Note that many TF domains are highly conserved, but that others display levels of conservation that are similar to those observed for domains involved in protein protein, protein-RNA, and enzyme substrate interactions (kinase domains, RNA recognition module (RRM), SH2, SH3, and Bromodomains).
COX11 proteins are essential for the assembly of cytochrome c oxidase; they display high levels of conservation among eukaryotes and play a role in hydrogen peroxide degradation (Banting and Glerum [2006]).
Notably, comparative analysis of the CENP-C homologues isolated from other species shows that the central and C-terminal regiof of the human CENP-C display different degrees of conservation [23].
Both methylated and unmethylated sites were observed to generally display high levels of conservation (fig. 1).
Based on available PWM, cross-species comparison suggests that putative cis-regulatory elements in miRNA promoters display different degree of conservation.
Although microbial G6PD homologues display lower degree of conservation compared with human counterpart, it has been shown that the bacterial form of G6PD exerts antioxidant activity in G6PD-nullizygous mouse embryonic stem cells.
CNEs have been shown to either display high levels of conservation over wide evolutionary periods, or otherwise occur as group-specific elements (e.g. vertebrate, amniote and eutherian-specific) [ 11- 13].
In plants, the CAF1 complex (Fig. 4A) is composed of FASCIATA1 (FAS2), Fand and MULTICOPY SUPRESSOR OF IRA1 (MSI1), all of which display high degrees of conservation of their functional domains with their animal counterparts and exhibit a similar histone chaperone activity (Kaya et al., 2001).
For example, SSPs functioning in cellular processes display higher degree of conservation that parallels taxonomic divergence patterns compared to those functioning at the interface between the organism and its niche (Transport & membrane proteins) or those that carryout species specific specialized functions [ 13].
In order to fully characterize both SIDER subgroups in the genomes of L. major, L. infantum, and L. braziliensis, we sought an efficient and automated method capable of producing reliable alignments when confronted with sequences displaying variable rates of conservation.
As the four sampled homoeologous regions have displayed varying levels of conservation in both genic and intergenic space, it is apparent that multiple sections of the genome need to be analysed in order to draw conclusions on the divergence of resident sub-genomes within allopolyploid species.
