As expected, protein coding gene exons contain the largest fraction of highly expressed bases (Figure 1B) as well as a disproportionately large fraction of total reads relative to their small (<3%) amount of genomic sequence (Figure S2). However, many regions of high expression do exist within intergenic regions, far more than are accounted for by current noncoding RNA gene annotations (Figure 1C). We reasoned that this unaccounted for intergenic transcription must derive from novel intergenic transcripts, and we next directed our efforts toward identification and analysis of these transcripts.
