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If this rearrangement was indeed recent, the expected sequence conservation at the breakpoints of inverted chromosomes should facilitate ongoing efforts to design a robust molecular diagnostic assay to detect the inversion in natural populations.
As expected, sequence conservation is seen primarily within the aligned granulin domains of the zebrafish precursors.
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In addition, strong functional conservation may lead to above-expected sequence conservation even at much higher evolutionary distances that separate the two pairs.
It has been shown that three-dimensional protein structure is evolutionarily more conserved than expected due to sequence conservation [45], [46].
In a series of papers, Lassig and coworkers demonstrated that that even modest positive selection is sufficient to create a TF-binding site in a relatively short time [ 39, 40] and that the calculated strength of TF-binding sites is more conserved than expected given the sequence conservation level [ 41], demonstrating specific purifying selection on the former.
Regulatory regions with functional importance can be expected to exhibit sequence conservation due to selection.
Regions of DNA involved in gene regulation are expected to exhibit sequence conservation between related species over evolutionary time due to functional constraints.
Sepsidae is more closely related to Tephritidae than the drosophilids [ 17], so it would be expected that higher sequence conservation exists between these two families, and that comparison to a tephritid would identify more transcripts.
It should be noted that only one case of sliding (FBgn0034221) has occurred within about 6 million years of evolution (between D. yakuba and D. melanogaster) [ 21] and was, therefore, expected to show sequence conservation between both introns of the NIP.
Such structural and functional constraints associated with coiled coil domains likely signify these motifs are under purifying selection and led us to expect and investigate sequence conservation.
As imprinted gene expression appears to be highly conserved among different mammalian species (Steinhoff et al. 2009), one might expect a tight sequence conservation in DMRs.
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