We excluded transcripts whose 5'-ends had been located inside the second or later exons of any other transcripts with compatible exon structure in the same locus. We accepted the transcripts whose 5'-ends were located inside of the first exons and considered as variations in the exact transcriptional start sites. Using similar concepts, we examined the completeness of the 3'-end using the same procedure and similarly removed all possible 3'-end truncated transcripts. The 3'-ends located inside of the last exons were allowed and concidered as alternative polyadenylation sites (Figure 1).
Figure 1. Scheme of truncated transcript decision
Reference: Kimura et al. (2006) Diversification of transcriptional modulation: Large-scale identification and characterization of putative alternative promoters of human genes. Genome Research 16, 55-65