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Topic: Pseudogene

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	Pseudogene
		Pseudogenes are inactive sequences of genomic DNA which have a similar sequence to known functional genes.
		Because of this similarity, pseudogenes are normally considered to be evolutionary relatives to normally functioning genes.
		Mutations in pseudogenes are typically neutral and free from selection because they are normally located in portions of the genome where modifications do not bring aobut a deleterious effect.
	www.iscid.org /encyclopedia/Pseudogene (183 words)

	Pseudogene function: more evidence
		Pseudogenes of protein-coding genes are usually compared with their certainly-functional gene paralogs (gene copies within the same organism), and inferences are made about lack of function based on deviations in sequence that are perceived to prevent the eventual synthesis of a functional peptide.
		Pseudogene nonfunctionality tacitly assumes that any functional peptide synthesized should be the same or very similar to that encoded by the paralogous protein-coding gene.
		Examination of the murine Makorin1-p1 pseudogene sequence indicates that it is riddled with insertions, deletions, and numerous nucleotide substitutions relative to the Makorin1 gene.
	www.answersingenesis.org /tj/v17/i2/pseudogene.asp (1974 words)

	Pseudogene function: regulation of gene expression
		Since pseudogenes are supposedly nothing more than inactivated copies of protein-coding genes, and the sole function of protein-coding genes was thought to synthesize peptides, it seemed self-evident that (the apparent) loss of normal protein-coding function, in any gene copy, was synonymous with the loss of all function.
		Moreover, the pseudogenic antisense RNA is an unlinked transcript.
		When antisense-mediated pseudogenic regulation of genes, by pseudogenes, was first proposed, the antisense RNA was envisioned as originating from a 5’ to 3’ transcription of the anticoding strand (not shown) of DNA.
	www.answersingenesis.org /tj/v17/i1/pseudogene.asp (3887 words)

	Pseudogene Research: Molecular History Research Center
		Unprocessed pseudogenes appear to be defective genes, yet others think that a function will one day be found for the pseudogenes we find in the genome.
		I am exploring the possibility that pseudogenes are indeed defective genes that have lost their original function.
		Pseudogenes most likely are the result of degradation.
	www.mhrc.net /research.htm (155 words)

	Pseudogene Summary
		Pseudogenes that are identical to sequences in mitochondrial DNA have been detected outside of the mitochondria, in the DNA in the cell's nucleus, and in a variety of organisms.
		Pseudogenes are characterized by a combination of homology to a known gene and nonfunctionality.
		Pseudogenes are quite difficult to identify and characterize in genomes, because the two requirements of homology and nonfunctionality are implied through sequence calculations and alignments rather than biologically proven.
	www.bookrags.com /Pseudogene (2359 words)

	Pseudogene
		Pseudogenes are believed to have resulted as mutation to an original functioning coding sequence.
		One scenario for the evolution of a pseudogene is that the environment of an organism changes sufficiently such that the gene product is no longer necessary for the survival of that organism (for example an enzyme may not be required at a different temperature).
		Similarly, pseudogenes are sometimes annotated as genes in genome sequences.
	www.wapipedia.org /wikipedia/mobiletopic.aspx?cur_title=Pseudogene (383 words)

	Pseudogene.org
		Pseudogenes are genomic DNA sequences similar to normal genes but non-functional; they are regarded as defunct relatives of functional genes.
		Pseudogenes are vitally important since they provide a record of how the genomic DNA has been changed without such evolutionary pressure and can be used as a model for determining the underlying rates of nucleotide substitution, insertion and deletion in the greater genome.
		The resulting pseudogenes or pseudogenic fragments have then been assigned to the paralog family of the most homologous gene (or assigned to a singleton gene if the probe gene has no obvious paralog).
	www.pseudogene.org /background.html (549 words)

	Pseudogene - EvoWiki (Site not responding. Last check: )
		A pseudogene is a non-coding section of DNA whose sequence resembles that of a functional gene, in that it has sequences homologous (similar) with those of functional genes, such as promotors and introns/exons, but which lacks the signals which allow it to be expressed.
		In the past the definition of pseudogene has been ambigious, with questions such as whether genes which produce RNA, but which are not translated into polypeptides (enzymes and proteins) should be classified as pseudogenes, but there is now a widespread concensus that "pseudogene" means only those "genes" which are not transcribed at all.
		Pseudogenes are "Junk DNA" and probably have no significant short term selective advantages or disadvantages.
	wiki.cotch.net /index.php?title=Pseudogene&redirect=no (384 words)

	Pseudogene Evolution (Site not responding. Last check: )
		Polymorphism and divergence at a Drosophila melanogaster pseudogene locus.
		A 630-bp fragment including the larval cuticle pseudogene locus (Lcp psi) was nucleotide sequenced in 10 strains of D. melanogaster and a 458-bp Lcp psi fragment from D. simulans was also sequenced.
		We used these data to test the hypotheses that the rates of synonymous and nonsynonymous substitution are equal, that the absolute levels of variation are higher than in functional genes, and that intraspecific polymorphism is correlated with interspecific divergence.
	pritch.bsd.uchicago.edu /publications/pseudo.html (227 words)

	ARS \| Publication request: A Processed Pseudogene Contributes to Apparent Mule Deer Prion Gene Heterogeneity (Site not responding. Last check: )
		This pseudogene is not expected to affect disease susceptibility but complicates genetic studies of mule deer because of its similarity to the normal gene.
		Selection of genotyping methods specific for the normal gene and the pseudogene are necessary for the large scale studies needed to determine whether CWD-resistance occurs in the mule deer population.
		Because susceptibility to the TSEs depends on the presence of the native prion protein, an untranslated pseudogene is not expected to affect disease resistance.
	www.ars.usda.gov /research/publications/publications.htm?SEQ_NO_115=151752 (487 words)

	Pseudogene.org
		Pseudogenes are vitally important since they provide a record of how the genomic DNA has been changed without such evolutionary pressure and can be used as a model for determining the underlying rates of nucleotide substitution, insertion and deletion in the greater genome.
		The resulting pseudogenes or pseudogenic fragments have then been assigned to the paralog family of the most homologous gene (or assigned to a singleton gene if the probe gene has no obvious paralog).
		In the case of pseudogenes, structural information can give extra evolutionary clues and facilitate analysis of the scope of folds in the pseudogene population ("pseudo"-folds) in contrast to those observed for the genes themselves.
	www.pseudogenes.org /background.html (549 words)

	Plagiarized Errors and Molecular Genetics
		The crucial observation relating the discovery of pseudogenes and retroposons to the theory of evolution is this: some pseudogenes and retroposons are shared between different species, as though they were copied from a pseudogene or retroposon in a common ancestor.
		A small section of the GLO pseudogene sequence was recently compared from human, chimpanzee, macaque and orangutan; all four pseudogenes were found to share a common crippling single nucleotide deletion that would cause the remainder of the protein to be translated in the wrong triplet reading frame (Ohta and Nishikimi BBA 1472:408, 1999).
		In addition, the galactosyltransferase pseudogene present in the human genome is shared with apes and Old World monkeys (Galili and Swanson, PNAS 88:7401, 1991) although the evolutionary interpretation of these shared galactosyltransferase pseudogenes is complex because there may have been selective pressure to inactivate this enzyme (see Box 2).
	www.talkorigins.org /faqs/molgen (16141 words)

	Potentially decisive evidence against pseudogene 'shared mistakes'
		Pseudogenes can serve non-coding functions as CpG islands (stretches of DNA that are enriched in cytosine and guanine at the expense of adenine and thymine), enhancers (a type of gene regulatory sequence), and matrix attachment regions (a DNA structural feature).
		Many pseudogenes have been identified in all sorts of organisms on the grounds that they are duplicated genes that exhibit stop codons or other disabling mutations in their DNA sequences, so that they cannot have the full function of the original genes from which derived.
		The striking degree of identicalness between the ‘lesions’ of presumably non-functional pseudogenes, unrelated by evolutionary ancestry, clearly dispenses with organic evolution as a necessary explanation for this overall phenomenon.
	www.creationontheweb.com /content/view/1578 (4641 words)

	Genome Annotation Worksheet
		A significant percentage of pseudogenes continue to be transcribed even as their protein-coding capability deteriorates (lost translational start or truncated or quickly degraded protein).
		For either kind of pseudogene, a subsequent deletion (perhaps millions of years later) may have caused the truncation; only for transcriptional pseudogenes could deletion boundaries plausibly be at intron-exon boundaries of the parent gene.
		A case is known of a pseudogene unexpressed for much of its evolutionary history that was later repaired and expressed, apparently after gene conversion by the parent gene.
	www.mad-cow.org /00/worksheet.html (1239 words)

	ScienceDaily: Researchers In Japan And UCSD Discover Novel Role For Pseudogenes
		Considered defective copies of DNA segments, the 20,000 pseudogenes in the human genome are thought to be non-participants in the protein-production assembly line.
		The researchers noted that the pseudogene, makorin1-p1, is a fragmented gene similar to a full-fledged protein-coding gene called makorin1, which is located on a different chromosome.
		In mice with the disabled makorin1-p1 pseudogene, the expression of the makorin1 gene appeared weak and irregular in the diseased kidney tissue.
	www.sciencedaily.com /releases/2003/05/030501080210.htm (870 words)

	Multiple Substitutions in the von Willebrand Factor Gene that Mimic the Pseudogene Sequence -- Eikenboom et al. 91 (6): ...
		We have analyzed a type IIB and a type I von Willebrand disease family for the presence of mutations in the region coding for the glycoprotein Ib binding domain of the von Willebrand factor.
		Since this sequence is also present in the highly homologous von Willebrand factor pseudogene, we have studied genomic DNA as well as cDNA, which was produced from RNA isolated from endothelial cells or platelets.
		The occurrence of multiple adjacent substitutions that exactly reflect a part of the sequence of the von Willebrand factor pseudogene is difficult to reconcile with sequential single mutational events.
	www.pnas.org /cgi/content/short/91/6/2221 (511 words)

	A Maximum Likelihood Method for Analyzing Pseudogene Evolution: Implications for Silent Site Evolution in Humans and ...
		gene, a pseudogene derived from the protein-coding gene, and
		A prediction of this hypothesis is that, in the pseudogene lineage,
		pseudogenes are disproportionately affected is that it is the
	mbe.oxfordjournals.org /cgi/content/full/19/1/110 (5311 words)

	ARS \| Publication request: Distinctly Different Msp2 Pseudogene Repertoires in Anaplasma Marginale Strains That Are ...
		However, we recently detected animals superinfected with different strains of A. marginale and hypothesized that the msp2 pseudogene repertoire would be distinct in these superinfecting strains, consistent with encoding different sets of surface variants.
		Five strains of A. marginale were selected in order to identify and compare msp2 pseudogene content; these included strains with similar and different msp1alpha genotypes, and genotypes that were representative of the strains that were found in the superinfected animals.
		Indeed, targeted sequence analysis of msp2 pseudogenes showed identical pseudogene repertoires in genotypically closely related strains and varying amounts of dissimilarity in the pseudogene repertoire in strains with distinctly different msp1alpha genotypes, but totally different msp2 pseudogene repertoires between the strains that were found in superinfected animals.
	www.ars.usda.gov /research/publications/publications.htm?SEQ_NO_115=190857 (433 words)

	Iterative gene prediction and pseudogene removal improves genome annotation -- van Baren and Brent 16 (5): 678 -- ...
		If the processed pseudogene in human was generated after the mouse–human split, it will not be present in the orthologous region in the mouse.
		To iteratively mask pseudogenes and rerun gene prediction, PPFINDER is run with a masking step after each of the methods (conserved synteny and intron alignment).
		First, the cycle of pseudogene finding and masking is run using the conserved synteny method, until no more pseudogenes are found.
	www.genome.org /cgi/content/full/16/5/678 (5054 words)

	The putatively functional Mkrn1-p1 pseudogene is neither expressed nor imprinted, nor does it regulate its source gene ...
		sequence of the pseudogene exhibits the hallmarks of retrotransposed
		The schematic shows the Mkrn1-p1 1.6-kb pseudogene (green) with the 0.7-kb region (yellow) previously claimed to be transcribed (6).
		that mammalian pseudogenes are indeed inactive gene relics.
	www.pnas.org /cgi/content/full/103/32/12039 (4812 words)

	Polymorphisms in the prion precursor functional gene but not the pseudogene are associated with susceptibility to ...
		and pseudogene alleles in a herd of white-tailed deer with a
		the pseudogene was identical to that of mule deer [5'-(aa)gaaaattcctgaga-3'].
		The pseudogene encodes either five octa/nonapeptide repeat units identical to those in the functional gene or six repeat units, with an additional 24 bp repeat unit inserted after the second unit.
	vir.sgmjournals.org /cgi/content/full/85/5/1339 (5382 words)

	Characterization of Allelic and Nucleotide Variation Between the RAGE Gene on Chromosome 6 and a Homologous Pseudogene ...
		Characterization of Allelic and Nucleotide Variation Between the RAGE Gene on Chromosome 6 and a Homologous Pseudogene Sequence to Its 5' Regulatory Region on Chromosome 3: Implications for Polymorphic Studies in Diabetes -- Hudson et al.
		Characterization of Allelic and Nucleotide Variation Between the RAGE Gene on Chromosome 6 and a Homologous Pseudogene Sequence to Its 5' Regulatory Region on Chromosome 3
		In contrast, chromosome 6 1139 RAGE/+2298 PBX2 is a constant C nucleotide because of the absence of the 185-bp band and the presence of both the 119- and 66-bp bands.
	diabetes.diabetesjournals.org /cgi/content/full/50/12/2646 (2751 words)

	Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation -- Karro et al. 35 ...
		groups of pseudogenes that are of interest to the research community.
		pseudogenes on chromosome 22 that correspond to the protein
		In (a) the user could choose to search all human pseudogenes, resulting in the search page shown (b), which can then be configured as shown.
	nar.oxfordjournals.org /cgi/content/full/35/suppl_1/D55 (3375 words)

	[No title]
		The pseudogene is already mutated to loss of function...
		so is it that in the case where no such pseudogene has ever been reported, we can assume the one is the 'true gene';....
		To avoid amplifying the pseudogene, use DNase-treated RNA as your template.
	www.protocol-online.org /forums/index.php?showtopic=11227&view=old (726 words)

	Pseudogene.org
		The site is developed and maintained by Yale Gerstein Group.
		This site contains a comprehensive database of identified pseudogenes, utilities used to find pseudogenes, various publication data sets and a pseudogene knowledgebase.
		Pseudogenes are genomic DNA sequences similar to normal genes but non-functional; they are regarded as defunct relatives of functional genes.
	www.pseudogene.org (52 words)

	Molecular History Research Center
		The MHR Center is currently looking at possible explanations for the formation of unprocessed pseudogenes.
		Are pseudogenes the result of unsuccessful biological experiments in the Evolutionary process or are pseudogenes the product of degradation since the time when God's original creation occured?
		Preliminary evidence suggests that there might be an answer to explain the existence of identical non-functional unprocessed pseudogenes in different species such as man, chimpanzee, gorilla, gibbons, baboon and other primates.
	www.mhrc.net (335 words)

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