Fig. 5

Relative position of retained introns and miRNA binding site enrichment. a Probability density function of the position of retained introns in relation to the other introns in the gene structure. Values between 0 and 1 represent the relative intron position, which is calculated by dividing the intron position by the total number of introns in a transcript. b Densities of 3′ UTR lengths as violin plots. Densities of 3′ UTR sequence lengths in transcripts with (IR) and without retained introns (Other). The solid and dashed horizontal lines mark the median 3′ UTR length of genes with and without retained introns, respectively, and the white dots their mean. Genes that do not contain retained introns (Other) include lowly and non-expressed genes. c Comparison of the number of predicted miRNA binding sites in the 3′ UTR sequences of genes with retained introns and non-intron-retaining genes. The white numbers indicate the median value, illustrated also by a horizontal line in each box. Genes that do not contain retained introns (Other) include lowly and non-expressed genes. d Sylamer [55] plots illustrating 6mer seed sites enriched in the 3′ UTR sequences (x-axis) of intron-retaining genes in human and mouse based on a hypergeometric significance test. The canonical polyadenylation signal (AATAAA), which is also enriched in both species, is not highlighted. Mutually enriched seed site sequences are underlined. The horizontal dotted line represents an E-value threshold (Bonferroni-corrected) of 0.01. The corresponding plots for dog, chicken, and zebrafish are in Additional file 2: Figure S17. e Model of intron-retaining transcripts as competing endogenous RNAs. Wilcoxon test was used to determine significance, denoted by ^*** (p < 0.001)