The sxy manuscript has been rejected! This was not what we expected, because it had been 'provisionally accepted', with the request that we do toeprinting or similar analyses to confirm our speculations that the secondary structure of sxy mRNA interferes with translation.
We didn't do the requested toeprinting, but instead used in vitro translation assays to confirm our speculations. We were a bit concerned that the editor/reviewers might not see these as an adequate substitute, but that turned out to not be a problem. But a combination of bad luck, bad judgement and bad mood let to it being rejected as not sufficiently improved for publication.
We still think this is an excellent piece of science, so we're going to instead submit it to another journal that's just as good, if not better. We're first giving the manuscript one more quick polish, taking into account all the reasonable and unreasonable comments from referees and making sure that all our explanations are as clear as possible. This should be done within the next couple of days. The new journal has a very fast turn-around time, so we'll know the outcome soon.
My sympathy. You seem to be taking the right tack. If you check in I'll be in that position in a couple of months. All part of the fun and games.
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