To assess whether a locus or transcript is full-length, it is necessary to identify the TSS and transcription termination site (TTS). TSSs may be tested by determining overlap with CAGE tags (Takahashi et al. 2012) and the TTS by the presence of polyadenylation feature (polyA signals and polyA sites) (Ara et al. 2006). The number of protein-coding genes with at least one polyadenylation feature annotated increased by ∼10% between 3c and 7, and in the later release, the majority (∼62%) of protein-coding loci have one or more polyA sites annotated. However, the mean number of individual transcripts with a polyA site decreased between versions 3c and 7 as the overall number of annotated transcripts increased (Supplemental Table 6). Transcripts at both coding and lncRNA loci show a reduction in the percentage with polyA site of ∼2.5%. Figure 5 shows the number of polyA features increases in every annotated chromosome between release 3c and 7 for protein-coding gene loci.
