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pombase-sequence — PomBase sequence analysis
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From: SourceForge.net <no...@so...> - 2012-10-08 23:00:29
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Sequence analysis item #2645099, was opened at 2009-02-27 03:57 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=2645099&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed Resolution: None Priority: 1 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: repeat expanded proteins Initial Comment: Re-curate this list mail Lee at Rockefeller ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-10-08 16:00 Message: all repeat expansion are annotated as "repeat containing" ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=2645099&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-10-08 22:32:21
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Sequence analysis item #2839846, was opened at 2009-08-18 13:49 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=2839846&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed Resolution: None Priority: 1 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: missing S. cerevisiae genes expected to be present Initial Comment: YLR119W ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-10-08 15:32 Message: this is ongoing, on the wiki https://sourceforge.net/apps/trac/pombase/wiki/OrthologInventoriesNoPom ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-04-10 12:36 Message: There are also 64 essential genes in budding yeast which do not appear to have a fission yeast ortholog recheck ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=2839846&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-10-08 22:18:12
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Sequence analysis item #2654313, was opened at 2009-03-02 03:47 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=2654313&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed Resolution: None Priority: 1 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: catalogue conserved S. c genes absent from pombe Initial Comment: divide into eukaryotically conserved and fungally conserved ------------------------------------------- YAT1 YAR035W carnitine O-acetyltransferase CYS4 YGR155W cystathionine beta-synthase TAZ1 YPR140W TAfaZzin YJL055W involved in the metabolism of purine and pyrimidine base analogues HMO1 YDR174W rDNA-binding component of the Pol I transcription system Glycogen metabolism GLC3 YEL011W glycogen branching enzyme GDB1YPR184W glycogen debranching enzyme GPH1, YPR160W glycogen debranching enzyme GPH1 YPR160W Glycogen PHosphorylase GDB1, GLG1, GLG2, GSY1, GSY2, FPS1 Tryptophan degradation/ de novo NAD biosynthesis BNA1 YJR025c tryptophan met 3-hydroxyanthranilate 3,4-dioxygenase activity BNA2 YJR078W tryptophan 2,3-dioxygenase activity BNA4 YBL098W tryptophan met kynurenine 3-monooxygenase BNA5 YLR231C tryptophan met kynureninase BNA6 YFR047C biosynthesis of NAD from tryptophan via kynurenine ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-10-08 15:18 Message: inventory on wiki https://sourceforge.net/apps/trac/pombase/wiki/OrthologInventoriesNoPom ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-08-29 08:14 Message: DLS1 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2010-06-24 02:15 Message: IPT1 inositol phosphotransferase ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2010-02-04 04:46 Message: cox23 yhr116w ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2009-11-30 01:17 Message: OGG1 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2009-11-20 04:07 Message: HPA2 histone acetyltransferase ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2009-04-02 08:33 Message: YPL123C ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=2654313&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-10-08 22:13:28
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Sequence analysis item #3407281, was opened at 2011-09-10 11:05 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3407281&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed Resolution: None Priority: 1 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: annotate telomeric features Initial Comment: sub telomeric regions? any telomeric repeats? anything else? Do this after sequence update ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-10-08 15:13 Message: see https://sourceforge.net/tracker/index.php?func=detail&aid=3353877&group_id=65526&atid=2096421 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3407281&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-10-08 22:11:28
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Sequence analysis item #3482833, was opened at 2012-02-01 13:46 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3482833&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed >Resolution: Duplicate Priority: 1 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: tRNA introns Initial Comment: check that all tRNAs with introns have intron features defined ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-10-08 15:11 Message: https://sourceforge.net/tracker/index.php?func=detail&aid=3316937&group_id=65526&atid=2096421 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3482833&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-10-08 22:06:59
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Sequence analysis item #3440217, was opened at 2011-11-19 03:13 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3440217&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed Resolution: None Priority: 5 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: possible small gene or RNA Initial Comment: Is there a little coding feature between SPAC1093.04/1093.05 (from ESTs ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-10-08 15:06 Message: There appears to be an intron here (flagged), but it cant make a protein coding gene. wait for Danny's data ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3440217&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-09-25 22:08:54
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Sequence analysis item #3274905, was opened at 2011-04-04 14:51 Message generated for change (Comment added) made by kim_rutherford You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3274905&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Closed Resolution: None Priority: 9 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Valerie Wood (val_wood) Summary: human ortholog set Initial Comment: fill in missing ---------------------------------------------------------------------- >Comment By: Kim Rutherford (kim_rutherford) Date: 2012-09-25 15:08 Message: I'm doing a new Chado load now. ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-09-25 03:58 Message: Finished annotating human orthologs. Need reloading and fixing any IDs which reject ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-08-28 05:43 Message: The following are also fixed: here are the latest warnings from running the ortholog loading: load Compara orthologs can't find feature in Chado for ENSG00000256511 load manual pombe to human orthologs: conserved_multi.txt can't find feature in Chado for NUDT310 can't find feature in Chado for METL21B can't find feature in Chado for CYP226Al can't find feature in Chado for C22orf16 can't find feature in Chado for RPSAP15 can't find feature in Chado for RPSAP15 can't find feature in Chado for HMT2 can't find feature in Chado for TCTEX1 can't find feature in Chado for CNHI4 can't find feature in Chado for FOLHB1 can't find feature in Chado for MSRBS2 can't find feature in Chado for CDS3 can't find feature in Chado for SUNC1 can't find feature in Chado for ZFS36L2 can't find feature in Chado for CTF2T can't find feature in Chado for SPCC13B11.04 can't find feature in Chado for HNRPUL1 can't find feature in Chado for 3 can't find feature in Chado for URG4 load manual pombe to human orthologs: conserved_one_to_one.txt can't find feature in Chado for PDSS5B except can't find feature in Chado for 3 can't find feature in Chado for SPCC13B11.04 and can't find feature in Chado for ENSG00000256511 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3274905&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-09-25 10:58:29
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Sequence analysis item #3274905, was opened at 2011-04-04 14:51 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3274905&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed Resolution: None Priority: 9 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Valerie Wood (val_wood) Summary: human ortholog set Initial Comment: fill in missing ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-09-25 03:58 Message: Finished annotating human orthologs. Need reloading and fixing any IDs which reject ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-08-28 05:43 Message: The following are also fixed: here are the latest warnings from running the ortholog loading: load Compara orthologs can't find feature in Chado for ENSG00000256511 load manual pombe to human orthologs: conserved_multi.txt can't find feature in Chado for NUDT310 can't find feature in Chado for METL21B can't find feature in Chado for CYP226Al can't find feature in Chado for C22orf16 can't find feature in Chado for RPSAP15 can't find feature in Chado for RPSAP15 can't find feature in Chado for HMT2 can't find feature in Chado for TCTEX1 can't find feature in Chado for CNHI4 can't find feature in Chado for FOLHB1 can't find feature in Chado for MSRBS2 can't find feature in Chado for CDS3 can't find feature in Chado for SUNC1 can't find feature in Chado for ZFS36L2 can't find feature in Chado for CTF2T can't find feature in Chado for SPCC13B11.04 can't find feature in Chado for HNRPUL1 can't find feature in Chado for 3 can't find feature in Chado for URG4 load manual pombe to human orthologs: conserved_one_to_one.txt can't find feature in Chado for PDSS5B except can't find feature in Chado for 3 can't find feature in Chado for SPCC13B11.04 and can't find feature in Chado for ENSG00000256511 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3274905&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-09-14 15:57:53
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Sequence analysis item #3567054, was opened at 2012-09-12 08:21 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3567054&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: next ortholog table Initial Comment: Hopefully the next version of the pombe/cereevisiae ortholog table will be the version written out of Chado. I still need to sort out the bunch of stuff at the top where there are gene fusions (protein maps to 2 different S. cerevisiae proteins or vice versa), and we need to decide how these should be represented in Chado. There is one more, which I didn't add yet SPAC1782.04 is both YLR204W (cox24) and YNL295w (pet20) ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-09-14 08:57 Message: SPAC10F6.08c added YDL002C SPCC16C4.20c remove YDL002C ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3567054&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-09-12 15:21:00
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Sequence analysis item #3567054, was opened at 2012-09-12 08:21 Message generated for change (Tracker Item Submitted) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3567054&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: next ortholog table Initial Comment: Hopefully the next version of the pombe/cereevisiae ortholog table will be the version written out of Chado. I still need to sort out the bunch of stuff at the top where there are gene fusions (protein maps to 2 different S. cerevisiae proteins or vice versa), and we need to decide how these should be represented in Chado. There is one more, which I didn't add yet SPAC1782.04 is both YLR204W (cox24) and YNL295w (pet20) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3567054&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-09-12 15:16:34
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Sequence analysis item #3352435, was opened at 2011-07-03 15:33 Message generated for change (Settings changed) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3352435&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed Resolution: None Priority: 8 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Valerie Wood (val_wood) Summary: next ortholog table update/candidates Initial Comment: consider splitting snf2/22 pair candidate SPAC144.01/YKL023W candidate SPBP8B7.02/YBR071W candidate SPCC1393.07/YDR544C- ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-09-12 08:16 Message: All fixed in new release ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-08-29 03:51 Message: Ortholog table update SPAC17G8.03c removed YBR278W reported by PMID:15388803 added YER159C removed human POLE4 ortholog and added DRAP1 SPCC16C4.22 added /controlled_curation="term=orthologous to S. cerevisiae YBR278W; db_xref=Treefam:TF103009; date=20120829" /controlled_curation="term=human POLE4 ortholog; db_xref=Treefam:TF103009; date=20120829" ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-08-18 11:22 Message: Added in art from Treefam SPBC902.06 YAL047C SPCC417.07c YIL106W; --- SPBC16C6.01c YDR257C (faster evolving suplicate) -- ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-08-11 02:51 Message: SPBC354.08c add S cerevisiae orthologs ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-08-11 02:49 Message: check SPBC215.11c | KCNAB2 KCNAB3 KCNAB1 SPAC977.14c | KCNAB2 KCNAB3 KCNAB1 -> YPL088W SPCC965.06 | KCNAB2 KCNAB3 KCNAB1 YCR107W? ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-08-09 00:56 Message: this is another one of those darned mitochondrial fusion proteins YNL295W pet20 YLR204W(QRI5 cox24) at the C-term ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-08-08 22:54 Message: >> SPAC12G12.15 | RMND1 + YDR282C >> SPCC16C4.01 | RMND1 + YDR282C > YLR045C) add 2 SPCC895.07 SPAC513.06c | DHDH YML051w check ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-08-08 08:51 Message: SPAC16A10.03c | VPS11 (add sc ortholog YMR231W faster evolving copy) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-07-16 04:27 Message: SPAC17G8.12 YER008C (SEC3) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-05-31 14:47 Message: SPBC32H8.07 remove YOR212W ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-05-31 09:33 Message: added YFL021W to SPCC1902.01 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-05-18 07:12 Message: added SPCC757.15 YML129C ( Pfam:PF14880) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-04-16 02:27 Message: SPAC25G10.03 added YIR017C ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-02-06 15:25 Message: SPAC6B12.16/ YBR076W; db_xref=Pfam:PF14616 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-01-18 10:59 Message: also need to sort N/C term /systematic_id="SPBC21C3.07c" /controlled_curation="term=phenotype, viable; qualifier=deletion; db_xref=PMID:20473289; cv=phenotype; date=20100406" /controlled_curation="term=orthologous to S. cerevisiae YOR239W; qualifier=C_term); date=19700101" On 21/07/2011 15:11, Valerie Wood wrote: > SPAC806.02C YIL003W(N)|YDR267C(C) > SPAC22A12.08C YKR070W(N)|YDL142C(C) > SPBC16A3.11 YDR419W(N)|YFR027W(C) > SPCC1450.15 YDR302W(N)|YBR265W(C) > SPAC6F12.05C YJR142W(N)|YOR143C(C) > SPBP4H10.15 YJL200C(N)|YJL096W(C) > SPAC22E12.10C YER141W(N)|YPL252C(C) > SPBC29A3.02C YCL030C(FUSION-N) > SPBC1711.13 YCL030C(FUSION-C) > SPAC8C9.10C YKL082C(FUSION-N) > SPBC947.07 YKL082C(FUSION-C) > SPAPB1A11.03 YML054C(FUSION-C) > SPBC530.12C YGR036C(FUSION-C) > SPBC1703.02 YML127W(FUSION-C) > SPAC15E1.04 YOR074C(FUSION-C) > SPCC1223.08C YOR236W(FUSION-C) > SPAC19B12.13 YPL132W(N)|YKL155C(C) > SPAC1420.04C YPL132W(N)|YKL155C(C) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-09-30 09:45 Message: SPAC1F5.05c added YNR049c ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-29 03:25 Message: IGNORE: NOT DONE SPCC1322.04 SPCC794.10 YKL035W and YHL012W split to SPCC1322.04 YKL035W SPCC794.10 NONE YHL012W NONE ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-29 03:09 Message: SPCC1322.04 SPCC794.10 YKL035W and YHL012W split to SPCC1322.04 YKL035W SPCC794.10 NONE YHL012W NONE ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-12 11:02 Message: check out Txt PSTPIP1 &2 maybe 1:1? GeneId SPAC20G8.05c ? ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-05 04:11 Message: YKL068W and YMR047C have been removed from SPAC1486.05 int eh contigs. These 2 only hve one of the domains and represent a shorter variant which fission yeast does not appear to have....... ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-05 04:11 Message: YKL068W and YMR047C have been removed from SPAC1486.05 int eh contigs. These 2 only hve one of the domains and represent a shorter variant which fission yeast does not appear to have....... ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-19 13:53 Message: split cluster? SPCPB1C11.02 YBR068C|YBR069C|YCL025C|YDR046C|YDR508C|YEL063C|YGR191W|YKR039W|YNL268W|YNL270C|YOL020W|YOR348C|YPL265W ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-19 13:13 Message: /product="proline specific plasma membrane permease Put4 (predicted)" /systematic_id="SPAC869.10c" /db_xref="SPD:34/34G09" /controlled_curation="term=phenotype, viable; qualifier=deletion; db_xref=PMID:20473289; cv=phenotype; date=20100406" /controlled_curation="term=orthologous to S. cerevisiae YBR068C and YBR069C and YCL025C and YDR046C and YDR508C and YEL063C and YGR191W and YKR039W and YNL268W and YNL270C and YOL020W and YOR348C and YPL265W; date=19700101" split cluster? ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-17 04:11 Message: When building a new protein family for S. cerevisiae EST3, Penny Coghill in the Pfam group pulled in Uniprot 014246 (fission yeast Tpz1) which seems to make sense functionally, and fits with the fact that we had not previously detected and S. cerevisiae/ S. pombe ortholog for Tpz1 or EST3. check next pfam release ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-14 12:39 Message: Testing in progress not fixed YOR099W and YKR061W and YJL139C and YDR483W and YBR205W and YBR199W and YPL053C YOR099W KTR1 YKR061W KTR2 YJL139C YUR1 YDR483W KRE2 YBR205W KTR3 YBR199W KTR4 YPL053C KTR6 ----------------------------- Txt consider adding SPCC1682.08 to cluster...check cpmpara FromEmail va...@sa... FromName val GeneId SPAC4G9.05 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-14 11:28 Message: Txt consider adding SPCC1682.08 to cluster...check cpmpara FromEmail va...@sa... FromName val GeneId SPAC4G9.05 (need to check all of these RNA binding proteins again) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-13 10:44 Message: Look at: SPAC26F1.08c S000002390; S000003108; S000003108; Could be both SPAC27D7.02c S000004300; S000001803; S000001201; GRIP DOMAIN these are tricky….not sure…… SPAPB24D3.02c S000001657;S000003045; S000002369; S000002369; SPAC11D3.08c S000001657;S000003045; S000002369; S000002369; I have YKL174C and YGL077C and YDL210W for 8 fission yeast transporters. Will look at this in more detail later ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-12 08:49 Message: reclusgter ace2 pwp1 and all PF10342 (SP and SC) MAPK-interacting Drmip-like superfamily (clan member) PF12748 YKL077w YDL049C YJL174W KRE9 family members PF05390 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-08 10:58 Message: Reassess this http://www.ncbi.nlm.nih.gov/pubmed/18701708?dopt=Abstract I think it is correct but I need to add the other 5 members of this tree: http://www.treefam.org/cgi-bin/TFinfo.pl?ac=TF105371 Tree fam has the fission yeast SPBC28F2.11 as an outgroup Tox3 family doesn't: http://www.treefam.org/cgi-bin/TFinfo.pl?ac=TF106481 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-07 03:34 Message: Look at SPAC26F1.08c S000002390; S000003108; S000003108; could be both SPAC27D7.02c S000004300; S000001803; S000001201; GRIP DOMAIN these are tricky….not sure…… SPAPB24D3.02c S000001657;S000003045; S000002369; S000002369; SPAC11D3.08c S000001657;S000003045; S000002369; S000002369; Not done yet I have YKL174C and YGL077C and YDL210W for 8 fission yeast transporters. Will look at this in more detail later ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-06 02:26 Message: SPBC28F2.11 YDL002C YKL032C from Treefam, but doesn't look right...needs checking ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-03 15:41 Message: sort N-term/C-term ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-03 15:39 Message: check SPBC3B9.15c /YPL006W could ncp1 not scap, or are they both both? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3352435&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-08-29 15:14:48
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Sequence analysis item #2654313, was opened at 2009-03-02 03:47 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=2654313&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 1 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: catalogue conserved S. c genes absent from pombe Initial Comment: divide into eukaryotically conserved and fungally conserved ------------------------------------------- YAT1 YAR035W carnitine O-acetyltransferase CYS4 YGR155W cystathionine beta-synthase TAZ1 YPR140W TAfaZzin YJL055W involved in the metabolism of purine and pyrimidine base analogues HMO1 YDR174W rDNA-binding component of the Pol I transcription system Glycogen metabolism GLC3 YEL011W glycogen branching enzyme GDB1YPR184W glycogen debranching enzyme GPH1, YPR160W glycogen debranching enzyme GPH1 YPR160W Glycogen PHosphorylase GDB1, GLG1, GLG2, GSY1, GSY2, FPS1 Tryptophan degradation/ de novo NAD biosynthesis BNA1 YJR025c tryptophan met 3-hydroxyanthranilate 3,4-dioxygenase activity BNA2 YJR078W tryptophan 2,3-dioxygenase activity BNA4 YBL098W tryptophan met kynurenine 3-monooxygenase BNA5 YLR231C tryptophan met kynureninase BNA6 YFR047C biosynthesis of NAD from tryptophan via kynurenine ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-08-29 08:14 Message: DLS1 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2010-06-24 02:15 Message: IPT1 inositol phosphotransferase ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2010-02-04 04:46 Message: cox23 yhr116w ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2009-11-30 01:17 Message: OGG1 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2009-11-20 04:07 Message: HPA2 histone acetyltransferase ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2009-04-02 08:33 Message: YPL123C ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=2654313&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-08-29 10:51:58
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Sequence analysis item #3352435, was opened at 2011-07-03 15:33 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3352435&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 8 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Valerie Wood (val_wood) Summary: next ortholog table update/candidates Initial Comment: consider splitting snf2/22 pair candidate SPAC144.01/YKL023W candidate SPBP8B7.02/YBR071W candidate SPCC1393.07/YDR544C- ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-08-29 03:51 Message: Ortholog table update SPAC17G8.03c removed YBR278W reported by PMID:15388803 added YER159C removed human POLE4 ortholog and added DRAP1 SPCC16C4.22 added /controlled_curation="term=orthologous to S. cerevisiae YBR278W; db_xref=Treefam:TF103009; date=20120829" /controlled_curation="term=human POLE4 ortholog; db_xref=Treefam:TF103009; date=20120829" ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-08-18 11:22 Message: Added in art from Treefam SPBC902.06 YAL047C SPCC417.07c YIL106W; --- SPBC16C6.01c YDR257C (faster evolving suplicate) -- ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-08-11 02:51 Message: SPBC354.08c add S cerevisiae orthologs ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-08-11 02:49 Message: check SPBC215.11c | KCNAB2 KCNAB3 KCNAB1 SPAC977.14c | KCNAB2 KCNAB3 KCNAB1 -> YPL088W SPCC965.06 | KCNAB2 KCNAB3 KCNAB1 YCR107W? ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-08-09 00:56 Message: this is another one of those darned mitochondrial fusion proteins YNL295W pet20 YLR204W(QRI5 cox24) at the C-term ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-08-08 22:54 Message: >> SPAC12G12.15 | RMND1 + YDR282C >> SPCC16C4.01 | RMND1 + YDR282C > YLR045C) add 2 SPCC895.07 SPAC513.06c | DHDH YML051w check ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-08-08 08:51 Message: SPAC16A10.03c | VPS11 (add sc ortholog YMR231W faster evolving copy) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-07-16 04:27 Message: SPAC17G8.12 YER008C (SEC3) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-05-31 14:47 Message: SPBC32H8.07 remove YOR212W ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-05-31 09:33 Message: added YFL021W to SPCC1902.01 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-05-18 07:12 Message: added SPCC757.15 YML129C ( Pfam:PF14880) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-04-16 02:27 Message: SPAC25G10.03 added YIR017C ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-02-06 15:25 Message: SPAC6B12.16/ YBR076W; db_xref=Pfam:PF14616 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-01-18 10:59 Message: also need to sort N/C term /systematic_id="SPBC21C3.07c" /controlled_curation="term=phenotype, viable; qualifier=deletion; db_xref=PMID:20473289; cv=phenotype; date=20100406" /controlled_curation="term=orthologous to S. cerevisiae YOR239W; qualifier=C_term); date=19700101" On 21/07/2011 15:11, Valerie Wood wrote: > SPAC806.02C YIL003W(N)|YDR267C(C) > SPAC22A12.08C YKR070W(N)|YDL142C(C) > SPBC16A3.11 YDR419W(N)|YFR027W(C) > SPCC1450.15 YDR302W(N)|YBR265W(C) > SPAC6F12.05C YJR142W(N)|YOR143C(C) > SPBP4H10.15 YJL200C(N)|YJL096W(C) > SPAC22E12.10C YER141W(N)|YPL252C(C) > SPBC29A3.02C YCL030C(FUSION-N) > SPBC1711.13 YCL030C(FUSION-C) > SPAC8C9.10C YKL082C(FUSION-N) > SPBC947.07 YKL082C(FUSION-C) > SPAPB1A11.03 YML054C(FUSION-C) > SPBC530.12C YGR036C(FUSION-C) > SPBC1703.02 YML127W(FUSION-C) > SPAC15E1.04 YOR074C(FUSION-C) > SPCC1223.08C YOR236W(FUSION-C) > SPAC19B12.13 YPL132W(N)|YKL155C(C) > SPAC1420.04C YPL132W(N)|YKL155C(C) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-09-30 09:45 Message: SPAC1F5.05c added YNR049c ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-29 03:25 Message: IGNORE: NOT DONE SPCC1322.04 SPCC794.10 YKL035W and YHL012W split to SPCC1322.04 YKL035W SPCC794.10 NONE YHL012W NONE ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-29 03:09 Message: SPCC1322.04 SPCC794.10 YKL035W and YHL012W split to SPCC1322.04 YKL035W SPCC794.10 NONE YHL012W NONE ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-12 11:02 Message: check out Txt PSTPIP1 &2 maybe 1:1? GeneId SPAC20G8.05c ? ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-05 04:11 Message: YKL068W and YMR047C have been removed from SPAC1486.05 int eh contigs. These 2 only hve one of the domains and represent a shorter variant which fission yeast does not appear to have....... ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-05 04:11 Message: YKL068W and YMR047C have been removed from SPAC1486.05 int eh contigs. These 2 only hve one of the domains and represent a shorter variant which fission yeast does not appear to have....... ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-19 13:53 Message: split cluster? SPCPB1C11.02 YBR068C|YBR069C|YCL025C|YDR046C|YDR508C|YEL063C|YGR191W|YKR039W|YNL268W|YNL270C|YOL020W|YOR348C|YPL265W ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-19 13:13 Message: /product="proline specific plasma membrane permease Put4 (predicted)" /systematic_id="SPAC869.10c" /db_xref="SPD:34/34G09" /controlled_curation="term=phenotype, viable; qualifier=deletion; db_xref=PMID:20473289; cv=phenotype; date=20100406" /controlled_curation="term=orthologous to S. cerevisiae YBR068C and YBR069C and YCL025C and YDR046C and YDR508C and YEL063C and YGR191W and YKR039W and YNL268W and YNL270C and YOL020W and YOR348C and YPL265W; date=19700101" split cluster? ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-17 04:11 Message: When building a new protein family for S. cerevisiae EST3, Penny Coghill in the Pfam group pulled in Uniprot 014246 (fission yeast Tpz1) which seems to make sense functionally, and fits with the fact that we had not previously detected and S. cerevisiae/ S. pombe ortholog for Tpz1 or EST3. check next pfam release ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-14 12:39 Message: Testing in progress not fixed YOR099W and YKR061W and YJL139C and YDR483W and YBR205W and YBR199W and YPL053C YOR099W KTR1 YKR061W KTR2 YJL139C YUR1 YDR483W KRE2 YBR205W KTR3 YBR199W KTR4 YPL053C KTR6 ----------------------------- Txt consider adding SPCC1682.08 to cluster...check cpmpara FromEmail va...@sa... FromName val GeneId SPAC4G9.05 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-14 11:28 Message: Txt consider adding SPCC1682.08 to cluster...check cpmpara FromEmail va...@sa... FromName val GeneId SPAC4G9.05 (need to check all of these RNA binding proteins again) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-13 10:44 Message: Look at: SPAC26F1.08c S000002390; S000003108; S000003108; Could be both SPAC27D7.02c S000004300; S000001803; S000001201; GRIP DOMAIN these are tricky….not sure…… SPAPB24D3.02c S000001657;S000003045; S000002369; S000002369; SPAC11D3.08c S000001657;S000003045; S000002369; S000002369; I have YKL174C and YGL077C and YDL210W for 8 fission yeast transporters. Will look at this in more detail later ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-12 08:49 Message: reclusgter ace2 pwp1 and all PF10342 (SP and SC) MAPK-interacting Drmip-like superfamily (clan member) PF12748 YKL077w YDL049C YJL174W KRE9 family members PF05390 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-08 10:58 Message: Reassess this http://www.ncbi.nlm.nih.gov/pubmed/18701708?dopt=Abstract I think it is correct but I need to add the other 5 members of this tree: http://www.treefam.org/cgi-bin/TFinfo.pl?ac=TF105371 Tree fam has the fission yeast SPBC28F2.11 as an outgroup Tox3 family doesn't: http://www.treefam.org/cgi-bin/TFinfo.pl?ac=TF106481 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-07 03:34 Message: Look at SPAC26F1.08c S000002390; S000003108; S000003108; could be both SPAC27D7.02c S000004300; S000001803; S000001201; GRIP DOMAIN these are tricky….not sure…… SPAPB24D3.02c S000001657;S000003045; S000002369; S000002369; SPAC11D3.08c S000001657;S000003045; S000002369; S000002369; Not done yet I have YKL174C and YGL077C and YDL210W for 8 fission yeast transporters. Will look at this in more detail later ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-06 02:26 Message: SPBC28F2.11 YDL002C YKL032C from Treefam, but doesn't look right...needs checking ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-03 15:41 Message: sort N-term/C-term ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-03 15:39 Message: check SPBC3B9.15c /YPL006W could ncp1 not scap, or are they both both? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3352435&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-08-28 12:43:29
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Sequence analysis item #3274905, was opened at 2011-04-04 14:51 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3274905&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 9 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Valerie Wood (val_wood) Summary: human ortholog set Initial Comment: fill in missing ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-08-28 05:43 Message: The following are also fixed: here are the latest warnings from running the ortholog loading: load Compara orthologs can't find feature in Chado for ENSG00000256511 load manual pombe to human orthologs: conserved_multi.txt can't find feature in Chado for NUDT310 can't find feature in Chado for METL21B can't find feature in Chado for CYP226Al can't find feature in Chado for C22orf16 can't find feature in Chado for RPSAP15 can't find feature in Chado for RPSAP15 can't find feature in Chado for HMT2 can't find feature in Chado for TCTEX1 can't find feature in Chado for CNHI4 can't find feature in Chado for FOLHB1 can't find feature in Chado for MSRBS2 can't find feature in Chado for CDS3 can't find feature in Chado for SUNC1 can't find feature in Chado for ZFS36L2 can't find feature in Chado for CTF2T can't find feature in Chado for SPCC13B11.04 can't find feature in Chado for HNRPUL1 can't find feature in Chado for 3 can't find feature in Chado for URG4 load manual pombe to human orthologs: conserved_one_to_one.txt can't find feature in Chado for PDSS5B except can't find feature in Chado for 3 can't find feature in Chado for SPCC13B11.04 and can't find feature in Chado for ENSG00000256511 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3274905&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-08-23 07:37:16
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Sequence analysis item #3482230, was opened at 2012-01-31 07:28 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3482230&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed Resolution: None Priority: 5 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Valerie Wood (val_wood) Summary: check species distribution Initial Comment: > SPAC17A2.08c sequence orphan extends > SPAC18G6.09c sequence orphan extends ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-08-23 00:37 Message: > SPAC17A2.08c sequence orphan changed to conserved fungal, cant sistinguish furhter > SPAC18G6.09c sequence orphan Kept as orphan, just hitting lots of random proline serine rich proteins ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3482230&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-08-23 07:15:00
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Sequence analysis item #3274905, was opened at 2011-04-04 14:51 Message generated for change (Settings changed) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3274905&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None >Priority: 9 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Valerie Wood (val_wood) Summary: human ortholog set Initial Comment: fill in missing ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3274905&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-08-23 07:14:23
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Sequence analysis item #3274371, was opened at 2011-04-04 09:16 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3274371&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None >Priority: 1 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: re-assesing the orphan set Initial Comment: Question from Charlie H and others: > > I was curious as to whether pombe proteins that have japonicus or > > octosporus homologs would then be removed from the orphan list, or will a > > "fission yeast only" category be created? I am not asking about any gene > > in particular, I was just wondering. Yes I intend to create classes conserved in Schizosaccharomyces pombe only conserved in Schizosaccharomyces only I am still waiting for all of the japonicus octosprus to be in Uniprot which will make this easier, but it is on the to-do list. We may find that when we build families for these with Pfam some of these build to other fungi, or even to higher eukaryotes, so it may change the observed levels of conservation quite a bit. ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-08-23 00:14 Message: No point doing this until the octosporus and japonicus updates are established and all of the translations are avaiable ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3274371&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-08-18 18:22:51
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Sequence analysis item #3352435, was opened at 2011-07-03 15:33 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3352435&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 8 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Valerie Wood (val_wood) Summary: next ortholog table update/candidates Initial Comment: consider splitting snf2/22 pair candidate SPAC144.01/YKL023W candidate SPBP8B7.02/YBR071W candidate SPCC1393.07/YDR544C- ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-08-18 11:22 Message: Added in art from Treefam SPBC902.06 YAL047C SPCC417.07c YIL106W; --- SPBC16C6.01c YDR257C (faster evolving suplicate) -- ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-08-11 02:51 Message: SPBC354.08c add S cerevisiae orthologs ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-08-11 02:49 Message: check SPBC215.11c | KCNAB2 KCNAB3 KCNAB1 SPAC977.14c | KCNAB2 KCNAB3 KCNAB1 -> YPL088W SPCC965.06 | KCNAB2 KCNAB3 KCNAB1 YCR107W? ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-08-09 00:56 Message: this is another one of those darned mitochondrial fusion proteins YNL295W pet20 YLR204W(QRI5 cox24) at the C-term ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-08-08 22:54 Message: >> SPAC12G12.15 | RMND1 + YDR282C >> SPCC16C4.01 | RMND1 + YDR282C > YLR045C) add 2 SPCC895.07 SPAC513.06c | DHDH YML051w check ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-08-08 08:51 Message: SPAC16A10.03c | VPS11 (add sc ortholog YMR231W faster evolving copy) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-07-16 04:27 Message: SPAC17G8.12 YER008C (SEC3) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-05-31 14:47 Message: SPBC32H8.07 remove YOR212W ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-05-31 09:33 Message: added YFL021W to SPCC1902.01 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-05-18 07:12 Message: added SPCC757.15 YML129C ( Pfam:PF14880) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-04-16 02:27 Message: SPAC25G10.03 added YIR017C ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-02-06 15:25 Message: SPAC6B12.16/ YBR076W; db_xref=Pfam:PF14616 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-01-18 10:59 Message: also need to sort N/C term /systematic_id="SPBC21C3.07c" /controlled_curation="term=phenotype, viable; qualifier=deletion; db_xref=PMID:20473289; cv=phenotype; date=20100406" /controlled_curation="term=orthologous to S. cerevisiae YOR239W; qualifier=C_term); date=19700101" On 21/07/2011 15:11, Valerie Wood wrote: > SPAC806.02C YIL003W(N)|YDR267C(C) > SPAC22A12.08C YKR070W(N)|YDL142C(C) > SPBC16A3.11 YDR419W(N)|YFR027W(C) > SPCC1450.15 YDR302W(N)|YBR265W(C) > SPAC6F12.05C YJR142W(N)|YOR143C(C) > SPBP4H10.15 YJL200C(N)|YJL096W(C) > SPAC22E12.10C YER141W(N)|YPL252C(C) > SPBC29A3.02C YCL030C(FUSION-N) > SPBC1711.13 YCL030C(FUSION-C) > SPAC8C9.10C YKL082C(FUSION-N) > SPBC947.07 YKL082C(FUSION-C) > SPAPB1A11.03 YML054C(FUSION-C) > SPBC530.12C YGR036C(FUSION-C) > SPBC1703.02 YML127W(FUSION-C) > SPAC15E1.04 YOR074C(FUSION-C) > SPCC1223.08C YOR236W(FUSION-C) > SPAC19B12.13 YPL132W(N)|YKL155C(C) > SPAC1420.04C YPL132W(N)|YKL155C(C) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-09-30 09:45 Message: SPAC1F5.05c added YNR049c ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-29 03:25 Message: IGNORE: NOT DONE SPCC1322.04 SPCC794.10 YKL035W and YHL012W split to SPCC1322.04 YKL035W SPCC794.10 NONE YHL012W NONE ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-29 03:09 Message: SPCC1322.04 SPCC794.10 YKL035W and YHL012W split to SPCC1322.04 YKL035W SPCC794.10 NONE YHL012W NONE ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-12 11:02 Message: check out Txt PSTPIP1 &2 maybe 1:1? GeneId SPAC20G8.05c ? ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-05 04:11 Message: YKL068W and YMR047C have been removed from SPAC1486.05 int eh contigs. These 2 only hve one of the domains and represent a shorter variant which fission yeast does not appear to have....... ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-05 04:11 Message: YKL068W and YMR047C have been removed from SPAC1486.05 int eh contigs. These 2 only hve one of the domains and represent a shorter variant which fission yeast does not appear to have....... ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-19 13:53 Message: split cluster? SPCPB1C11.02 YBR068C|YBR069C|YCL025C|YDR046C|YDR508C|YEL063C|YGR191W|YKR039W|YNL268W|YNL270C|YOL020W|YOR348C|YPL265W ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-19 13:13 Message: /product="proline specific plasma membrane permease Put4 (predicted)" /systematic_id="SPAC869.10c" /db_xref="SPD:34/34G09" /controlled_curation="term=phenotype, viable; qualifier=deletion; db_xref=PMID:20473289; cv=phenotype; date=20100406" /controlled_curation="term=orthologous to S. cerevisiae YBR068C and YBR069C and YCL025C and YDR046C and YDR508C and YEL063C and YGR191W and YKR039W and YNL268W and YNL270C and YOL020W and YOR348C and YPL265W; date=19700101" split cluster? ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-17 04:11 Message: When building a new protein family for S. cerevisiae EST3, Penny Coghill in the Pfam group pulled in Uniprot 014246 (fission yeast Tpz1) which seems to make sense functionally, and fits with the fact that we had not previously detected and S. cerevisiae/ S. pombe ortholog for Tpz1 or EST3. check next pfam release ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-14 12:39 Message: Testing in progress not fixed YOR099W and YKR061W and YJL139C and YDR483W and YBR205W and YBR199W and YPL053C YOR099W KTR1 YKR061W KTR2 YJL139C YUR1 YDR483W KRE2 YBR205W KTR3 YBR199W KTR4 YPL053C KTR6 ----------------------------- Txt consider adding SPCC1682.08 to cluster...check cpmpara FromEmail va...@sa... FromName val GeneId SPAC4G9.05 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-14 11:28 Message: Txt consider adding SPCC1682.08 to cluster...check cpmpara FromEmail va...@sa... FromName val GeneId SPAC4G9.05 (need to check all of these RNA binding proteins again) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-13 10:44 Message: Look at: SPAC26F1.08c S000002390; S000003108; S000003108; Could be both SPAC27D7.02c S000004300; S000001803; S000001201; GRIP DOMAIN these are tricky….not sure…… SPAPB24D3.02c S000001657;S000003045; S000002369; S000002369; SPAC11D3.08c S000001657;S000003045; S000002369; S000002369; I have YKL174C and YGL077C and YDL210W for 8 fission yeast transporters. Will look at this in more detail later ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-12 08:49 Message: reclusgter ace2 pwp1 and all PF10342 (SP and SC) MAPK-interacting Drmip-like superfamily (clan member) PF12748 YKL077w YDL049C YJL174W KRE9 family members PF05390 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-08 10:58 Message: Reassess this http://www.ncbi.nlm.nih.gov/pubmed/18701708?dopt=Abstract I think it is correct but I need to add the other 5 members of this tree: http://www.treefam.org/cgi-bin/TFinfo.pl?ac=TF105371 Tree fam has the fission yeast SPBC28F2.11 as an outgroup Tox3 family doesn't: http://www.treefam.org/cgi-bin/TFinfo.pl?ac=TF106481 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-07 03:34 Message: Look at SPAC26F1.08c S000002390; S000003108; S000003108; could be both SPAC27D7.02c S000004300; S000001803; S000001201; GRIP DOMAIN these are tricky….not sure…… SPAPB24D3.02c S000001657;S000003045; S000002369; S000002369; SPAC11D3.08c S000001657;S000003045; S000002369; S000002369; Not done yet I have YKL174C and YGL077C and YDL210W for 8 fission yeast transporters. Will look at this in more detail later ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-06 02:26 Message: SPBC28F2.11 YDL002C YKL032C from Treefam, but doesn't look right...needs checking ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-03 15:41 Message: sort N-term/C-term ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-03 15:39 Message: check SPBC3B9.15c /YPL006W could ncp1 not scap, or are they both both? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3352435&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-08-11 09:51:52
|
Sequence analysis item #3352435, was opened at 2011-07-03 15:33 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3352435&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 8 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Valerie Wood (val_wood) Summary: next ortholog table update/candidates Initial Comment: consider splitting snf2/22 pair candidate SPAC144.01/YKL023W candidate SPBP8B7.02/YBR071W candidate SPCC1393.07/YDR544C- ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-08-11 02:51 Message: SPBC354.08c add S cerevisiae orthologs ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-08-11 02:49 Message: check SPBC215.11c | KCNAB2 KCNAB3 KCNAB1 SPAC977.14c | KCNAB2 KCNAB3 KCNAB1 -> YPL088W SPCC965.06 | KCNAB2 KCNAB3 KCNAB1 YCR107W? ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-08-09 00:56 Message: this is another one of those darned mitochondrial fusion proteins YNL295W pet20 YLR204W(QRI5 cox24) at the C-term ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-08-08 22:54 Message: >> SPAC12G12.15 | RMND1 + YDR282C >> SPCC16C4.01 | RMND1 + YDR282C > YLR045C) add 2 SPCC895.07 SPAC513.06c | DHDH YML051w check ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-08-08 08:51 Message: SPAC16A10.03c | VPS11 (add sc ortholog YMR231W faster evolving copy) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-07-16 04:27 Message: SPAC17G8.12 YER008C (SEC3) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-05-31 14:47 Message: SPBC32H8.07 remove YOR212W ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-05-31 09:33 Message: added YFL021W to SPCC1902.01 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-05-18 07:12 Message: added SPCC757.15 YML129C ( Pfam:PF14880) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-04-16 02:27 Message: SPAC25G10.03 added YIR017C ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-02-06 15:25 Message: SPAC6B12.16/ YBR076W; db_xref=Pfam:PF14616 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-01-18 10:59 Message: also need to sort N/C term /systematic_id="SPBC21C3.07c" /controlled_curation="term=phenotype, viable; qualifier=deletion; db_xref=PMID:20473289; cv=phenotype; date=20100406" /controlled_curation="term=orthologous to S. cerevisiae YOR239W; qualifier=C_term); date=19700101" On 21/07/2011 15:11, Valerie Wood wrote: > SPAC806.02C YIL003W(N)|YDR267C(C) > SPAC22A12.08C YKR070W(N)|YDL142C(C) > SPBC16A3.11 YDR419W(N)|YFR027W(C) > SPCC1450.15 YDR302W(N)|YBR265W(C) > SPAC6F12.05C YJR142W(N)|YOR143C(C) > SPBP4H10.15 YJL200C(N)|YJL096W(C) > SPAC22E12.10C YER141W(N)|YPL252C(C) > SPBC29A3.02C YCL030C(FUSION-N) > SPBC1711.13 YCL030C(FUSION-C) > SPAC8C9.10C YKL082C(FUSION-N) > SPBC947.07 YKL082C(FUSION-C) > SPAPB1A11.03 YML054C(FUSION-C) > SPBC530.12C YGR036C(FUSION-C) > SPBC1703.02 YML127W(FUSION-C) > SPAC15E1.04 YOR074C(FUSION-C) > SPCC1223.08C YOR236W(FUSION-C) > SPAC19B12.13 YPL132W(N)|YKL155C(C) > SPAC1420.04C YPL132W(N)|YKL155C(C) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-09-30 09:45 Message: SPAC1F5.05c added YNR049c ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-29 03:25 Message: IGNORE: NOT DONE SPCC1322.04 SPCC794.10 YKL035W and YHL012W split to SPCC1322.04 YKL035W SPCC794.10 NONE YHL012W NONE ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-29 03:09 Message: SPCC1322.04 SPCC794.10 YKL035W and YHL012W split to SPCC1322.04 YKL035W SPCC794.10 NONE YHL012W NONE ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-12 11:02 Message: check out Txt PSTPIP1 &2 maybe 1:1? GeneId SPAC20G8.05c ? ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-05 04:11 Message: YKL068W and YMR047C have been removed from SPAC1486.05 int eh contigs. These 2 only hve one of the domains and represent a shorter variant which fission yeast does not appear to have....... ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-05 04:11 Message: YKL068W and YMR047C have been removed from SPAC1486.05 int eh contigs. These 2 only hve one of the domains and represent a shorter variant which fission yeast does not appear to have....... ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-19 13:53 Message: split cluster? SPCPB1C11.02 YBR068C|YBR069C|YCL025C|YDR046C|YDR508C|YEL063C|YGR191W|YKR039W|YNL268W|YNL270C|YOL020W|YOR348C|YPL265W ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-19 13:13 Message: /product="proline specific plasma membrane permease Put4 (predicted)" /systematic_id="SPAC869.10c" /db_xref="SPD:34/34G09" /controlled_curation="term=phenotype, viable; qualifier=deletion; db_xref=PMID:20473289; cv=phenotype; date=20100406" /controlled_curation="term=orthologous to S. cerevisiae YBR068C and YBR069C and YCL025C and YDR046C and YDR508C and YEL063C and YGR191W and YKR039W and YNL268W and YNL270C and YOL020W and YOR348C and YPL265W; date=19700101" split cluster? ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-17 04:11 Message: When building a new protein family for S. cerevisiae EST3, Penny Coghill in the Pfam group pulled in Uniprot 014246 (fission yeast Tpz1) which seems to make sense functionally, and fits with the fact that we had not previously detected and S. cerevisiae/ S. pombe ortholog for Tpz1 or EST3. check next pfam release ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-14 12:39 Message: Testing in progress not fixed YOR099W and YKR061W and YJL139C and YDR483W and YBR205W and YBR199W and YPL053C YOR099W KTR1 YKR061W KTR2 YJL139C YUR1 YDR483W KRE2 YBR205W KTR3 YBR199W KTR4 YPL053C KTR6 ----------------------------- Txt consider adding SPCC1682.08 to cluster...check cpmpara FromEmail va...@sa... FromName val GeneId SPAC4G9.05 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-14 11:28 Message: Txt consider adding SPCC1682.08 to cluster...check cpmpara FromEmail va...@sa... FromName val GeneId SPAC4G9.05 (need to check all of these RNA binding proteins again) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-13 10:44 Message: Look at: SPAC26F1.08c S000002390; S000003108; S000003108; Could be both SPAC27D7.02c S000004300; S000001803; S000001201; GRIP DOMAIN these are tricky….not sure…… SPAPB24D3.02c S000001657;S000003045; S000002369; S000002369; SPAC11D3.08c S000001657;S000003045; S000002369; S000002369; I have YKL174C and YGL077C and YDL210W for 8 fission yeast transporters. Will look at this in more detail later ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-12 08:49 Message: reclusgter ace2 pwp1 and all PF10342 (SP and SC) MAPK-interacting Drmip-like superfamily (clan member) PF12748 YKL077w YDL049C YJL174W KRE9 family members PF05390 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-08 10:58 Message: Reassess this http://www.ncbi.nlm.nih.gov/pubmed/18701708?dopt=Abstract I think it is correct but I need to add the other 5 members of this tree: http://www.treefam.org/cgi-bin/TFinfo.pl?ac=TF105371 Tree fam has the fission yeast SPBC28F2.11 as an outgroup Tox3 family doesn't: http://www.treefam.org/cgi-bin/TFinfo.pl?ac=TF106481 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-07 03:34 Message: Look at SPAC26F1.08c S000002390; S000003108; S000003108; could be both SPAC27D7.02c S000004300; S000001803; S000001201; GRIP DOMAIN these are tricky….not sure…… SPAPB24D3.02c S000001657;S000003045; S000002369; S000002369; SPAC11D3.08c S000001657;S000003045; S000002369; S000002369; Not done yet I have YKL174C and YGL077C and YDL210W for 8 fission yeast transporters. Will look at this in more detail later ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-06 02:26 Message: SPBC28F2.11 YDL002C YKL032C from Treefam, but doesn't look right...needs checking ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-03 15:41 Message: sort N-term/C-term ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-03 15:39 Message: check SPBC3B9.15c /YPL006W could ncp1 not scap, or are they both both? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3352435&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-08-11 09:49:19
|
Sequence analysis item #3352435, was opened at 2011-07-03 15:33 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3352435&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 8 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Valerie Wood (val_wood) Summary: next ortholog table update/candidates Initial Comment: consider splitting snf2/22 pair candidate SPAC144.01/YKL023W candidate SPBP8B7.02/YBR071W candidate SPCC1393.07/YDR544C- ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-08-11 02:49 Message: check SPBC215.11c | KCNAB2 KCNAB3 KCNAB1 SPAC977.14c | KCNAB2 KCNAB3 KCNAB1 -> YPL088W SPCC965.06 | KCNAB2 KCNAB3 KCNAB1 YCR107W? ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-08-09 00:56 Message: this is another one of those darned mitochondrial fusion proteins YNL295W pet20 YLR204W(QRI5 cox24) at the C-term ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-08-08 22:54 Message: >> SPAC12G12.15 | RMND1 + YDR282C >> SPCC16C4.01 | RMND1 + YDR282C > YLR045C) add 2 SPCC895.07 SPAC513.06c | DHDH YML051w check ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-08-08 08:51 Message: SPAC16A10.03c | VPS11 (add sc ortholog YMR231W faster evolving copy) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-07-16 04:27 Message: SPAC17G8.12 YER008C (SEC3) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-05-31 14:47 Message: SPBC32H8.07 remove YOR212W ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-05-31 09:33 Message: added YFL021W to SPCC1902.01 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-05-18 07:12 Message: added SPCC757.15 YML129C ( Pfam:PF14880) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-04-16 02:27 Message: SPAC25G10.03 added YIR017C ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-02-06 15:25 Message: SPAC6B12.16/ YBR076W; db_xref=Pfam:PF14616 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-01-18 10:59 Message: also need to sort N/C term /systematic_id="SPBC21C3.07c" /controlled_curation="term=phenotype, viable; qualifier=deletion; db_xref=PMID:20473289; cv=phenotype; date=20100406" /controlled_curation="term=orthologous to S. cerevisiae YOR239W; qualifier=C_term); date=19700101" On 21/07/2011 15:11, Valerie Wood wrote: > SPAC806.02C YIL003W(N)|YDR267C(C) > SPAC22A12.08C YKR070W(N)|YDL142C(C) > SPBC16A3.11 YDR419W(N)|YFR027W(C) > SPCC1450.15 YDR302W(N)|YBR265W(C) > SPAC6F12.05C YJR142W(N)|YOR143C(C) > SPBP4H10.15 YJL200C(N)|YJL096W(C) > SPAC22E12.10C YER141W(N)|YPL252C(C) > SPBC29A3.02C YCL030C(FUSION-N) > SPBC1711.13 YCL030C(FUSION-C) > SPAC8C9.10C YKL082C(FUSION-N) > SPBC947.07 YKL082C(FUSION-C) > SPAPB1A11.03 YML054C(FUSION-C) > SPBC530.12C YGR036C(FUSION-C) > SPBC1703.02 YML127W(FUSION-C) > SPAC15E1.04 YOR074C(FUSION-C) > SPCC1223.08C YOR236W(FUSION-C) > SPAC19B12.13 YPL132W(N)|YKL155C(C) > SPAC1420.04C YPL132W(N)|YKL155C(C) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-09-30 09:45 Message: SPAC1F5.05c added YNR049c ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-29 03:25 Message: IGNORE: NOT DONE SPCC1322.04 SPCC794.10 YKL035W and YHL012W split to SPCC1322.04 YKL035W SPCC794.10 NONE YHL012W NONE ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-29 03:09 Message: SPCC1322.04 SPCC794.10 YKL035W and YHL012W split to SPCC1322.04 YKL035W SPCC794.10 NONE YHL012W NONE ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-12 11:02 Message: check out Txt PSTPIP1 &2 maybe 1:1? GeneId SPAC20G8.05c ? ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-05 04:11 Message: YKL068W and YMR047C have been removed from SPAC1486.05 int eh contigs. These 2 only hve one of the domains and represent a shorter variant which fission yeast does not appear to have....... ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-05 04:11 Message: YKL068W and YMR047C have been removed from SPAC1486.05 int eh contigs. These 2 only hve one of the domains and represent a shorter variant which fission yeast does not appear to have....... ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-19 13:53 Message: split cluster? SPCPB1C11.02 YBR068C|YBR069C|YCL025C|YDR046C|YDR508C|YEL063C|YGR191W|YKR039W|YNL268W|YNL270C|YOL020W|YOR348C|YPL265W ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-19 13:13 Message: /product="proline specific plasma membrane permease Put4 (predicted)" /systematic_id="SPAC869.10c" /db_xref="SPD:34/34G09" /controlled_curation="term=phenotype, viable; qualifier=deletion; db_xref=PMID:20473289; cv=phenotype; date=20100406" /controlled_curation="term=orthologous to S. cerevisiae YBR068C and YBR069C and YCL025C and YDR046C and YDR508C and YEL063C and YGR191W and YKR039W and YNL268W and YNL270C and YOL020W and YOR348C and YPL265W; date=19700101" split cluster? ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-17 04:11 Message: When building a new protein family for S. cerevisiae EST3, Penny Coghill in the Pfam group pulled in Uniprot 014246 (fission yeast Tpz1) which seems to make sense functionally, and fits with the fact that we had not previously detected and S. cerevisiae/ S. pombe ortholog for Tpz1 or EST3. check next pfam release ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-14 12:39 Message: Testing in progress not fixed YOR099W and YKR061W and YJL139C and YDR483W and YBR205W and YBR199W and YPL053C YOR099W KTR1 YKR061W KTR2 YJL139C YUR1 YDR483W KRE2 YBR205W KTR3 YBR199W KTR4 YPL053C KTR6 ----------------------------- Txt consider adding SPCC1682.08 to cluster...check cpmpara FromEmail va...@sa... FromName val GeneId SPAC4G9.05 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-14 11:28 Message: Txt consider adding SPCC1682.08 to cluster...check cpmpara FromEmail va...@sa... FromName val GeneId SPAC4G9.05 (need to check all of these RNA binding proteins again) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-13 10:44 Message: Look at: SPAC26F1.08c S000002390; S000003108; S000003108; Could be both SPAC27D7.02c S000004300; S000001803; S000001201; GRIP DOMAIN these are tricky….not sure…… SPAPB24D3.02c S000001657;S000003045; S000002369; S000002369; SPAC11D3.08c S000001657;S000003045; S000002369; S000002369; I have YKL174C and YGL077C and YDL210W for 8 fission yeast transporters. Will look at this in more detail later ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-12 08:49 Message: reclusgter ace2 pwp1 and all PF10342 (SP and SC) MAPK-interacting Drmip-like superfamily (clan member) PF12748 YKL077w YDL049C YJL174W KRE9 family members PF05390 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-08 10:58 Message: Reassess this http://www.ncbi.nlm.nih.gov/pubmed/18701708?dopt=Abstract I think it is correct but I need to add the other 5 members of this tree: http://www.treefam.org/cgi-bin/TFinfo.pl?ac=TF105371 Tree fam has the fission yeast SPBC28F2.11 as an outgroup Tox3 family doesn't: http://www.treefam.org/cgi-bin/TFinfo.pl?ac=TF106481 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-07 03:34 Message: Look at SPAC26F1.08c S000002390; S000003108; S000003108; could be both SPAC27D7.02c S000004300; S000001803; S000001201; GRIP DOMAIN these are tricky….not sure…… SPAPB24D3.02c S000001657;S000003045; S000002369; S000002369; SPAC11D3.08c S000001657;S000003045; S000002369; S000002369; Not done yet I have YKL174C and YGL077C and YDL210W for 8 fission yeast transporters. Will look at this in more detail later ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-06 02:26 Message: SPBC28F2.11 YDL002C YKL032C from Treefam, but doesn't look right...needs checking ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-03 15:41 Message: sort N-term/C-term ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-03 15:39 Message: check SPBC3B9.15c /YPL006W could ncp1 not scap, or are they both both? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3352435&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-08-09 07:56:41
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Sequence analysis item #3352435, was opened at 2011-07-03 15:33 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3352435&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 8 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Valerie Wood (val_wood) Summary: next ortholog table update/candidates Initial Comment: consider splitting snf2/22 pair candidate SPAC144.01/YKL023W candidate SPBP8B7.02/YBR071W candidate SPCC1393.07/YDR544C- ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-08-09 00:56 Message: this is another one of those darned mitochondrial fusion proteins YNL295W pet20 YLR204W(QRI5 cox24) at the C-term ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-08-08 22:54 Message: >> SPAC12G12.15 | RMND1 + YDR282C >> SPCC16C4.01 | RMND1 + YDR282C > YLR045C) add 2 SPCC895.07 SPAC513.06c | DHDH YML051w check ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-08-08 08:51 Message: SPAC16A10.03c | VPS11 (add sc ortholog YMR231W faster evolving copy) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-07-16 04:27 Message: SPAC17G8.12 YER008C (SEC3) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-05-31 14:47 Message: SPBC32H8.07 remove YOR212W ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-05-31 09:33 Message: added YFL021W to SPCC1902.01 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-05-18 07:12 Message: added SPCC757.15 YML129C ( Pfam:PF14880) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-04-16 02:27 Message: SPAC25G10.03 added YIR017C ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-02-06 15:25 Message: SPAC6B12.16/ YBR076W; db_xref=Pfam:PF14616 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-01-18 10:59 Message: also need to sort N/C term /systematic_id="SPBC21C3.07c" /controlled_curation="term=phenotype, viable; qualifier=deletion; db_xref=PMID:20473289; cv=phenotype; date=20100406" /controlled_curation="term=orthologous to S. cerevisiae YOR239W; qualifier=C_term); date=19700101" On 21/07/2011 15:11, Valerie Wood wrote: > SPAC806.02C YIL003W(N)|YDR267C(C) > SPAC22A12.08C YKR070W(N)|YDL142C(C) > SPBC16A3.11 YDR419W(N)|YFR027W(C) > SPCC1450.15 YDR302W(N)|YBR265W(C) > SPAC6F12.05C YJR142W(N)|YOR143C(C) > SPBP4H10.15 YJL200C(N)|YJL096W(C) > SPAC22E12.10C YER141W(N)|YPL252C(C) > SPBC29A3.02C YCL030C(FUSION-N) > SPBC1711.13 YCL030C(FUSION-C) > SPAC8C9.10C YKL082C(FUSION-N) > SPBC947.07 YKL082C(FUSION-C) > SPAPB1A11.03 YML054C(FUSION-C) > SPBC530.12C YGR036C(FUSION-C) > SPBC1703.02 YML127W(FUSION-C) > SPAC15E1.04 YOR074C(FUSION-C) > SPCC1223.08C YOR236W(FUSION-C) > SPAC19B12.13 YPL132W(N)|YKL155C(C) > SPAC1420.04C YPL132W(N)|YKL155C(C) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-09-30 09:45 Message: SPAC1F5.05c added YNR049c ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-29 03:25 Message: IGNORE: NOT DONE SPCC1322.04 SPCC794.10 YKL035W and YHL012W split to SPCC1322.04 YKL035W SPCC794.10 NONE YHL012W NONE ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-29 03:09 Message: SPCC1322.04 SPCC794.10 YKL035W and YHL012W split to SPCC1322.04 YKL035W SPCC794.10 NONE YHL012W NONE ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-12 11:02 Message: check out Txt PSTPIP1 &2 maybe 1:1? GeneId SPAC20G8.05c ? ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-05 04:11 Message: YKL068W and YMR047C have been removed from SPAC1486.05 int eh contigs. These 2 only hve one of the domains and represent a shorter variant which fission yeast does not appear to have....... ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-05 04:11 Message: YKL068W and YMR047C have been removed from SPAC1486.05 int eh contigs. These 2 only hve one of the domains and represent a shorter variant which fission yeast does not appear to have....... ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-19 13:53 Message: split cluster? SPCPB1C11.02 YBR068C|YBR069C|YCL025C|YDR046C|YDR508C|YEL063C|YGR191W|YKR039W|YNL268W|YNL270C|YOL020W|YOR348C|YPL265W ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-19 13:13 Message: /product="proline specific plasma membrane permease Put4 (predicted)" /systematic_id="SPAC869.10c" /db_xref="SPD:34/34G09" /controlled_curation="term=phenotype, viable; qualifier=deletion; db_xref=PMID:20473289; cv=phenotype; date=20100406" /controlled_curation="term=orthologous to S. cerevisiae YBR068C and YBR069C and YCL025C and YDR046C and YDR508C and YEL063C and YGR191W and YKR039W and YNL268W and YNL270C and YOL020W and YOR348C and YPL265W; date=19700101" split cluster? ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-17 04:11 Message: When building a new protein family for S. cerevisiae EST3, Penny Coghill in the Pfam group pulled in Uniprot 014246 (fission yeast Tpz1) which seems to make sense functionally, and fits with the fact that we had not previously detected and S. cerevisiae/ S. pombe ortholog for Tpz1 or EST3. check next pfam release ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-14 12:39 Message: Testing in progress not fixed YOR099W and YKR061W and YJL139C and YDR483W and YBR205W and YBR199W and YPL053C YOR099W KTR1 YKR061W KTR2 YJL139C YUR1 YDR483W KRE2 YBR205W KTR3 YBR199W KTR4 YPL053C KTR6 ----------------------------- Txt consider adding SPCC1682.08 to cluster...check cpmpara FromEmail va...@sa... FromName val GeneId SPAC4G9.05 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-14 11:28 Message: Txt consider adding SPCC1682.08 to cluster...check cpmpara FromEmail va...@sa... FromName val GeneId SPAC4G9.05 (need to check all of these RNA binding proteins again) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-13 10:44 Message: Look at: SPAC26F1.08c S000002390; S000003108; S000003108; Could be both SPAC27D7.02c S000004300; S000001803; S000001201; GRIP DOMAIN these are tricky….not sure…… SPAPB24D3.02c S000001657;S000003045; S000002369; S000002369; SPAC11D3.08c S000001657;S000003045; S000002369; S000002369; I have YKL174C and YGL077C and YDL210W for 8 fission yeast transporters. Will look at this in more detail later ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-12 08:49 Message: reclusgter ace2 pwp1 and all PF10342 (SP and SC) MAPK-interacting Drmip-like superfamily (clan member) PF12748 YKL077w YDL049C YJL174W KRE9 family members PF05390 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-08 10:58 Message: Reassess this http://www.ncbi.nlm.nih.gov/pubmed/18701708?dopt=Abstract I think it is correct but I need to add the other 5 members of this tree: http://www.treefam.org/cgi-bin/TFinfo.pl?ac=TF105371 Tree fam has the fission yeast SPBC28F2.11 as an outgroup Tox3 family doesn't: http://www.treefam.org/cgi-bin/TFinfo.pl?ac=TF106481 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-07 03:34 Message: Look at SPAC26F1.08c S000002390; S000003108; S000003108; could be both SPAC27D7.02c S000004300; S000001803; S000001201; GRIP DOMAIN these are tricky….not sure…… SPAPB24D3.02c S000001657;S000003045; S000002369; S000002369; SPAC11D3.08c S000001657;S000003045; S000002369; S000002369; Not done yet I have YKL174C and YGL077C and YDL210W for 8 fission yeast transporters. Will look at this in more detail later ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-06 02:26 Message: SPBC28F2.11 YDL002C YKL032C from Treefam, but doesn't look right...needs checking ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-03 15:41 Message: sort N-term/C-term ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-03 15:39 Message: check SPBC3B9.15c /YPL006W could ncp1 not scap, or are they both both? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3352435&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-08-09 05:54:33
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Sequence analysis item #3352435, was opened at 2011-07-03 15:33 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3352435&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 8 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Valerie Wood (val_wood) Summary: next ortholog table update/candidates Initial Comment: consider splitting snf2/22 pair candidate SPAC144.01/YKL023W candidate SPBP8B7.02/YBR071W candidate SPCC1393.07/YDR544C- ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-08-08 22:54 Message: >> SPAC12G12.15 | RMND1 + YDR282C >> SPCC16C4.01 | RMND1 + YDR282C > YLR045C) add 2 SPCC895.07 SPAC513.06c | DHDH YML051w check ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-08-08 08:51 Message: SPAC16A10.03c | VPS11 (add sc ortholog YMR231W faster evolving copy) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-07-16 04:27 Message: SPAC17G8.12 YER008C (SEC3) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-05-31 14:47 Message: SPBC32H8.07 remove YOR212W ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-05-31 09:33 Message: added YFL021W to SPCC1902.01 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-05-18 07:12 Message: added SPCC757.15 YML129C ( Pfam:PF14880) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-04-16 02:27 Message: SPAC25G10.03 added YIR017C ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-02-06 15:25 Message: SPAC6B12.16/ YBR076W; db_xref=Pfam:PF14616 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-01-18 10:59 Message: also need to sort N/C term /systematic_id="SPBC21C3.07c" /controlled_curation="term=phenotype, viable; qualifier=deletion; db_xref=PMID:20473289; cv=phenotype; date=20100406" /controlled_curation="term=orthologous to S. cerevisiae YOR239W; qualifier=C_term); date=19700101" On 21/07/2011 15:11, Valerie Wood wrote: > SPAC806.02C YIL003W(N)|YDR267C(C) > SPAC22A12.08C YKR070W(N)|YDL142C(C) > SPBC16A3.11 YDR419W(N)|YFR027W(C) > SPCC1450.15 YDR302W(N)|YBR265W(C) > SPAC6F12.05C YJR142W(N)|YOR143C(C) > SPBP4H10.15 YJL200C(N)|YJL096W(C) > SPAC22E12.10C YER141W(N)|YPL252C(C) > SPBC29A3.02C YCL030C(FUSION-N) > SPBC1711.13 YCL030C(FUSION-C) > SPAC8C9.10C YKL082C(FUSION-N) > SPBC947.07 YKL082C(FUSION-C) > SPAPB1A11.03 YML054C(FUSION-C) > SPBC530.12C YGR036C(FUSION-C) > SPBC1703.02 YML127W(FUSION-C) > SPAC15E1.04 YOR074C(FUSION-C) > SPCC1223.08C YOR236W(FUSION-C) > SPAC19B12.13 YPL132W(N)|YKL155C(C) > SPAC1420.04C YPL132W(N)|YKL155C(C) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-09-30 09:45 Message: SPAC1F5.05c added YNR049c ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-29 03:25 Message: IGNORE: NOT DONE SPCC1322.04 SPCC794.10 YKL035W and YHL012W split to SPCC1322.04 YKL035W SPCC794.10 NONE YHL012W NONE ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-29 03:09 Message: SPCC1322.04 SPCC794.10 YKL035W and YHL012W split to SPCC1322.04 YKL035W SPCC794.10 NONE YHL012W NONE ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-12 11:02 Message: check out Txt PSTPIP1 &2 maybe 1:1? GeneId SPAC20G8.05c ? ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-05 04:11 Message: YKL068W and YMR047C have been removed from SPAC1486.05 int eh contigs. These 2 only hve one of the domains and represent a shorter variant which fission yeast does not appear to have....... ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-05 04:11 Message: YKL068W and YMR047C have been removed from SPAC1486.05 int eh contigs. These 2 only hve one of the domains and represent a shorter variant which fission yeast does not appear to have....... ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-19 13:53 Message: split cluster? SPCPB1C11.02 YBR068C|YBR069C|YCL025C|YDR046C|YDR508C|YEL063C|YGR191W|YKR039W|YNL268W|YNL270C|YOL020W|YOR348C|YPL265W ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-19 13:13 Message: /product="proline specific plasma membrane permease Put4 (predicted)" /systematic_id="SPAC869.10c" /db_xref="SPD:34/34G09" /controlled_curation="term=phenotype, viable; qualifier=deletion; db_xref=PMID:20473289; cv=phenotype; date=20100406" /controlled_curation="term=orthologous to S. cerevisiae YBR068C and YBR069C and YCL025C and YDR046C and YDR508C and YEL063C and YGR191W and YKR039W and YNL268W and YNL270C and YOL020W and YOR348C and YPL265W; date=19700101" split cluster? ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-17 04:11 Message: When building a new protein family for S. cerevisiae EST3, Penny Coghill in the Pfam group pulled in Uniprot 014246 (fission yeast Tpz1) which seems to make sense functionally, and fits with the fact that we had not previously detected and S. cerevisiae/ S. pombe ortholog for Tpz1 or EST3. check next pfam release ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-14 12:39 Message: Testing in progress not fixed YOR099W and YKR061W and YJL139C and YDR483W and YBR205W and YBR199W and YPL053C YOR099W KTR1 YKR061W KTR2 YJL139C YUR1 YDR483W KRE2 YBR205W KTR3 YBR199W KTR4 YPL053C KTR6 ----------------------------- Txt consider adding SPCC1682.08 to cluster...check cpmpara FromEmail va...@sa... FromName val GeneId SPAC4G9.05 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-14 11:28 Message: Txt consider adding SPCC1682.08 to cluster...check cpmpara FromEmail va...@sa... FromName val GeneId SPAC4G9.05 (need to check all of these RNA binding proteins again) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-13 10:44 Message: Look at: SPAC26F1.08c S000002390; S000003108; S000003108; Could be both SPAC27D7.02c S000004300; S000001803; S000001201; GRIP DOMAIN these are tricky….not sure…… SPAPB24D3.02c S000001657;S000003045; S000002369; S000002369; SPAC11D3.08c S000001657;S000003045; S000002369; S000002369; I have YKL174C and YGL077C and YDL210W for 8 fission yeast transporters. Will look at this in more detail later ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-12 08:49 Message: reclusgter ace2 pwp1 and all PF10342 (SP and SC) MAPK-interacting Drmip-like superfamily (clan member) PF12748 YKL077w YDL049C YJL174W KRE9 family members PF05390 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-08 10:58 Message: Reassess this http://www.ncbi.nlm.nih.gov/pubmed/18701708?dopt=Abstract I think it is correct but I need to add the other 5 members of this tree: http://www.treefam.org/cgi-bin/TFinfo.pl?ac=TF105371 Tree fam has the fission yeast SPBC28F2.11 as an outgroup Tox3 family doesn't: http://www.treefam.org/cgi-bin/TFinfo.pl?ac=TF106481 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-07 03:34 Message: Look at SPAC26F1.08c S000002390; S000003108; S000003108; could be both SPAC27D7.02c S000004300; S000001803; S000001201; GRIP DOMAIN these are tricky….not sure…… SPAPB24D3.02c S000001657;S000003045; S000002369; S000002369; SPAC11D3.08c S000001657;S000003045; S000002369; S000002369; Not done yet I have YKL174C and YGL077C and YDL210W for 8 fission yeast transporters. Will look at this in more detail later ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-06 02:26 Message: SPBC28F2.11 YDL002C YKL032C from Treefam, but doesn't look right...needs checking ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-03 15:41 Message: sort N-term/C-term ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-03 15:39 Message: check SPBC3B9.15c /YPL006W could ncp1 not scap, or are they both both? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3352435&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-08-08 15:51:03
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Sequence analysis item #3352435, was opened at 2011-07-03 15:33 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3352435&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 8 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Valerie Wood (val_wood) Summary: next ortholog table update/candidates Initial Comment: consider splitting snf2/22 pair candidate SPAC144.01/YKL023W candidate SPBP8B7.02/YBR071W candidate SPCC1393.07/YDR544C- ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-08-08 08:51 Message: SPAC16A10.03c | VPS11 (add sc ortholog YMR231W faster evolving copy) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-07-16 04:27 Message: SPAC17G8.12 YER008C (SEC3) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-05-31 14:47 Message: SPBC32H8.07 remove YOR212W ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-05-31 09:33 Message: added YFL021W to SPCC1902.01 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-05-18 07:12 Message: added SPCC757.15 YML129C ( Pfam:PF14880) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-04-16 02:27 Message: SPAC25G10.03 added YIR017C ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-02-06 15:25 Message: SPAC6B12.16/ YBR076W; db_xref=Pfam:PF14616 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-01-18 10:59 Message: also need to sort N/C term /systematic_id="SPBC21C3.07c" /controlled_curation="term=phenotype, viable; qualifier=deletion; db_xref=PMID:20473289; cv=phenotype; date=20100406" /controlled_curation="term=orthologous to S. cerevisiae YOR239W; qualifier=C_term); date=19700101" On 21/07/2011 15:11, Valerie Wood wrote: > SPAC806.02C YIL003W(N)|YDR267C(C) > SPAC22A12.08C YKR070W(N)|YDL142C(C) > SPBC16A3.11 YDR419W(N)|YFR027W(C) > SPCC1450.15 YDR302W(N)|YBR265W(C) > SPAC6F12.05C YJR142W(N)|YOR143C(C) > SPBP4H10.15 YJL200C(N)|YJL096W(C) > SPAC22E12.10C YER141W(N)|YPL252C(C) > SPBC29A3.02C YCL030C(FUSION-N) > SPBC1711.13 YCL030C(FUSION-C) > SPAC8C9.10C YKL082C(FUSION-N) > SPBC947.07 YKL082C(FUSION-C) > SPAPB1A11.03 YML054C(FUSION-C) > SPBC530.12C YGR036C(FUSION-C) > SPBC1703.02 YML127W(FUSION-C) > SPAC15E1.04 YOR074C(FUSION-C) > SPCC1223.08C YOR236W(FUSION-C) > SPAC19B12.13 YPL132W(N)|YKL155C(C) > SPAC1420.04C YPL132W(N)|YKL155C(C) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-09-30 09:45 Message: SPAC1F5.05c added YNR049c ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-29 03:25 Message: IGNORE: NOT DONE SPCC1322.04 SPCC794.10 YKL035W and YHL012W split to SPCC1322.04 YKL035W SPCC794.10 NONE YHL012W NONE ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-29 03:09 Message: SPCC1322.04 SPCC794.10 YKL035W and YHL012W split to SPCC1322.04 YKL035W SPCC794.10 NONE YHL012W NONE ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-12 11:02 Message: check out Txt PSTPIP1 &2 maybe 1:1? GeneId SPAC20G8.05c ? ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-05 04:11 Message: YKL068W and YMR047C have been removed from SPAC1486.05 int eh contigs. These 2 only hve one of the domains and represent a shorter variant which fission yeast does not appear to have....... ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-05 04:11 Message: YKL068W and YMR047C have been removed from SPAC1486.05 int eh contigs. These 2 only hve one of the domains and represent a shorter variant which fission yeast does not appear to have....... ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-19 13:53 Message: split cluster? SPCPB1C11.02 YBR068C|YBR069C|YCL025C|YDR046C|YDR508C|YEL063C|YGR191W|YKR039W|YNL268W|YNL270C|YOL020W|YOR348C|YPL265W ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-19 13:13 Message: /product="proline specific plasma membrane permease Put4 (predicted)" /systematic_id="SPAC869.10c" /db_xref="SPD:34/34G09" /controlled_curation="term=phenotype, viable; qualifier=deletion; db_xref=PMID:20473289; cv=phenotype; date=20100406" /controlled_curation="term=orthologous to S. cerevisiae YBR068C and YBR069C and YCL025C and YDR046C and YDR508C and YEL063C and YGR191W and YKR039W and YNL268W and YNL270C and YOL020W and YOR348C and YPL265W; date=19700101" split cluster? ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-17 04:11 Message: When building a new protein family for S. cerevisiae EST3, Penny Coghill in the Pfam group pulled in Uniprot 014246 (fission yeast Tpz1) which seems to make sense functionally, and fits with the fact that we had not previously detected and S. cerevisiae/ S. pombe ortholog for Tpz1 or EST3. check next pfam release ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-14 12:39 Message: Testing in progress not fixed YOR099W and YKR061W and YJL139C and YDR483W and YBR205W and YBR199W and YPL053C YOR099W KTR1 YKR061W KTR2 YJL139C YUR1 YDR483W KRE2 YBR205W KTR3 YBR199W KTR4 YPL053C KTR6 ----------------------------- Txt consider adding SPCC1682.08 to cluster...check cpmpara FromEmail va...@sa... FromName val GeneId SPAC4G9.05 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-14 11:28 Message: Txt consider adding SPCC1682.08 to cluster...check cpmpara FromEmail va...@sa... FromName val GeneId SPAC4G9.05 (need to check all of these RNA binding proteins again) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-13 10:44 Message: Look at: SPAC26F1.08c S000002390; S000003108; S000003108; Could be both SPAC27D7.02c S000004300; S000001803; S000001201; GRIP DOMAIN these are tricky….not sure…… SPAPB24D3.02c S000001657;S000003045; S000002369; S000002369; SPAC11D3.08c S000001657;S000003045; S000002369; S000002369; I have YKL174C and YGL077C and YDL210W for 8 fission yeast transporters. Will look at this in more detail later ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-12 08:49 Message: reclusgter ace2 pwp1 and all PF10342 (SP and SC) MAPK-interacting Drmip-like superfamily (clan member) PF12748 YKL077w YDL049C YJL174W KRE9 family members PF05390 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-08 10:58 Message: Reassess this http://www.ncbi.nlm.nih.gov/pubmed/18701708?dopt=Abstract I think it is correct but I need to add the other 5 members of this tree: http://www.treefam.org/cgi-bin/TFinfo.pl?ac=TF105371 Tree fam has the fission yeast SPBC28F2.11 as an outgroup Tox3 family doesn't: http://www.treefam.org/cgi-bin/TFinfo.pl?ac=TF106481 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-07 03:34 Message: Look at SPAC26F1.08c S000002390; S000003108; S000003108; could be both SPAC27D7.02c S000004300; S000001803; S000001201; GRIP DOMAIN these are tricky….not sure…… SPAPB24D3.02c S000001657;S000003045; S000002369; S000002369; SPAC11D3.08c S000001657;S000003045; S000002369; S000002369; Not done yet I have YKL174C and YGL077C and YDL210W for 8 fission yeast transporters. Will look at this in more detail later ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-06 02:26 Message: SPBC28F2.11 YDL002C YKL032C from Treefam, but doesn't look right...needs checking ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-03 15:41 Message: sort N-term/C-term ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-03 15:39 Message: check SPBC3B9.15c /YPL006W could ncp1 not scap, or are they both both? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3352435&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-07-16 11:27:54
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Sequence analysis item #3352435, was opened at 2011-07-03 15:33 Message generated for change (Settings changed) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3352435&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None >Priority: 8 Private: No Submitted By: Valerie Wood (val_wood) >Assigned to: Valerie Wood (val_wood) Summary: next ortholog table update/candidates Initial Comment: consider splitting snf2/22 pair candidate SPAC144.01/YKL023W candidate SPBP8B7.02/YBR071W candidate SPCC1393.07/YDR544C- ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-07-16 04:27 Message: SPAC17G8.12 YER008C (SEC3) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-05-31 14:47 Message: SPBC32H8.07 remove YOR212W ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-05-31 09:33 Message: added YFL021W to SPCC1902.01 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-05-18 07:12 Message: added SPCC757.15 YML129C ( Pfam:PF14880) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-04-16 02:27 Message: SPAC25G10.03 added YIR017C ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-02-06 15:25 Message: SPAC6B12.16/ YBR076W; db_xref=Pfam:PF14616 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-01-18 10:59 Message: also need to sort N/C term /systematic_id="SPBC21C3.07c" /controlled_curation="term=phenotype, viable; qualifier=deletion; db_xref=PMID:20473289; cv=phenotype; date=20100406" /controlled_curation="term=orthologous to S. cerevisiae YOR239W; qualifier=C_term); date=19700101" On 21/07/2011 15:11, Valerie Wood wrote: > SPAC806.02C YIL003W(N)|YDR267C(C) > SPAC22A12.08C YKR070W(N)|YDL142C(C) > SPBC16A3.11 YDR419W(N)|YFR027W(C) > SPCC1450.15 YDR302W(N)|YBR265W(C) > SPAC6F12.05C YJR142W(N)|YOR143C(C) > SPBP4H10.15 YJL200C(N)|YJL096W(C) > SPAC22E12.10C YER141W(N)|YPL252C(C) > SPBC29A3.02C YCL030C(FUSION-N) > SPBC1711.13 YCL030C(FUSION-C) > SPAC8C9.10C YKL082C(FUSION-N) > SPBC947.07 YKL082C(FUSION-C) > SPAPB1A11.03 YML054C(FUSION-C) > SPBC530.12C YGR036C(FUSION-C) > SPBC1703.02 YML127W(FUSION-C) > SPAC15E1.04 YOR074C(FUSION-C) > SPCC1223.08C YOR236W(FUSION-C) > SPAC19B12.13 YPL132W(N)|YKL155C(C) > SPAC1420.04C YPL132W(N)|YKL155C(C) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-09-30 09:45 Message: SPAC1F5.05c added YNR049c ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-29 03:25 Message: IGNORE: NOT DONE SPCC1322.04 SPCC794.10 YKL035W and YHL012W split to SPCC1322.04 YKL035W SPCC794.10 NONE YHL012W NONE ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-29 03:09 Message: SPCC1322.04 SPCC794.10 YKL035W and YHL012W split to SPCC1322.04 YKL035W SPCC794.10 NONE YHL012W NONE ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-12 11:02 Message: check out Txt PSTPIP1 &2 maybe 1:1? GeneId SPAC20G8.05c ? ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-05 04:11 Message: YKL068W and YMR047C have been removed from SPAC1486.05 int eh contigs. These 2 only hve one of the domains and represent a shorter variant which fission yeast does not appear to have....... ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-05 04:11 Message: YKL068W and YMR047C have been removed from SPAC1486.05 int eh contigs. These 2 only hve one of the domains and represent a shorter variant which fission yeast does not appear to have....... ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-19 13:53 Message: split cluster? SPCPB1C11.02 YBR068C|YBR069C|YCL025C|YDR046C|YDR508C|YEL063C|YGR191W|YKR039W|YNL268W|YNL270C|YOL020W|YOR348C|YPL265W ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-19 13:13 Message: /product="proline specific plasma membrane permease Put4 (predicted)" /systematic_id="SPAC869.10c" /db_xref="SPD:34/34G09" /controlled_curation="term=phenotype, viable; qualifier=deletion; db_xref=PMID:20473289; cv=phenotype; date=20100406" /controlled_curation="term=orthologous to S. cerevisiae YBR068C and YBR069C and YCL025C and YDR046C and YDR508C and YEL063C and YGR191W and YKR039W and YNL268W and YNL270C and YOL020W and YOR348C and YPL265W; date=19700101" split cluster? ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-17 04:11 Message: When building a new protein family for S. cerevisiae EST3, Penny Coghill in the Pfam group pulled in Uniprot 014246 (fission yeast Tpz1) which seems to make sense functionally, and fits with the fact that we had not previously detected and S. cerevisiae/ S. pombe ortholog for Tpz1 or EST3. check next pfam release ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-14 12:39 Message: Testing in progress not fixed YOR099W and YKR061W and YJL139C and YDR483W and YBR205W and YBR199W and YPL053C YOR099W KTR1 YKR061W KTR2 YJL139C YUR1 YDR483W KRE2 YBR205W KTR3 YBR199W KTR4 YPL053C KTR6 ----------------------------- Txt consider adding SPCC1682.08 to cluster...check cpmpara FromEmail va...@sa... FromName val GeneId SPAC4G9.05 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-14 11:28 Message: Txt consider adding SPCC1682.08 to cluster...check cpmpara FromEmail va...@sa... FromName val GeneId SPAC4G9.05 (need to check all of these RNA binding proteins again) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-13 10:44 Message: Look at: SPAC26F1.08c S000002390; S000003108; S000003108; Could be both SPAC27D7.02c S000004300; S000001803; S000001201; GRIP DOMAIN these are tricky….not sure…… SPAPB24D3.02c S000001657;S000003045; S000002369; S000002369; SPAC11D3.08c S000001657;S000003045; S000002369; S000002369; I have YKL174C and YGL077C and YDL210W for 8 fission yeast transporters. Will look at this in more detail later ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-12 08:49 Message: reclusgter ace2 pwp1 and all PF10342 (SP and SC) MAPK-interacting Drmip-like superfamily (clan member) PF12748 YKL077w YDL049C YJL174W KRE9 family members PF05390 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-08 10:58 Message: Reassess this http://www.ncbi.nlm.nih.gov/pubmed/18701708?dopt=Abstract I think it is correct but I need to add the other 5 members of this tree: http://www.treefam.org/cgi-bin/TFinfo.pl?ac=TF105371 Tree fam has the fission yeast SPBC28F2.11 as an outgroup Tox3 family doesn't: http://www.treefam.org/cgi-bin/TFinfo.pl?ac=TF106481 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-07 03:34 Message: Look at SPAC26F1.08c S000002390; S000003108; S000003108; could be both SPAC27D7.02c S000004300; S000001803; S000001201; GRIP DOMAIN these are tricky….not sure…… SPAPB24D3.02c S000001657;S000003045; S000002369; S000002369; SPAC11D3.08c S000001657;S000003045; S000002369; S000002369; Not done yet I have YKL174C and YGL077C and YDL210W for 8 fission yeast transporters. Will look at this in more detail later ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-06 02:26 Message: SPBC28F2.11 YDL002C YKL032C from Treefam, but doesn't look right...needs checking ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-03 15:41 Message: sort N-term/C-term ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-03 15:39 Message: check SPBC3B9.15c /YPL006W could ncp1 not scap, or are they both both? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3352435&group_id=65526 |
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From: SourceForge.net <no...@so...> - 2012-05-31 21:47:31
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Sequence analysis item #3352435, was opened at 2011-07-03 15:33 Message generated for change (Comment added) made by val_wood You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3352435&group_id=65526 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 1 Private: No Submitted By: Valerie Wood (val_wood) Assigned to: Nobody/Anonymous (nobody) Summary: next ortholog table update/candidates Initial Comment: consider splitting snf2/22 pair candidate SPAC144.01/YKL023W candidate SPBP8B7.02/YBR071W candidate SPCC1393.07/YDR544C- ---------------------------------------------------------------------- >Comment By: Valerie Wood (val_wood) Date: 2012-05-31 14:47 Message: SPBC32H8.07 remove YOR212W ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-05-31 09:33 Message: added YFL021W to SPCC1902.01 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-05-18 07:12 Message: added SPCC757.15 YML129C ( Pfam:PF14880) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-04-16 02:27 Message: SPAC25G10.03 added YIR017C ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-02-06 15:25 Message: SPAC6B12.16/ YBR076W; db_xref=Pfam:PF14616 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2012-01-18 10:59 Message: also need to sort N/C term /systematic_id="SPBC21C3.07c" /controlled_curation="term=phenotype, viable; qualifier=deletion; db_xref=PMID:20473289; cv=phenotype; date=20100406" /controlled_curation="term=orthologous to S. cerevisiae YOR239W; qualifier=C_term); date=19700101" On 21/07/2011 15:11, Valerie Wood wrote: > SPAC806.02C YIL003W(N)|YDR267C(C) > SPAC22A12.08C YKR070W(N)|YDL142C(C) > SPBC16A3.11 YDR419W(N)|YFR027W(C) > SPCC1450.15 YDR302W(N)|YBR265W(C) > SPAC6F12.05C YJR142W(N)|YOR143C(C) > SPBP4H10.15 YJL200C(N)|YJL096W(C) > SPAC22E12.10C YER141W(N)|YPL252C(C) > SPBC29A3.02C YCL030C(FUSION-N) > SPBC1711.13 YCL030C(FUSION-C) > SPAC8C9.10C YKL082C(FUSION-N) > SPBC947.07 YKL082C(FUSION-C) > SPAPB1A11.03 YML054C(FUSION-C) > SPBC530.12C YGR036C(FUSION-C) > SPBC1703.02 YML127W(FUSION-C) > SPAC15E1.04 YOR074C(FUSION-C) > SPCC1223.08C YOR236W(FUSION-C) > SPAC19B12.13 YPL132W(N)|YKL155C(C) > SPAC1420.04C YPL132W(N)|YKL155C(C) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-09-30 09:45 Message: SPAC1F5.05c added YNR049c ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-29 03:25 Message: IGNORE: NOT DONE SPCC1322.04 SPCC794.10 YKL035W and YHL012W split to SPCC1322.04 YKL035W SPCC794.10 NONE YHL012W NONE ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-29 03:09 Message: SPCC1322.04 SPCC794.10 YKL035W and YHL012W split to SPCC1322.04 YKL035W SPCC794.10 NONE YHL012W NONE ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-12 11:02 Message: check out Txt PSTPIP1 &2 maybe 1:1? GeneId SPAC20G8.05c ? ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-05 04:11 Message: YKL068W and YMR047C have been removed from SPAC1486.05 int eh contigs. These 2 only hve one of the domains and represent a shorter variant which fission yeast does not appear to have....... ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-08-05 04:11 Message: YKL068W and YMR047C have been removed from SPAC1486.05 int eh contigs. These 2 only hve one of the domains and represent a shorter variant which fission yeast does not appear to have....... ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-19 13:53 Message: split cluster? SPCPB1C11.02 YBR068C|YBR069C|YCL025C|YDR046C|YDR508C|YEL063C|YGR191W|YKR039W|YNL268W|YNL270C|YOL020W|YOR348C|YPL265W ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-19 13:13 Message: /product="proline specific plasma membrane permease Put4 (predicted)" /systematic_id="SPAC869.10c" /db_xref="SPD:34/34G09" /controlled_curation="term=phenotype, viable; qualifier=deletion; db_xref=PMID:20473289; cv=phenotype; date=20100406" /controlled_curation="term=orthologous to S. cerevisiae YBR068C and YBR069C and YCL025C and YDR046C and YDR508C and YEL063C and YGR191W and YKR039W and YNL268W and YNL270C and YOL020W and YOR348C and YPL265W; date=19700101" split cluster? ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-17 04:11 Message: When building a new protein family for S. cerevisiae EST3, Penny Coghill in the Pfam group pulled in Uniprot 014246 (fission yeast Tpz1) which seems to make sense functionally, and fits with the fact that we had not previously detected and S. cerevisiae/ S. pombe ortholog for Tpz1 or EST3. check next pfam release ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-14 12:39 Message: Testing in progress not fixed YOR099W and YKR061W and YJL139C and YDR483W and YBR205W and YBR199W and YPL053C YOR099W KTR1 YKR061W KTR2 YJL139C YUR1 YDR483W KRE2 YBR205W KTR3 YBR199W KTR4 YPL053C KTR6 ----------------------------- Txt consider adding SPCC1682.08 to cluster...check cpmpara FromEmail va...@sa... FromName val GeneId SPAC4G9.05 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-14 11:28 Message: Txt consider adding SPCC1682.08 to cluster...check cpmpara FromEmail va...@sa... FromName val GeneId SPAC4G9.05 (need to check all of these RNA binding proteins again) ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-13 10:44 Message: Look at: SPAC26F1.08c S000002390; S000003108; S000003108; Could be both SPAC27D7.02c S000004300; S000001803; S000001201; GRIP DOMAIN these are tricky….not sure…… SPAPB24D3.02c S000001657;S000003045; S000002369; S000002369; SPAC11D3.08c S000001657;S000003045; S000002369; S000002369; I have YKL174C and YGL077C and YDL210W for 8 fission yeast transporters. Will look at this in more detail later ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-12 08:49 Message: reclusgter ace2 pwp1 and all PF10342 (SP and SC) MAPK-interacting Drmip-like superfamily (clan member) PF12748 YKL077w YDL049C YJL174W KRE9 family members PF05390 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-08 10:58 Message: Reassess this http://www.ncbi.nlm.nih.gov/pubmed/18701708?dopt=Abstract I think it is correct but I need to add the other 5 members of this tree: http://www.treefam.org/cgi-bin/TFinfo.pl?ac=TF105371 Tree fam has the fission yeast SPBC28F2.11 as an outgroup Tox3 family doesn't: http://www.treefam.org/cgi-bin/TFinfo.pl?ac=TF106481 ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-07 03:34 Message: Look at SPAC26F1.08c S000002390; S000003108; S000003108; could be both SPAC27D7.02c S000004300; S000001803; S000001201; GRIP DOMAIN these are tricky….not sure…… SPAPB24D3.02c S000001657;S000003045; S000002369; S000002369; SPAC11D3.08c S000001657;S000003045; S000002369; S000002369; Not done yet I have YKL174C and YGL077C and YDL210W for 8 fission yeast transporters. Will look at this in more detail later ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-06 02:26 Message: SPBC28F2.11 YDL002C YKL032C from Treefam, but doesn't look right...needs checking ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-03 15:41 Message: sort N-term/C-term ---------------------------------------------------------------------- Comment By: Valerie Wood (val_wood) Date: 2011-07-03 15:39 Message: check SPBC3B9.15c /YPL006W could ncp1 not scap, or are they both both? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=2096387&aid=3352435&group_id=65526 |