PROOF against evolution

I don't really want to get into the main topic of this argument i.e. Proof against evolution, but I have to agree with crashfrog that "junk DNA" is a horrid term. 9% of the genome is composed of human endogenous retroviruses. Their LTRs serve as promoters, potential promoters, sites likely to recombine (important for evolution), some are transcriptionally active, and some have known function. This is just HERVs...non-LTR retrotransposons and other retroelements make up over 50% of the genome. Some of these are also active. Of the open reading frames identified by the various genome projects (not retroelements) a huge number have no known function....lumping all of this into the term junk DNA is probably part of the reason we don't know why the same medicine affects people differently, to how different developmental pathways are regulated...because most of the genome is considered junk since it cannot be assigned to the few biochemical pathways that are well studied a lot of data is ignored. There are clearly sequences that have no function and are hanging around for the ride like a lot of mitochondrial pseudogenes for example. But a better term would be sequences of unknown function for most of the genome... and reserve junk DNA for the examples where this has been shown to be the case...my two cents.

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Another way to remember the difference is that EXons are EXpressed, and INTrons are INTervening sequences.

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Also, technically, introns and exons related to RNA, not DNA.

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To nitpick, introns are also "expressed" i.e. transcribed, but are spliced out as a posttranscriptional modification.Also, not all exons make it into the protein for example the prion gene has 2-3 exons, the entire ORF contained ona single exon.re chimp-human sequence divergence, there was a recent paper that suggested a much higher divergence in sequences when indels are taken into account. This will have to be factored in once the chimp genome sequence is completed.Proc Natl Acad Sci U S A. 2002 Oct 15; 99(21): 13633-5. Epub 2002 Oct 04. Related Articles, LinksDivergence between samples of chimpanzee and human DNA sequences is 5%, counting indels.Britten RJ.California Institute of Technology, 101 Dahlia Avenue, Corona del Mar, CA 92625, USA. rbritten@cco.caltech.eduFive chimpanzee bacterial artificial chromosome (BAC) sequences (described in GenBank) have been compared with the best matching regions of the human genome sequence to assay the amount and kind of DNA divergence. The conclusion is the old saw that we share 98.5% of our DNA sequence with chimpanzee is probably in error. For this sample, a better estimate would be that 95% of the base pairs are exactly shared between chimpanzee and human DNA. In this sample of 779 kb, the divergence due to base substitution is 1.4%, and there is an additional 3.4% difference due to the presence of indels. The gaps in alignment are present in about equal amounts in the chimp and human sequences. They occur equally in repeated and nonrepeated sequences, as detected by REPEATMASKER (http://ftp.genome.washington.edu/RM/RepeatMasker.html).

Hi DNAunion
There are in some cases, expressed intronsDNA Res. 2000 Feb 28; 7(1): 27-30. Related Articles, LinksmRNAs encoding zinc finger protein isoforms are expressed by alternative splicing of an in-frame intron in fission yeast.Okazaki K, Niwa O.Kazusa DNA Research Institute, Kisarazu, Chiba, Japan. kokazaki@kazusa.or.jpWe report here that a gene encoding a protein with three zinc fingers is expressed predominantly to produce a protein containing only two zinc fingers in the fission yeast Schizosaccharomyces pombe. A third zinc finger resides within the in-frame intron that is normally spliced out. By RT-PCR analysis, we detected a minor transcript encoding a protein with three zinc fingers. Such alternative splicing for assortment of zinc finger domains have been reported in animals and implicated in switching of the target genes expressed specifically during development. This is the first report of the occurrence of such zinc finger assortment in lower eucaryotes.Another issue, if one studies gene expression, one can examine total RNA or mRNA. Total RNA will measure transcripts containing introns which have been expressed, hence gene expression. This is different from actually making a protein which does not necessarily correlate all that well with total mRNA levels in any case.There are even functional genes in intronsBiochem J. 2002 Aug 1; 365(Pt 3): 833-40. Related Articles, LinksAn open reading frame in intron seven of the sea urchin DNA-methyltransferase gene codes for a functional AP1 endonuclease.Cioffi AV, Ferrara D, Cubellis MV, Aniello F, Corrado M, Liguori F, Amoroso A, Fucci L, Branno M.Biochemistry and Molecular Biology Laboratory, Stazione Zoologica A. Dohrn, Villa Comunale 80121 Naples, Italy.Analysis of the genome structure of the Paracentrotus lividus (sea urchin) DNA methyltransferase (DNA MTase) gene showed the presence of an open reading frame, named METEX, in intron 7 of the gene. METEX expression is developmentally regulated, showing no correlation with DNA MTase expression. In fact, DNA MTase transcripts are present at high concentrations in the early developmental stages, while METEX is expressed at late stages of development. Two METEX cDNA clones (Met1 and Met2) that are different in the 3' end have been isolated in a cDNA library screening. The putative translated protein from Met2 cDNA clone showed similarity with Escherichia coli endonuclease III on the basis of sequence and predictive three-dimensional structure. The protein, overexpressed in E. coli and purified, had functional properties similar to the endonuclease specific for apurinic/apyrimidinic (AP) sites on the basis of the lyase activity. Therefore the open reading frame, present in intron 7 of the P. lividus DNA MTase gene, codes for a functional AP endonuclease designated SuAP1.RNA. 2000 Apr; 6(4): 616-27. Related Articles, LinksExpression of the Naegleria intron endonuclease is dependent on a functional group I self-cleaving ribozyme.Decatur WA, Johansen S, Vogt VM.Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.NaSSU1 is a complex nuclear group I intron found in several species of Naegleria, consisting of a large self-splicing group I ribozyme (NaGIR2), which itself is interrupted by a small, group I-like ribozyme (NaGIR1) and an open reading frame (ORF) coding for a homing endonuclease. The GIR1 ribozyme cleaves in vitro transcripts of NaSSU1 at two internal processing sites about 400 nt downstream of the 5' end of the intron, proximal to the endonuclease ORF. Here we demonstrate that self-cleavage of the excised intron also occurs in vivo in Naegleria gruberi, generating an ORF-containing RNA that possesses a short leader with a sequence element likely to be involved in gene expression. To assess the functional significance of self-cleavage, we constructed a genetic system in Saccharomyces cerevisiae. First, a mutant yeast strain was selected with a mutation in all the rRNA genes, rendering the rDNA resistant to cleavage by the Naegleria endonuclease. Active endonuclease, which is otherwise lethal, could be expressed readily in these cells. Endonuclease activity also could be detected in extracts of yeast harboring plasmids in which the endonuclease ORF was embedded in its native context in the intron. Analysis of the RNA from these yeast cells showed that the excised intron RNA was processed as in N. gruberi. A mutant intron constructed to prevent self-cleavage of the RNA failed to express endonuclease activity. These results support the hypothesis that the NaGIR1-catalyzed self-cleavage of the intron RNA is a key event in expression of the endonuclease.The problem with science textbooks is they are too general and usually take to long to update given the rapid pace of science and the near futility of keeping up with the primary literature.RE: chimp human comparisons, as I understand it, how the comparisons are made is still controversial. Some only compare expressed sequences like EST sequences. Whether the initial studies will include transposons, HERVs, microsatellites, etc. is not clear..but inclusion will be essential ultimately in getting an accurate measure of the human-chimp genomic differences.