Repeated sequences sequence analysis

Horie N, Aiba H, Oguro K et al. Functional analysis and DNA polymorphism of the tandemly repeated sequences in the 5 -terminal regulatory region of the human gene for thymidylate synthase. Cell Stmct Funct 1995 20 191-197. 

Sequence analysis of cDNA clones shows that the 540-bp consensus repeats on DNA segment B, H, and O1 are contained within an open... 

Figure 15. Statistical analysis of the sharp jumps detected in the S profiles of the 22 human autosomal chromosomes by the WT microscope at scale a = 200 kbp for repeat-masked sequences [38, 39]. AS = S(3 ) — S(5 ), where the averages were computed over the two adjacent 20-kbp windows, respectively, in the 3 and 5 direction from the detected jump location, (a) Histograms Af( AS ) of AS values, (b) A( AS > AS ) versus AS. In (a) and (b), the black (respectively, grey) line corresponds to downward AS < 0 (respectively, upward AS > 0) jumps. R = 3 corresponds to the ratio of upward over downward jumps presenting an amphmde AS > 12.5% (see text).

Figure 16. Statistical analysis of the sharp jumps detected in the S profiles of the 22 human autosomal chromosomes by the WT microscope at scale a — 200 kbp for repeat-masked sequences [109]. The detected jumps have been classified into three categories according to the GC content found in a 100-kbp window centered at the position of the jump. Same as in Fig. 15 (a, a )...

Kawakami K, Watanabe G. Identification and functional analysis of single nucleotide polymorphism in the tandem repeat sequence of thymidylate synthase gene. Cancer Res 2003 63 6004-6007. 

Studies of overall genome composition based on reassociation kinetics (Simpson et ai, 1982 Cox et ai, 1990 Marx et a/., 2000) and analysis of fully sequenced bacterial artificial chromosome (BAC) clones from the 5. mansoni genome project show that platyhelminth genomes contain abundant highly and moderately repetitive sequence (Fig. 2.1). Much of the repetitive DNA comprises two classes of integrated mobile elements class I elements, which include long terminal repeat (LTR) retrotransposons and retroviruses, non-LTR retro-transposons and short interspersed nuclear elements (SINES) and transpose via an RNA intermediate, and class II elements (trans-posons), which transpose as DNA (Brindley et ai, 2003). Additionally, small dispersed or tandemly repeated sequences are common. A wide variety of these sequences have been isolated and characterized from a variety of taxa (Table 2.4). 

Structural analysis of N-24 based on amino acid sequence (derived from its cDNA sequence) revealed some very interesting features. The finding that exons 2, 3 and 4 represent the same repeat sequence has led to the suggestion that this repeated domain may have been generated by duplication of an insertion sequence (Katinakis Verma, 1985). The first and last exons are unique and contain hydrophobic domains. While the first hydrophobic domain at the amino-terminal seems to act as a signal sequence, the hydrophobic domain in the last exon may act as a mem-... 

Trichohyalin contains extensive repeat sequence blocks, which are predicted to form an elongated, flexible single-stranded o-helical rod (Lee et al, 1993). These predictions are consistent with biochemical and electron microscopical analysis showing an extended shape with overall dimensions of 85 nm. Similar to profilaggrin, the N-terminus comprises an S-100 protein-like calcium-binding domain. 

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