Selenoprotein evolution: update blog

This cluster of genomeWiki articles on selenoprotein evolution in vertebrates is updated regularly by various contributers. Because those changes can be scattered across diverse long articles, this simple directory to articles and significant updates can be helpful for following developments.

• Tracking significant updates (this page)
• Selenoprotein curated sequence collection
• Evolution of GPX glutathione peroxidases
• SECIS elements, binding proteins, and selenocysteine insertion

Reverse Chronological Update Blog

18 Dec 08 (Tom): fixed egregious GenBank error on SEPN1 alt splice, tracked gene back to sponge divergence
16 Dec 08 (Tom): annotated questionable 3' alt splice of SELS and exon-skipping frame-shifting alt splice of SEP15
15 Dec 08 (Tom): analyzed processed pseudogenes of SELW in various placentals, finding no viable active retrogenes
14 Dec 08 (Tom): added 49 deuterostome sequences for RDX12 (aka C17orf37, SEPW2A)and dated selenocystein loss to amphibian stem
03 Jul 08 (Tom): brought outgroup total to 230 sequences (atlantogenata to frog)
02 Jul 08 (Tom): 30 tetrapod outgroup SECIS added (with greatly increasing difficulty): {[(chicken,finch),lizard],frog}.
30 Jun 08 (Tom): 128 SECIS placental outgroups added: [(sloth, armadillo),(elephant, tenrec, hyrax)],[(wallaby, brushtail),opossum].
15 Jun 08 (Tom): added SELL diselenide, prototyped custom SECIS track
11 Jun 08 (Tom): put up gene-by-gene anchored alignment of SECIS elements, seq error discussion, asked admin for sortable tables 
10 Jun 08 (Tom): added gene-by-gene SECIS alignment screenshots; SECIS elements subsorted by structural features
07 Jun 08 (Tom): brought SECIS elements up to 380 across 36 proteins using multiz genomic alignment orthology
05 Jun 08 (Tom): added 17 SECIS insertion sequences for TXNRD1, 9 for TXNRD3 and 10 for TXNRD1
04 Jun 08 (Tom): added 10 SECIS insertion sequences for SELV, 20 for SELS, 21 for SELT and 5 for SELO
03 Jun 08 (Tom): further KIAA0256 analysis; put up 18 SECIS insertion sequences for SELH to enable type 1,2 classification program
01 Jun 08 (Tom): good grief ...8 years of researchers using erroneous gene model for KIAA0256 SECIS binding protein
29 May 08 (Tom): added section on L30 kink-turn binding and evolutionary origin of selenocysteine insertion
28 May 08 (Perry): corrected thioredoxin reductase names (these are a bit confusing TrxR3 = TGR = TR2 and TrxR2 = TR3)
28 May 08 (Tom): added GPX3 in two further marsupials (still no GPX5 or GPX6); located 17 SECIS elements for each of GPX1 and GPX2
26 May 08 (Tom): began new page on detailed evolution of glutathione peroxidases based on 240 sequences
25 May 08 (Tom): added GPX sequences from urchin, amphioxus, tunicate, lamprey, and chondrichthyes; assimilated Perry's GPX sequences
23 May 08 (Tom): brought SELI to 10 deuterostome sequences
22 May 08 (Tom): upped GPX4 collection to 26 coding and 14 SECIS sequences
21 May 08 (Tom): added 30 GPX8 sequences (all cysteine except serine in most fish)
20 May 08 (Tom): located SECIS elements for GPX3, added screenshots of 3' UTR context.
18 May 08 (Tom): added 78 seqs for GPX3 and GPX5-GPX6 inverted tandem, patterns of U loss, fixed GPX classifer.
16 May 08 (Tom): found a new SECIS binding protein KIAA0256; moved all things SECIS to a new page
14 May 08 (Tom): moved stuff around, added summary matrix for genome project species, fixed fasta headers
14 May 08 (Perry): Put all GPX sequences I've collected into one group-not formatted correctly, just present for reference
12 May 08 (Tom): parsed TXNRD1-3 exons in human and added about 30 species each for terminal GCuG exons.
11 May 08 (Tom): found metazoan outgroup species with selenocysteine in SELU3 and additional lophotrochozoans for SELU2
10 May 08 (Tom): fixed SELK, added new SeCis collection, integrated hagfish/lamprey/eshark collections
09 May 08 (Tom): added 15 SEPP1, colorized the selenocysteines for clarity
08 May 08 (Perry): In the AM, added some to GPx1 and GPx2
08 May 08 (Perry): Started sections for the remaining human selenoproteins
08 May 08 (Tom): Started sections on SELO, SEPN1, SEPHS1, SEPHS2, SELK, SELT, GPX1, etc
06 May 08 (Tom): Added special section on basal jawless vertebrates: 16 genes from lamprey, 8 from hagfish.
28 Apr 08 (Tom): Brought total sequence count to 341, greatly expanded DIO1 and SELV collections and gene highlights
25 Apr 08 (Tom): Fixed DIO deiodinase sequences
24 Apr 08 (Tom): Added echidna and platypus selenoproteins from 454 search
23 Apr 08 (Tom): Added and analyzed 13 boreoeuthere SELV sequences
20 Apr 08 (Tom): Selenoprotein wiki launch
16 Apr 08 (Tom): Platypus and echidna selenoproteins from 454 transcripts
15 Apr 08 (Tom): SELU and SEPW1 updated to 50 vertebrate genome projects