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TIGR Rice - Repeat Database Background Simple repeats: Based on previous experimental and bioinformatic genome analysis we know that repetitive sequences are found in tandemly repeated microsatellites (1-7 bp), longer and more complex minisatellite repeating units (up to 40 bp), and satellite DNAs with lengths of 140 to 360 bp. This Rice Repeat Database is a compilation of sequences that can aid in the identification and annotation of such elements in the rice genome. Other repeats: Analysis of rice centromeric sequences indicates that the centromere is a complex region with stretches of tandemly repeated sequences intermixed with middle repetitive sequences. www.tigr.org /tdb/e2k1/osa1/repeatinfo.shtml   (565 words)

IRLC (Inverted Repeat-lacking clade) The Inverted Repeat-lacking clade or IRLC (Wojciechowski et al., 2000), so-called because it is uniquely marked by the loss of one copy of the large inverted repeat (approx. Liston, A. Use of the polymerase chain reaction to survey for the loss of the inverted repeat in the legume chloroplast genome. Chloroplast genomes of two conifers lack a large inverted repeat and are extensively rearranged. tolweb.org /IRLC_(Inverted_Repeat-lacking_clade)/60358   (1271 words)

Welcome Where a third inverted repeat is present on a molecule, the likelihood of intramolecular movement of Tn3 is reduced. The synthesis of five bp repeats by DNA Polymerase I, joins the ends of the target molecule to the transposon and new DNA is synthesised along the lengths of the two strands of transposon DNA. Activation is caused by the strong influence of the RNA polymerase promoter regions in the terminal repeats when they are inserted into a suitable region in the vicinity of a susceptible gene, transcription of that gene occurs along with the transcription of the Ty element genes (Watson et al, 1992; Singleton and Sainsbury, 1993). www.freya.u-net.com /transposon/transpson.html   (4312 words)

Single-copy inverted repeats associated with regional genetic duplications in gamma fibrinogen and immunoglobulin genes ...   (Site not responding. Last check: 2007-09-17) We have found that a portion (150 base pairs) of the seventh exon of the human gamma fibrinogen gene is duplicated in the preceding intron. As in the fibrinogen pseudoexon, the portion of the immunoglobulin mu-delta region containing the duplication and the inverted repeat was reported to be single-copy in the mouse genome. Since both of the first two single-copy inverted repeats to be sequenced are associated with regional duplications, it is likely that many of the single-copy inverted repeat sequences, which make up 1 to 2 percent of the genome, are also associated with regional duplications. www.sciencemag.org /cgi/content/abstract/224/4645/161   (330 words)

Symmetrical Structures in Genetic Texts Direct and inverted repeats are examples of pure spatial symmetry while the potential hair pins represent the symmetry in respect to both spatial transformation and the transformation of the DNA alphabet according to the rule : {a <-> t, c <-> g}. As far as this repeat is present in SP at the fixed distance, it is possible to assume, that restrictase may play an essential role in process of replication initiation. The sequences { pa, pp } are grouped by repeats of the same six types of symmetry, as for group { ec, ea, kp, sd, st }, and the distances between repeats in the majority of cases are also strictly fixed (Fig. www.netsci.org /Science/Bioinform/feature05.html   (2211 words)

Insertion Sequences Comparison revealed that the inverted terminal repeats were in each case flanked externally by direct repeats of the same length, but of different sequence (asterisks in the above alignment). The length of the variable sequence direct repeats is characteristic of a family and varies from 3 to 12 among families. The direct repeats externally flanking the inverted repeats are not part of the insertion sequence. opbs.okstate.edu /~melcher/mg/MGW3/MG32211.html   (444 words)

Methods for the isothermal amplification of nucleic acid molecules - Patent 5354668 The sequences of the two adaptor molecules are selected such that the nucleotide sequence of the external inverted repeat sequence of the first of the two adaptor molecules is different from the external inverted repeated sequence of the second of the two adaptor molecules. The nucleotide sequence of the internal inverted repeated sequences of the two adaptor molecules is preferably the same, or at least sufficiently similar to allow the respective internal repeated sequences of the adaptor molecules to hybridize to one another. For example, the "inverted repeated sequence-inverted repeated sequence," "inverted repeated sequence-spacer sequence-inverted repeated sequence" or the "external inverted repeated sequence-internal inverted repeated sequence-internal inverted repeated sequence-external inverted repeated sequence" segment of the adaptor molecules can be obtained by cloning such a sequence, propagating the vector, and then excising the sequence using a restriction endonuclease. www.freepatentsonline.com /5354668.html   (13896 words)

3[prime]-Inverted repeats in plant mitochondrial mRNAs are processing signals rather than transcription terminators The inverted repeat structures found at the 3'-termini of mRNAs in plant mitochondria are thus recognized as processing and most likely also stabilizing signals in transcript maturation, but do not terminate transcription. The double inverted repeat located in the 3'-untranslated region of the mitochondrial pea atp9 gene (Morikami and Nakamura, 1993) was amplified by PCR between primers PA-11 (5'-GTATCGATGTAGTCCCTGAGGAC-3') and PA-12 (5'-TTATCGATGCTCTCTCCAAAACG-3') from a clone containing the type I allele of the atp1. Drager RG, Zeidler M, Simpson CL and Stern DB (1996) A chloroplast transcript lacking the 3' inverted repeat is degraded by 3' to 5' exoribonuclease activity. www.nature.com /emboj/journal/v16/n16/full/7590484a.html   (6004 words)

Interarm Interaction of DNA Cruciform Forming at a Short Inverted Repeat Sequence -- Kato et al. 85 (1): 402 -- ... Supercoiled recombinant plasmid containing the inverted repeat was treated with S1 nuclease in a reaction buffer containing 200 mM NaCl for 1 min (lane 1), 2 min (lane 2), or 5 min (lane 3) at 25°C followed by DraI digestion. Asterisks and arrows at the left of the panels indicate the positions of the inverted repeat symmetry. The plasmid pBan1 retains the inverted repeat of 17 bp complementary stretches (17 + 2 + 17 = 36 bp in total); the length of potential stem-loop may be around 6 nm (0.34 nm/bp). www.biophysj.org /cgi/content/full/85/1/402   (3819 words)

EMBOSS: einverted It will find inverted repeats that include a proprtion of mismatches and gaps (bulges in the stem loop). Secondary structures like inverted repeats in genomic sequences may be implicated in initiation of DNA replication. Maximum separation between the start of repeat and the end of the inverted repeat (the default is 4000 bases). www.psc.edu /general/software/packages/emboss/einverted.html   (608 words)

Allosteric Negative Regulation of smt O/P Binding of the Zinc Sensor, SmtB, by Metal Ions: A Coupled Equilibrium ... For example, given the clearly palindromic nature of the S2/S1 inverted repeat and the fact that SmtB exists in solution as a dissociable homodimer, it seemed reasonable to speculate that a single SmtB dimer would bind specifically to an oligonucleotide containing a single 6-2-6 core consensus sequence of the inverted repeat (3). S2xMut destroys the one half of the direct repeat as well as the inside portion of the S1 5'-TGAA sequence; this mutation was designed on the basis of a previously described mutant smt O/P characterized in vivo (13). The fundamental stoichiometry of the binding of the SmtB homodimer to a single 12-2-12 inverted repeat is two dimers per repeat, with the affinity and calorimetric enthalpy of each dimer binding increasing significantly when the number of flanking base pairs on both sides of the repeat is extended to 6 or 7 bp (Table 1). pubs.acs.org /cgi-bin/jtextd?bichaw/asap/html/bi020178t.html   (6914 words)

An Internal Rearrangement in an Arabidopsis Inverted Repeat Locus Impairs DNA Methylation Triggered by the Locus -- ... An Internal Rearrangement in an Arabidopsis Inverted Repeat Locus Impairs DNA Methylation Triggered by the Locus -- Melquist and Bender 166 (1): 437 -- Genetics An Internal Rearrangement in an Arabidopsis Inverted Repeat Locus Impairs DNA Methylation Triggered by the Locus inverted repeat (Fig 2 Fig 3 Fig 4). www.genetics.org /cgi/content/full/166/1/437   (6376 words)

Critical nucleotides in the interaction of CatR with the pheBA promoter: conservation of the CatR-mediated regulation ... The sequence of IBS is located in IS1472, between the left inverted repeat (indicated by a triangle) and the transposase gene tnpA (shown in fl) of the element. The nucleotides of the interrupted inverted repeat are underlined and the boldface italic represents the T and A residues of the conserved T-N of the interrupted inverted repeat of the RBS sequence (Fig. mic.sgmjournals.org /cgi/content/full/146/1/173   (6009 words)

Space Studies Board Baculovirus genomes are circular, iridoviruses and phage T4 have linear circular permuted genomes with terminal reduncancy, and the linear genomes of herpesviruses have sequences from both termini that are repeated internally in an inverted form. Four PBCV-1 ORFs reside in the 2.2 kb inverted terminal repeat region of the PBCV-1 genome and consequently are present twice in the PBCV-1 genome (Strasser et al., 1991; Lu et al., 1995). The termini of the chlorella virus PBCV-1 genome are identical 2.2-kbp inverted repeats. www7.nationalacademies.org /ssb/nanopanel2vanetten.html   (2961 words)

Promoter Analysis of the cap8 Operon, Involved in Type 8 Capsular Polysaccharide Production in Staphylococcus aureus ... repeat of one of the repeats was required for promoter activity. of the 10-bp inverted repeat, we constructed a strain with a mutation To determine whether the inverted repeat is required for the transcription of the cap8 genes, we compared, by RNA dot blot jb.asm.org /cgi/content/full/181/8/2492   (5243 words)

Mechanisms of sod2 Gene Amplification in Schizosaccharomyces pombe -- Albrecht et al. 11 (3): 873 -- Molecular Biology ... The proposed structure of the amplicon is shown, together with the PCR primers For 5, For 13, and Rev B. Open arrows represent the inverted repeat. sod2 is shown as a shaded oval, the inverted repeats are shown as rectangles, and the helicase/replication complex is shown as an elongated oval. After ligase seals the nick, a larger hairpin, consisting of a duplication of the region from the inverted repeat to the telomere, is formed. www.molbiolcell.org /cgi/content/full/11/3/873   (6419 words)

A Linker Region of the Yeast Zinc Cluster Protein Leu3p Specifies Binding to Everted Repeat DNA -- Mamane et al. 273 ... Hydrophobic residues found at positions a and d of the heptad repeats (dimerization domain) are in bold characters. Borders between the zinc cluster domain, the linker region, and the dimerization domains were defined according to previous studies (11, 12, 27, 28) and this work. Drawings are based on the crystal structure of the DNA binding domains of Gal4p (11) and Ppr1p (12), the analysis of Hap1p-Ppr1p chimeras (28), and Leu3p-Ppr1p chimeras (this study). www.jbc.org /cgi/content/full/273/29/18556   (4298 words)

Inverted repeat-stimulated sister-chromatid exchange events are RAD1-independent but reduced in a msh2 mutant -- Nag et ... Inverted repeats (IRs) and trinucleotide repeats (TNRs) that Inverted repeats (IRs) and trinculeotide repeats (TNRs) are A DSB formed due to nicking of the secondary structure within the triplet repeat sequence may be repaired by an intra-chromosomal single-strand annealing-like event, leading to contraction of the repeat tract. nar.oxfordjournals.org /cgi/content/full/33/16/5243   (3807 words)

BioMed Central | Full text | SmTRC1, a novel Schistosoma mansoniDNA transposon, discloses new families of animal and ... An inverted repeat motif was found at both extremities (the left with 54 bp and the right missing only one base), suggesting that this intron is an inserted mobile element (Figure 1B). A TRC element of approximately 5.2 kb was detected in the Tribolium castaneum genomic sequence [GenBank:AAJJ01002287.1], and displays at its extremities an inverted repeat of 27 bp with the sequence CCCTAGTAGCACCGAATATTTGTAAAA. Both elements have a 2 bp direct repeat adjacent to each inverted repeat (Figure 2B), suggesting that target site duplication occurred when the mobile elements were inserted, analogous to the situation in the S. www.biomedcentral.com /1471-2148/6/89   (6119 words)

untitled If a repeat sign occurs at the end of the piece, it indicates that you should repeat the entire piece once from the beginning. If a repeat sign occurs in the middle of a piece, go back to the beginning and repeat the section before going on. Here the inverted repeat sign means that you should skip the first measure when you repeat the piece. www.music-mind.com /Music/mpage6.HTM   (799 words)

Diverse Sequences within Tlr Elements Target Programmed DNA Elimination in Tetrahymena thermophila -- Wuitschick and ... Either side of the Tlr1 terminal inverted repeat is sufficient to promote programmed DNA elimination within the context of normal Tlr1 flanking sequences. Inverted repeats as genetic elements for promoting DNA inverted duplication: implications in gene amplification. Long inverted repeats are an at-risk motif for recombination in mammalian cells. ec.asm.org /cgi/content/full/2/4/678   (7131 words)

Inverted Repeat Structure of the Human Genome: The X-Chromosome Contains a Preponderance of Large, Highly Homologous ... Inverted Repeat Structure of the Human Genome: The X-Chromosome Contains a Preponderance of Large, Highly Homologous Inverted Repeats That Contain Testes Genes -- Warburton et al. Inverted Repeat Structure of the Human Genome: The X-Chromosome Contains a Preponderance of Large, Highly Homologous Inverted Repeats That Contain Testes Genes Repeat (IR) structure in the human genome, using a novel and www.genome.org /cgi/content/abstract/14/10a/1861   (529 words)

Mitochondrial Genome of the Colorless Green Alga Polytomella parva: Two Linear DNA Molecules with Homologous Inverted ... The sequences flanking the left terminus of the 13.5-kb mtDNA and the two termini of the 3.5-kb mtDNA were obtained from PCR products produced with primer pairs, including in each case an outside primer designed from the outermost region of fragment H51 and an inner sequence of the closest cloned region. Thick solid arrows near the ends of the maps denote terminal inverted repeats; the two flags within these regions represent two direct subrepeats. A 44-bp sequence is present in the repeat region downstream of nad1, that is missing from the other three repeat regions; single copies of a 7-bp sequence located at one end of and immediately following the other end of this extra 44 bp sequence are underlined. mbe.oxfordjournals.org /cgi/content/full/19/7/999   (5021 words)

Multiple inverted DNA repeats of Bacteroides fragilis that control polysaccharide antigenic variation are similar to ... Multiple inverted DNA repeats of Bacteroides fragilis that control polysaccharide antigenic variation are similar to the hin region inverted repeats of Salmonella typhimurium -- Patrick et al. Multiple inverted DNA repeats of Bacteroides fragilis that control polysaccharide antigenic variation are similar to the hin region inverted repeats of Salmonella typhimurium fragilis NCTC 9343 inverted repeat regions (fix1–7) at the left (top strand) and right (inverse bottom strand) end of the invertible regions upstream of PS biosynthesis loci 1–7 with the promoter in the correct orientation for PS expression and top-strand left-hand inverted repeats of the ‘Hin’ family (hix, pix, cix, gix, M. mic.sgmjournals.org /cgi/content/full/149/4/915   (3797 words)

C. elegans Project With the advent of genomic sequence a number of repeat families have now been determined. victor is a subset of the Tc3 terminal inverted repeat Sanford C. and Perry M.D. Asymmetrically distributed oligonucleotide repeats in the Caenorhabditis elegans genome sequence that map to regions important for meiotic chromosome segregation. www.sanger.ac.uk /Projects/C_elegans/REPEATS   (359 words)

Interaction of EF-C/RFX-1 with the Inverted Repeat of Viral Enhancer Regions Is Required for Transactivation -- David ... EF-C is a ubiquitous binding activity that interacts with an inverted repeat sequence in the HBV and Py enhancer regions. To test the possibility that the interaction of EF-C with a Py EF-C site inverted repeat may be intrinsically more stable than binding to the RFX DRA half-site, we performed off-rate analyses using these sites with purified EF-C as shown in Fig. Nuclear factor EF-C binds as a dimer to inverted repeat sequences in the polyomavirus and hepatitis B virus enhancer regions (Fig. www.jbc.org /cgi/content/full/270/14/8353   (6453 words)

An imperfect inverted repeat is critical for DNA binding of the response regulator RegR of Bradyrhizobium japonicum -- ... An imperfect inverted repeat is critical for DNA binding of the response regulator RegR of Bradyrhizobium japonicum -- Emmerich et al. An imperfect inverted repeat is critical for DNA binding of the response regulator RegR of Bradyrhizobium japonicum an imperfect inverted repeat in the fixR UAS (GCGAC-N nar.oxfordjournals.org /cgi/content/full/28/21/4166   (3638 words)

Gene Expression Induced by Copper Stress in the Diatom Thalassiosira pseudonana -- Davis et al. 5 (7): 1157 -- ... inverted repeats in the genome, and novel genes in one inverted The figure is shown to scale except for the intervening region between the inverted repeats, which is indicated by a double bar. Nitrate reductase (NR) was identified in a subtracted cDNA library enriched in genes down-regulated by 1 h of copper exposure and is included as an example of a down-regulated gene. ec.asm.org /cgi/content/full/5/7/1157   (6570 words)

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