It should be noted that GENCODE-coding transcripts are not all considered equally. First, transcripts with identical CDS (in other words those that undergo alternative splicing only in 3′- or 5′-UTR) are regarded as identical for the purposes of selecting a principal protein isoform in APPRIS. Second, transcripts that are annotated as NMD targets are annotated with protein features, but cannot be selected as the principal variant by APPRIS. The same is also true of all transcripts annotated as fragments.
