    3:Introns in part, may appear to do nothing, but in reality they don’t. God wouldn’t give us something that has no function. Everything inside of the human body has a function, whether the function has been discovered or not, there is a function for everything. Introns are involved in the making of rRNA, and like the article I found, sex structures.
    4:Why Introns? Because they are in our basic DNA, even though they are taken out by the spliceosome, they are highly functional.

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  2. 1 The role of Introns is to do al lot more than rejoin exon regions that are on the DNA, they are a major benefit to cells because by Splicing the DNA it lets you unzip the genetic message so those cells that would be receiving it would be able to read it before that certain protein is made, and therefore giving it a head-start on preparing to receive the protein.
    I will answer the rest tomorrow hopefully.

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  3. As a first approximation, it is possible to view introns as unimportant sequences whose only function is to be removed from an unspliced precursor RNA in order to generate the functional mRNA, rRNA or tRNA product. However, recent studies show that this perspective is, in many cases, overly simplistic. It is now well-established that some introns themselves encode specific proteins or can be further processed after splicing to generate noncoding RNA molecules.
    Introns are advantageous in eukaryotes because they enhance within-gene recombination and therefore increase selection efficacy.

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  4. My, I like your point and the way you said it.

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  5. Prokaryotes don’t have introns, and they are simple organisms. As a general rule, the simpler the organism, the more introns it is going to have. If they were not important to the complexity of the organism, why would we have them? And why would cells put so much effort into creating these introns? The only answer is there must be a reason for them. Research has shown that there is a high level of conservation of some introns, which indicates that there is some purpose to them. In an essay I found a man named Jerry Bergman points out that introns are a “complex mix of different DNA, much of which are vital to the life of the cell.” It has been discovered that intron alterations are directly related to the development of cancer. It has also been found that DNA can function as both exons and introns, meaning that there are different pathways which produce a greater protein variety. Sometimes introns are even coded to produce a specialized protein. These factors alone support that there is purpose in introns. The above finding seems to suggest that introns can simply be dormant DNA that can be activated if it is needed. And as for the complex splicing operation, if the introns are inactive we need them removed. But there are some times when these introns are not going to be removed, it all depends on which protein is being coded. Introns are not useless, nor are they junk DNA, as previously though. They do have a purposes.

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  6. Its possible that introns play a function in DNA expression or conservation. If there was a mutation in the DNA, and it occurred in an intron region that is never coded to a protein, the mutation would then have no effect on proteins created, so its possible that an amount of noncoding DNA acts a buffer to mutations. Another idea is that introns are involved in DNA expression. If DNA is unwound by a helicase but a section of the DNA shouldn't be coded for, its possible that the intron region could be used to form a stem loop so that the DNA binds to itself in the region and is then unable to be transcripted into functional RNA until the proper time.

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  7. I found research from two different sources that suggest theories for the purpose of introns. According to the first source,

    “There are a number of hypotheses about the function of introns. One hypothesis is that alternative splicing may allow a single gene to code for more than one version of a protein.” http://highered.mcgraw-hill.com/sites/0072995246/student_view0/chapter14/how_spliceosomes_process_rna.html

    The article also mentioned the idea of spatial separation. Here is my crude analogy of this concept: Imagine a yard stick with a line marked on it every inch. You need a piece of yardstick that is 12 inches long, but only has 6 lines on it. Impossible. Now, imagine the same yardstick with 6 inch blank segments every 6 inches. Out of this yardstick you can get the piece you need. Same idea with introns. They are in the DNA so that when a length of DNA is removed, only the needed genes are on the section.

    The second source:

    “Mining existing data from genome-wide studies on yeast, it was discovered that intron containing genes produce more RNA, more protein and are more likely to be haploinsufficient than non-intronic genes... These data provide evidence that introns improve transcriptional and translational yield and are required for competitive growth of yeast.” http://www.genetics.org/cgi/content/short/genetics.106.058560v1

    I also like what frendtem had to say about being a buffer against mutations.

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  8. Research has shown that introns can promote transcriptional and translational yield in a cell. Introns can produce more RNA and thus more proteins.
    They have been found to cause growth rates in the cell after it has been deleted by the spliceosome.
    To say that introns have no use and are simply 'nonsense' would be innacurate. There is a purpose for every cell and every function in our body. These introns have been found to possibly aid in cell growth and development so they do have structural importance for the cell.

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  10. Introns are hugely important for DNA and transcription and translations. The product that is brought about in this process is RNA which leads to proteins. By splicing the RNA you can then view the DNA in the cell. I am going to research it more!!

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  11. One of the purposes of intron is to accommodate sequences for gene expression where the intron resides, and introns have some indentifiable functions. Some intron alterations are directly related to the development of cancer. "Some introns also function as control sequences in the process of chromosome X inactivation, which is necessary for dosage compensation in females". Introns have genes for small nuclear RNA which involve in translation of mRNA. Introns are ubiquitous in our genes therefore they should be performing a major role in our genes which scientists haven't discover its role yet.

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  12. This source that I got seemed to hint at introns being important in stabilizing the structure of the DNA and RNA. If we took out this seemingly meaningless piece, it could drastically change the shape of the DNA and RNA and thus their packaging within the nucleus. "Some evidence also exists that introns structurally stabilize the pre-mRNA to protect it against degradation. Marculis and Sagan noted that DNA is packed into a chromosome so effectively that it is 1/8,000 of its former size after packing.55 They concluded from studies on ciliates that at least some introns, and possibly other noncoding DNA, may be involved in DNA packaging in eukaryotes and perhaps in some prokaryotes." 56

    55Margulis and Sagan, Origins of Sex, 115.
    56M. I. Baldi, E. Mattaccia, E. Bufardeci, S. Fabbri, and G. P. Tocchini-Valenti, "Participation of the Intron in the Reaction Catalyzed bv the Xenopus TRNA Splicing Endonuclease," Science @55 (1992): 1404-8.

    Compiled in a Journal: The Functions of Introns: From Junk DNA to Designed DNA (http://www.rae.org/introns.html)

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  14. So apparently the majority of eukaryotic protein-encoding genes contain intron sequences that disrupt the protein encoding-frame and therefore must be removed from the sequence. Apparently these introns are removed by genetic splicing machinery but this splicing machinery isn't very efficient and the cell must compensate with what is called nonsense-mediated decay, which targets and destroys nonsense mutations in mRNA. This nonsense-mediated decay is essential in that it constantly destroys mRNA mutations that might otherwise be translated. The interesting thing about this is that evolutionist say that the mechanism must have co-evolved with intron acquisition for quality control, otherwise mutations would just run rampant.

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  15. 1. Since Eukaryotes have a defined nuclear membrane unlike the Prokaryotes wouldn't there be a more complex RNA processing process than that of the Prokaryotes because it actually has to cross the nuclear membrane which is not a easy thing to do. And since Eukaryotes tend to have to be more precise in how they cut their RNA it should be logical to think it would have preset dotted lines that designate where to cut since it could be more consequential for it and the organism at large. While bacterium are far more "durable" organisms that can take quite a beating and so they wouldn't have to be as precise with their RNA processing.

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  16. I liked Sam's analogy with the measuring stick. And the bit about increased RNA production in regions with introns. Is could be possible that introns also serve a purpose in maintaining the strucural aspects of the chromosomes, or since they are involved in gene expression, could they be used to code for proteins as back up in case the expressed proteins' genes become compromised? We lose genetic material over time so it makes sense that there would be mechanisms inplace, like introns, that would safeguard against losing too much.

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  17. While researching introns, I found this:

    "It is now well-established that some introns themselves encode specific proteins or can be further processed after splicing to generate noncoding RNA molecules."

    So it seems that introns have more purpose than just to be eliminated from the DNA sequence. Perhaps having introns and exons can allow the DNA sequence to hold more information. In other words, the exons can be coded to make most proteins, but the introns can have more specific roles. The fact that they are cut out of the regular DNA sequence could mean they are being set aside to make something else. Just because they are cut out of the regular DNA sequence does not mean they are discarded. Eukaryotes have more complex systems than prokaryotes. Therefore, perhaps the introns help give some of that complexity that the prokaryotes lack.

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  18. Not much is known about introns, but this is what I have found. It is now thought that introns are a total mix of DNA, and the mixture is what is helpful to the cell. Scientists compare them to the human language, and the parts of the introns are like letters and words, which carries vital information to make them work correctly. Introns also are involved in splicing, especially shifting, which causes the DNA to be read in a completely different way. Another way that introns are involved in splicing are alterations, where the introns cause "base hopping in which large DNA segments are skipped when the mRNA is produced".

    Bergman also says that even though not much is known about introns, it would be wrong to say that they are simply junk in the cell. They are just as important as DNA, if not more so. He continues, "We now know that DNA sequences not only carry information for making proteins, but also play many supportive roles in protein synthesis including manufacturing transfer RNAs that help to assemble amino acids into proteins and rRNA, as well as other forms of RNA." This leads me to think about the irreducible complexity of cells, and how every part, regardless of how small is needed to have successful life. God thought of everything!

    http://www.rae.org/introns.html

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  19. Although I found that little is known of introns it seems that they would have a rather important function. It is clear that introns are not needed for proteins since they are cut out of the mRNA. The intron segments in the DNA could have another function though. I would suggest that these intron segments are used by the cell to locate DNA segments which correspond to the device needed that they would produce in the cell, perhaps by using transcription factors. There is much that goes on in the nucleus that occurs to carry out transcription and the introns would help mediate all the operations.

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  21. As I was researching the purpose of introns, people had a lot of theories about what they did and why they do it and sometimes their theories would conflict with each other. But I did notice something that the majority seems to agree on. It is that they genetically serve as bridges or "spacers" between the spaces of DNA that are coded for specific proteins.

    Also, most agree that they don't do much, even to the point of giving them the nickname "junk DNA" but research is still in progress. What motivates them to research about introns is the fact that they believe that it must have some important function as to why it has survived evolution. I believe that it should have an important function because our Intelligent Creator created it.

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  22. I think the main purpose of introns is widely ignored and trivialized by the secular scientific community. The complexity of introns and the intron splicing mechanism strongly suggests that intelligent design was involved. Introns aren’t merely “junk” DNA like so many scientists would propose but actually have been thought to be a means of gene diversification and are thought to carry important structural and regulatory purposes. Since introns carry functional information on non-protein coding sequences it is possible that they serve a preventative purpose in the DNA. Perhaps they are a “safety net” alerting the cell of miscoded mRNA and helping prevent malformed proteins or maybe they help separate out the exons so that the code for the mRNA is put together correctly and doesn’t get mixed up.

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  23. Introns separate exons. Many proteins are made through many different combinations of exons which come from the same gene. Introns provide a separation and provide different sequences which then can be arranged when SnRNPs cut out the introns.
    Having separate exons allows for a larger range of combinations from which to make different kinds of proteins.
    Introns do have a function in DNA as well. You need separation between genes and promoters.
    One conjecture on the purpose of introns "is that alternative splicing may allow a single gene to code for more than one version of a protein. In other words a piece of the gene may be an intron in one case and an exon in another case. Another possible explanation is that each exon codes for a module of a protein. Spatially separating the exons may allow for the development of many different proteins by removing, adding, or replacing entire modules."

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  24. Introns are involved in the production of RNA and sometimes are used in the production of specialized proteins. Splicing could be part of a cells immune function. They could remove sections of DNA that have been infected. Because they already remove introns (the DNA that isn’t coded) , they could be involved with cutting out all sections of the DNA that wont be coded for the specific protein. Also, eukaryotes have far more diversity. Perhaps it would be more practical for eukaryotes to have this splicosome function instead of having even more DNA.

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  25. Introns are nucleotide sequences that, when removed, help create the final product of RNA. "It is now well-established that some introns themselves encode specific proteins or can be further processed after splicing to generate noncoding RNA molecules." I think...God is too awesome to make something super simple ...I mean, in our eyes, intron splicing may seem complicated, but to God this is simple! Introns are like the middle men in life that God still uses for the sake of...His glory! ;D

    -Sarah Gonzales

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  26. So what is the purpose of introns? What overall function do they provide for eukaryotes?
    "A segment of a gene situated between exons that is removed before translation of messenger RNA and does not function in coding for protein synthesis."-yahoo. Introns were also described as this: " You could think of introns as long commercials, in a language you don't understand, interrupting your favorite television show right in the middle of the action." lol!

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  27. The purpose of introns seems to still be a highly debated topic. Evolutionists believe that introns are the remnants of past genes that were cut out due to a lack of need, but left part behind. This however is mostly discounted as if evolution were true, the introns would have been completely removed, as opposed to staying.
    Another theory is that since only complex organisms contain introns, they must serve some purpose, even if not major. While there is still no proof for this, it is quite possible that the introns help to code for minor things before the proteins are made.

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  28. Introns generate the final mature RNA product of a gene. "Introns provide an opportunity for a particular gene to be spliced in several different ways, so that gene can produce different proteins in different cells or under different developmental circumstances." Dr. Jeff Schloss

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  29. Introns allow for greater gene diversity within a cell. They allow genes to be spliced in many different ways, creating different proteins, which leads to different phenotypes in the specimen.The potential for diversity is exponentiated by the fact that many introns can move around in the genome. Something that may not cause a change in one gene if spliced differently, could cause a change in another gene. This diversity is a good thing because it allows eukaryotes to more easily adapt to their environment. So if these introns are so helpful for adaptation, then why is there no trace of introns in Prokarytoes? This seems like it might be a hard question for evolutionists to answer. Introns can also be recycled by the cell to create non coding RNA.

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  30. I found this article from a Creationist named Dr. Wile who first begins by explaining introns, their previous view of being “junk DNA” and their assistance in alternative splicing. He continues to argue why introns are useful and not junk.

    “Is that the only thing introns do? Are they just “spacers” that separate the exons so the exons can be spliced together in different ways? Probably not. You certainly wouldn’t expect that in such an elegantly-designed system. In the end, there are probably other jobs introns perform as well. As an article in the journal Science says:Introns may play other vital roles, however. For instance, a slew of so-called small nucleolar RNAs (snoRNAs) are encoded by introns. Because snoRNAs accumulate in the nucleolus, where the protein-making ribosomes are formed, researchers speculate that they play a role in ribosome assembly.4

    In addition, we know that certain introns play a vital role in the regulation of genes.5,6
    So far from being the “junk” that many first imagined, introns are clearly a very important part of the genome. Indeed, as Dr. John S. Mattick, director of the Institute for Molecular Bioscience at the University of Queensland said: The failure to recognize the full implications of this—particularly the possibility that the [introns] may be transmitting parallel information in the form of RNA molecules—may well go down as one of the biggest mistakes in the history of molecular biology.

    The more we learn about the genome, the less junk there appears to be. This, of course, supports the creationist view of the genome.”

    http://blog.drwile.com/?p=1477

    Basically, the majority of articles I’ve been reading through all say the same thing: introns serve mainly to regulate genes and provide for alternative splicing. I’m sure there’s much more than that, and I’ve probably way oversimplified it but I don’t know how else to say it simply.

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  31. Though previously introns had been thought to serve no purpose, recent studies have found several functions introns serve. One indication that introns are important was seen by intron alterations which led to the development of cancer. Also, different reading frames cause some introns to become exons and some exons to become introns. Therefore introns allow more proteins to be coded from one strand of RNA. Introns also function as a way to control which genes are expressed and which are not. For example the Sx1 gene which functions as a control sequence in chromosome X inactivation, tells the cell not to remove introns from certain genes, and therefore not to make the proteins the genes code for. Overall I think that this “junk DNA” doesn’t point to evolution, but to creation. Why would a more complex system evolve to cut out this junk DNA? And how could this complicated splicing process have evolved little by little?

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  32. The purpose of introns is a part of the process where RNA is made, and this helps make more proteins. They can promote transcriptional and translational yield in the cell. The help eukaryotes sequence for gene expression for certain functions. The overall function that they can provide for eukaryotes is that will sequence themselves in an organized way. You have to use the complex splicing operation for this function because they are needed to make rRNA. Even though introns appear to not have a greater function that rejoins with the exon regions, they provide pathways that can provide a greater protein variety. Even though we don’t know what function they are, they were obviously put in our body by God for some reason. It’s just going to take us and our sinful nature a little bit longer to figure out their purpose.

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  33. Introns are an adaptation for error-correction, by providing safe-haven for the stem-loop potential needed to initiate recombination. Prokaryote DNA polymerases have the ability to proof read, yet most eukaryotic DNA polymerases do not have this ability Prokaryotes do not have a variety of histones, which are the major protein components of nucleosomes. This is why Eukaryotes need Introns to proof read and correct errors for the Eukaryote. Also the complex splicing is very necessary to make sure it cuts the right thing. It has to cut the Intron not the exon. It may very well have to cut to a certain point of the intron for the intron to be able to correct errors. Introns fill in very nicely with the exons. Everything seems to work perfectly and it is very complex, but introns are crucial to the spliceosome.

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  34. Apparently, the common view is that introns are a necessary component. It has been suggested that prokaryotic organisms don’t have introns because bacteria need streamlined genomes, or may have less need for whatever functions introns serve. One hypothesis is “alternative splicing may allow a single gene to code for more than one version of a protein. In other words a piece of the gene may be an intron in one case and an exon in another case.” (http://highered.mcgraw-hill.com/sites/9834092339/student_view0/chapter15/how_spliceosomes_process_rna.html) If this is the case, it would allow overall greater complexity in eukaryotes. The complex splicing operation could ensure the exon regions are joined correctly and in the needed order.

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  35. The main purpose that everyone seems to agree on is that they are spacers that separate the exon. In eukaryotes they serve in production of RNA and splicing. But scientists seem to be stumped to why they are there. One article I was reading said “Introns are interruptions in the text of eukaryotic genes. Every time the genome is replicated, they are replicated right along with it. For Richard Dawkins, introns are an example of pure "selfish DNA," out for its own survival only”. I’m just thinking out loud here, but it seems that the introns would splice just to rejoin so that the initial copy of DNA would be protected, like an organization factor maybe. Protect the original and rejoin where it can be sent out and checked for error?

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  36. Intron function, as previously stated, is related to the synthesis of many proteins as they are sometimes preserved instead of discarded.
    Alternative splicing and the synthesis of peptides normally synthesized by exons show the design element of introns. Introns are homeostatically controlled by maturases, which are formed by introns that are sometimes kept as exons by alternative splicing. Maturases are enzymes involved in the removal of introns.

    On the evolutionary side, it has been supposed that introns mutate and add functional genes to more complex organisms. While the mutation of introns is feasible, the loss of functions that they already perform and the unlikelihood of their mutations being so favorable as to produce a 'higher' life form rules this out.

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  38. Introns do have identifiable and significant functions. For example, introns contain genes for small nuclear RNA, which is important for the translation of mRNA. Also nuclear introns can be significant in a process called alternative splicing, in which there is more variability for making more proteins. Furthermore, introns are required for regulation of gene transcription.

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  39. introns are a "spacer" of sorts for the exons in the DNA. Some experts think that the introns seem to serve an error checking role in the transcription process. Also introns contain rRNA that is necessary for the production of Ribosomes.

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  40. Prokaryotes and Eukaryotes as we have learnt throughout this semester is that although evolutionarily biologists would like to think that these marvelous organisms are some how from the same ancestor. How they work on the inside is is vastly different and although they share some common things like protien and RNA they use them differently. Knowing this it is quite possible to accept tha tonly eukaryotes carry SnrPS, which i think would be as crucial for a prokariotic cell than for a eukariotic cell. A bacteria can live and thrive even if there is a miniscule mistake for coding but im pretty sure if one of the cells of a eukariotic organisms where to code the wrong protein it could have terrible repercussions, i think that the SnrPs are a crucial part of quality control that we fond throughout organisms.

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  41. Introns as what everyone seems to be having the same opinion and the random journals online have been stating is that, introns are spacers which separate the exons. And no introns are not related to any transformer whether it may be a deceptecon or an autobot and certainly not related to megan fox. Introns in a way act like a movie preview, by unzipping and showing the codes it lets other cells know what they are getting into.

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