The most conserved pattern in NLPs, the GHRHDWE sequence (η in Figure 4), is between the putative C (β3) and D (β4) β-strands.
The most conserved pattern was observed at the amino acid level: strong alanine over-representation was observed at the second amino acid position of highly expressed proteins.
If more than one CDS of α-keratin genes were predicted, we aligned the identified CDS and checked the predicted protein sequences to identify the most conserved pattern.
While it is unarguable that the later stages of embryogenesis are not conserved among species, two major models have been proposed: the "funnel-like" model, in which the earliest embryo shows the most conserved pattern, and the "hourglass" model, in which the middle point of development is imposed with the most evolutionary constraints [ 1].
The above cited set of residues and their accompanying protein:DNA contacts (when present) comprise the most conserved pattern at these respective positions between the non-3-ketosteroid receptors (the basic residues at the positions 160-161 being also extensive to the 3-ketosteroid receptors and other divergent NR classes - see below).
Additionally, we identified the 50 transcripts with the most conserved expression patterns in each subspecies (Additional files 8 and 9).
Furthermore, the Fingers-like domains start with a beta strand-alpha helix element and ends by a helix-beta-strand element, which are the two most conserved structural patterns in RAMPs (see above and Additional File 1).
Seemingly, the differentiation of the insect compound eye is one of the most conserved cellular patterning processes known.
Contig_67454, which is annotated, has the second most conserved expression pattern, with an average RPKM = 13 across all tissues in both subspecies.
We found the biological process of "neuropeptide-signaling pathway" to be the most significantly enriched (Table 2) in the class 1 gene set, which subsumes the most conserved expression pattern across the two species.
