Table 2 Examples of other possible, logical splice junctions derived from the gene model in Figure 1 example
Splice junction aAnnotated? (Y/N)Annotated frequency (unique, common, constitutive)Exon-skipping? (Y/N)Alternative donor? (Y/N)Alternative acceptor? (Y/N)Exon-intron border? (Y/N)
Exon A:Exon F|Exon A:Exon G*Nn/aYYNN
Exon A:Exon ENn/aYYNN
Exon C:Exon HNn/aYYNN
Exon A:Exon INn/aYYNN
Exon B:Exon JNn/aYYYN
Exon D:Exon JNn/aYNYN
Exon D:Exon KNn/aYNYN
Exon H:Exon KNn/aYNYN
Exon H:Exon LNn/aYNYN
Exon I:Exon JNn/aNNYN
Exon C donor:intronNn/aNYNY
Exon E donor:intronNn/aNNNY
Exon H acceptor:intronNn/aNNNY
  • Full list of all possible junctions are listed in Supplementary Table 1 in Additional File 1.

  • a Junctions here are denoted with the 5′most exon/intron first. The second exon/intron is separated from the first using a colon. Events with identical donors and acceptors are separated by a “|”

  • * Junction is not unique as exons F and G share the same acceptor site.

  • ES = exon skipping, AD = alternative donor, AA = alternative acceptor.