Figure 2.

(A) Schematic illustration of the irak3-cDNA variants. The encoded protein domains are colored as in Figure 1 (upper panel) and drawn to scale. Flanking light gray lines indicate UTR sequences; the black triangle and square mark the start and stop of the ORF, respectively. Non-synonymous SNCs are represented by longitudinal white lines; the longitudinal red line indicates the point mutation that leads to the shortened variant j. Arrows indicate the locations of the primers used for fragment amplification and the 3′-RACE. The scissors symbol indicates the end of the truncated irak3-cDNAs. (B) List display of the 45 SNCs in trout Irak3-encoding cDNA sequences predicted by RNA-sequencing and those confirmed via cloning. The SNCs are numbered in the first row together with their exon-related occurrences and the exact positions in the ORF, with “1” assigned to the first nucleotide of the translational start triplet. Twenty-three of the SNCs were also confirmed by sequencing 100 randomly picked clones from batch-cloned irak3 amplicons. SNCs not represented in that clone collection are shown in gray characters. Nucleotide variations and the affected aa residues are marked with the same colors (adenine, green; guanine, red; thymine, blue; cytosine, orange). Characteristic domains carrying the affected aa residues are indicated by differently shaded table fields. Note that variants a and c share the same SNCs, but bear an additional nt exchange at position 407 (C) Dendrogram of trout irak3 cDNA variants. The bootstrap analysis of transcript relatedness involved 17 trout-specific nucleotide sequences (abbreviated as numbers and digits as indicated in (B) in the left column of the table).