RRF-3 is one of the four putative RNA-directed RNA polymerases (RdRPs) in C. elegans and plays a major role in endogenous synthesis of siRNAs. By deep sequencing of mRNA tags (mRNA-seq) from N2 worms and from worms with mutational backgrounds, at different stages, we found that the annotated seventh exon of rrf-3 contains an intron. The position of the intron is chrII: 8165255-8165300 (WS190 version of the C. elegans genome), and it is 45 bp long (Figure 1). The 5' end of the intron starts with GTATATTCTA and the 3' ends with AAATATTCAG. The intron does not change the reading frame and shortens the protein by 15 amino acids.
Figures
Figure 1: (A) PCR and RT-PCR on a region in rrf-3 ’s seventh exon spanning the newly defined intron. (B) View of the rrf-3 gene by UCSC genome browser with the WS190 version of the C. elegans genome. The primers that were used for (A) are shown in red. Sanger sequencing of the RT-PCR is shown in black and validates the intron. The purple arrow points to the newly identified intron.
