Selenoprotein evolution: update blog: Difference between revisions
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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. | 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. | ||
* [ | * [[Selenoprotein_evolution:_update_blog|Tracking significant updates (this page)]] | ||
* [ | * [[Selenoprotein_evolution:_introduction|Selenoprotein curated sequence collection]] | ||
* [ | * [[Selenoprotein_evolution:_GPX|Evolution of GPX glutathione peroxidases]] | ||
* [ | * [[Selenoprotein_evolution:_SECIS|SECIS elements, binding proteins, and selenocysteine insertion]] | ||
<pre>Reverse Chronological Update Blog | <pre>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 | 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 | 04 Jun 08 (Tom): added 10 SECIS insertion sequences for SELV, 20 for SELS, 21 for SELT and 5 for SELO |
Latest revision as of 00:42, 15 January 2009
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