Fig. 1

Massively parallel reporter assay (MPRA) reveals a high frequency of cryptic splice sites. a Schematic of MPRA employed for cryptic splice site identification. b Splice sites identified in the MPRA on BRCA1, BRCA2, and LDLR. The blue and red bars represent 5′ splice sites (5′ss) and 3′ splice sites (3′ss), respectively. The height of the bars corresponds to the original enrichment score (not log10 transformed), with taller bars indicating higher scores. The plot within the dashed box provides a zoomed-in representation of the splice sites identified in BRCA1 intron 3. c The proportion of splice sites identified in the MPRA that were found in the Sequence Read Archive (SRA). d Comparison of enrichment scores for splice sites found in SRA and those not found in SRA (Mann–Whitney test). e Sequence logos depicting the consensus sequence for cryptic 5′ and 3′ splice sites identified in the MPRA. The dotted boxes represent the dinucleotides present in the 5′ and 3′ splice sites. f RT-PCR validation of pseudo-exons created by cryptic sites in BRCA2 using TaqMan® Control Total RNA. Each lane represents one of three pseudo-exons created by cryptic sites identified in our MPRA. The blue and yellow boxes represent exons and the gray lines denote intron, the red dots indicate cryptic splice sites and arrows represent the primers used for RT-PCR