Extended Data Figure 7: Promoter-dependent inclusion of RS-exons in CADM2 and NTM genes.

a, Number of cassette and constitutive exons starting with motif GURAG. b–d, RT–PCR of CADM2 gene in the frontal cortex using primers indicated in b or Fig. 4a. RT–PCR was carried out on one (b) or four (c, d) human brains. In c, the inclusion of the second RS-exon occurs together with the minor promoter. Two bands are present for both PCR reactions due to the presence of an alternatively spliced exon following the RS-exon. This can result in two distinct long or short isoforms. In d, the inclusion of the second RS-exon occurs when the first RS-exon is included. Schematics in c and d represent examined splicing products together with expected length of products. e, RNA-seq read density patterns for the NTM gene and expected human isoforms. RNA-seq reads are grouped in 5-kb windows and linear regression performed on resulting histograms. A cryptic minor promoter/exon detected by RNA-seq is indicated by vertical red line. The annotated RS-exon is indicated by the vertical blue line. Zoomed area represents RS-site sequence at start of the annotated RS-exon. Primers to assess the major and minor promoter products associated with the RS-exon are indicated by coloured arrows. f, RT–PCR of NTM gene around RS-exon using indicated primers. g, RT–PCR analysis of NTM products in which the upstream exon is either derived from the major upstream promoter or the cryptic upstream promoter/exon. RT–PCR was performed in the frontal cortex of three human brains using primer sets indicated by coloured arrows in e. Schematics represent possible splicing products together with expected length of products. Top panel assesses RS-exon inclusion, bottom panel assesses RS-site junction detection.