Interestingly, ESR2 and AR kept very few targets in the absence of FOXL2, whereas NR5A1 conserved a similar number of targets.
If a word is found to be genome-wide conserved, a large number of redundant, highly similar (e.g. slightly more degenerate) variants of that word may also appear in the final output of the method.
The rapid increase in the number of genome sequencing projects [3] has resulted in a growing number of so called "conserved hypothetical protein families" which denote predicted proteins conserved across a number of organisms, but without detectable sequence similarity to proteins of known function.
Therefore, in order to conserve the overall gene diversity, it is generally recommended to conserve a large number of breeds with small population sizes rather than a small number of breeds with large population sizes.
As shown in this figure, not only is the Env peptide highly conserved in a number of different human proteins, but a single cross-conserved epitope can be found in 32 alleles of the same human protein (source protein highlighted in orange).
The functions of core members of the σE regulon are conserved in a number of bacterial species [9].
T3SS is highly conserved among a number of Gram-negative bacteria and functions as an injector of virulence molecules (i.e., effectors) into the host cell through a needle-like injection apparatus [20], [21].
The dystrophin gene is evolutionarily well conserved and a number of animal models of DMD have been described including mouse (mdx) [33], [34], dog (GRMD) [35], zebra fish [36], C. elegans [37] and Drosophila melanogaster (dmDys) [15], [38], [39], [40], [41], [42] with mutations existing in the dystrophin gene in vertebrates or invertebrates genes [15], [43].
Most of these phospho-acceptor sites are conserved over a number of species (data not shown).
Interestingly, the cysteine/methionine cluster is conserved in a number of norovirus 3C proteases.
