Figure 2. The schematic picture of CDS consistency.

The reconstructed full-length cDNA is consistent with the reference gene if the exon-intron structure of the true CDS was completely contained in the exon-intron structure of the reference gene. Inconsistency was caused by different exon boundaries, sequence gaps or missing links between exons (i.e., introns). Sequence gaps were categorized into three types: (1) a gap in the middle of exons, (2) the 5′-end (or 3′-end) of the cDNA clone was missing, or (3) a link between two adjacent exons was missing. Note that in the case (3) we cannot exclude a possibility that some exon(s) between them is missing; therefore, the output transcript needs manual finishing in such a case.