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)eve1.18 (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)bxd110 (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 α 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)SD5rv3 (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)dph27 (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-δ5 (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 β 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)odd4.13 (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