Seed enhancers have increased sequence conservation and show preferential usage in downstream somatic tissues, often expanding into super enhancers.
As expected, consistent NFR segments showed increased sequence conservation.
This increased SNP density in genes was likely due to increased sequence conservation between the A- and D-genomes.
It has been noted previously that easily alignable eukaryotic mRNAs are over-represented for multi-subunit complexes [ 63] due to increased sequence conservation.
Several GO categories were found to be under-represented, indicating increased sequence conservation and possible constraint of these processes, functions, and components in the D. yakuba lineage (see Additional file 1; representatives with asterisk on Figure 6).
In our datasets we find patients (mostly therapy-experienced) who exhibit an increase in sequence conservation with a reduction of the CD4+ T-cell counts (example in Figure 10B).
Alignment of this part of the passenger domain in our model illustrated an increase in sequence conservation among proteins of the SPATE family compared to the N-terminal part, further indicating that this region might encode a shared functional aspect.
They reported that CRMs do indeed share common features such as elevated GC contents, increased levels of interspecific sequence conservation, and tendency to be transcribed into RNA [ 8].
Therefore, high sequence conservation would increase the interaction between RNA molecules from different strains and recombination could occur as a result of homologous interaction [ 31, 47].
Interestingly, we show here that the high identity quartile of binding sites (i.e. the binding regions with the highest sequence conservation) displayed increased retention of C/EBPα and PPARγ binding independent of conservation of their respective consensus sites.
