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In three independent plants lines in which Cre recombinase was employed to excise the ABF3 transgene from the T-DNA insertion, only a small number of genes were found to be differentially expressed (Table 1).
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Overall, these data indicate that these retrotransposon insertions constitute only a small fraction of the total retrotransposon DNA content of the grape genome.
Further analysis using the Sybil tool at www.aspgd.org (Crabtree et al. 2007) demonstrated that the amylolytic cluster (amyA– aglA– amyR) is highly conserved in all eight sequenced Aspergilli, with only a small insertion downstream of amyR in Aspergillus terreus (Suppl. Fig. 1).
Furthermore, these libraries show bias towards certain insertion points, and even the largest libraries sample only a small fraction of the immense possibilities in sequence space [ 38].
The insertion mutagenesis used in this study relied on random non-homologous recombination, where a vast majority of transformants have unstable, circularized vector DNA and only a small portion have stable insertions.
Suffix is mainly transcribed from different sites of insertion as a component of longer RNA molecules, and only a small portion of these correspond to F elements.
Many research groups over the past 20 years have created mutant libraries of which only a small number of single-copy insertion mutants were successfully analysed [ 21, 22].
When there is only little overlap between the sequence spaces of two organisms, we assume that only a small number of C-terminal insertion signals from one organism will be recognized by another organism's BAM complex.
Local mutations affect only a small number of nucleotides and include nucleotide substitution and insertion or deletion of nucleotides.
To minimize the impact of these gaps on the outcome of our analyses, we used two alignment algorithms (ClustalW and Bali-Phy) and excluded regions where only a small proportion (less than one-third) of sequences shared insertions.
Only a small minority of the proteins in the dataset had short insertions relative to engrailed.
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