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. 2010 Nov 24;6(11):e1001016. doi: 10.1371/journal.pcbi.1001016

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Corvelo et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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BP location relative to the 3SS (a1) is dependent on presence/absence additional AG dinucleotides in the intron. The most common situation is the absence of AGs in the region between the BP and the 3SS. However, these can occur either at locations close to the 3SS (i.e. a2 in r1) where they may compete with the 3SS signal, or very close to the BP (i.e a3 in r3), where they are bypassed possibly due to steric constraints. Any AG occurring in r2 is likely to be recognized as 3SS. Therefore, BPs are usually located inside region defined as r1+r2+r3 – the AG exclusion zone (AGEZ).