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EIN3 binding regions were then associated to a gene if located within 5 kbp.
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Once an ancestral sequence has been inferred, the rate of evolution from the ancestor to the target species (i.e., the number of substitutions that are fixed in the primer binding regions) is then a major determining factor of amplification success.
These same regions were then searched for conserved transcription factor binding sites from the TRANSFAC database using rVISTA 2.0 (Loots and Ovcharenko 2004).
Differences across regions were then examined.
Any overlapping regions were then joined into larger meta-regions.
Further analysis on such complexes was carried out [ 8, 9], predictors were developed [ 10, 11], and these binding regions were first named molecular recognition elements [ 11] then molecular recognition features (MoRFs) [ 8].
208 binding regions were annotated for these 19 factors.
ChIP-seq binding regions overlapped by ChIP-chip binding regions were used for downstream analysis.
These regions are then contracted to create seed regions for region growing.
These putative regions are then compared to the normalized control and the regions that are significantly enriched with mapped sequence tags relative to the control are identified as binding sites.
Three nucleotides of the putative 7 nucleotide seed region were then mutated as shown in Figure 5B by site directed mutagenesis to disrupt the binding of miR-886-3p miR-886-3p miR-886-3p
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