Deleted protein_ids - part 1. - Whitfield, E.J. (2000)
Subject: deleted protein_ids - part 1 Hi, I have been working through the list of deleted protein_ids in the new release. In some cases when the gene/translation was deleted from release 1 it was not replaced by another gene/translation in release 2. For these we have deleted the TrEMBL entry as it is no longer supported by a translation. I have found that some of the protein_IDs still exist in the genes file so the following updates delete them. You may want to only delete the protein_ID and maintain the accession number - upto you, but please be sure to delete protein_ID and TrEMBL. For those cases where there is homology data are these lines being kept? I ask as it seems strange to keep them if you have no DNA or protein to generate the homology from, unless you want to keep it to maintain the history of the translation? updates follow: \*a CG15700 - \*g AE003808; AAF58058 \*m SPTREMBL:Q9V7J5 # \*a CG16803 - \*g AE003800; AAF57743 \*m SPTREMBL:Q9V8C4 # \*a CG17487 - \*g AE003752; AAF56486 \*m SPTREMBL:Q9VBP4 # \*a CG15687 - \*g AE003731; AAF55787 \*m SPTREMBL:Q9VDK4 # \*a CG11602 - \*g AE003677; AAF54186 \*m SPTREMBL:Q9VHW3 # \*a CG11046 - \*g AE003677; AAF54182 \*m SPTREMBL:Q9VHW7 # \*a CG17485 - \*g AE003667; AAF53900 \*m SPTREMBL:Q9VIL7 # \*a CG4711 - \*g AE003652; AAF53550 \*m SPTREMBL:Q9VJJ5 # \*a BG:DS02252.3 - \*g AE003648; AAF53486 \*m SPTREMBL:Q9VJN3 # \*a CG16917 - \*g AE003631; AAF53090; AAF53091 \*m SPTREMBL:Q9VKH7 \*m SPTREMBL:Q9VKH8 not sure how Gillians pers comm for this gene should be treated as there is no adjacent gene to merge! # \*a CG14278 - \*g AE003620; AAF52608 \*m SPTREMBL:Q9VLS6 # \*a CG12353 - \*g AE003599; AAF51865 \*m SPTREMBL:Q9VNQ8 # \*a CG18618 - \*g AE003598; AAF51839 \*m SPTREMBL:Q9VNT1 # \*a CG15384 - \*g AE003584; AAF51287 \*m SPTREMBL:Q9VQ90 # \*a CG3381 - \*g AE003577; AAF51039 \*m SPTREMBL:Q9VQX2 # \*a CG10078 \*g AE003561; AAF50638; AAF50639 > \*g AE003561; AAF50639 - \*m SPTREMBL:Q9VRZ2 # \*a CG18587 - \*g AE003546; AAF50097 \*m SPTREMBL:Q9VTF4 # \*a CG13378 - \*g AE003519; AAF49232 \*m SPTREMBL:Q9VVS7 # \*a CG18168 - \*g AE003519; AAF49217 \*m SPTREMBL:Q9VVU0 # \*a CG11341 - \*g AE003481; AAF47888 \*m SPTREMBL:Q9VZD6 # \*a CG9178 - \*g AE003471; AAF47488 \*m SPTREMBL:Q9W0G0 # \*a CG10485 - \*g AE003462; AAF47153 \*m SPTREMBL:Q9W1B8 # \*a CG18093 - \*g AE003460; AAF46996 \*m SPTREMBL:Q9W1Q7 # \*a CG11478 - \*g AE003456; AAF46790 \*m SPTREMBL:Q9W2A2 # \*a CG14433 - \*g AE003439; AAF46217 \*m SPTREMBL:Q9W3U6 # \*a CG17679 - \*g AE003379; AAF45334 \*m SPTREMBL:Q9W5H3 # \*a CG17452 - \*g AE003122; AAF45433 \*m SPTREMBL:Q9W5L5 # thanks Ele Subject: deleted protein_ids - part 2 Hi again, These are the cases where a translation has been deleted in release 1 but has been replaced by a new/changed translation in release 2. In the genes file these are the simpler updates for this category of change - the protein_ID/TrEMBL accession may or may not be deleted so the updates complete the task. updates are: \*a CG18812 + \*m SPTREMBL:Q9V4R6 Q9V4R6 is now annotated to show CG18812 instead of CG12040 # \*a CG8029 \*g AE003834; AAF58965; AAF58966 > \*g AE003834; AAF58966 - \*m SPTREMBL:Q9V555 splice variant associated with AAF58965 has been deleted by Celera. # \*a CG18189 \*m SPTREMBL:Q9V627 > \*m SPTREMBL:Q9I7F3 # \*a Vha100-2 - \*m SPTREMBL:Q9VE76 \*m SPTREMBL:Q9XZ27 secondary to Q9VE75 \*g AE003722; AAF55551; AAF55552 > \*g AE003722; AAF55552 AAF55551 is now dead and replaced by second version of AAF55552 # \*a CG18749 + \*m SPTREMBL:Q9VHU6 # \*a BG:DS09218.1 - \*g AE003650; AAF53529 \*m SPTREMBL:Q9VJL1 now secondary to Q9NK54 # \*a CG18787 + \*m SPTREMBL:Q9I7N2 # \*a CG10712 \*g AE003599; AAF51877; AAF51878 > \*g AE003599; AAF51877 AAF51878 protein_ID is deleted from the new release also why does this gene have 3 locations?! \*c 25C1 \*c Limits inferred from genome sequence \*c 79F5--6 \*c Limits inferred from genome sequence \*c 89E9--10 \*c Limits inferred from genome sequence # \*a CG7611 \*g AE003594; AAF51739; AAG22180; AAG22181; AAG22182 > \*g AE003594; AAG22180; AAG22181; AAG22182 # \*a slgA - \*m SPTREMBL:Q9VRH7 \*m SPTREMBL:Q9VRH9 secondary to Q9VRH8 # \*a CG18768 \*m SPTREMBL:Q9VSA0 \*m SPTREMBL:Q9VSA1 > \*m SPTREMBL:Q9I7Q8 both are now secondary to Q9I7Q8 # \*a Eip63F-1 \*m SPTREMBL:Q9VZL0 > \*m SPTREMBL:Q9I7T4 Q9VZL0 is secondary to Q9I7T4 # \*a Sox14 - \*m SPTREMBL:Q9W1E3 secondary to Q9W1E2 # \*a Caps - \*m SPTREMBL:Q9W5K5 secondary to Q9W5K6 # \*a CG18769 \*m SPTREMBL:Q9VRX4 > \*m SPTREMBL:Q9I7Q7 Q9VRX4 is secondary to Q9I7Q7 # thanks Ele Subject: deleted protein_ids - part 3 These are the more complicated updates from the previous category: translation has been deleted in release 1 but has been replaced by a new/changed translation in release 2. The genes file seems to have a few scenarios for the same category of change. 1) a CG has been 'eliminated' but it existed as a synonym of a known gene by previous work - these entries are fine, CG maintained, protein_ID and TrEMBL accession deleted in previous email 2) There are cases of a CG being eliminated and the new/changed translation has been assigned a new CG - for these cases I thought the original CG would become a synonym of the new CG? In some cases this appears to be true so for the following update I am simply reporting the problem but not suggesting the solution. They should either: look like this: \*a CG18474 \*z FBgn0037691 \*W Was AE003682; AAF54376; SPTREMBL:Q9VHD9 \*c 85D15--17 \*c Limits inferred from genome sequence \*K Deficiency: Df(3R)by416 (inferred from cytology) \*K Duplication: Dp(3;3)M86D[+]2 (inferred from cytology) \*u Eliminated in the July 2000 Celera release of annotated sequence. # ie demoting \*g and \*m lines to \*W or become synonyms for those genes the translation matches - ie CG18474 could be a synonym of alpha-Man-II as AAF54375 and AAF54376 were splice variants of the same gene (although Celera incorrectly gave one of the variants a CG symbol)? the updates are: please note synonymy has been determined by sequence comparison or known splice variant. \*a CG17983 \*z FBgn0040781 \*c 43E4--5 \*c Limits inferred from genome sequence \*K Deficiency: Df(2R)tor-rx6 (inferred from cytology) \*K Duplication: Dp(2;Y)cn[+] (inferred from cytology) \*g AE003840; AAF59223 \*m SPTREMBL:Q9V4P3 \*u Eliminated in the July 2000 Celera release of annotated sequence. # AAF59223 is now dead, replaced by second version of AAF59222 Q9V4P3 is now a secondary accession CG17983 become a synonym of BcDNA:GH02712? \*a CG2074 \*z FBgn0033200 \*c 43E5--7 \*c Limits inferred from genome sequence \*K Deficiency: Df(2R)tor-rx6 (inferred from cytology) \*K Duplication: Dp(2;Y)cn[+] (inferred from cytology) \*g AE003840; AAF59217 \*m SPTREMBL:Q9V4P8 \*j species == Arabidopsis thaliana; gene == 'putative ribotol dehydrogenase'; EMBL:AC004684; gi:3236237; score == 323; expect == 2.e-40 \*j species == Caenorhabditis elegans; gene == 'predicted using Genefinder; Similarity to dehydrogenases; cDNA EST'; EMBL:Z81035; protein_id:CAB02732; gi:3874345; score == 325; expect == 9.e-41 \*j species == Homo sapiens; gene == 'putative oxidoreductase'; gi:4758530; score == 128.4; expect == 1.e-09 \*j species == Mus musculus; gene == 'NAD(+)-dependent 15-hydroxyprostaglandin dehydrogenase'; EMBL:U44389; gi:1171436; score == 51.5; expect == 2.e-05 \*j species == Saccharomyces cerevisiae; gene == 'probable membrane protein YOR246c'; PIR:S67139; gi:2132926; score == 165.1; expect == 2.e-16 \*u Eliminated in the July 2000 Celera release of annotated sequence. \*x FBrf0126705 == FamiliarityBreedsContempt, 1999.11, automatic genome annotation \*d lipid metabolism ; GO:0006629 ; score == 84 | inferred from electronic annotation \*F enzyme ; GO:0003824 ; score == 302 | inferred from electronic annotation \*f cell ; GO:0005623 ; score == 46.5 | inferred from electronic annotation # AAF59217 is now dead, replaced by second version of AAF59216 Q9V4P8 is now a secondary accession CG2074 become a synonym of CG17986? \*a CG8698 \*z FBgn0033290 \*c 44C1 \*c Limits inferred from genome sequence \*K Deficiency: Df(2R)NCX10 (inferred from cytology) \*K Duplication: Dp(2;3)eve[1.18] (inferred from cytology) \*g AE003837; AAF59098 \*m SPTREMBL:Q9V4S7 \*j species == Caenorhabditis elegans; gene == 'gene unc-93 protein 2'; PIR:S23353; gi:102476; score == 52.7; expect == 2.e-06 \*j species == Homo sapiens; gene == 'dJ366N23.1 (putative C. elegans UNC-93 (protein 1, C46F11.1) LIK'; EMBL:AL021331; protein_id:CAA16149; gi:3355533; score == 57.8; expect == 5.e-08 \*u Eliminated in the July 2000 Celera release of annotated sequence. # AAF59098 is now dead, replaced by second version of AAF59099 Q9V4S7 is now a secondary accession CG8698 become a synonym of CG2121? \*a CG13147 \*z FBgn0040757 \*c 49B7--8 \*c Limits inferred from genome sequence \*K Deficiency: Df(2R)vg-C (inferred from cytology) \*K Duplication: Dp(2;2)Y3b (inferred from cytology) \*g AE003821; AAF58473 \*m SPTREMBL:Q9V6F4 \*u Eliminated in the July 2000 Celera release of annotated sequence. # AAF58473 is now dead, replaced by AAG22277 Q9V6F4 is now a secondary accession CG13147 become a synonym of CG8776? \*a CG13327 \*z FBgn0033796 \*c 49F6--7 \*c Limits inferred from genome sequence \*K Deficiency: Df(2R)vg-B (inferred from cytology) \*K Duplication: Dp(2;2)M14 (inferred from cytology) \*g AE003819; AAF58424 \*m SPTREMBL:Q9V6J9 \*u Eliminated in the July 2000 Celera release of annotated sequence. # AAF58424 is now dead, replaced by second version of AAF58425 Q9V6J9 is now a secondary accession CG13327 become a synonym of CG17054? \*a CG13351 \*z FBgn0033892 \*c 50C22--23 \*c Limits inferred from genome sequence \*K Duplication: Dp(2;2)SMG45 (inferred from cytology) \*g AE003816; AAF58304 \*m SPTREMBL:Q9V6W4 \*u Eliminated in the July 2000 Celera release of annotated sequence. # AAF58304 is now dead, replaced by AAG22270 Q9V6W4 is now a secondary accession CG13351 become a synonym of RN-tre? \*a CG12968 \*z FBgn0034043 \*c 52C7--8 \*c Limits inferred from genome sequence \*K Deficiency: Df(2R)WMG (inferred from cytology) \*K Duplication: Dp(2;2)SMG45 (inferred from cytology) \*g AE003809; AAF58106 \*m SPTREMBL:Q9V7F1 \*u Eliminated in the July 2000 Celera release of annotated sequence. # AAF58106 is now dead, replaced by second version of AAF58107 Q9V7F1 is now a secondary accession CG12968 become a synonym of CG8242? \*a CG15900 \*z FBgn0033034 \*c 41F9 \*c Limits inferred from genome sequence \*K Deficiency: Df(2R)nap1 (inferred from cytology) \*K Duplication: Dp(2;2)BG (inferred from cytology) \*g AE003785; AAF57319 \*m SPTREMBL:Q9V9H0 \*u Eliminated in the July 2000 Celera release of annotated sequence. # AAF57319 is now dead, replaced by second version of AAF57320 Q9V9H0 is now a secondary accession CG15900 become a synonym of CG11066? \*a CG5951 \*z FBgn0032989 \*c 40D2--3 \*c Limits inferred from genome sequence \*K Deficiency: Df(2L)lt2 (inferred from cytology) \*K Duplication: Dp(2;f)Bl (inferred from cytology) \*g AE003783; AAF57261 \*m SPTREMBL:Q9V9M5 \*u Eliminated in the July 2000 Celera release of annotated sequence. # AAF57261 is now dead, replaced by second version of AAF57260 Q9V9M5 is now a secondary accession CG5951 become a synonym of CG3278? \*a CG10180 \*z FBgn0039082 \*c 95A2 \*c Limits inferred from genome sequence \*K Duplication: Dp(3;3)M95A[+]13 (inferred from cytology) \*g AE003743; AAF56140 \*m SPTREMBL:Q9VCL8 \*u Eliminated in the July 2000 Celera release of annotated sequence. # AAF56140 is now dead, replaced by second version of AAF56139 Q9VCL8 is now a secondary accession CG10180 become a synonym of CG4370? \*a CG14287 \*z FBgn0038670 \*c 91E2--3 \*c Limits inferred from genome sequence \*K Deficiency: Df(3R)Cha9 (inferred from cytology) \*K Duplication: Dp(3;3)bxd[110] (inferred from cytology) \*g AE003724; AAF55619 \*m SPTREMBL:Q9VE14 \*u Eliminated in the July 2000 Celera release of annotated sequence. # AAF55619 is now dead, replaced by second version of AAF55620 Q9VE14 is now a secondary accession CG14287 become a synonym of CG6003? \*a CG18479 \*z FBgn0037927 \*c 86E19--F1 \*c Limits inferred from genome sequence \*K Deficiency: Df(3R)M-Kx1 (inferred from cytology) \*K Duplication: Dp(3;3)M86D[+]2 (inferred from cytology) \*g AE003692; AAF54671 \*m SPTREMBL:Q9VGK6 \*u Eliminated in the July 2000 Celera release of annotated sequence. # AAF54671 is now dead, the translation is overlapping with AAF54672 Q9VGK6 is now a secondary accession CG18479 become a synonym of CG14713? \*a CG9382 \*z FBgn0037706 \*c 85D23--25 \*c Limits inferred from genome sequence \*K Deficiency: Df(3R)by416 (inferred from cytology) \*K Duplication: Dp(3;3)M86D[+]2 (inferred from cytology) \*g AE003683; AAF54395 \*m SPTREMBL:Q9VHC1 \*u Eliminated in the July 2000 Celera release of annotated sequence. # AAF54395 is now dead, replaced by second version of AAF54394 Q9VHC1 is now a secondary accession CG9382 become a synonym of CG9381? \*a CG11746 \*z FBgn0037598 \*c 85A3--4 \*c Limits inferred from genome sequence \*K Deficiency: Df(3R)CA3 (inferred from cytology) \*K Duplication: Dp(3;3)Tpl-J23 (inferred from cytology) \*g AE003679; AAF54253 \*m SPTREMBL:Q9VHP8 \*u Eliminated in the July 2000 Celera release of annotated sequence. # AAF54253 is now dead, replaced by second version of AAF54252 Q9VHP8 is now a secondary accession CG11746 become a synonym of CG11745? \*a CG11743 \*z FBgn0037595 \*c 85A3--4 \*c Limits inferred from genome sequence \*K Deficiency: Df(3R)CA3 (inferred from cytology) \*K Duplication: Dp(3;3)Tpl-J23 (inferred from cytology) \*g AE003679; AAF54250 \*m SPTREMBL:Q9VHQ1 \*j species == Arabidopsis thaliana; gene == 'putative protein binding protein'; EMBL:AL035356; protein_id:CAA22992; gi:4220519; score == 294; expect == 6.e-79 \*j species == Caenorhabditis elegans; gene == F10B5.5; WP:CE01547; score == 240; expect == 2.e-62 \*j species == Homo sapiens; gene == 'HPV16 E1 protein binding protein'; EMBL:U96131; gi:2232019; score == 305; expect == 3.e-82 \*j species == Mus musculus; gene == Vcp; MGI:99919; score == 143.6; expect == 2.e-13 \*j species == Saccharomyces cerevisiae; gene == 'HYPOTHETICAL 60.5 KD PROTEIN IN MBA1-RPS13 INTERGENIC REGION'; SWP:P38126; gi:586317; score == 172; expect == 4.e-42 \*u Eliminated in the July 2000 Celera release of annotated sequence. \*x FBrf0126650 == Anonymous, 1999.11, curated genome annotation \*x FBrf0126705 == FamiliarityBreedsContempt, 1999.11, automatic genome annotation \*F chaperone ; GO:0003754 | inferred from sequence similarity annotation \*d intracellular protein traffic ; GO:0006886 ; score == 262.6 | inferred from electronic annotation \*F endopeptidase ; GO:0004175 ; score == 212 | inferred from electronic annotation \*F enzyme ; GO:0003824 ; score == 262.2 | inferred from electronic annotation \*f cytosol ; GO:0005829 ; score == 587.7 | inferred from electronic annotation # AAF54250 is now dead, replaced by second version of AAF54251 Q9VHQ1 is now a secondary accession CG11743 become a synonym of CG11744? \*a CG7553 \*z FBgn0037558 \*c 84F4--5 \*c Limits inferred from genome sequence \*K Deficiency: Df(3R)CA3 (inferred from cytology) \*K Duplication: Dp(3;3)D1 (inferred from cytology) \*g AE003678; AAF54203 \*m SPTREMBL:Q9VHU6 \*j species == Caenorhabditis elegans; gene == 'Y43F8B.4'; EMBL:AL032623; protein_id:CAA21512; gi:3947627; score == 165.4; expect == 8.e-19 \*j species == Homo sapiens; gene == 'prolyl 4-hydroxylase ? subunit (EC 1.14.11.2)'; EMBL:M24487; gi:190788; score == 132; expect == 3.e-30 \*j species == Mus musculus; gene == P4ha1; MGI:97463; score == 129; expect == 2.e-29 \*j species == Rattus; gene == 'PROLYL 4-HYDROXYLASE ALPHA SUBUNIT PRECURSOR'; SWP:P54001; gi:1709530; score == 130; expect == 8.e-30 \*u Eliminated in the July 2000 Celera release of annotated sequence. \*x FBrf0126705 == FamiliarityBreedsContempt, 1999.11, automatic genome annotation \*F enzyme ; GO:0003824 ; score == 351 | inferred from electronic annotation \*f endoplasmic reticulum ; GO:0005783 ; score == 229 | inferred from electronic annotation # AAF54203 is now dead, replaced with new translation AAG22134 Q9VHU6 now represents CG18749 CG7553 become a synonym of CG18749? \*a CG18092 \*z FBgn0032903 \*c 38F3--4 \*c Limits inferred from genome sequence \*K Deficiency: Df(2L)DS6 (inferred from cytology) \*K Duplication: Dp(2;f)Bl (inferred from cytology) \*g AE003668; AAF53944 \*m SPTREMBL:Q9VIH5 \*u Eliminated in the September 2000 Celera release of annotated sequence # AAF53944 is now dead, replaced by second version of AAF53947 Q9VIH5 is now a secondary accession CG18092 become a synonym of CG18078? \*a CG18621 \*z FBgn0040997 \*c 38C6--8 \*c Limits inferred from genome sequence \*K Deficiency: Df(2L)pr76 (inferred from cytology) \*K Duplication: Dp(2;1)C239 (inferred from cytology) \*g AE003666; AAF53883 \*m SPTREMBL:Q9VIN4 \*u Eliminated in the July 2000 Celera release of annotated sequence. # AAF53883 is now dead, replaced by second version of AAF53884 Q9VIN4 is now a secondary accession CG18621 become a synonym of spir? \*a CG10048 \*z FBgn0032792 \*c 37E4--5 \*c Limits inferred from genome sequence \*K Deficiency: Df(2L)E55 (inferred from cytology) \*K Duplication: Dp(2;1)C239 (inferred from cytology) \*g AE003663; AAF53810 \*m SPTREMBL:Q9VIV4 \*j species == Mus caroli; gene == 'RP2 protein, testosterone-regulated'; PIR:A39798; gi:109490; score == 127; expect == 1.e-28 \*j species == Mus musculus; gene == D7Rp2e; MGI:94203; score == 125; expect == 6.e-28 \*u Eliminated in the July 2000 Celera release of annotated sequence. # AAF53810 is now dead, replaced by second version of AAF53809 Q9VIV4 is now a secondary accession CG10048 become a synonym of CG18094? \*a CG10441 \*z FBgn0032737 \*c 37B9 \*c Limits inferred from genome sequence \*K Deficiency: Df(2L)VA16 (inferred from cytology) \*K Duplication: Dp(2;1)C239 (inferred from cytology) \*g AE003661; AAF53737 \*m SPTREMBL:Q9VJ20 \*Y ATP-binding cassette transporter-like \*j species == Caenorhabditis elegans; gene == 'multidrug resistance related protein 1'; EMBL:U66260; gi:1518135; score == 1522.7; expect == 0 \*j species == Homo sapiens; gene == 'ABC transporter MOAT-B'; EMBL:AF071202; gi:3335173; score == 1967; expect == 0 \*j species == Mus musculus; gene == 'multidrug resistance protein'; EMBL:AF022908; gi:2511759; score == 1394; expect == 0 \*j species == Oryctolagus cuniculus; gene == 'multidrug resistance-associated protein 2'; EMBL:Z49144; protein_id:CAA89004; gi:1430907; score == 1612.4; expect == 0 \*j species == Saccharomyces cerevisiae; gene == 'cadmium resistance protein YCF1'; PIR:S51863; gi:1077042; score == 1341; expect == 0 \*u Eliminated in the July 2000 Celera release of annotated sequence. \*x FBrf0126705 == FamiliarityBreedsContempt, 1999.11, automatic genome annotation \*x FBrf0126677 == Ketchum, 1999.11, curated genome annotation annotation \*d small molecule transport ; GO:0006832 ; score == 998.6 | inferred from electronic annotation \*F ion channel ; GO:0005216 ; score == 3016.6 | inferred from electronic annotation \*f plasma membrane ; GO:0005886 ; score == 2818.9 | inferred from electronic annotation \*F transporter ; GO:0005215 | inferred from sequence similarity # AAF53737 is now dead, replaced by second version of AAF53736 Q9VJ20 is now a secondary accession CG10441 become a synonym of CG17338? \*a CG10666 \*z FBgn0032722 \*c 37B7--8 \*c Limits inferred from genome sequence \*K Deficiency: Df(2L)OD15 (inferred from cytology) \*K Duplication: Dp(2;1)C239 (inferred from cytology) \*g AE003661; AAF53721 \*m SPTREMBL:Q9VJ36 \*u Eliminated in the July 2000 Celera release of annotated sequence. # AAF53721 is now dead, replaced by second version of AAF53722 Q9VJ36 is now a secondary accession CG10666 become a synonym of CG18397? \*a CG17937 \*z FBgn0032610 \*c 36A10 \*c Limits inferred from genome sequence \*K Deficiency: In(2L)b88e16 (inferred from cytology) \*K Duplication: Dp(2;2)SD5[rv3] (inferred from cytology) \*g AE003652; AAF53576 \*m SPTREMBL:Q9VJH3 \*Y diacylglycerol O-acyltransferase-like \*j species == Arabidopsis thaliana; gene == 'diacylglycerol O-acyltransferase'; EMBL:AJ131831; protein_id:CAB44774.1; gi:5050913; score == 224; expect == 5.e-58 \*j species == Caenorhabditis elegans; gene == 'cDNA EST yk453a2.3 comes from this gene; cDNA EST yk453a2.5 comes'; EMBL:Z75526; protein_id:CAA99773; gi:3874043; score == 277; expect == 5.e-74 \*j species == Homo sapiens; gene == 'ACAT related gene product 1'; EMBL:AF059202; gi:3746533; score == 282; expect == 2.e-75 \*j species == Mus musculus; gene == 'diacylglycerol acyltransferase'; EMBL:AF078752; gi:3859934; score == 279; expect == 2.e-74 \*j species == Saccharomyces cerevisiae; gene == 'acyl-CoA:sterol acyltransferase'; EMBL:U55383; gi:1389739; score == 113; expect == 1.e-24 \*u Eliminated in the July 2000 Celera release of annotated sequence. \*x FBrf0126705 == FamiliarityBreedsContempt, 1999.11, automatic genome annotation \*x FBrf0126677 == Ketchum, 1999.11, curated genome annotation annotation \*f plasma membrane ; GO:0005886 ; score == 41.8 | inferred from electronic annotation \*F enzyme ; GO:0003824 | inferred from sequence similarity # AAF53576 is now dead, replaced by second version of AAF53577 Q9VJH3 is now a secondary accession CG17937 become a synonym of CG17938? \*a CG14276 \*z FBgn0040956 \*c 28E4--7 \*c Limits inferred from genome sequence \*K Duplication: Dp(2;3)dp[h27] (inferred from cytology) \*g AE003620; AAF52602 \*m SPTREMBL:Q9VLT2 \*u Eliminated in the July 2000 Celera release of annotated sequence. # AAF52602 is now dead, replaced by second version of AAF52603 Q9VLT2 is now a secondary accession CG14276 become a synonym of CG8683? \*a CG13774 \*z FBgn0031870 \*c 27C4--6 \*c Limits inferred from genome sequence \*K Deficiency: Df(2L)Dwee-?5 (inferred from cytology) \*K Duplication: Dp(2;2)C619 (inferred from cytology) \*g AE003615; AAF52459 \*m SPTREMBL:Q9VM66 \*j species == Caenorhabditis elegans; gene == 'F35D11.11 gene product'; EMBL:U29381; gi:868224; score == 255.9; expect == 2.e-21 \*j species == Entamoeba histolytica; gene == 'myosin heavy chain'; EMBL:L03534; gi:1850913; score == 283.6; expect == 2.e-27 \*j species == Homo sapiens; gene == 'myosin ? heavy chain, cardiac and skeletal muscle'; PIR:S12458; gi:107132; score == 207.1; expect == 1.e-22 \*j species == Mus musculus; gene == Myhca; MGI:97255; score == 200.7; expect == 2.e-22 \*j species == Saccharomyces cerevisiae; gene == 'integrin homolog'; PIR:S30782; gi:320776; score == 112; expect == 3.e-23 \*u Eliminated in the July 2000 Celera release of annotated sequence. \*x FBrf0126705 == FamiliarityBreedsContempt, 1999.11, automatic genome annotation \*d cytoskeleton organization and biogenesis ; GO:0007010 ; score == 2120.7 | inferred from electronic annotation \*F motor ; GO:0003774 ; score == 3255.5 | inferred from electronic annotation \*f cytoskeleton ; GO:0005856 ; score == 5960.9 | inferred from electronic annotation # AAF52459 is now dead, replaced by second version of AAF52458 Q9VM66 is now a secondary accession CG13774 become a synonym of CG18304? \*a CG14576 \*z FBgn0037111 \*c 78E5--F1 \*c Limits inferred from genome sequence \*K Deficiency: Df(3L)XS1155 (inferred from cytology) \*g AE003595; AAF51759 \*m SPTREMBL:Q9VP03 \*j species == ACICA; gene == 'ALDOSE 1-EPIMERASE PRECURSOR (MUTAROTASE)'; SWP:P05149; gi:127542; score == 69.9; expect == 7.e-12 \*j species == Caenorhabditis elegans; gene == 'similar to aldose 1-epimerases (Pfam:PF01263, Score=216.9, E=3.1e'; EMBL:AF125952; protein_id:AAD14698; gi:4262570; score == 54.7; expect == 3.e-07 \*j species == Homo sapiens; gene == 'Ibd1'; EMBL:U11036; gi:836883; score == 47.3; expect == 4.e-05 \*u Eliminated in the July 2000 Celera release of annotated sequence. \*x FBrf0126705 == FamiliarityBreedsContempt, 1999.11, automatic genome annotation \*d carbohydrate metabolism ; GO:0005975 ; score == 44.9 | inferred from electronic annotation \*F enzyme ; GO:0003824 ; score == 44.9 | inferred from electronic annotation \*f cytoplasm ; GO:0005737 ; score == 44.9 | inferred from electronic annotation # AAF51759 is now dead, replaced by second version of AAF51760 Q9VP03 is now a secondary accession CG14576 become a synonym of CG12562? \*a CG17647 \*z FBgn0031363 \*c 22B2 \*c Limits inferred from genome sequence \*K Deficiency: Df(2L)frtz11 (inferred from cytology) \*K Duplication: Dp(2;Y)odd[4.13] (inferred from cytology) \*g AE003585; AAF51340 \*m SPTREMBL:Q9VQ42 \*j species == Homo sapiens; OMIM:603076; score == 83.1; expect == 1.e-15 \*j species == Mus musculus; gene == Abc8; MGI:107704; score == 84.7; expect == 4.e-16 \*u Eliminated in the July 2000 Celera release of annotated sequence. \*x FBrf0126705 == FamiliarityBreedsContempt, 1999.11, automatic genome annotation \*d small molecule transport ; GO:0006832 ; score == 84.7 | inferred from electronic annotation \*F enzyme ; GO:0003824 ; score == 84.7 | inferred from electronic annotation \*F ion channel ; GO:0005216 ; score == 84.7 | inferred from electronic annotation \*F ligand binding or carrier ; GO:0005488 ; score == 84.7 | inferred from electronic annotation \*f plasma membrane ; GO:0005886 ; score == 84.7 | inferred from electronic annotation # AAF51340 is now dead, replaced by second version of AAF51341 Q9VQ42 is now a secondary accession CG17647 become a synonym of CG17646? \*a CG17981 \*z FBgn0036167 \*c 68C4--5 \*c Limits inferred from genome sequence \*K Deficiency: Df(3L)vin66 (inferred from cytology) \*K Duplication: Dp(3;3)M67C[+]4 (inferred from cytology) \*g AE003544; AAF50057 \*m SPTREMBL:Q9VTJ1 \*u Eliminated in the July 2000 Celera release of annotated sequence. # remove protein_ID and TrEMBL accession \*a CG14139 \*z FBgn0040819 \*c 68C7--8 \*c Limits inferred from genome sequence \*K Deficiency: Df(3L)vin66 (inferred from cytology) \*K Duplication: Dp(3;3)M67C[+]4 (inferred from cytology) \*g AE003544; AAF50048 \*m SPTREMBL:Q9VTK0 \*u Eliminated in the July 2000 Celera release of annotated sequence. # AAF50048 is now dead, replaced by second version of AAF50047 Q9VTK0 is now a secondary accession CG14139 become a synonym of CG6100? \*a CG18230 \*z FBgn0036797 \*c 75D1 \*c Limits inferred from genome sequence \*K Deficiency: Df(3L)Cat (inferred from cytology) \*K Duplication: Dp(3;3)M35 (inferred from cytology) \*g AE003520; AAF49252 \*m SPTREMBL:Q9VVQ8 \*u Eliminated in the July 2000 Celera release of annotated sequence. # AAF49252 is now dead, replaced by second version of AAF49251 Q9VVQ8 is now a secondary accession CG18230 become a synonym of CG13382? \*a CG6918 \*z FBgn0036957 \*c 77A4--B1 \*c Limits inferred from genome sequence \*K Deficiency: Df(3L)rdgC-co2 (inferred from cytology) \*K Duplication: Dp(3;3)M72 (inferred from cytology) \*g AE003514; AAF49049 \*m SPTREMBL:Q9VW99 \*j species == Caenorhabditis elegans; gene == 'cDNA EST yk257c2.5 comes from this gene; cDNA EST yk257c2.3 comes'; EMBL:Z79598; protein_id:CAB01869; gi:3979721; score == 54.3; expect == 2.e-06 \*u Eliminated in the July 2000 Celera release of annotated sequence. # AAF49049 is now dead, replaced by second version of AAF49048 Q9VW99 is now a secondary accession CG6918 become a synonym of CG17233? \*a CG6266 \*z FBgn0036971 \*c 77B3--4 \*c Limits inferred from genome sequence \*K Deficiency: Df(3L)rdgC-co2 (inferred from cytology) \*K Duplication: Dp(3;3)M72 (inferred from cytology) \*g AE003514; AAF49031 \*m SPTREMBL:Q9VWB5 \*Y serpin \*j species == Homo sapiens; OMIM:600517; score == 73; expect == 1.e-12 \*j species == Mus musculus; gene == At3; MGI:88095; score == 68.3; expect == 4.e-11 \*j species == Ovis aries; gene == 'ANTITHROMBIN-III PRECURSOR (ATIII)'; SWP:P32262; gi:416622; score == 62.8; expect == 2.e-09 \*u Eliminated in the July 2000 Celera release of annotated sequence. \*x FBrf0126651 == Ashburner, 1999.11, curated genome annotation \*x FBrf0126705 == FamiliarityBreedsContempt, 1999.11, automatic genome annotation \*F serpin ; GO:0004868 | inferred from sequence similarity annotation \*F enzyme inhibitor ; GO:0004857 ; score == 342.9 | inferred from electronic annotation # AAF49031 is now dead, replaced by second version of AAF49032 Q9VWB5 is now a secondary accession CG6266 become a synonym of CG6663? \*a CG1579 \*z FBgn0030335 \*c 10E2--3 \*c Limits inferred from genome sequence \*K Deficiency: Df(1)HA85 (inferred from cytology) \*K Duplication: Dp(1;2)v[+]65b (inferred from cytology) \*g AE003487; AAF48096 \*m SPTREMBL:Q9VYU2 \*u Eliminated in the July 2000 Celera release of annotated sequence. \*x FBrf0126705 == FamiliarityBreedsContempt, 1999.11, automatic genome annotation \*F chaperone ; GO:0003754 ; score == 122.6 | inferred from electronic annotation \*F enzyme ; GO:0003824 ; score == 61.3 | inferred from electronic annotation \*f endoplasmic reticulum ; GO:0005783 ; score == 61.3 | inferred from electronic annotation # AAF48096 is now dead, it was contained within AAF48095 Q9VYU2 is now a secondary accession CG1579 become a synonym of Hsc70-3? thanks Ele Subject: Re: remaining eliminated genes this update (and the earlier messages) should take care of all protein_IDs and TrEMBL accession in 'eliminated' genes. when you have done these could you do one last check? (sorry to be paranoid!) \*a BG:DS02252.4 + \*g AE003648 to treat the same as the others, ie delete protein_ID, keep accession number # \*a BG:DS09218.1 \*g AE003650; AAF53529 > \*g AE003650 protein_ID is dead # \*a Cyp318a1 \*g AE003488; AAF48137 > \*g AE003488 protein_ID is dead # \*a CG13945 \*g AE003815; AAF58278 \*m SPTREMBL:Q9V6Y9 > \*g AE003815 protein_ID is dead # AAF46284 is dead and the translation is exactly matched by AAF46285 so: \*a CG18624 \+ \*i CG15328 \*m SPTREMBL:Q9W3N7 # \*a CG8810 \*g AE003821; AAF58480 \*m SPTREMBL:Q9V6E7 > \*g AE003821 protein_ID is dead # \*a CG16994 \*z FBgn0029544 \*c 1C5--D1 \*c Limits inferred from genome sequence \*K Deficiency: Df(1)tR15 (inferred from cytology) \*K Duplication: Dp(1;2)E1 (inferred from cytology) \*g AE003419; AAF45567 \*m SPTREMBL:Q9W5C3 \*u Eliminated in the July 2000 Celera release of annotated sequence. # AAF45567 is now dead and replaced by AAG22365 please merge CG16994 and CG18830, deleting AAF45567 \*a CG18830 \*z FBgn0042153 \*W New in Celera 0007 dump. ag000818 \*c 1C5--D1 \*c Limits inferred from genome sequence \*g AE003419; AAG22365 # \*a CG17937 \*g AE003652; AAF53576 \*m SPTREMBL:Q9VJH3 \*u Eliminated in the July 2000 Celera release of annotated sequence. # from previous email: AAF53576 is now dead, replaced by second version of AAF53577 Q9VJH3 is now a secondary accession CG17937 become a synonym of CG17938? thanks Ele