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Cis-regulatory elements can be predicted by sequence conservation analysis, as tight clusters of functional TFBSs can be under strong evolutionary constraint [ 4- 7].
This conclusion is in line with the expectation that contact residues are in general much more likely to be under strong evolutionary constraint compared with noncontact residues.
On the other hand, the likely enrichment of recent positive selections at the subcentral positions can be explained: Genes with protein products of very high centrality could be under strong evolutionary constraints and hence accommodate fewer selective events, whereas genes at the periphery may not contribute strongly enough to phenotypic effects for selection due to their network locations.
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Indeed, DNA-binding domains are often highly conserved across species and, in many cases, appear to be under stronger evolutionary constraints than other regions of the protein (Hirsch and Aggarwal 1995; Luscombe and Thornton 2002; Rorick and Wagner 2010).
Although robust purifying selection was encountered in most of the analyses, the secretory protein genes were found to be under stronger evolutionary selection pressure than non-secretary protein genes in symbiotic and pathogenic strains.
This indicated that the younger bZIP proteins may be under stronger evolutionary constraints than older proteins, but supported the notion that the legume bZIP gene family is essential for the regulation of cellular processes.
These studies and others (Barbosa-Morais et al., 2012; Brawand et al., 2011) suggest that regulation in other somatic tissues evolves similarly, though embryonic tissues and their enhancers may be under stronger evolutionary constraint (Faure et al., 2012; He et al., 2011; Nord et al., 2013).
The changes indicate that the gene has been under strong evolutionary pressure in humans.
As the major physiological process that provides plants with carbon and energy, photosynthesis is under strong evolutionary selection that gives rise to variability in nearly all parts of the photosynthetic apparatus.
The prediction of [27], [28] is that those sequences falling on the scaling curve from genomic alignments are under strong evolutionary constraint; however, their functions – if not miRNAs - are most likely novel, presenting an intangible experimental challenge.
These observations suggest that MblC is under strong evolutionary pressure since it has not changed significantly over at least 13 million years (almost 100% protein identity in melanogaster group species) and can be found in Nematoda.
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