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Each individual, VMs-to-PMs assignment, resulting from the selection is mutated using the mutation probability.
Notably, we have reanalysed several DNA samples from patients previously found not mutated using the AS-PCR approach, but failed to find any additional mutated patient.
hDAT pcDNA3.1 was mutated using the QuikChange Mutagenesis kit (Stratagene).
The pCDNA5-HA-FilGAP [12] was directly mutated using the QuickChange site-directed mutagenesis kit.
phaseoli (Xap) [40], was mutated using the manganese method (see Materials and Methods).
Putative PPREs were mutated using the QuickChange Site Directed Mutagenesis kit according to the manufacturer's instructions (Stratagene, http://www.stratagene.com).com
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For each mutation rate, the original sequences were randomly mutated using this rate and then the intron phase distribution was predicted using the same protocol for the all-pattern model, but with C i and D ij taken from the mutated sequences instead of the original sequences.
Base pairs that were different from the reference sequence (NCBI Genbank ID, BC114376) were mutated using QuickChange (Stratagene, La Jolla, CA) via the manufacturer's protocols to match the reference and non-synonymous polymorphic variant sequences.
The others in M i are mutated using a random model based on the observed characteristics of the glioblastoma data.
Human CLR with an N-terminal haemagglutinin (HA) epitope tag, human RAMP2 with an N-terminal FLAG epitope tag (Qi et al., 2013) and untagged human RAMP3 were mutated using a method based on the Quik Change II site-directed mutagenesis kit (Stratagene, Cambridge, UK) as described previously (Conner et al., 2005; Bailey and Hay, 2007).
To generate mutant promoter/reporter constructs, the SRY binding consensus sites in the promoter were mutated using complementary oligos (Table S3).
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