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Figure 1. Comparison of nomenclatures for alternative splicing.Examples of splicing structures in the 5 human genes VEGFA (A), CLEC10A (B), TCL6 (C), AURKC (D), and AIF1 (E). In each case a schema of the exon–intron structure is shown where variable sites are numbered consecutively from 5′ to 3′. Subsequently, the splicing structure is described with the Malko's 5-component strings, Nagasaki's bit matrices and integer vectors, the nomenclature of the ASD/ATD/AEdb databases and with the AS code we propose in this work. The nomenclature of ASD/ATD/AEdb assigns ambiguously the same identifier to the structures in VEGFA (A) and TCL6 (C), respectively in CLEC10A (B) and AURKC (D). In CLEC10A (B), the bit matrix system assumes independence between both sides of the exon and therefore can not identify a single AS event. In AURKC (D), the vector (1,3) is assignable from the bit matrices, but it is not considered as part of the alternative donor event (9,13). Authors of the ASD/ATD/AEdb nomenclature propose the term “CIR” for complex intron retention structures. However, as in AIF1 (E), the selection of the central intron can be problematic as the names “CIR-II-5p3p-5p-IR-3p”, “CIR-CIR-II5p3p-5p-5p”, or “CIR-II5p4p-CIR-IR-3p-3p” could be imaginable. Image published in: Sammeth M et al. (2008) Sammeth et al. This image is reproduced with permission of the journal and the copyright holder. This is an open-access article distributed under the terms of the Creative Commons Attribution license Larger Image Printer Friendly View

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