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Based on the phylogenetic conservation with known pre-miRNAs and miRNAs and their stability of folding stem-loop structures, 108 sequences [64 unique sequences with high conservation (E value≤e−4) and 44 with less conservation (E value>e−4)] were selected to predict conserved mature miRNAs in the Asian seabass.
The GTPase (G) domain is overall well conserved, particularly in the nucleotide binding loops, with less conservation seen in the exposed loops in between.
Sequence conservation was greater at 5' end up to central hinge domain, with less conservation in the 3' hairpin region.
These two mRNAs share 100% identity in the domain 5′ to the intron processing locus with less conservation 3′ to the cyclic product.
> -wrap-foot> ExtramoCoC designates amoC copies outside the amoCAB operon in Nitrosomonas europaea ATCC 19718 and Nitrosospira multiformis ATCC 25196 aOnly one sequence was available Local changes in sequence conservation were inspected throughout the alignments to identify regions with less conservation in the different genes of the amoCAB operon.
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In contrast to the CYPs that have principally endogenous functions, these CYP genes are much more diverse, with much less conservation of sequence between zebrafish and human.
Our identification of novel miRNAs highlights the importance of miRNAs with low abundance and less conservation between species.
A comparison with S. agalactiae revealed less conservation of genome structure, suggesting a more distant genetic relationship.
Indeed, we found that the mean per-gene phyloP score calculated based on a 46-way primate comparison was significantly reduced (reflecting less conservation) for genes with detectable eQTL in both species, and greatest for genes in which eQTL were not detected in either case (p < 10−53; Figure 3A).
Less conservation of synteny was observed with the other species studied, with less than 20%% of the chestnut genome aligning to the Medicago, papaya, Arabidopsis and tomato genomes (Fig. 2).
Of these nine pairs of ohnologs, the faster evolving copy was associated with less synteny conservation in seven instances.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com