Figure 2

Specific cases of RNA editing in nuclear transcripts. (A) U-to-C (orange) and C-to-U (blue) editing in the mRNA of AT1G29930. (B) U-to-C (orange) and C-to-U (blue) editing in the mRNAs of AT1G52400. U-to-C editing sites that reside only in the mRNA of AT1G52400.1 are in green. (C) A-to-G (purple) editing in the mRNAs of AT2G21660. For (A), (B), and (C), the gene model IDs and the gene annotations are shown. The exons are represented by light blue boxes, the UTR regions by gray boxes, and the introns by lines. The transcript length is measured by x axis; y axis indicates the number of distinct short-read sequences supporting a specific editing site. (D) Secondary structure transformation of edited ath-miR854c. The secondary structure was predicted by RNAfold. Different editing patterns are indicated by different colors; the editing site position and the number of distinct short reads (in the parentheses) supporting this editing site are also shown. The mini stem-loop structure near the main stem region of ath-miR854c disappeared after editing is in light blue shadow. Mature miRNA is indicated by a pink bar.