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Using dn/ ds analysis for interspecies comparisons, we found that the PSG protein amino-terminal N and N1 domains are relatively conserved, consistent with conservation of function in rodents and primates.
In Fig. 2 A most places are high peaks and in Fig. 2 B most areas are in red color, meaning that in many sequence positions the residues are highly conserved, consistent to the high conservation of PDZ family.
Since microRNAs were originally identified by strong evolutionary homology, we surmised that newly-described microRNAs observed in hESC could be less conserved, consistent with a more recent evolutionary appearance, as has been predicted [24].
Over the entire MgPa operon the four repeat regions exhibit extensive variation within and among strains while the non-repeat regions are relatively conserved, consistent with previous observations that the repeat regions are undergoing rapid genetic changes by recombination with MgPars, presumably due to immune or microenvironmental selection pressure [1], [10] [13].
The overall structure of the duplications we examined is well conserved, consistent with the idea that duplication occurred in an ancestral grass genome and assumed much of the modern structure before the divergence of the rice, Brachypodium and temperate grass lineages.
These data suggest that CIDE-N domain is evolutionarily conserved, consistent with an observation previously reported [ 32].
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That B1 and B4 are highly conserved is consistent with their being largely comprised of structural homologies.
The synteny of these genes is conserved and consistent with other members in Ascomycota.
We also found that functional variants are depleted in highly conserved genes, consistent with constraint on gene expression patterns.
Comparisons of translated octocoral mtMutS sequences with bacterial MutS and eukaryotic MSH genes identified conserved residues consistent with MutS-protein functional sites in all octocoral sequences.
Interestingly, 7 of 8 positions of RNA editing lie within conserved blocks, consistent with their functional importance, a hallmark of RNA editing in plant mitochondria [ 36].
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