Figure 4

Novel and known spliced transcript isoforms identified with long single-end 454 RNA-seq split reads. (A) Transcript isoforms of the p53 gene. In addition to previously reported isoforms, (i) to (iv) [24], we identified three novel canonically spliced isoforms, (v) to (vii). Consistent with [24], the β and γ isoforms were not expressed here. Each splice junction is labeled with its read support, i.e. the number of reads that map across this junction. For better comparability with [24], the p53 gene, encoded on the minus strand of chromosome 17, is shown in the direction of transcription from left to right. The junctions marked with an asterisk have been experimentally validated. (B) Unannotated transcripts in the vicinity of the TACSTD2 and MYSM1 genes recovered from a HUVEC RNA data set [27]. segemehl revealed the exon structure of two novel transcript isoforms comprising at least four exons. One exon common to both isoforms was mapped to the TACSTD2 gene. The associated introns enclose the MYSM1 gene locus. The putative gene structure is supported by three exemplary multi-split reads (not strand-reversing). Some of the splice junctions have already been reported by ENCODE/CSHL (HUVEC polyA+ RNA-seq). The strandedness of the isoforms cannot be inferred.