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We examined the nature of the positional conservation pattern in plants, and found a relatively longer conserved motif, wherein two conservation blocks were apparent: positions 2-13, and 16-19, with position 4 completely conserved.
The list of non-exonic conservation blocks was obtained after the subtraction of conserved exons (UCSC browser exoniphy track) to the PhastCons most conserved elements (17-way Vertebrate Multiz Alignment) [3].
Considering 75% as the threshold for positional conservation across species, two distinct conservation blocks were identified: 2-13 and 16-19.
These results showed that WGD or segmental duplication and dispersed gene duplication played critical roles in the expansion of the Hsf gene family in the Rosaceae.> Collinearity and synteny are traditionally identified by looking for both intra- and intergenomic pairwise conservation blocks.
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The distance (bp) between all DpnII fragments and their respective nearest non-exonic conservation block was measured center to center.
Within pre-miRNAs, variations are more likely to occur in the central part of the conservation block, which corresponds to the loop part when the sequence is folded into a stem-loop structure.
Interestingly, there are significantly shorter distances between the DpnII fragments in the CNC libraries and the nearest conservation block in comparison with either a simulation (wilcoxon rank test P = 0.00017), or control CNC libraries in the absence of formaldehyde cross linking (P = 0.00532) (Figure 4A).
Residue conservation was observed for all 6 candidate enzymes and reported as the longest continuous sequence conservation block containing the active site residue.
We calculated the autocorrelation of the conservation pattern of the conserved blocks and compared this to the autocorrelation in known exonic regions (see Methods).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com