Fig. 3

Highly expressed circRNAs. a Expression pattern of CSPP1, HDAC2 and RIMS2 circRNAs. b Expression relative to linear host expression for CSPP1, HDAC2 and RIMS2 circRNAs. c Genome browser view of CSSP1 circRNA (red). TopHat2-mapped RNA-seq reads from cortex at E60 are shown in green. Intron–exon structure of the CSSP1 gene region is shown below (black). Exons contained in the CSSP1 circRNA have larger read density than other exons in the CSSP1 gene. Note that TopHat2 is not able to correctly map back-spliced sequences, so the outermost exonic sequence of a circRNA will appear to have lower coverage than the internal exonic sequences. d Northern blots showing RNase R-resistant CSSP1, HDAC2 and RIMS2 circRNAs in cortex at E42 and E60 with linear GAPDH transcript as RNase R-sensitive control. A faint RNase R-sensitive band corresponding to the HDAC2 linear transcript is detected with northern blotting (asterisk). Uncropped northern blot lanes are shown in Additional file 4. e Quantitative PCR across the back-splice junction of circRNAs from the same RNA samples used in panel (d). Error bars represent standard deviation