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Although yielding many more conserved introns than in this study, the complexity of the used algorithms to select a set of genes and align them, makes it difficult to interpret different intron characteristics within the given set of conserved introns.
We found that our method picks up many more conserved segments than BLAST and discontiguous MegaBLAST in these regions.
Characterized genes encode many more conserved Pfam domains than uncharacterized genes, and genes with maintained large UIRs (and often large UTRs) may represent a specific subset of regulators with wide domain activity.
For example, we have identified a large set of LCNS among birds, and we find many more conserved regions between these two taxa than we found between human and mouse, which diverged approximately at the same time.
This criterion is likely the reason why we found many more conserved codon pairs as opposed to other findings [ 22], where the universal rules were searched only among the first ten most conserved codon pairs in each separate domain.
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First, there may be many more sequences conserved between human and mouse than we currently estimate, which is consistent with the argument in a recent paper [ 20].
If one views the TFBS Conserved track in juxtaposition to the sno/miRNA track (which indicates the positions of 70- to 110-nt long small hairpin precursor (pre-miR) sequences of microRNA genes taken from miRBase), it can readily be appreciated that many pre-miRs contain one or more conserved TFBS.
In many biologically relevant motifs, some positions are more conserved than others.
Another advantage of our approach is that it is not dependent on any previous alignment of homologous regions conserved for many species, which might introduce a bias toward more conserved loci resulting in a reduced sample size.
The other genes within the subgroup are more conserved in chicken while in tetraodon many independent duplication events occurred (Fig. 6E).
Although the cp genome is more conserved than the nuclear genome in plants, many mutation events in the chloroplast DNA sequence have been identified, including indels, substitutions, and inversions (Ingvarsson et al. 2003).
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