Those HBs which did not contain at least one significantly conserved position (conservation level > 0) were discarded.
Thus, the AUGs in CONSTIT and ALT regions are significantly conserved compared to the background levels of conservation, but that conservation is considerably more pronounced in CONSTIT regions.
Murine HOTAIR, indeed, has a first exon significantly conserved with respect to human sequence but the second exon shows high conservation only in a subdomain.
The regions with significantly conserved strong / weak folding signals cannot be explained based only on sequence conservation.
Indeed, the three genes identified here are significantly conserved throughout primate genomes only.
We call a putative binding site significantly conserved if its p-value is less than 0.01.
According to a BLAST analysis, none of these 23 sequences contains a significantly conserved part of a gene.
As expected, the N- and C-terminal coding regions are significantly conserved between the two genes (Figure 6).
The proportion of significantly conserved binding sites among all the binding sites of each transcription factor is shown in supplementary Tables S5 and S6.
Most notably, there is a significantly conserved region spanning ∼700 bp that is found ∼10,000 bp downstream of the MaSp1 and MaSp2 ORFs (Figure 6).
With the p-value cutoff of 0.01, we calculated the proportion of the significantly conserved binding sites among the over-represented putative binding sites.
