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The accuracy of computational predictions is usually better for methods that consider "fold recognition": structure is usually more conserved than sequence, and the functional core regions are usually more conserved at all levels.
This result agreed with previous reports that nucleotide sequences were more conserved at the NCRs than the coding region due to the preservation of conserved RNA structure elements within the NCR[31], [32].
In β-turns, hydropathy at positively selected sites is more conserved than at all other sites, unlike the other three structures, which show the opposite trend; hydropathy is more conserved at sites that are not undergoing selection.
Related to our observation that LNK pairs are usually have a high inclusion level, Plass et al. showed that the exonic structure is more conserved at higher inclusion levels, and that this correlates with the sequence conservation of the alternative exons [ 39].
Further, NBiPs are more conserved at the DNA sequence level than KBiPs (Kolmogorov Smirnov test, p < 0.001), while both types of bidirectional promoters are more conserved than UniPs (Kolmogorov-Smirnov test, p < 0.0001, Figure 5c).
A lower value suggests lower entropy more conserved at a position and vice versa.
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Buffering effect of translation on gene transcription divergence was also revealed in another study (Khan et al. 2013), which demonstrated more conserved evolution at the protein level than the gene transcript level, indicating that gene transcription divergence could overestimate the speciation difference in gene regulation.
So, the genes at the waist of a DGEN tend to be more conserved than genes at earlier or later stages.
For example, amino acids buried in protein cores have been found to be far more conserved than those at surface positions [ 9].
In general, information content tends to be larger at more conserved sites.
Are some protein families more conserved than others, either at the level of protein sequence, gene regulation, or copy number?
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