Subject: [Encode] Summary of pseudogene call on Thu. 5-Jan-06 at 11 AM EDT [PGENE] From: Date: Mon, 09 Jan 2006 17:25:10 -0500 Hi, I very much enjoyed the call after the holidays. Below I have attached a summary of the last call . cheers, marK ## ## Summary of 5-Jan-06 Call ## The main focus was to come to an agreement on the final consensus Jan freeze list of pseudogenes. 1. Robert found 9 new pgenes that have to be verified by Adam 2. Yantao's list of pgenes have been verified by Adam. There were two main classes of pgenes that were under discussion. a. Some pgenes have a large portion of UTR aligned to parent gene, but very little of the coding region was aligned. It was decided that since all the initial analysis was based on protein alignments, we would stick with that criteria and therefore not include the 4 pgenes which fell in this category. b. In Slide 8, Yontao illustrated an example of a pgene that was debatable because Adam's initial Gencode annotation around the locus of AK054891 indicated that it enclosed a big block of transcriptional unit which included the parent gene and several duplications. After discussion, it was agreed that it was a pgene because it seemes like a candidate for NMD. Tom would check this to see if it indeed is a candidate for NMD. There was discussion about adopting a consistent criterion to 'call' a pgene. It was agreed that even when there is transcriptional evidence, if the mrna is likely to undergo NMD, then it will be called pgene. This has to be mentioned as an important point in the methods section of a pseudogene focussed paper. 3. It was agreed that Adam would look over Robert's new list of 9 pgenes and will finalize the January pgene freeze list to be circulated around, presumably by end of Friday. This list will be tagged with a version number to distinguish it from the October freeze. Adam: Please remember to send the parent gene along with the pseudogene. 4. Another call will be scheduled after Alex is back from vacation to discuss the RACE experiments.