Figure 3.

Transcript variants of the P. andruzzii per2 gene. (a) Schematic representation of the portion of the cavefish per2 gene, between exon 17 and exon 19, where alternative splicing and transcript processing generates the three mRNA transcript variants (tv_1, tv_2 and tv_3). Open boxes denote the coding exons 17, 18 and 19 while a filled dark grey box (Tr) shows the location of transposon-derived sequences which are inserted by aberrant splicing into the per2 mRNA in transcript variant tv_3. “Stop” indicates the premature termination codon and “AAAAAA” the site of premature polyadenylation in the transcript variant tv_3. The filled light grey box, present in transcript variant tv_2, shows the 3′ untranslated sequence generated in exon 19 by a frame shift caused by the removal of exon 18. Dotted lines indicate the positions of alternative splicing in the three transcripts. (b) qPCR analysis of the relative expression levels of the three different per2 transcript variants in total RNA prepared from cavefish brain, heart and the fin clip-derived cavefish cell line, CF1. Primers used are reported in Table S1. Statistical analysis was performed by Kruskal-Wallis test.