From midori at ebi.ac.uk Tue Jul 3 22:00:05 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Wed, 4 Jul 2007 05:00:05 UT Subject: [annotation] SourceForge Annotation Tracker Update Message-ID: <200707040500.l64505q1219671@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20070704/af91d44a/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20070704/af91d44a/attachment.pl From midori at ebi.ac.uk Mon Jul 16 22:00:05 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Tue, 17 Jul 2007 05:00:05 UT Subject: [annotation] SourceForge Annotation Tracker Update Message-ID: <200707170500.l6H505Z1269518@mozart.ebi.ac.uk> An HTML attachment was scrubbed... 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Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20070717/8a054ea3/attachment.pl From pfey at northwestern.edu Wed Jul 18 14:19:12 2007 From: pfey at northwestern.edu (Petra Fey) Date: Wed, 18 Jul 2007 16:19:12 -0500 Subject: [annotation] pseudouridine synthase vs. pseudouridylate synthase Message-ID: <5D533AD0-A5C4-4C71-91FC-1E9185DB227C@northwestern.edu> Hello, I'm curating the Dicty ortholog of human RPUSD2 (RNA pseudouridylate synthase domain containing 2), and like the human protein, it has the InterPro hits to IPR006145, IPR006224, IPR006225 with the following GO annotations IPR006145 Pseudouridine synthase: GO:0009982 pseudouridine synthase activity IPR006224 Pseudouridine synthase, Rlu: GO:0004730 pseudouridylate synthase activity IPR006225 Pseudouridine synthase, Rlu: GO:0004730 pseudouridylate synthase activity When checking GO: GO:0009982 Catalysis of the reaction: RNA uridine = RNA pseudouridine. Note that this term should not be confused with 'pseudouridylate synthase activity ; GO:0004730', which refers to the formation of free pseudouridine from uracil and ribose-5-phosphate. GO:0004730 Catalysis of the reaction: uracil + D-ribose 5-phosphate = pseudouridine 5'-phosphate + H2O. Note that this term should not be confused with 'pseudouridine synthase activity ; GO:0009982', which refers to the intramolecular isomerization of uridine to pseudouridine. I just submitted this SF item https://sourceforge.net/tracker/? func=detail&atid=605890&aid=1756470&group_id=36855 However, there seems to be a larger issue: Why are the human and mouse proteins called 'RNA pseudouridylate synthase'? What complicates this further, PF00849, on which IPR006145 (!) is based on, also calls it 'RNA pseudouridylate synthase'. http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00849 Is this all a consequence of the easy confusion the GO note alerts to? Thanks, Petra -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20070718/3838495e/attachment.html From midori at ebi.ac.uk Wed Jul 18 22:00:06 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Thu, 19 Jul 2007 05:00:06 UT Subject: [annotation] SourceForge Annotation Tracker Update Message-ID: <200707190500.l6J506n1373459@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20070719/5459c5ca/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20070719/5459c5ca/attachment.pl From midori at ebi.ac.uk Fri Jul 20 22:00:07 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Sat, 21 Jul 2007 05:00:07 UT Subject: [annotation] SourceForge Annotation Tracker Update Message-ID: <200707210500.l6L507J1385073@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20070721/197f9ffd/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20070721/197f9ffd/attachment.pl From midori at ebi.ac.uk Wed Jul 25 22:00:05 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Thu, 26 Jul 2007 05:00:05 UT Subject: [annotation] SourceForge Annotation Tracker Update Message-ID: <200707260500.l6Q505d1157012@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20070726/332b4764/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20070726/332b4764/attachment.pl From midori at ebi.ac.uk Thu Jul 26 22:00:04 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Fri, 27 Jul 2007 05:00:04 UT Subject: [annotation] SourceForge Annotation Tracker Update Message-ID: <200707270500.l6R505f1201265@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20070727/4bcb1c83/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20070727/4bcb1c83/attachment.pl From midori at ebi.ac.uk Fri Jul 27 22:00:05 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Sat, 28 Jul 2007 05:00:05 UT Subject: [annotation] SourceForge Annotation Tracker Update Message-ID: <200707280500.l6S506i1240545@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20070728/8e9a8bd7/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... 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Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20070731/6893f1d9/attachment.pl From midori at ebi.ac.uk Tue Jul 31 22:00:05 2007 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Wed, 1 Aug 2007 05:00:05 UT Subject: [annotation] SourceForge Annotation Tracker Update Message-ID: <200708010500.l71505x1390351@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/annotation/attachments/20070801/640b4512/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://fafner.stanford.edu/pipermail/annotation/attachments/20070801/640b4512/attachment.pl