However, samples from subfamilies Secamonoideae and Periplocoideae did not amplify using these primers, indicating that either the pseudogene is not present or the PCR priming sites are divergent or absent.
This is not an inconsistent result, as our correlations appear to be mainly driven by the Her14 locus, and it is clear that the Rügen site is divergent enough to strongly affect the results of broad scale correlation analyses.
Including another four sites in the proline-knot motif, 36 of 38 (94.74 %) sites were functionally divergent, and all seven sites under positive selection were also located in this region.
We found that about 40% of the sites were under divergent selection pressures, with the UCP1 clade experiencing a greater number of substitutions at replacement sites relative to silent sites.
However, it is known that various integrases can have secondary attachment sites that are divergent from the sequence of the primary attachment site, which may explain the variety of putative att sites [ 31– 31].
Recent analysis of several large data sets of RNA sequences expressed in embryonic stem cells shows that a majority of long non-coding RNAs originated from initiation sites that are divergent from known protein-encoding genes or sites with chromatin marks indicating enhancer elements.
Of note, although Smad4 is a positive regulator of all three LM-332 chains the underlying mechanisms are surprisingly complex and binding sites involved are divergent for the LAMA3 promoter on the one hand and for the LAMB3 and LAMC2 promoters on the other side.
Sites with the strongest CTCF binding intensities were highly conserved (77% of the top 0.1 percentile), while lower-intensity CTCF binding sites were enriched for divergent binding (57% of mouse-divergent sites).
Conversely, motifs underlying the divergent sites were evolutionarily dynamic and diverged in strong correlation to divergent binding intensity.
Clade model C showed 79%and62%2% of sites are under divergent selection in OBPs and CSPs, respectively.
