Figure 3.

De novo assembled transcripts connect genomic supercontigs. Schematic overview of end regions of two genomic supercontigs, v31.005068 (left) and v31.000152 (right; reverse complemented, showing previous MAKER predictions in green). Shown are de novo transcripts from the Illumina+ assembly (purple), a blastn alignment of the Mus musculus Hy-3 protein to both supercontigs (grey), transcripts assembled from 454 data alone (red), an experimentally validated PCR amplicon spanning both supercontigs (orange), and transcriptome sequencing coverage summed over all Illumina (non-stranded) or SOLiD samples (strand-specific, coverage of plus and minus strands are shown in separate panels).