Disparate evolution of prion protein domains and the distinct origin of Doppel- and prion-related loci revealed by fish-to-mammal comparisons FASEB J. Rivera-Milla et al.
10.1096/fj.05-4279fje
Supplemental Data
Files in this Data Supplement:
Supplemental Table 1 -
(SupplementalTable1.pdf; 68 KB) PCR primers sequences, along with public software and databases used in this study.
Supplemental Table 2 -
(SupplementalTable2.pdf; 48 KB) Estimated pairwise average rates of nonsynonymous/synonymous substitutions among vertebrate PrP genes, based on Jukes-Cantor distance values.
Supplemental Table 3 -
(SupplementalTable3.pdf; 72 KB) Pairwise standardized values of synonymous substitutions per synonymous site (upper blue matrix) and non-synonymous substitutions per non-synonymous site (lower black matrix) in vertebrate PrP genes, based on Jukes-Cantor distance values.
Supplemental Table 4 -
(SupplementalTable4.pdf; 53 KB) Estimated degree of structural conservation at the different regions of the globular domain. Numbers and ratios of amino acid replacements maintaining secondary structure over the number of total replacements were scored and compared between different vertebrate classes (Phase I). The loop connecting α-helix-2 and -3 was excluded from the analysis due to large indels between classes.
Supplemental Figure 6 -
(SupplementalFigure6.pdf; 112 KB) Amino acid alignment of repetitive elements in vertebrate PrPs. Type A and B repeats are shown in green and dark blue respectively. Residues that define basic repeat cores are highlighted in bold. Other residues are shown as follows: NH2-flanks in red, COOH-flanks in brown, and non-repetitive stretch in orange.
