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The LRR-domain itself might not be under functional conservation.
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Here, to examine whether each orthologous target site has been under functional constraints, we computed the expected time of conservation of a target site under neutral evolution.
The conservation level, coverage of SNV, GC content, and overlap with previously reported regulatory signatures as well as DAF analysis support that the CNSs identified are under functional constraint and may have regulatory functions.
As suggested by Fedorova and Fedorov [ 28], conservation of the first intron at the 5'end of many genes also appears to be under stringent functional constraints.
Of these nine SbRPG genes, four encoded nuclear genes targeted to the chloroplast and/or implicated in photosynthetic-related functions, supporting the notion that this class of genes is under strong pressure for functional conservation.
Using the functional residue information at the DDX3X ATPase site, we showed that most of these residues are under strong functional constraints and that validates their conservation pattern (Figure 3).
As primate unique CNSs are under lowest functional constraint, we checked whether the conservation level is different from that of randomly retrieved sequences.
These results suggest that the sequence conservation in the 5' non-transcribed region is indeed indicative of functional conservation.
miRNA targeted genes were predicted according to functional conservation and binding sites.
Given that HSV is a viral pathogen, this functional conservation has most certainly not been under direct selection during evolution.
Epigenetic conservation was functional, with higher conservation at promoters and expressed genes compared to non-coding regions.
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