Fig. 3

Genomic features of circRNAs expressed during human pre-implantation development. a Distribution of the number of different types of circRNA transcripts from each circRNA hosting gene. b Distribution of the back-spliced exons in circRNAs. Nearly all (99.9 %) back-spliced exons that contribute to circRNAs are located in the middle of their hosting genes, whereas six are in the first exon and none are in the last exon, as annotated. c An example in which potential extra exons are located upstream of the annotated first exon that participates in the circularization of FAT3. Back-spliced reads of FAT3 circRNA are presented as a red curve. The peaks connected by the green dashed line are the reads mapped to the first exon that participates in the circularization, and the extra exon which is not annotated, simultaneously. d Distribution of the number of back-spliced exons in each circRNA. More than 95 % of circRNAs contain multiple back-spliced exons and more than half of them contain 2–6 exons. The maximum number of exons in a single circRNA was 56. e Length distribution of back-spliced exons. The box plots show that the exon length distribution from the circRNA consisted of a different number of back-spliced exons (***P value = 7.4E-32, Student’s t-test). f Distribution of the number of Alu elements in flanking and all other introns. The median number is given in the bracket. The number of Alu elements in flanking intron (upstream in blue and downstream in purple) is much higher than that in the randomly selected control introns no matter in circRNA (in green) or not (in red)