A bioinformatics analysis of the relationship between stowaway-like transposable elements and scaffold/matrix attachment regions

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Grybas, Anna E.
Blakey, C. Ann
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Thesis (B.?.)
Honors College
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Predictions of a relationship between transposons and S/MARs were made by Tikhonov, Bennetzen, and Avramova (2000) and Christoffers (1998). This analysis compares the presence of transposons from the Stowaway family relative to two specific plant S/MARs, pTMX4 and pSR14, isolated by Christoffers (1998). Homologous sequences were identified using both pTMX4 and pSR14 by BLASTn and MEGABIast searches. These sequences were further analyzed for the presence of Stowaway elements. General Stowaway patterns were observed with respect to the level of homology to the S/MAR, the species, and the quantity of Stowaways per sequence. These patterns suggest there is a positive relationship between Stowaway quantity and the level of S/MAR homology. Detailed Stowaway patterns were observed among individual Stowaways within the sequences with respect to location, order, and fragmentation of individual Stowaway elements. These Stowaways revealed probable insertion patterns of nested Stowaway elements and models were subsequently generated to represent them. The complete description of the Stowaway analysis of pTMX4 and SR14 are provided.