Supplementary Figure 8: Detailed analysis of ERG exon 6 alt, the alternative first exon in the ERGalt transcript.

RNA–seq read coverage, the region mapped by RACE and RT–PCR, and read pair mapping at the ERGalt first exon and canonical exon 7 in SJERG026. Coverage for RNA–seq is shown at the top, with the black line marking the exon boundary determined by RACE and RT–PCR. RNA–seq read pairs were sorted by ERGalt exon start site. The forward and reverse reads in a read pair are shown in red and blue, respectively. Cyan color indicates a ‘skipped’ region, i.e., a spliced intron, while gray color indicates a region where a forward read overlaps with a reverse read in a read pair. The black arrow points to the transcription initiation site determined on the basis of RACE that shows a strong bias for reverse reads, as expected from a first exon. The initiation site also matches the highest RNA–seq coverage peak in this region. A small proportion of reads aligned in forward orientation were from unspliced read pairs for which the reverse reads clustered to two additional potential alternative transcription start sites for ERGalt (marked by gray arrows).