
	Where results make sense

Topic: Alu repeats

Related Topics

Transposon

Breast cancer

White carrot

Recombination

Antihistamine

Offutt AFB, Nebraska

Kamchadal

PPG 16

Hualalai

Circulatory system

Tetbury

Chromatography

Jim Black

Retroperitoneal

Pancreas

In the News (Mon 6 Jul 09)

Northern Trust

Marvin Harrison

Peter Chernin

Gary Locke

Match Play

Penelope Cruz

Mickey Rourke

AR Rahman

Danny Boyle

Hugh Jackman

	Alu sequence - Wikipedia, the free encyclopedia
		The Alu endonuclease is so-named because it was isolated from Arthrobacter luteus.
		The recognition sequence of the Alu endonuclease is 5' AG/CT 3'; that is, the enzyme splits the DNA segment between the guanine and cytosine residues.
		Alu sequences in primates form a fossil record that is relatively easy to decipher because Alu sequence insertion events have a characteristic signature that is both easy to read and faithfully recorded in the genome from generation to generation.
	en.wikipedia.org /wiki/Alu_sequence (486 words)

	Quantifying the mechanisms for segmental duplications in mammalian genomes by statistical analysis and modeling -- Zhou ...
		Mode 1 may have been caused by the random pairing of Alu repeats that are not related to duplications in the flanking regions, or by erosions in the duplicated sequences due to mutation accumulation after the initial duplication events.
		The shifts in the positions of the matching repeats could have been caused by insertions and deletions after the initial duplication events or the random pairing of Alu repeats that are not related to the duplication process in the flanking regions.
		The fitting of the model to the distribution of Alu and long interspersed transposable element 1 (L1) repeats in the duplication flanking regions in the human genome hg15 assembly, and the distribution of L1 repeats in mouse (mm3) and rat (rn3) genomes.
	www.pnas.org /cgi/content/full/0407957102/DC1 (1424 words)

	Mark A. Batzer
		Many of these "young" Alu repeats have inserted so recently within the human genome that individuals can be polymorphic for the presence or absence of an Alu element at a particular chromosomal location.
		First, the presence of an Alu element represents identity by descent, since the probability that two different young Alu repeats would integrate independently in the same chromosomal location is negligible.
		Second, the ancestral state of each Alu insertion polymorphism is known to be the absence of the Alu element, which can be used to root trees of population relationships.
	www.biology.lsu.edu /faculty_listings/fac_pages/mbatzer.html (529 words)

	Not just junk - Deccan Herald (Site not responding. Last check: 2007-11-01)
		“Repeats like Alu may have key roles in regulating the functions of other genes and hereby making a difference between a human and a fly,” says Dr Mukherjee, stressing that her studies have indicated towards a possible correlation between these so-called useless repeats and gene functions.
		Alu repeats appear to play a role in the development of a particular type of blood cancer as well as in blood pressure regulation.
		A statistically significant correlation between Alu and gene densities across various human chromosomes indicates that gene density is a major factor for Alu accumulation within a particular chromosome and these elements are actually preferred in genes.Some of the Alu repeats, might also be the evolutionary relics of the past.
	www.deccanherald.com /deccanherald/jan222004/snt2.asp (592 words)

	BioMed Central \| Full text \| The association of Alu repeats with the generation of potential AU-rich elements (ARE) at ...
		Alu repeats are sequences of approximately 300 nucleotides (nt) transcribed by RNA polymerase III.
		Alu amplification appears to have reached a maximum rate between 35 and 60 mya, and is currently amplifying at only 1% of the maximum rate [26].
		Alu repeats account for 6–13% of the human genome [31] and were identified in 5% of 1,616 human full-length cDNA.
	www.biomedcentral.com /1471-2164/5/97 (3221 words)

	Glossary
		The Alu family of retroposons is present at an extremely large copy number within the human genome (500,000 copies/genome equivalent), represent approximately 10% of the mass of the human genome.
		Alu retroposons have been divided into subfamilies of related sequences based on nucleotide divergence that appear to be of different genetic ages.
		The distribution of the polymorphic Alu insertions appears to be variable within members of the human population from different geographic origins, and is not random along individual human chromosomes.
	www.sanger.ac.uk /Software/formats/glossary (656 words)

	The Panda's Thumb: Evolvability: ALU repeats and hominid phylogenetics
		ALU repeats are transponson related repeats about 250-300 base pairs long and unique to the genome of primates.
		ALU repeats are very common, perhaps as many as one ALU repeat per 3000 base pairs.
		ALU repeats are believed to be very suitable for tree reconstruction since they are essentially unidirectional, in other words, once they appear, they are hard to remove from the genome.
	www.pandasthumb.org /archives/2004/10/evolvability_al.html (1324 words)

	[Full text] A SINE in the genome of the cephalochordate amphioxus is an Alu element
		A SINE in the genome of the cephalochordate amphioxus is an Alu element.
		The best-known SINEs are the Alu elements of primates, which are thought to have a common origin with the B1 elements of rodents [1, 3, 4].
		Alu elements have previously been described only in primates [15], raising the question of whether Amphi-Alu and primate Alu elements are descended from a common ancestral Alu, or whether the presence of Alu sites in these two SINEs from primates and amphioxus represent convergent evolution.
	www.biolsci.org /v02p0061.htm (2784 words)

	[No title]
		Alu / Palu dataset BACKGROUND ---------- A possible artifact of genomic sequencing is to overlook common repeat elements, and eventually incorporate them into erroneous coding regions.
		While scanning Swissprot or Pir with a newly determined amino-acid sequence, any significant similarity with one of these Alu entries should be taken as a serious warning that the coding region determination might be wrong (usually a stop codon is missed due to a frame shift error).
		Alu sequences are common within vertebrate introns and appear with a 10% frequency in partial cDNA sequences (either due to Alu being presentin 3' untranslated regions, partially spliced mRNAs, true Alu transcription, or genomic DNA contamination).
	blast.wustl.edu /pub/jmc/alu/HELP.Alu.6.OLD (646 words)

	ALFRED
		HS4.14 polymorphic Alu element belongs to the young (Ya5/8) subfamily of human-specfic Alu repeats.
		The composition of the 3' oligo (dA) tail is denoted by the appropriate nucleotide in parenthesis followed by the length in subscripts.
		The nucleotide sequences comprising the flanking direct repeats of each Alu element are in bold.
	alfred.med.yale.edu /alfred/recordinfo.asp?UNID=SI000821L (172 words)

	[No title]
		The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).
		On average, interspersed repeats have diverged 18% in human (~35% in mouse) from their consensus since the mammalian orders separated, so typing '-div 18' in the advanced options box limits masking to most primate specific repeats.
		Interspersed repeats are specific to a (group of) species, dependent on the time of activity of the source transposable element.
	www.repeatmasker.org /webrepeatmaskerhelp.html (6035 words)

	Widespread RNA Editing of Embedded Alu Elements in the Human Transcriptome.
		Alu elements are divided into several subfamilies whose relative ages are estimated based on sequence divergence from an Alu consensus sequence.
		Almost all Alus, except for the youngest AluY subfamily, are fixed in the human population (Batzer and Deininger 2002).
		Thus, from an evolutionary perspective, dimerization of the Alu structure (doubling of Alu length by fusing left and right monomers) and the subsequent burst of Alu retrotransposition during early primate evolution (Batzer and Deininger 2002) have likely contributed to the elevated level of repeat-associated RNA editing in humans.
	www.euchromatin.com /KimDDY01.htm (5565 words)

	Repetitive DNA
		These may be short repeats just a few nt long, like CACACA etc. They can also range up to a few hundred nt long.
		In shorter repeats like di- and tri-nucleotide repeats, the number of repeating units can occasionally change during evolution and descent.
		They are thus useful markers for familial relationships and have been used in paternity testing, forensic science and in the identification of human remains.
	www.iscid.org /encyclopedia/Repetitive_DNA (118 words)

	Characterization of Alu Repeats That Are Associated with Trinucleotide and Tetranucleotide Repeat Microsatellites -- ...
		Characterization of Alu Repeats That Are Associated with Trinucleotide and Tetranucleotide Repeat Microsatellites -- Yandava et al.
		Characterization of Alu Repeats That Are Associated with Trinucleotide and Tetranucleotide Repeat Microsatellites
		The poly(A) tract of Alu repetitive elements is polymorphic in the human genome.
	www.genome.org /cgi/content/full/7/7/716 (3221 words)

	Bioinformatics Lab at UCSD (Professor Pevzner's Group) - Software
		Alu repeats are the most abundant family of repeats in the human genome, with over 1 million copies comprising 10% of the genome.
		Alu repeat elements are believed to have arisen from the replication of a small number of source elements, whose evolution over time gives rise to the 31 Alu subfamilies currently reported in Repbase Update.
		Read assignment in repeat regions are often ambiguous, causing errors in base-assignment in the final assembly.
	www-cse.ucsd.edu /groups/bioinformatics/software.html (1750 words)

	Batzer Laboratory featured on the cover of Genome Research
		The stealth Alu element, represented by the shadow of the Stealth Fighter aircraft, generates proxy active source elements (represented by yellow Alu RNA secondary structures).
		Only the active elements are conspicuous to the "genomic radar" of selection (depicted as blips on the radar screen) and, thus, are purged from the population.
		In contrast, the stealth driver element and nonactive Alu elements remain undetected and exist under the genomic radar.
	www.biology.lsu.edu /highlights/batzer_gr.html (597 words)

	Sperm nuclear matrix association of the PRM1{->}PRM2{->}TNP2 domain is independent of Alu methylation -- Schmid et al. ...
		Alu elements that are evolutionarily young tend to
		Positions of the Alu repeats surrounding the matrix attachment region (MAR) are shown as arrows indicating their orientation.
		Rubin, C.M., Vandevoort, C.A., Teplitz, R.L. and Schmid, C.W. (1994) Alu repeated DNAs are differentially methylated in primate germ cells.
	molehr.oxfordjournals.org /cgi/content/full/7/10/903 (4446 words)

	Alu Insertion Polymorphisms for the Study of Human Genomic Diversity -- Roy-Engel et al. 159 (1): 279 -- Genetics
		Alu Insertion Polymorphisms for the Study of Human Genomic Diversity -- Roy-Engel et al.
		Alu subfamilies derived from the Alu Y and Yb8 subfamilies.
		The origins of the Yb9, Yc1, and Yc2 Alu subfamilies are shown after the divergence of the Yb8 and the Y subfamily, respectively.
	www.genetics.org /cgi/content/full/159/1/279 (3552 words)

	Initial Sequencing and Analysis of the Human Genome.
		It is possible to recognize cohorts of repeats 'born' at the same time and to follow their fates in different regions of the genome or in different species.
		Bases covered by interspersed repeats were sorted by their divergence from their consensus sequence (which approximates the repeat's original sequence at the time of insertion).
		The repeats in the other organisms may have been slightly underestimated because the repeat databases for the other organisms are less complete than for the human, especially with regard to older elements; on the other hand, recent additions to these databases appear to increase the repeat content only marginally.
	www.euchromatin.org /Collins1.htm (16299 words)

	AluGene: a database of Alu elements incorporated within protein-coding genes -- Dagan et al. 32 (Supplement 1): D489 -- ...
		Alu sequences are scattered throughout incompatible and unconnected
		Alu repeats of different evolutionary ages have been identified.
		Alu sequence was aligned to the consensus sequence of its subfamily
	nar.oxfordjournals.org /cgi/content/full/32/suppl_1/D489 (2523 words)

	SINE Insertions in Cladistic Analyses and the Phylogenetic Affiliations of Tarsius bancanus to Other Primates -- ...
		PCR analyses of orthologous Alu elements, their target sites, and a diagrammatic representation of their location corresponding to the human representative (drawn to scale) in primate and nonprimate outgroups.
		Alu repeats were identified as members of the human Alu J subfamily
		PCR analyses of nonorthologous Alu elements and a diagrammatic representation of their location in primates corresponding to the human representative (drawn to scale).
	www.genetics.org /cgi/content/full/157/2/777 (4405 words)

	FuturePundit: What Drove Divergence Of Humans From Chimpanzees?
		The spread of the Alu DNA repeats was written into the chemistry of human chromosomes.
		I question Dugaiczyk's assertion that the spread of Alu repeats was not selected for.
		But possibly a mechanism that increased the rate at which Alu repeats accumulated was selected for.
	www.futurepundit.com /archives/002333.html (1623 words)

	BLAST Help Document
		Furthermore, in some cases, sequences are masked in their entirety, indicat ing that the statistical significance of any matches reported against the unfil tered query sequence should be suspect.
		Filtering for repeats can inc rease the speed of a search especially with very long sequences (>100 kb) and a gainst databases which contain large number of repeats (htgs).
		Human Repeat F iltering is still experimental and under development, so it may change in the n ear future.
	www.swbic.org /origin/proc_man/Blast/blastcgihelp.html (2074 words)

	CIS526 Demo Lecture
		Furthermore, in some cases, sequences are masked in their entirety, indicating that the statistical significance of any matches reported against the unfiltered query sequence should be suspect.
		Filtering for repeats can increase the speed of a search especially with very long sequences (>100 kb) and against databases which contain large number of repeats (htgs).
		Human Repeat Filtering is still experimental and under development, so it may change in the near future.
	distancelearning.ksi.edu /demo/526/cis526.htm (5264 words)

	RNA polymerase III transcribes human microRNAs - Nature Structural & Molecular Biology (Site not responding. Last check: 2007-11-01)
		This miRNA-Alu arrangement is remarkable; 42 of 43 miRNAs are separated from proximal Alus by an average of 100 bp.
		Additionally, Alus found upstream of the miRNAs within C19MC belong to either the AluJ or AluS subfamilies, and, as evolutionarily older Alu sequences, they are probably not retrotranspositionally active.
		Transcripts arising from these 3' Alus would typically consist of only one stem of the pre-miRNA, as approximately 74% contain a Pol III terminator (TTTT) between the two stems of the pre-miRNA (Supplementary Table 4) when read from the negative-strand Alu.
	www.nature.com /nsmb/journal/v13/n12/full/nsmb1167.html (3720 words)

	Interindividual variability and parent of origin DNA methylation differences at specific human Alu elements -- ...
		Alu repeats are differentially methylated in germ cells, with
		Alu insertions with parent of origin methylation differences are typed in bold: those labeled in blue are Alu insertions exhibiting stronger methylation through paternal meiosis and the single insertion labeled in red indicates the Alu insertion with stronger methylation after maternal meiosis.
		Rubin, C.M., Vande Voort, C.A., Teplitz, T.L. and Schmid, C.W. (1994) Alu repeated DNAs are differentially methylated in primate germ cells.
	hmg.oxfordjournals.org /cgi/content/full/14/15/2135 (4241 words)

	Homologous and Nonhomologous Recombination Resulting in Deletion: Effects of p53 Status, Microhomology, and Repetitive ...
		In contrast to the observed stability of repeats in p53 wild-type cells, when the plasmid variants were integrated into two
		repeat may be a hot spot for p53 action.
		repeat to excise the 3' arm of the hairpin.
	mcb.asm.org /cgi/content/full/20/11/4028 (4947 words)

	Humans march to a faster genetic 'drummer' than primates, UC Riverside research says (Site not responding. Last check: 2007-11-01)
		Or maybe he's just speaking poorly, and he means that once the cellular environment was altered (presumably randomly) in order to favor heightened Alu production, the outcome (i.e., increased Alu repeats) was a deterministic result of that modified environment, and was not itself due to additional random Alu introductions.
		It would mean that the Alu repeats were not involved in whatever DNA differences made us human.
		The result of the Alu repetitions were not "silent" -- that is, they made some contribution to whatever DNA differences make us human.
	www.freerepublic.com /focus/f-news/1203812/posts (5242 words)

	Chapter 4: Bioinformatics and Functional Genomics
		Translations of select Alu repeats from REPBASE, suitable for masking Alu repeats from query sequences.
		Genome Survey Sequence, includes single-pass genomic data, exon-trapped sequences, and Alu PCR sequences.
		Select Alu repeats from REPBASE, suitable for masking Alu repeats from query sequences (available by anonymous FTP from ncbi.nlm.nih.gov under the /pub/jmc/alu directory).
	www.bioinfbook.org /chapt4.htm (258 words)

	FISH guide - Alu-PCR, Alu-banding
		Although hybridizations with nick-translated and interAlu-PCR labeled YACs may yield similar FISH results, it is likely that interAlu-PCR does not really amplify the human sequence 100%, as the amplification depends on the density and orientations of the Alu repeats in the clone.
		The 77mer primer and the PCR products probably hybridize on more defined, longer Alu sequences, and the banding pattern becomes visible.
		Alu banding can be used along during FISH with other probes, to help identify human chromosomes.
	info.med.yale.edu /genetics/ward/tavi/fi11.html (431 words)

Try your search on: Qwika (all wikis)