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Fig. 3 | BMC Bioinformatics

Fig. 3

From: TrancriptomeReconstructoR: data-driven annotation of complex transcriptomes

Fig. 3

Comparison of called exon borders to TAIR10 and Araport11. A Overlaps of called internal exons vs TAIR10 and Araport11. On top, the schematic outline shows the possible overlap types for internal exons: (i) exact match (within 5 bp offset) at both borders of the same annotated exon; (ii) exact match at borders of two adjacent exons (intron retention); (iii) exact match only at 5' exon border (alternative acceptor site); (iv) exact match only at 3' exon border (alternative donor site). Notably, it is also possible that a called exon has no overlap with any annotated exon, or that the overlapping pattern is more complicated than those shown on the schematic. The bottom stacked barplot shows the counts of called internal exons with different type of pairwise overlaps, colored as in the schematic above, with their best mate exons in either TAIR10 or Araport11. B Histogram shows the distribution of called 5' or 3' exon borders (left and right panel, respectively) relative to the acceptor and donor sites from their best mates in TAIR10. The central (zero) position on X-axis corresponds to exact match between called and annotated exon borders. C Metagene plot shows the average density of spliceosome intermediate reads in the plaNET-seq dataset over 50 bp windows centered at 3' exon borders (donor splice sites) of either re-discovered (blue) or newly discovered (red) called exons. The shaded areas show the normal-based confidence intervals for the mean. The presence of sharp peaks exactly at the called 3' exon borders (at zero position on the X axis) in the newly discovered exons indicate that they represent functional donor sites. The absolute peak height is proportional to the average expression levels of genes in each group

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