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Topic: Repeat When Necessary

    Note: these results are not from the primary (high quality) database.

Table of Contents Moreover, the presence of the trinucleotide repeat in SRP14 DNA and the corresponding C-terminal tail in SRP14 are associated with a significant increase in SRP14 polypeptide and Alu RNA-binding activity. Sequences containing Alu repeats were eliminated because unique primers could not be designed. Forty-four of the 57 cloned Alu repeats were monomorphic in the sample and 13 Alu repeats were dimorphic for insertion presence/absence. www.chronicillnet.org /reports/ci_report_8.html

Inverted repeat -- Facts, Info, and Encyclopedia article An inverted repeat is a sequence of (A phosphoric ester of a nucleoside; the basic structural unit of nucleic acids (DNA or RNA)) nucleotides that is the reversed complement of another sequence further downstream. Inverted repeats define the boundaries in (A segment of DNA that can become integrated at many different sites along a chromosome (especially a segment of bacterial DNA that can be translocated as a whole)) transposons. Inverted repeat -- Facts, Info, and Encyclopedia article www.absoluteastronomy.com /encyclopedia/i/in/inverted_repeat.htm   (77 words)

[Frontiers in Bioscience 3, d408-418, March 27, 1998] The inverted repeat is illustrated by the opposing arrows. Anticipation is associated with expansion of the triplet repeat sequence in the disease associated gene. Figure 3: Deletion mutation of DNA mediated by an inverted repeat. www.bioscience.org /1998/v3/d/bissler/7.htm   (2869 words)

Inverted repeat - Wikipedia, the free encyclopedia An inverted repeat is a sequence of nucleotides that is the reversed complement of another sequence further downstream. When no nucleotides intervene between the sequence and its downstream complement, it is called a palindrome. en.wikipedia.org /wiki/Inverted_repeat   (60 words)

Rednova NEWS Interarm interaction of DNA cruciform forming at a short inverted repeat sequence An inverted repeat consisting of 17 bp complementary sequences was isolated from the bluegill sunfish Lepomis macrochirus (Perciformes) and subcloned into the pUC19 plasmid, after which the supercoiled recombinant plasmid was subjected to enzymatic and chemical modification. The inverted repeat sequences of the guanine-rich 5'-half are expected to have a higher potential of forming the hairpin triplex. According to the hairpin triplex model, one 5'-half of the inverted repeat becomes the third strand and should be arranged in parallel with the 5'-half of the stem-loop structure, as shown in Fig. www.rednova.com /modules/news/tools.php?tool=print&id=11380   (4325 words)

Interspersed Repeats Moreover, for short or highly diverged repeats, the joined portions may be detectable when the separated pieces are not. Primates have Alu elements and mice have B1, B2, etc. The process of insertion of a LINE or SINE into the genome causes a short sequence (7-21 bp for Alus) to be repeated, with one copy (in the same orientation) at each end of the inserted sequence. The Alu family descended from 7SL RNA (a component of the signal recognition particle), as did the mouse B1 repeats, and because of this, an Alu and a B1 will be recognizably similar in a sequence comparison. globin.cse.psu.edu /globin/html/courses/spring2000/repeats.html   (4325 words)

Tandem repeat - Wikipedia, the free encyclopedia Tandem repeats can be very useful in determining parentage. Tandem repeats and variable number tandem repeats in DNA are two or more This is a term from genetics, which describes a pattern that helps determine an individual's inherited traits. en.wikipedia.org /wiki/Tandem_repeat   (4325 words)

Pharyngula::Tandem repeats and morphological variation Tandem repeats are subject to very high mutation rates, up to 100,000 times greater probability than a point mutation, because they are prone to a kind of error called slipped-strand mispairing. Tandem repeats are short lengths of DNA that are repeated multiple times within a gene, anywhere from a handful of copies to more than a hundred. These tandem repeats are common in the vertebrate genome, so this could clearly be a reservoir of variation and a robust and flexible way to add new variations to a population. pharyngula.org /index/weblog/comments/tandem_repeats_and_morphological_variation   (4325 words)

Maintenance of heterochromatin by RNA interference of tandem repeats - Nature Genetics The reverse strand of the pericentromeric repeats of fission yeast is transcribed. Tandem repeats are prone to epigenetic silencing regulated by RNA interference. A similar mechanism could maintain heterochromatin through RNAi of transcribed tandem repeats. www.nature.com /ng/journal/v35/n3/full/ng1252.html   (4325 words)

The Scientist :: Tandem repeats take, make shape , Dec. 14, 2004 Tandem repeat units can be added or subtracted by slipped-strand mispairing during DNA replication. Tandem repeats of sequences in developmental genes may contribute to morphological evolution, according to a paper in this week's PNAS. They found repeat polymorphisms in at least one of the repeats in every species, which suggests that tandem repeat lengths may also control morphology in these species, Fondon said. www.biomedcentral.com /news/20041214/01   (4325 words)

Directory of open access journals Tandem repeats contained within coding regions can mediate phase variation when the repeated units change the reading frame of the coding sequence in a copy number dependent manner. Coding tandem repeats are those which do not alter the reading frame with copy number, and the changes in copy number of these repeats may then potentially alter the function or antigenicity of the protein encoded. Of these, 22 contain coding tandem repeats that vary in copy number between the three sequenced strains, three strain specific genes were included for investigation on the basis of having >90% identity between repeated units, and three genes with repeated elements of >250 bp were included although no length variations were seen in the genomes. www.doaj.org /abstract?id=83032&toc=y   (4325 words)

COUNTERPOINT - LoveToKnow Article on COUNTERPOINT The plaintive expression of the whole variation is largely due to the fact that the flowing semiquaver counterpoint below the main theme is on each repeat inverted in the 12th, with the result that its chief emphasis falls upon the most plaintive parts of the scale. Moreover, the artistic value of the device is at its highest in three-part polyphonic harmony, which, whether invertible or not, is always a fine test of artistic economy, while the inversions are as evident to the ear, especially where the top part is concerned, as those in double counterpoint. Two of the most striking illustra- tions of this effect are to be found in the last chorus of Brahmss Triumphlied and in the fourth of his variations on a theme by Haydn. 99.1911encyclopedia.org /C/CO/COUNTERPOINT.htm   (1282 words)

Delila Program: rep repeats that meet the criteria of minimum length and minimum and/or maximum distance between half repeats are reported in fout. helices are interpreted as repeats, direct or inverted depending upon the input sequences. * distance: if direct repeats, the number of bases from five prime end to five prime end of each repeat; if inverted repeats, the number of bases from three prime end to five prime end (i.e., pseudo-loop distance). www-lmmb.ncifcrf.gov /~toms/delila/rep.html   (396 words)

Inverted repeat near position 46500 The inverted repeat can extend from position 46384 to 46422 and from 46495 to 46534; however, this repeat is only at 87% sequence identity. The sequence from positions 46407 to 46422 and from 46495 to 46510 comprise a 16-bp inverted repeat. nucleus.cshl.org /protarab/T10M13-IR1-annotation.html   (57 words)

Amplification of a Circular Episome Carrying an Inverted Repeat of the DFR1 Locus and Adjacent Autonomously Replicating Sequence Element of Saccharomyces cerevisiae -- Huang and Campbell 270 (16): 9607 -- Journal of Biological Chemistry In particular, the inverted repeat structure and the association of a putative origin of replication is similar to a recently characterized mouse ADA amplisome (14, 28), although the extent of the amplified region is much smaller in yeast. Inverted repeats are a common, though not invariant, feature of both episomal and chromosomal amplified DNAs (18). The second class of models, that is, intrachromosomal formation of the inverted duplication, is embodied by the chromosomal spiral model of gene amplification (20). www.jbc.org /cgi/content/full/270/16/9607   (7153 words)

BioMed Central Full text The association of Alu repeats with the generation of potential AU-rich elements (ARE) at 3' untranslated regions. Alu repeats are sequences of approximately 300 nucleotides (nt) transcribed by RNA polymerase III. Alu repeats account for 6–13% of the human genome [ 31 ] and were identified in 5% of 1,616 human full-length cDNA. 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 ]. www.biomedcentral.com /1471-2164/5/97   (7153 words)

Repetitive DNA In shorter repeats like di- and tri-nucleotide repeats, the number of repeating units can occasionally change during evolution and descent. These may be short repeats just a few nt long, like CACACA etc. They can also range up to a few hundred nt long. 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   (7153 words)

INVARIANT SECONDARY STRUCTURE OF ALU REPEATS PREDETERMINES CLUSTERIZATION OF REGULATORY ELEMENTS IN HUMAN GENOME Alu repeats are divided into several families, differing in their evolutionary age, basing on DNA divergence and certain "diagnostic" substitutions. Hence, the increasing volume of data concerning the role of Alu repeats in regulation of cell differentiation and tissue-specific gene expression are not unexpected. Thus, a discrete location of Alu repeats in the genome reflects not only the traces of Alu expansion but is also likely to be connected with a novel function: alternative interaction between Alu repeats that determines the dynamic unfolding of the information contained in the genome (Alu code). www.bionet.nsc.ru /bgrs/thesis/89   (7153 words)

Inverted Alu repeats unstable in yeast are excluded from the human genome -- Lobachev et al. 19 (14): 3822 -- The EMBO Journal Ruskin,B. and Fink,G.R. (1993) Mutations in POL1 increase the mitotic instability of tandem inverted repeats in Saccharomyces cerevisiae. Henderson,S.T. and Petes,T.D. (1993) Instability of a plasmid borne inverted repeat in Saccharomyces cerevisiae. The length of the spacer region separating the Alu repeats and the extent of homology in the Alu pairs are shown. embojournal.npgjournals.com /cgi/content/full/19/14/3822   (7153 words)

Cancer Immunity 3:3 (2003) Antisera to the tandem repeat region detected the recombinant protein, and this binding was blocked by the addition of the immunizing peptide. In this context, antibody responses to the extracellular tandem repeat domain of MUC1 are frequently observed, especially in breast and ovarian cancer patients, and have been shown to have prognostic significance ( 7). Analysis of the sequence of OGFr revealed similarities between the carboxyl-terminal tandem repeats of this protein and the tandem repeats in the extracellular domain of MUC1 (20% identity, Figure 1), with striking positional conservation of 4 of the 5 prolines in each repeat ( 11, 12). www.cancerimmunity.org /v3p3/030203.htm   (7153 words)

BioMed Central Full text Identification of polymorphic tandem repeats by direct comparison of genome sequence from different bacterial strains : a web-based resource Tandem repeats in pathogenic bacteria were initially identified within genes associated with bacterial virulence [ 11, 12 ]. The finding that polymorphic tandem repeats have, on average, a higher internal conservation, total length, and copy number than monomorphic ones is in agreement with previous observations that TR polymorphism is correlated with conservation in Yersinia pestis and with total length in Bacillus anthracis [ 9 ]. We compared the distribution of tandem repeats sequence characteristics among the group of "polymorphic" loci (differing in at least two of the strains compared, excluding length differences between strains that resulted from microdeletions in the flanking sequences) and the others. www.biomedcentral.com /1471-2105/5/4   (7153 words)

DNA Repeats Repeats with pattern size in the range from 1 to 500 bases are detected. A tandem repeat in DNA is two or more adjacent, approximate copies of a pattern of nucleotides. Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences. www.hgmp.mrc.ac.uk /GenomeWeb/nuc-repeats.html   (7153 words)

Eva Strawbridge If the repeat length is long and the loop length is small, then in order to prevent cruciform extrusion, the inverted repeat may be "imperfect" and therefore have a higher energy when extruded, thereby possibly preventing the formation of a cruciform. In simplified terms, for a given loop size (the number of base-pairs between the inverted repeats), the greater the number of base-pairs in the repeat, the greater the likelihood of extrusion. Consequently, one would expect that the distribution and location of inverted repeats in Eukaryotes would reflect a more stable environment in which the replication functions of DNA are still maintained but the danger of mutation is minimized. genomics.ucdavis.edu /strawbridge.html   (305 words)

PhD.html The upstream half of the nrd inverted repeat was shown to be essential for nrd cell cycle regulation. A 45 bp inverted repeat was found to be required for nrd induction during DNA synthesis inhibition. Alterations in the downstream half of the inverted repeat decreased nrd expression, however, this mutant induced expression during thymine starvation. biosci.cbs.umn.edu /~blake/PhD.html   (336 words)

PG-I: 28pg1 In order to characterize the number and location of replication origins, subclones of the inverted repeat and adjacent regions are being prepared for in vitro DNA replication reactions using a partially purified tobacco chloroplast enzyme fraction. Significant hybridization was observed only to the Sal 1 and 4 fragments in the inverted repeat region near the rRNA genes, similar to the location which has been reported in other chloroplast genomes. This location agrees with the single D-loop in each inverted repeat recently reported for tobacco proplastid DNA from cultured cells [Y. Takeda, H. Hirokawa and T. Nagata, Mol. www.intl-pag.org /1/abstracts/28pg1.html   (336 words)

[Frontiers in Bioscience 3, d408-418, March 27, 1998] a 136 bp inverted repeat that is unstable when cloned into a bacterial system (43, 44). Inverted repeats whether perfect or imperfect are imbedded in genomes and have critical functions. The SV40 virus contains inverted repeats that are critical for DNA replication; however, evidence thus far suggests their function is the linear form (42). www.bioscience.org /1998/V3/d/bissler/6.htm   (602 words)

Developmentally Regulated Excision of a 28-Base-Pair Sequence from the Paramecium Genome Requires Flanking DNA -- Ku et al. 20 (22): 8390 -- Molecular and Cellular Biology The previously identified inverted repeats that are adjacent to the flanking TA are indicated by thin arrows, and the perfect 8-bp inverted repeat flanking the element (identified in this study) is indicated by thick arrows and underlines. (B) The inverted repeats flanking (underlined) and adjacent to the 29-bp internal IES of IES6649. Consensus inverted terminal repeat sequence of Paramecium IESs: resemblance to termini of Tc1-related and Euplotes Tec transposons. mcb.asm.org /cgi/content/full/20/22/8390   (5024 words)

Energy Citations Database (ECD) - Energy and Energy-Related Bibliographic Citations The mechanism of dynamic mutation is discussed, and a number of observations of simple tandem repeat mutation that could assist in understanding this phenomenon are commented on. Arrays of up to 5 or 6 nt are known as simple tandem repeats, and these are widely dispersed and highly polymorphic. Members of one group of the simple tandem repeats, the trinucleotide repeats, can undergo an increase in copy number by a process of dynamic mutation. www.osti.gov /energycitations/product.biblio.jsp?osti_id=96324   (5024 words)

Independently Regulated Neocentromere Activity of Two Classes of Tandem Repeat Arrays -- Hiatt et al. 14 (2): 407 -- THE PLANT CELL Chromatin is shown in white, the 180-bp repeat is shown in green, and the TR-1 repeat is shown in orange. In (E) and (F), the chromatin is shown in lavender, the centromere repeat CentC is shown in magenta, and the 180-bp knob repeat is shown in white. primarily of the 180-bp repeat (14 of 28 knobs in the strains www.plantcell.org /cgi/content/full/14/2/407   (5024 words)

Algorithms for Detection and Analysis of Tandem Repeats in DNA Sequences by Gary Benson Tandem repeats occur frequently in the human genome, including the centromeres and telomeres which are important chromosomal components. An interesting feature of tandem repeats is that the duplicated copies are preserved together, making it possible to do "phylogenetic analysis" on a single sequence. In this process, a stretch of nucleotides is duplicated to produce two or more adjacent copies, resulting in a tandem repeat. www.ima.umn.edu /biology/wkshp_abstracts/benson1.html   (5024 words)

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