By contrast, the right peaks for single putative CREs in CDRs and the randomly selected short k-mers are much larger than their own left peaks, indicating that there are much more conserved short sequences than non-conserved ones in CDRs, which is expected as most CDRs are highly conserved.
Hence, putative CREs in a CRM as a whole are much more conserved than the randomly selected NCRs, and also more conserved than spacer sequences in the putative CRMs.
The TLR2 intracellular domains were generally much more conserved through strong purifying selection, reaching maximum conservation in the TIR domain with ω < 0.1 for the vast majority of sites.
For positions that are much more conserved, the joint probability between them and other less conserved positions is approximately equal to the product of the individual probabilities of the latter position, resulting in low MI (see Equation 1 in Methods).
These results indicate that analogously to the genetic code, which is more conserved than protein-coding DNA (Moura et al., 2010), the gene regulatory code is much more conserved than the regulatory sequences themselves.
Altogether the His-kinase domain is also much more conserved than the two VFT domains, with only 11 variable positions harbouring essentially conservative substitutions over a total of 223 residues (4.9%).
Traditional sequence-based searches are inefficient, however, as the secondary structure of the element is much more conserved than the nucleic acid sequence.
CNEs are much more conserved than the sequences of known enhancers, but many of these elements clearly regulate gene expression [32].
The perhaps most important finding was that upon in vitro evolution position −5 became much more conserved than observed in nature.
Therefore, the upstream intronic regions and the downstream intronic regions are not symmetric and the upstream intronic regions of conditional exons are much more conserved.
Interestingly, the residues near the central catalytic core region were much more conserved when the malate dehydrogenase sequences were removed from the alignment.
