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The Enterobacteriaceae are closely related to the Vibrionaceae but appear to have a more conserved set of proteins.
The studies also vary in the level of conservation of the initial set of elements-Pollard et al. started with a smaller and more conserved set than we did.
In addition, the majority of conserved and legume-specific miRNA families produce 21 nt long mature miRNAs with distinct nucleotide distribution and regulate a more conserved set of target mRNAs compared to soybean-specific families.
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In this case we can see that one list is clearly a subset of the other, and moving from a less conserved setting to a more conserved setting reduced the number of predicted targets by 30% (Figure 1C, right panel).
Additionally, CEGMA (Core Eukaryotic Genes Mapping Approach) analysis of conserved eukaryotic genes (CEGs), determined that our filtered transcriptome contained 453 full-length CEGs of the complete set of 458 CEGs (99%), and 238 of the more-conserved set of 248 CEGs (96%) [ 51, 52].
Still, the specific Nc nucleotide observed at a given SS is usually more conserved than the set of all Nc nucleotides (cnuc > cset), indicating that some site-specific selection may be present.
This strictness could have biased our data set toward more conserved sequences.
This pattern was not accounted by a bias in our methods of detecting potentially more conserved regulatory regions (supplementary data set S1 and results, Supplementary Material online) nor does it reflect a distribution bias for Helitron insertions in the genome (supplementary data set S2 and results, Supplementary Material online).
These two folds differ from the ancient α/β3-layered sandwich domains like the Rossmannoid and P-loop NTPase domains, which appear to have begun their existence as enzymatic domains and more-or-less retained a conserved set of basic biochemical activities throughout their evolution [ 121, 122].
Finally, we found that LUAT-associated promoters contain more conserved elements than the other two sets in regions close to and downstream of the TSS (t-test in region [TSS; +500 bp]; p < 10-166 and p < 10-224, respectively; Figure 5D).
We noticed that autoimmune disease genes are more conserved than other immunological disease genes and both sets of genes evolved significantly at a slower rate than immunological genes.
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