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Benos, T. (2000.12.13). FlyBase error report on Wed Dec 13 14:35:56 2000. 
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FBrf0133222
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Personal communication to FlyBase
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Text of Personal Communication
From benos@XXXX Wed Dec 13  14:36:42  2000
Envelope-to: gm119@XXXX
Delivery-date: Wed, 13 Dec 2000  14:36:42  \+0000
Date: Wed, 13 Dec 2000  14:35:56  \+0000 (GMT)
From: Takis Benos <benos@XXXX>
To: flybase-updates@XXXX
cc: Eleanor Whitfield <eleanor@XXXX>
Subject: EDGP-CG gene comparison....
MIME-Version: 1.0
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Hello, dear All:
Please, find attached a text file with the results of the comparison we
performed between EDGP genes and the ones reported by Celera in the version
1.0 of the Drosophila Genome.
The differences between the genes are divided in the following categories:
\# 0. less than 1% differences \--> IDENTICAL
\# A. differences on ATG selection
\# B. additional/missing internal exon
\# C. differences on termination codon selection
\# D. major differences indicating very different gene model
Genes of category D were analysed in detail (as well as some of the other
categories). File EDGPvsCG.takis.for_FB contains the results of the
analysis. Note that some of the CG genes (category D) were found to be
wrong, based on EST hits. Also two of the genes were 'splitted' between
two EDGP clones; therefore their corresponding entries need to be joined.
Best regards,
takis ;)
From benos@XXXX Wed Dec 13  14:32:39  2000
Date: Wed, 13 Dec 2000  08:30:26  \-0600
From: Takis Benos <benos@XXXX>
To: benos@XXXX
\#
\#23456789012345678901234567890123456789012345678901234567890123456789012345
\#
\# This file is summarising the differences between EDGP and CG
\# a.a. sequences, as reported by Melanie Gatt in the form of ClustalW
\# output. THe categories of differences that are considered are:
\#
\# 0. less than 1% differences \--> IDENTICAL
\#
\# A. differences on ATG selection
\# B. additional/missing internal exon
\# C. differences on termination codon selection
\# D. major differences indicating very different gene model
\#
\# Plus/minus symbols mean that EDGP gains/misses in sequence length over CG
\# gene.
\#
\# PVB-000724
\#
>CG17636|FBan0017636|CT38919|FBan0017636  last_updated:000321 
 >EG:23E12 .1
>Diff : 0
>CG17617|FBan0017617|CT38862|FBan0017617  last_updated:000321 
 >EG:23E12 .5
>Diff : 0
>CG17960|FBan0017960|CT40020|FBan0017960  last_updated:000321 
 >EG:23E12 .2
>Diff : B-
>CG17707|FBan0017707|CT39230|FBan0017707  last_updated:000321 
 >EG:23E12 .3
>Diff : 0
>CG3038|FBan0003038|CT10170|FBan0003038  last_updated:000321 
 >EG:BACR37P7 .1
>Diff : 0
>CG2995|FBan0002995|CT10081|FBan0002995  last_updated:000321 
 >EG:BACR37P7 .2
>Diff : 0
>CG13377|FBan0013377|CT32709|FBan0013377  last_updated:000321 
 >EG:BACR37P7 .9
>Diff : A-
>CG13375|FBan0013375|CT32707|FBan0013375  last_updated:000321 
 >EG:BACR37P7 .8
>Diff : B-
>CG18104|FBan0018104|CT40671|FBan0018104  last_updated:000321 
 >EG:171D11 .4
>Diff : C+
>CG17829|FBan0017829|CT39573|FBan0017829  last_updated:000321 
 >EG:115C2 .6
>Diff : 0
>CG5254|FBan0005254|CT16777|FBan0005254  last_updated:000321 
 >EG:BACR19J1 .2
>Diff : 0
>CG5273|FBan0005273|CT16821|FBan0005273  last_updated:000321 
 >EG:BACR19J1 .3
>Diff : 0
>CG12467|FBan0012467|CT32681|FBan0012467  last_updated:000321 
 >EG:34F3 .2
\#>Diff : A-- B- C+
>Diff : D
\#
\#Comments:
\#
\# A : differences in NH2- terminus are probably due to different prediction
\# methods used: in this case gene CG12467 should be  EG:34F3 .1 \+
\#  EG:34F3 .2.
\# B : CG12467 has one additional exon: this probably comes from Genie
\# prediction. None of Genfinder/Genscan predictions support this exon.
\# C : differences on the \-COOH are probably due to different prediction
\# methods used. In this case, the two last exons of  EG:34F3 .2 (starting
\# 'APSATPII...' should form another CG gene).
\#
\# There is no supporting evidence to favour of EDGP or CG model.
\# (and the EST hits cannot enlighten us further on that)
\#
\#CONCLUSION: Ambigious
\#
>CG16785|FBan0016785|CT32689|FBan0016785  last_updated:000321 
 >EG:34F3 .6
>Diff : A--
>CG11664|FBan0011664|CT34394|FBan0011664  last_updated:000321 
 >EG:BACR7A4 .3
>Diff : 0
>CG3711|FBan0003711|CT12449|FBan0003711  last_updated:000321 
 >EG:BACR7A4 .19
>Diff : 0
>CG3034|FBan0003034|CT10206|FBan0003034  last_updated:000321 
 >EG:BACR7A4 .6
>Diff : 0
>CG3708|FBan0003708|CT12445|FBan0003708  last_updated:000321 
 >EG:BACR7A4 .18
>Diff : A+
>CG3706|FBan0003706|CT12435|FBan0003706  last_updated:000321 
 >EG:BACR7A4 .20
>Diff : 0
>CG11642|FBan0011642|CT36631|FBan0011642  last_updated:000321 
 >EG:BACR7A4 .5
>Diff : 0
>CG3704|FBan0003704|CT12427|FBan0003704  last_updated:000321 
 >EG:BACR7A4 .17
>Diff : 0
>CG3026|FBan0003026|CT10194|FBan0003026  last_updated:000321 
 >EG:BACR7A4 .16
>Diff : 0
>CG3703|FBan0003703|CT12417|FBan0003703  last_updated:000321 
 >EG:BACR7A4 .15
>Diff : A-
>CG3699|FBan0003699|CT12411|FBan0003699  last_updated:000321 
 >EG:BACR7A4 .14
>Diff : D-
\#
\#Comments:
\#
\#The \-COOH terminus (70-90 last a.a.) is completely different between the
\#two genes. That is very strange, because  EG:BACR7A4 .14 is single-exon
\#gene. Obviously, CG3699 has a splice site at some point which leads to
\#different \-COOH sequence.
\#However, ESTs AI293564 and AI294621 support the view that the exon
\#predicted by EDGP is terminal.
\#
\#CONCLUSION:  EG:BACR7A4 .14 is more correct.
\#
>CG3690|FBan0003690|CT12383|FBan0003690  last_updated:000321 
 >EG:BACR7A4 .13
>Diff : 0
>CG11638|FBan0011638|CT36619|FBan0011638  last_updated:000321 
 >EG:BACR7A4 .12
>Diff : A++
>CG18091|FBan0018091|CT40606|FBan0018091  last_updated:000321 
 >EG:190E7 .1
>Diff : 0
>CG3051|FBan0003051|CT10258|FBan0003051  last_updated:000321 
 >EG:132E8 .2|FBgn0023169;SNF1A
>Diff : 0
>CG3719|FBan0003719|CT12473|FBan0003719  last_updated:000321 
 >EG:132E8 .3
>Diff : 0
>CG11448|FBan0011448|CT36231|FBan0011448  last_updated:000321 
 >EG:132E8 .4
>Diff : 0
>CG18531|FBan0018531|CT42308|FBan0018531  last_updated:000321 
 >EG:BACN32G11 .1
>Diff : 0
>CG3021|FBan0003021|CT10176|FBan0003021  last_updated:000321 
 >EG:BACR7A4 .8
>Diff : C-
>CG14630|FBan0014630|CT34388|FBan0014630  last_updated:000321 
 >EG:BACR7A4 .9
>Diff : A-
>CG14629|FBan0014629|CT34387|FBan0014629  last_updated:000321 
 >EG:103E12 .2
>Diff : 0
>CG3655|FBan0003655|CT12291|FBan0003655  last_updated:000321 
 >EG:103E12 .3
>Diff : 0
>CG11392|FBan0011392|CT31794|FBan0011392  last_updated:000321 
 >EG:BACR42I17 .1
>Diff : B+
>CG11382|FBan0011382|CT31774|FBan0011382  last_updated:000321 
 >EG:BACR42I17 .10
>Diff : 0
>CG11398|FBan0011398|CT31827|FBan0011398  last_updated:000321 
 >EG:BACR42I17 .11
>Diff : 0
>CG14628|FBan0014628|CT34385|FBan0014628  last_updated:000321 
 >EG:BACR42I17 .12
>Diff : 0
>CG11378|FBan0011378|CT31764|FBan0011378  last_updated:000321 
 >EG:BACR42I17 .2
>Diff : 0
>CG11384|FBan0011384|CT31776|FBan0011384  last_updated:000321 
 >EG:BACR42I17 .3
>Diff : 0
>CG11379|FBan0011379|CT31766|FBan0011379  last_updated:000321 
 >EG:BACR42I17 .4
>Diff : 0
>CG14627|FBan0014627|CT34384|FBan0014627  last_updated:000321 
 >EG:BACR42I17 .5
>Diff : A++
>CG14626|FBan0014626|CT34383|FBan0014626  last_updated:000321 
 >EG:BACR42I17 .6
>Diff : A-
>CG11380|FBan0011380|CT31768|FBan0011380  last_updated:000321 
 >EG:BACR42I17 .7
>Diff : A++
>CG14625|FBan0014625|CT34382|FBan0014625  last_updated:000321 
 >EG:BACR42I17 .8
>Diff : A+
>CG11491|FBan0011491|CT36317|FBan0011491  last_updated:000321 
 >EG:17A9 .1_altrn_1|FBgn0000210;br /alternative
>Diff : 0
>CG3791|FBan0003791|CT12681|FBan0003791  last_updated:000321 
 >EG:73D1 .1
>Diff : 0
>CG14813|FBan0014813|CT34626|FBan0014813  last_updated:000321 
 >EG:63B12 .10
>Diff : 0
>CG16903|FBan0016903|CT37506|FBan0016903  last_updated:000321 
 >EG:67A9 .2
>Diff : C--
>CG3981|FBan0003981|CT13223|FBan0003981  last_updated:000321 
 >EG:67A9 .1
>Diff : A-
>CG3954|FBan0003954|CT37554|FBan0003954  last_updated:000321 
 >EG:BACN25G24 .2|FBgn0000382;csw
>Diff : 0
>CG3895|FBan0003895|CT12875|FBan0003895  last_updated:000321 
 >EG:BACN25G24 .3|FBgn0004860;ph-d
>Diff : A-- B+ C+
> \##### WARNING Known gene \! \#####
>CG3540|FBan0003540|CT11900|FBan0003540  last_updated:000321 
 >EG:152A3 .2
>Diff : 0
>CG10755|FBan0010755|CT30144|FBan0010755  last_updated:000321 
 >EG:152A3 .6|FBgn0015036;Cyp4e4
>Diff : 0
>CG18031|FBan0018031|CT40356|FBan0018031  last_updated:000321 
 >EG:103B4 .2
\#>Diff : B C-
>Diff : D
\#
\#Comments:
\#
\# B : differences on internal exon(s) are due to different prediction
\# EDGP followed Genefinder; Genscan (and \-presumambly Genie- supports
\# one more exon. Similarity hits from both SW and TrEMBL though,
\# favour EDGP's (a.k.a. Genefinder's) prediction. (although the hits
\# are not very strong)
\# C : differences in \-COOH terminus are probably due to different
\# prediction methods used. There is no supporting evidence for any of
\# the gene structures there.
\#
\#CONCLUSION: Ambigious or  EG:103B4 .2 is more correct.
\#
>CG3218|FBan0003218|CT10801|FBan0003218  last_updated:000321 
 >EG:30B8 .5|FBgn0000810;fs(1)K10
>Diff : 0
>CG14050|FBan0014050|CT33609|FBan0014050  last_updated:000321 
 >EG:BACH48C10 .1
>Diff : 0
>CG2854|FBan0002854|CT9762|FBan0002854  last_updated:000321 
 >EG:BACH48C10 .2
>Diff : C-
>CG14048|FBan0014048|CT33607|FBan0014048  last_updated:000321 
 >EG:BACH48C10 .6
>Diff : 0
>CG2841|FBan0002841|CT9712|FBan0002841  last_updated:000321 
 >EG:BACH48C10 .5
>Diff : A+
>CG14047|FBan0014047|CT33606|FBan0014047  last_updated:000321 
 >EG:BACH48C10 .4
\#>Diff : A-- B- B+ B+ C-
>Diff : D
\#
\#Comments:
\#
\# A : differences in NH2- terminus are probably due to incomplete analysis
\# of EDGP. Gene  EG:BACH48C10 .4 is located at the end of BAC H48C10
\# (reverse orientation) and is probably continuing on BAC H7M4. In
\# this case gene  EG:BACH7M4 .1 should match the NH2- terminus of
\# CG14047.
\# B : differences on internal exons should be due to different prediction
\# algorithms used. Although, in this case, EDGP followed the Genscan
\# prediction (which should be similar to Genie that Celera used), it is
\# possible that the two software programs are utilising different exons.
\# C : differences on the \-COOH are probably due to different prediction
\# methods used. It applies the same as in (B).
\#
\# (There is no supportive evidence to favour one or the other prediction.)
\#
>CG13756|FBan0013756|CT33235|FBan0013756  last_updated:000321 
 >EG:BACH59J11 .2
>Diff : B+
>CG14045|FBan0014045|CT33604|FBan0014045  last_updated:000321 
 >EG:BACH7M4 .1
>Diff : A--
>CG14045|FBan0014045|CT33604|FBan0014045  last_updated:000321 
 >EG:BACH7M4 .2
>Diff : A- C-
>CG12496|FBan0012496|CT33234|FBan0012496  last_updated:000321 
 >EG:BACH7M4 .4
>Diff : C-
>CG12497|FBan0012497|CT33237|FBan0012497  last_updated:000321 
 >EG:BACR25B3 .2
>Diff : A+ B+
>CG13758|FBan0013758|CT33238|FBan0013758  last_updated:000321 
 >EG:BACR25B3 .3
\#>Diff : A+ B C+
>Diff : D
\#
\#Comments:
\#
\# A : differences in NH2- terminus are due to different prediction methods
\# used. Although, in this case, EDGP followed the Genscan prediction
\# (which should be similar to Genie that Celera used), it is possible
\# that the two software programs are utilising different starting
\# exons. There is no other evidence to favour one or the other
\# version.
\# B : differences on internal exons should be due to frameshift errors
\# (most probably).
\# C : differences in \-COOH terminus are due to different prediction methods
\# used. Although, in this case, EDGP followed the Genscan prediction
\# (which should be similar to Genie that Celera used), it is possible
\# that the two software programs are utilising different end exons. In
\# fact, the last exon that Genscan/EDGP predicts (not present in
\# Genefinder prediction) is some 1.5 kb downstream of the previous one.
\# There is no supportive evidence to favour one or the other prediction.
\#
\#CONCLUSION: Ambigious.
\#
>CG13759|FBan0013759|CT33239|FBan0013759  last_updated:000321 
 >EG:BACR25B3 .5
>Diff : B+
>CG13760|FBan0013760|CT33241|FBan0013760  last_updated:000321 
 >EG:BACR25B3 .6
>Diff : A--
>CG17437|FBan0017437|CT33240|FBan0017437  last_updated:000321 
 >EG:BACR25B3 .7
>Diff : 0
>CG13761|FBan0013761|CT33242|FBan0013761  last_updated:000321 
 >EG:BACR7C10 .4
>Diff : C+
>CG10742|FBan0010742|CT30103|FBan0010742  last_updated:000321 
 >EG:BACR7C10 .6
>Diff : 0 (6/302)
>CG9904|FBan0009904|CT27892|FBan0009904  last_updated:000321 
 >EG:BACR7C10 .1
>Diff : 0
>CG13762|FBan0013762|CT33244|FBan0013762  last_updated:000321 
 >EG:BACR7C10 .7
>Diff : B-
>CG10260|FBan0010260|CT28483|FBan0010260  last_updated:000321 
 >EG:BACR7C10 .2
>Diff : A+ B- B+ (over 2160 a.a.)
>Diff : D
\#
\#Comments:
\#
\# A : differences in NH2- terminus are minor and involve different starting
\# ATG selection (2 a.a. apart).
\# B : the initial differences on internal exon should be due to different
\# prediction algorithms used. EDGP follows Genefinder prediction,
\# which in this case seems more trustworthy (Genscan predicts a tiny
\# intron in the region). Both programs however, agree on the 'main
\# body' of the prediction, i.e. region starting at 'ADKLCG...'. Thus,
\# the absence of one region in CG10260 is unexplainable there.
\#
\#CONCLUSION: Ambigious or  EG:BACR7C10 .2 is more correct.
\#
>CG12498|FBan0012498|CT33246|FBan0012498  last_updated:000321 
 >EG:BACR43E12 .1
>Diff : 0
>CG14416|FBan0014416|CT34073|FBan0014416  last_updated:000321 
 >EG:BACR43E12 .7
>Diff : 0
>CG3588|FBan0003588|CT11992|FBan0003588  last_updated:000321 
 >EG:100G7 .6
>Diff : A-- C+
>CG14424|FBan0014424|CT34081|FBan0014424  last_updated:000321 
 >EG:100G7 .5
>Diff : 0
>CG7981|FBan0007981|CT23996|FBan0007981  last_updated:000321 
 >EG:BACR25B3 .11
>Diff : D (identity starts at 3285 a.a. of CG)
\#
\#Comments:
\#
\# A : differences in NH2- terminus are due to different prediction methods
\# used. EDGP follows the Genfinder prediction, whereas CG7981 seems to
\# be similar to the Genscan one. In this case the NH2- terminus of the
\# CG7981 should be  EG:BACR25B3 .10.
\# C : differences in \-COOH terminus are also due to different prediction
\# methods used. Genscan, suggests a highly unprobable 'long' gene
\# structure (big introns, small exons), probably derived from its
\# 'human' training set. I don't know whether Genie (the primary used
\# Celera program) was trained on similar data set.
\#
\#CONCLUSION: Ambigious.
\#
>CG7981|FBan0007981|CT23996|FBan0007981  last_updated:000321 
 >EG:BACR25B3 .10
>Diff : D (identity starts at 2448 a.a. of CG)
\#
>CG7981|FBan0007981|CT23996|FBan0007981  last_updated:000321 
 >EG:BACR25B3 .1
>Diff : A++ C-
\#
\#==================================================================
\#GENERAL Comments for  EG:BACR25B3 .1,  EG:BACR25B3 .10,  EG:BACR25B3 .11
\#==================================================================
\#
\#This was one of the most difficult regions to annotate (PVB did it during
\#his visit to Cambridge, Feb. 2000). It seems like it has undergone
\#multiple duplications. Genscan, predicts one very very very long gene
\#there (biased from its Human training set, i suppose); so does Celera.
\#(based on Genie; from which organism Genie's training set was derived?)
\#This is 'the longest Drosophila gene' that is described on the paper.
\#PVB has split the gene into three 'smaller' ones and XDrosDB comments say
\#that 'TVB-990205: i'm not sure about this gene; ...'.
\#However, based on similarity matches (considering the ranges of the hits),
\#we can safely say that 'the longest Drosophila gene' does NOT exist (not
\#as such, anyway).
\#
\#CONCLUSION:  EG:BACR25B3 .1,  EG:BACR25B3 .10,  EG:BACR25B3 .11 should be more
correct.
\#
>CG12467|FBan0012467|CT32681|FBan0012467  last_updated:000321 
 >EG:34F3 .1
\#>Diff : A++ C
>Diff : D (CG extends 800 a.a. further down)
\#
\#Comments:
\#
\# A : differences in NH2- terminus are due to different selection of
\# starting ATG. CG12467 chooses an in-frame ATG 39 a.a. downstream of
\# the one of  EG:34F3 .1, for no obvious reason.
\# C : differences in \-COOH terminus are probably due to different
\# prediction methods used. EDGP follows the Genefinder prediction;
\# Celera, follows Genie's one. I'm expecting that the 'missing' 800
\# a.a. are part of  EG:34F3 .2 gebe (which is downstream of  EG:34F3 .1).
\#
\#Mel_Comments:
\#
\#Takis you suggested that  EG:34F3 .1 and 34F3.2 equal CG12467 and I agree.
\#
\#34F3.1 starts at \+40 of the CG gene
\# it has a perfect match until aa position 524
\#
\#34F3.2 starts at \+525 of the CG gene
\# one gap is present and the C terminus is messed up.
\#
\#You have suggested that the last two exons of 34F3.2 should form anothe
\#CG gene but I have been unable to find another matching CG gene for
\#their aa sequence.
\#
\#CONCLUSION: Ambigious or  EG:34F3 .1 is more correct.
\#
 >EG:87B1 .5|FBgn0004861_ph-p
 >EG:BACN25G24 .3|FBgn0004860_ph-d
>Diff : D
> \##### WARNING Known gene!#####
\#
\#Comments:
\#
\# It seems like Celera has a mis-assembly on the genomic sequence,
\# resulting in incorrect model. The mis-assembly is probably due to a
\# genomic duplication that resulted into ph-p and ph-d.
\#
>CG4857|FBan0004857|CT15601|FBan0004857  last_updated:000321 
 >EG:EG0007 .12; CAA21828.1
>Diff : D
\#
\#Comments:
\#
\# EG:EG0007 .12 is a mere Genefinder prediction, although with very very high
\#score (137.81, when our cutoff is 50 and BDGP's cutoff was 20). ESTs
\#support practically the 2nd and 3rd exon; but there is no other evidence
\#to favour EDGP's or CG's version.
\#
\#CONCLUSION: Ambigious.
\#
>CG4857|FBan0004857|CT15601|FBan0004857  last_updated:000321 
 >EG:EG0007 .4; CAA21827.1
\#>Diff : B- C
>Diff : D (CG extends 1000 a.a. further down)
\#
\#Comments:
\#
\# C : differences in \-COOH terminus are probably due to different
\# prediction methods used. EDGP follows the Genefinder prediction;
\# Celera, follows Genie's one.
\#
\#CONCLUSION: Ambigious.
\#
>CG2766|FBan0002766|CT9405|FBan0002766  last_updated:000321 
 >EG:BACN33B1 .2
\#>Diff : A+
>Diff : D
\#
\#Comments:
\#The first 61 a.a. of  EG:BACN33B1 .2 are matching the first 61 a.a. of
\#CG2766, whereas the rest of the gene matches CG2716.
\#
\#I checked the genomic structure and all data. Gene  EG:BACN33B1 .2 is a
\#mere Genscan prediction. Genefinder predicts two genes (probably the
\#equivalent of CG2766 and CG2766). However, EST AI512291, which covers the
\#first 4 exons of the gene, supports  EG:BACN33B1 .2 over CG2766 \+ CG2766.
\#
\#CONCLUSION:  EG:BACN33B1 .2 is more correct.
\#
>CG2716|FBan0002716|CT9237|FBan0002716  last_updated:000321 
 >EG:BACN33B1 .2
>Diff : D
\#
\#Comments:
\#
\#The first 61 a.a. of  EG:BACN33B1 .2 matches exactly the corresponding
\#CG2766 region. The whole gene matches CT9237 (from  CT9237:140  onwards).
\# EG:BACN33B1 .2 is a mere Genscan prediction supported by multiple ESTs on
\#all but its last exon.
\#I don't know where CG2716 comes from or why CG2716 is different than
\#CT9237.
\#
\#CONCLUSION: Ambigious or  EG:BACN33B1 .2 is more correct.
\#
\#General Comments:
\#Based on EST hit(s), genes CG2766 \+ CG2716 should concatanate to
\# EG:BACN33B1 .2.
\#
>CG3713|FBan0003713|CT12463|FBan0003713  last_updated:000321 
 >EG:BACR7A4 .2
>Diff : 0 (suspicious... only 83 a.a. long)
>CG4015|FBan0004015|CT41858|FBan0004015  last_updated:000321 
 >EG:140G11 .3
>Diff : 0
>CG3526|FBan0003526|CT11880|FBan0003526  last_updated:000321 
 >EG:BACR43E12 .4
>Diff : A++
>CG3939|FBan0003939|CT13113|FBan0003939  last_updated:000321 
 >EG:140G11 .5
>Diff : A+
>CG14265|FBan0014265|CT33887|FBan0014265  last_updated:000321 
 >EG:96G10 .8
>Diff : 0
>CG18166|FBan0018166|CT40990|FBan0018166  last_updated:000321 
 >EG:171D11 .6
>Diff : D
\#
\#Comments:
\#
\#Completely different gene structure.
\# EG:171D11 .6 follows the 'consensus' prediction of Genefinder and Genscan
\#(practically identical except the last exon(s)); and is supported by
\#multiple ESTs.
\#One thing that might misled the Celera annotators is that this region/gene
\#seems to be duplicated (as shown by the multiple hits of some of the ESTs
\#(e.g. AA438842).
\#
\#CONCLUSION:  EG:171D11 .6 is more correct.
\#
>CG18273|FBan0018273|CT41446|FBan0018273  last_updated:000321 
 >EG:171D11 .6
>Diff : B+ C++
\#
\#General Comments:
\#Both genes CG18166 & CG18273 match gene  EG:171D11 .6, but in a 'weird'
\#way.  EG:171D11 .6 follows both Genefinder and Genscan predictions, as well
\#as the corresponding EST matches. If there is not a mis-assembly case, i
\#don't know how to explain it...
\#
\#Mel_Comments:
\#The two clustal analysis of this gene which you looked at were incorrect.
\#I can only assume that Michael tried clustals on these two CG genes,
\#CG18166 and CG18273, before he found the correct matching CG gene which is
\#CG13372.
\#
\#This is matched perfectly until aa positon 1006, gapped for 50 aa and
\#finally the CG gene misses the last 250aa of the EG gene.
\#
\#CONCLUSION:  EG:171D11 .6 is more correct.
\#
>CG18503|FBan0018503|CT42214|FBan0018503  last_updated:000321 
 >EG:171D11 .3_altrn_1|FBgn0004648;svr /alternative
>Diff : D
\#
\#Comments:
\#This is the ALTERNATIVE transcript/protein, based on EST and protein
\#hits. The two transcripts differ on their 5' exon(s). CG18503 attaches
\#the 5'-most exon in a completely different gene.
\#PVB believes that  EG:171D11 .3_altrn_1 is the correct gene structure for
\#the alternatively spliced  EG:171D11 .3 gene.
\#
\#CONCLUSION:  EG:171D11 .3_altrn_1 (svr alternative) is correct.
\#
>CG14624|FBan0014624|CT34381|FBan0014624  last_updated:000321 
 >EG:BACR42I17 .9
\#>Diff : A++
>Diff : D (CG extends 460 a.a. further up)
\#
\#Comments:
\#
\# A : differences in NH2- terminus are due to different prediction methods
\# used. EDGP follows the Genefinder prediction. Probably, the first
\# 460 a.a. are part of  EG:BACR42I17 .8 gene.
\#
\#Mel_Comments:
\#
\#There are two clustals of this gene.
\#The clustal of 42I17.9 with CG11381 begins at \+25 of the CG gene \- if you
\#look closely you notice that the first 6 aa of the EG gene match the
\#begining of the CG gene. This then has a perfent match until position 446
\#and the CG gene misses the next ~260aa.
\#In the clustal of 42I17.9 with CG14624 the CG gene begins at \+463 and is
\#matched perfectly until the end.
\#
\#CONCLUSION: Ambigious.
\#
>CG11381|FBan0011381|CT31772|FBan0011381  last_updated:000321 
 >EG:BACR42I17 .9
>Diff : A-- C+
>CG18089|FBan0018089|CT40590|FBan0018089  last_updated:000321 
 >EG:100G7 .1|FBgn0014096;anon-3Ca
>Diff : 0 (suspicious... only 56 a.a. long)
>CG2945|FBan0002945|CT9961|FBan0002945  last_updated:000321 
 >EG:BACR37P7 .3|FBgn0000316;cin
>Diff : 0
>CG3114|FBan0003114|CT10322|FBan0003114  last_updated:000321 
 >EG:BACR37P7 .7|FBgn0005427;ewg
>Diff : B+
>CG12470|FBan0012470|CT32706|FBan0012470  last_updated:000321 
 >EG:BACR37P7 .5
>Diff : 0
> \##### WARNING Cant find translation for  EG:BACR37P7 .5!#####
\#
\#Comments:
\#Translation found and is 100% identical to CG12470.
\#
>CG3777|FBan0003777|CT12604|FBan0003777  last_updated:000321 
 >EG:125H10 .1
>Diff : 0
>CG3757|FBan0003757|CT12485|FBan0003757  last_updated:000321 
 >EG:125H10 .2|FBgn0004034;y
>Diff : 0
>CG3796|FBan0003796|CT12661|FBan0003796  last_updated:000321 
 >EG:125H10 .3|FBgn0000022;ac
>Diff : 0
>CG3827|FBan0003827|CT12777|FBan0003827  last_updated:000321 
 >EG:198A6 .1|FBgn0004170;sc
>Diff : 0
>CG3839|FBan0003839|CT12815|FBan0003839  last_updated:000321 
 >EG:198A6 .2|FBgn0002561;l(1)sc
>Diff : 0
>CG13374|FBan0013374|CT32705|FBan0013374  last_updated:000321 
 >EG:EG0001 .1|FBgn0011822;pcl
>Diff : 0
>CG3258|FBan0003258|CT10959|FBan0003258  last_updated:000321 
 >EG:165H7 .2|FBgn0000137;ase
>Diff : 0
>CG3972|FBan0003972|CT13187|FBan0003972  last_updated:000321 
 >EG:165H7 .1|FBgn0011757;ASC-T1
>Diff : 0
>CG3923|FBan0003923|CT13059|FBan0003923  last_updated:000321 
 >EG:165H7 .3
\#>Diff : A+ C+ (probably different selection of starting exon)
>Diff : D+
\#
\#Comments:
\#
\#Only a.a.  EG:165H7 . 3:40-190  match CG3923.
\# EG:165H7 .3 is the 'consensus' prediction of Genefinder and Genscan (aggree
\#on all but one exon). I had added one more NH2- exon, following multiple
\#EST hits (e.g. AA439864).
\#I don't know where the rest of CG3923 comes from or why Celera missed this
\#gene.
\#
\#CONCLUSION:  EG:165H7 .3 is correct.
\#
>CG13372|FBan0013372|CT32701|FBan0013372  last_updated:000321 
 >EG:171D11 .6
>Diff : B+ C+
>CG3156|FBan0003156|CT10534|FBan0003156  last_updated:000321 
 >EG:171D11 .2
>Diff : A-
>CG17896|FBan0017896|CT39849|FBan0017896  last_updated:000321 
 >EG:171D11 .1
>Diff : 0
>CG17896|FBan0017896|CT39849|FBan0017896  last_updated:000321 
 >EG:171D11 .1_altrn_1 /alternative
>Diff : A-
>CG17778|FBan0017778|CT13856|FBan0017778  last_updated:000321 
 >EG:171D11 .5
>Diff : 0
>CG4122|FBan0004122|CT41466|FBan0004122  last_updated:000321 
 >EG:171D11 .3|FBgn0004648;svr
\#>Diff : A+ B+ D
>Diff : D
\#
\#Comments:
\#
\#Gene  EG:171D11 .3 is KNOWN (FBgn0004648;svr) and is (or should be)
\#identical to U29591; apart from the last exon, where the original cloning
\#should had contained a frameshift.
\#I don't know why CG4122 doesn't match.
\#
\#CONCLUSION:  EG:171D11 .3 is correct.
\#
>CG18503|FBan0018503|CT42214|FBan0018503  last_updated:000321 
 >EG:171D11 .3_altrn_1|FBgn0004648;svr /alternative, mismatched
>Diff : D
\#
\#General Comments:
\#Only the first 152 a.a. of  EG:171D11 .3a match the CG18503.
\#
\#This is the alternative svr gene, which corresponds to U29592.
\#
\#CONCLUSION:  EG:171D11 .3a is correct.
\#
>CG4262|FBan0004262|CT13920|FBan0004262  last_updated:000321 
 >EG:65F1 .2|FBgn0000570;elav
>Diff : 0
>CG4293|FBan0004293|CT14025|FBan0004293  last_updated:000321 
 >EG:65F1 .1
>Diff : 0
>CG7727|FBan0007727|CT23451|FBan0007727  last_updated:000321 
 >EG:65F1 .5|FBgn0000108;Appl
>Diff : A+
>CG6172|FBan0006172|CT19338|FBan0006172  last_updated:000321 
 >EG:118B3 .1|FBgn0003986;vnd
>Diff : 0
>CG13366|FBan0013366|CT32693|FBan0013366  last_updated:000321 
 >EG:118B3 .2
>Diff : 0
>CG17828|FBan0017828|CT39571|FBan0017828  last_updated:000321 
 >EG:115C2 .5
>Diff : 0
>CG13369|FBan0013369|CT32698|FBan0013369  last_updated:000321 
 >EG:115C2 .1
>Diff : 0
>CG18451|FBan0018451|CT32691|FBan0018451  last_updated:000321 
 >EG:115C2 .12
>Diff : 0
\#
\#WARNING: Only 64 a.a. long!?
>CG7622|FBan0007622|CT23257|FBan0007622  last_updated:000321 
 >EG:115C2 .7|FBgn0002579;RpL36
>Diff : 0
>CG6189|FBan0006189|CT19398|FBan0006189  last_updated:000321 
 >EG:115C2 .2|FBgn0001341;l(1)1Bi
>Diff : 0
>CG7486|FBan0007486|CT22949|FBan0007486  last_updated:000321 
 >EG:115C2 .9|FBgn0020381;Dredd
>Diff : B-
>CG6222|FBan0006222|CT19476|FBan0006222  last_updated:000321 
 >EG:115C2 .3|FBgn0003575;su(s)
>Diff : 0
>CG13367|FBan0013367|CT32696|FBan0013367  last_updated:000321 
 >EG:115C2 .8
>Diff : A-
>CG16982|FBan0016982|CT32695|FBan0016982  last_updated:000321 
 >EG:115C2 .11
>Diff : B+
>CG13363|FBan0013363|CT32690|FBan0013363  last_updated:000321 
 >EG:115C2 .10
>Diff : C-
>CG16983|FBan0016983|CT32694|FBan0016983  last_updated:000321 
 >EG:115C2 .4
>Diff : 0
>CG5227|FBan0005227|CT16627|FBan0005227  last_updated:000321 
 >EG:BACR19J1 .1|FBgn0021764;sdk
>Diff : B+
>CG7434|FBan0007434|CT22861|FBan0007434  last_updated:000321 
 >EG:BACR19J1 .4|FBgn0015288;RpL22
>Diff : 0
>CG7359|FBan0007359|CT22657|FBan0007359  last_updated:000321 
 >EG:34F3 .8
>Diff : 0
>CG13358|FBan0013358|CT32683|FBan0013358  last_updated:000321 
 >EG:34F3 .1059
>Diff : A+
>CG13359|FBan0013359|CT32684|FBan0013359  last_updated:000321 
 >EG:34F3 .9
>Diff : B-
>CG7413|FBan0007413|CT22763|FBan0007413  last_updated:000321 
 >EG:34F3 .3|FBgn0015799;Rbf
>Diff : 0
>CG16989|FBan0016989|CT32688|FBan0016989  last_updated:000321 
 >EG:34F3 .4
>Diff : 0
>CG13360|FBan0013360|CT32685|FBan0013360  last_updated:000321 
 >EG:34F3 .5
>Diff : 0
>CG12311|FBan0012311|CT21087|FBan0012311  last_updated:000321 
 >EG:34F3 .7
>Diff : A- C-
>CG3658|FBan0003658|CT12303|FBan0003658  last_updated:000321 
 >EG:BACR7A4 .11|FBgn0026143;CDC45L
>Diff : 0
>CG3019|FBan0003019|CT10162|FBan0003019  last_updated:000321 
 >EG:BACR7A4 .10|FBgn0003638; su(wa) (/partial; this is the 5' terminus)
>Diff : B-
\#### WARNING: check the 3' terminus too....
\# identity up to  EG:BACR7A4 .10 1-224
>CG3638|FBan0003638|CT12157|FBan0003638  last_updated:000321 
 >EG:33C11 .3
>Diff : A+ C--
>CG11403|FBan0011403|CT31837|FBan0011403  last_updated:000321 
 >EG:33C11 .2
>Diff : 0
>CG11405|FBan0011405|CT31841|FBan0011405  last_updated:000321 
 >EG:33C11 .1
>Diff : 0
>CG11408|FBan0011408|CT31847|FBan0011408  last_updated:000321 
 >EG:114D9 .1
>Diff : 0
>CG14622|FBan0014622|CT34379|FBan0014622  last_updated:000321 
 >EG:114D9 .2
>Diff : A--
>CG11411|FBan0011411|CT31859|FBan0011411  last_updated:000321 
 >EG:8D8 .1
>Diff : 0
>CG11409|FBan0011409|CT31851|FBan0011409  last_updated:000321 
 >EG:8D8 .2
>Diff : 0
>CG11412|FBan0011412|CT31863|FBan0011412  last_updated:000321 
 >EG:8D8 .6
>Diff : B+
>CG11418|FBan0011418|CT31875|FBan0011418  last_updated:000321 
 >EG:8D8 .8
>Diff : 0
>CG11415|FBan0011415|CT31869|FBan0011415  last_updated:000321 
 >EG:8D8 .7
>Diff : 0
>CG12773|FBan0012773|CT31881|FBan0012773  last_updated:000321 
 >EG:8D8 .3
>Diff : 0
 >EG:8D8 .4
>CG11417|FBan0011417|CT31873|FBan0011417  last_updated:000321 
>Diff : 0
>CG11420|FBan0011420|CT31887|FBan0011420  last_updated:000321 
 >EG:8D8 .5
>Diff : 0
>CG3056|FBan0003056|CT10284|FBan0003056  last_updated:000321 
 >EG:132E8 .1
>Diff : 0
>CG3064|FBan0003064|CT10298|FBan0003064  last_updated:000321 
 >EG:49E4 .1
\#>Diff : A- B- C+++
>Diff : D
\#
\#Comments:
\#
\#Gene  EG:49E4 .1 is a mere Genefinder prediction with very high score
\#(404.95). Genscan prediction is practically the same, except it has a
\#couple of additional NH2- terminus exons. Exons 3, 4, 5, 6, 8 and 9 are
\#supported further by protein similarity hits (e.g. MAPB_HUMAN).
\#I don't know where CG3064 comes from.
\#
\#CONCLUSION:  EG:49E4 .1 is more correct.
\#
>CG14785|FBan0014785|CT34595|FBan0014785  last_updated:000321 
 >EG:BACN32G11 .2
>Diff : 0
>CG14786|FBan0014786|CT34596|FBan0014786  last_updated:000321 
 >EG:BACN32G11 .3
>Diff : 0
>CG14787|FBan0014787|CT34597|FBan0014787  last_updated:000321 
 >EG:BACN32G11 .4
>Diff : A-
>CG14788|FBan0014788|CT34598|FBan0014788  last_updated:000321 
 >EG:BACN32G11 .5
>Diff : 0
>CG14789|FBan0014789|CT34599|FBan0014789  last_updated:000321 
 >EG:BACN32G11 .6
>Diff : A-
>CG14777|FBan0014777|CT34587|FBan0014777  last_updated:000321 
 >EG:80H7 .10
>Diff : 0
\##### WARNING: No corresponding CG to  EG:80H7 .1 \!
\##### WARNING: Can't find translation of  EG:80H7 .2 \!
>CG14780|FBan0014780|CT34590|FBan0014780  last_updated:000321 
 >EG:80H7 .3
>Diff : 0
>CG14791|FBan0014791|CT34601|FBan0014791  last_updated:000321 
 >EG:80H7 .4
>Diff : B-
>CG14781|FBan0014781|CT34591|FBan0014781  last_updated:000321 
 >EG:80H7 .11
>Diff : B+
>CG14782|FBan0014782|CT34592|FBan0014782  last_updated:000321 
 >EG:80H7 .5
>Diff : 0
>CG14792|FBan0014792|CT34602|FBan0014792  last_updated:000321 
 >EG:80H7 .6|FBgn0003517;sta
\#>Diff : A- B C+
>Diff : A- B C+
>CG14793|FBan0014793|CT34603|FBan0014793  last_updated:000321 
 >EG:80H7 .7
>Diff : D
\#
\#Comments:
\#
\#Differences in COOH- terminus are probably due to different prediction
\#methods used. In this case,  EG:80H7 .7 follows the Genefinder prediction
\#and protein similarity hits.
\#Genscan prediction extends downstream to include two more exons, which in
\#fact correspond to gene sta (or  EG:80H7 .6).
\#If this is true, the \-COOH terminus of CG14793 should align with 80H7.6.
\#
\#CONCLUSION:  EG:80H7 .7 is more correct.
\#
>CG14795|FBan0014795|CT34605|FBan0014795  last_updated:000321 
 >EG:196F3 .3
>Diff : A+
>CG14783|FBan0014783|CT34593|FBan0014783  last_updated:000321 
 >EG:196F3 .2
>Diff : C+
>CG14796|FBan0014796|CT34607|FBan0014796  last_updated:000321 
 >EG:56G7 .1
>Diff : 0
>CG11491|FBan0011491|CT36317|FBan0011491  last_updated:000321 
>CG11509|FBan0011509|CT36379|FBan0011509  last_updated:000321 
>CG11511|FBan0011511|CT34608|FBan0011511  last_updated:000321 
>CG11514|FBan0011514|CT36387|FBan0011514  last_updated:000321 
 >EG:17A9 .1|FBgn0000210;br
>Diff : B--
\##### Note: There are alternatively spliced products for br.
>CG3093|FBan0003093|CT10396|FBan0003093  last_updated:000321 
 >EG:171E4 .1|FBgn0000482;dor
>Diff : 0
>CG3740|FBan0003740|CT12509|FBan0003740  last_updated:000321 
 >EG:171E4 .4
>Diff : D
\#
\#Comments:
\#
\#Only the first 55 a.a. of the two genes match.
\#
\# EG:171E4 .4 is a small two-exon gene, located betwen  EG:171E4 .1 (dor) and
\# EG:171E4 .2 (on their opposite strand). It is a modified prediciton of
\#both Genefinder and Genscan programs; but both give relatively low score.
\#The reason it was reported is that matches EST AA142192 (on the correct
\#orientation).
\#I don't know where \-COOH terminus of gene CG3740 is located though.
\#
\#CONCLUSION:  EG:171E4 .4 is more correct.
\#
>CG3095|FBan0003095|CT10406|FBan0003095  last_updated:000321 
 >EG:171E4 .2
>Diff : A+ C+
>CG3737|FBan0003737|CT12505|FBan0003737  last_updated:000321 
 >EG:171E4 .3
>Diff : 0
>CG3100|FBan0003100|CT10412|FBan0003100  last_updated:000321 
 >EG:9D2 .1|FBgn0024897;b6
>Diff : 0
>CG3783|FBan0003783|CT12641|FBan0003783  last_updated:000321 
 >EG:9D2 .2
>Diff : D
\##### Note: Only one exon of  EG:9D2 .2 matches CG3783!
\#
\#Comments:
\#
\# EG:9D2 .2 is the intact Genscan prediction. The first 4 exons match the
\#genomic sequence for gene a6 (Y16065), but i decided to leave them in
\#because: (a) the ORF of a6 gene 700-800 bp upstream and (b) exon 4 matches
\#EST AI403894, which further extends to exons 5 and 6.
\#Maybe Celera didn't include the first 4 exons, because of their overlap
\#with Y16065
\#
\#CONCLUSION:  EG:9D2 .2 is more correct.
\#
>CG3771|FBan0003771|CT12608|FBan0003771  last_updated:000321 
 >EG:9D2 .3|FBgn0023130;a6
>Diff : C-
>CG3795|FBan0003795|CT12705|FBan0003795  last_updated:000321 
 >EG:9D2 .4
>Diff : 0
>CG14808|FBan0014808|CT34621|FBan0014808  last_updated:000321 
 >EG:4F1 .1
>Diff : 0
>CG12598|FBan0012598|CT34611|FBan0012598  last_updated:000321 
 >EG:BACN35H14 .1
>Diff : A+
>CG17968|FBan0017968|CT40057|FBan0017968  last_updated:000321 
 >EG:137E7 .1
>Diff : 0
\##### Note: Only 64 a.a. long!
>CG14801|FBan0014801|CT34614|FBan0014801  last_updated:000321 
 >EG:131F2 .2
>Diff : A-
>CG14812|FBan0014812|CT34625|FBan0014812  last_updated:000321 
 >EG:131F2 .3
>Diff : 0
>CG14814|FBan0014814|CT34627|FBan0014814  last_updated:000321 
 >EG:63B12 .6
>Diff : A-
>CG14802|FBan0014802|CT34615|FBan0014802  last_updated:000321 
 >EG:63B12 .13
>Diff : 0
>CG14815|FBan0014815|CT34628|FBan0014815  last_updated:000321 
 >EG:63B12 .5
>Diff : 0
>CG14803|FBan0014803|CT34616|FBan0014803  last_updated:000321 
 >EG:63B12 .9
>Diff : B+
>CG14816|FBan0014816|CT34629|FBan0014816  last_updated:000321 
 >EG:63B12 .4
>Diff : 0
>CG14804|FBan0014804|CT34617|FBan0014804  last_updated:000321 
 >EG:63B12 .8
>Diff : 0
>CG14817|FBan0014817|CT34630|FBan0014817  last_updated:000321 
 >EG:63B12 .11
>Diff : 0
>CG14805|FBan0014805|CT34618|FBan0014805  last_updated:000321 
 >EG:63B12 .7
>Diff : B+
>CG14818|FBan0014818|CT34631|FBan0014818  last_updated:000321 
 >EG:63B12 .12
>Diff : 0
>CG3848|FBan0003848|CT12853|FBan0003848  last_updated:000321 
 >EG:63B12 .3
>Diff : B++
>CG3109|FBan0003109|CT10436|FBan0003109  last_updated:000321 
 >EG:63B12 .2
>Diff : B+
>CG11579|FBan0011579|CT12773|FBan0011579  last_updated:000321 
 >EG:86E4 .6|FBgn0000117;arm
>Diff : A+
>CG3810|FBan0003810|CT36539|FBan0003810  last_updated:000321 
 >EG:86E4 .2
>Diff : C+
>CG17766|FBan0017766|CT39345|FBan0017766  last_updated:000321 
 >EG:86E4 .3
>Diff : A-
>CG3480|FBan0003480|CT11715|FBan0003480  last_updated:000321 
 >EG:86E4 .4
>Diff : 0
>CG3806|FBan0003806|CT12735|FBan0003806  last_updated:000321 
 >EG:86E4 .1
>Diff : 0
>CG3573|FBan0003573|CT11908|FBan0003573  last_updated:000321 
 >EG:86E4 .5
>Diff : 0
>CG11596|FBan0011596|CT12035|FBan0011596  last_updated:000321 
 >EG:39E1 .1
>Diff : 0
>CG3857|FBan0003857|CT12883|FBan0003857  last_updated:000321 
 >EG:39E1 .3
>Diff : 0
>CG3587|FBan0003587|CT12059|FBan0003587  last_updated:000321 
 >EG:39E1 .2
>Diff : 0
>CG3600|FBan0003600|CT12107|FBan0003600  last_updated:000321 
 >EG:BACH61I5 .1
>Diff : 0
>CG16902|FBan0016902|CT37504|FBan0016902  last_updated:000321 
 >EG:133E12 .2
\#>Diff : B B- B+ C++
>Diff : D
\#
\#Comments:
\#
\#Gene  EG:133E12 .2 is a 'consensus' prediction of both Genfinder and Genscan
\#programs.
\# B : So, differences on internal exons should be due to the different
\# prediction algorithms used.
\# C : I had decided to not include the last exons (that both Genfinder and
\# Genscan predict), because it was indicated by the protein similarity
\# hits (e.g. O161228, THR4 gene).
\#
\#CONCLUSION:  EG:133E12 .2 is more correct.
\#
>CG4406|FBan0004406|CT14360|FBan0004406  last_updated:000321 
 >EG:133E12 .3
>Diff : A+
>CG4399|FBan0004399|CT14236|FBan0004399  last_updated:000321 
 >EG:133E12 .4
>Diff : 0
>CG4376|FBan0004376|CT14163|FBan0004376  last_updated:000321 
 >EG:133E12 .1|FBgn0000667;Actn
>Diff : 0
>CG4380|FBan0004380|CT14272|FBan0004380  last_updated:000321 
 >EG:22E5 .1|FBgn0003964;usp
>Diff : 0
>CG4325|FBan0004325|CT14153|FBan0004325  last_updated:000321 
 >EG:22E5 .12
>Diff : 0
>CG4322|FBan0004322|CT14137|FBan0004322  last_updated:000321 
 >EG:22E5 .11
>Diff : C+
>CG4313|FBan0004313|CT14076|FBan0004313  last_updated:000321 
 >EG:22E5 .10
>Diff : 0
>CG4290|FBan0004290|CT14053|FBan0004290  last_updated:000321 
 >EG:22E5 .8
>Diff : 0
>CG4281|FBan0004281|CT14023|FBan0004281  last_updated:000321 
 >EG:22E5 .7
\#>Diff : A- B- C+
>Diff : D
\#
\#Comments:
\#
\# EG:22E5 .7 is mainly a Genefinder prediction apart from the first exon.
\#Both Genefinder and Genscan aggree on the prediction of the first 3-4
\#exons, but Genescan extends the gene further down (in the area of
\# EG:22E5 .8).
\#
\# A : I had decided to 'truncate' the first exon (appeared on both
\# predictions), because this was suggested by EST hits
\# (e.g. AI133907). Thus, i adopted the first ATG found in this EST, as
\# the starting ATG for gene  EG:22E5 .7.
\# CG4281 probably follows the Genscan prediction.
\# B : I cannot explain gthe differences in the internal exon, since both
\# Genefinder and Genscan predictions aggree on them.
\# C : If Celera followed the Genscan (or Genie) prediction 'blindly', then
\# the \-COOH of CG4281 should match part of  EG:22E5 .8.
\# I believe  EG:22E5 .8 is a different gene, because of EST hits
\# (e.g. AI108139) and protein similarity hits of different type.
\#
\#CONCLUSION:  EG:22E5 .7 is more correct.
\#
>CG4199|FBan0004199|CT13610|FBan0004199  last_updated:000321 
 >EG:22E5 .5
>Diff : A+
>CG4194|FBan0004194|CT13604|FBan0004194  last_updated:000321 
 >EG:22E5 .6
>Diff : 0
>CG4061|FBan0004061|CT13484|FBan0004061  last_updated:000321 
 >EG:22E5 .3
>Diff : 0
>CG4045|FBan0004045|CT13392|FBan0004045  last_updated:000321 
 >EG:22E5 .4
>Diff : C+
>CG4025|FBan0004025|CT13374|FBan0004025  last_updated:000321 
 >EG:22E5 .9
>Diff : 0
>CG3835|FBan0003835|CT42116|FBan0003835  last_updated:000321 
 >EG:87B1 .3
>Diff : 0
>CG3724|FBan0003724|CT12475|FBan0003724  last_updated:000321 
 >EG:87B1 .4|FBgn0004654;Pgd
>Diff : 0
>CG3717|FBan0003717|CT12461|FBan0003717  last_updated:000321 
 >EG:87B1 .6|FBgn0013432;bcn92
>Diff : 0
>CG3707|FBan0003707|CT42114|FBan0003707  last_updated:000321 
 >EG:87B1 .2|FBgn0004655;wapl
>Diff : A+
\##### WARNING: Known gene \!
>CG3656|FBan0003656|CT12233|FBan0003656  last_updated:000321 
 >EG:87B1 .1|FBgn0005670;Cyp4d1
>Diff : 0
>CG3630|FBan0003630|CT12189|FBan0003630  last_updated:000321 
 >EG:152A3 .3
>Diff : 0
>CG3621|FBan0003621|CT12175|FBan0003621  last_updated:000321 
 >EG:152A3 .7
>Diff : 0
>CG3466|FBan0003466|CT11675|FBan0003466  last_updated:000321 
 >EG:152A3 .4|FBgn0011576;Cyp4d2
>Diff : A-
\##### WARNING: Known gene \!?
>CG3461|FBan0003461|CT11665|FBan0003461  last_updated:000321 
 >EG:152A3 .5|FBgn0003116;pn
>Diff : 0
>CG3460|FBan0003460|CT11655|FBan0003460  last_updated:000321 
 >EG:152A3 .1
>Diff : 0
>CG3457|FBan0003457|CT11649|FBan0003457  last_updated:000321 
 >EG:17E2 .1
>Diff : B-
>CG3456|FBan0003456|CT11643|FBan0003456  last_updated:000321 
 >EG:103B4 .3
>Diff : A-
>CG18033|FBan0018033|CT40358|FBan0018033  last_updated:000321 
 >EG:103B4 .4
>Diff : 0
>CG3299|FBan0003299|CT11081|FBan0003299  last_updated:000321 
 >EG:103B4 .1|FBgn0004397;Vinc
>Diff : 0
>CG3443|FBan0003443|CT40368|FBan0003443  last_updated:000321 
 >EG:30B8 .4|FBgn0003048;pcx
>Diff : B--
>CG3228|FBan0003228|CT10831|FBan0003228  last_updated:000321 
 >EG:30B8 .2|FBgn0001330;kz
>Diff : 0
>CG3206|FBan0003206|CT10765|FBan0003206  last_updated:000321 
 >EG:30B8 .7
>Diff : C
>CG3193|FBan0003193|CT10256|FBan0003193  last_updated:000321 
 >EG:30B8 .1|FBgn0000377;crn
>Diff : 0
>CG3191|FBan0003191|CT10198|FBan0003191  last_updated:000321 
 >EG:30B8 .3
>Diff : 0
>CG3078|FBan0003078|CT9973|FBan0003078  last_updated:000321 
 >EG:30B8 .6
>Diff : D
\#
\#Comments:
\#
\# EG:30B8 .6 is the intact prediction of both Genefinder and Genscan with
\#good scores. The two first exons supported by EST hits and exon-2 has
\#also some protein hits (not very strong though).
\#CG3078 matches  EG:30B8 .6 only in the first 184 a.a.
\#I don't know what happened with the rest of the prediction.
\#
\#CONCLUSION: Ambigious or  EG:30B8 .6 is more correct.
\#
>CG3071|FBan0003071|CT41361|FBan0003071  last_updated:000321 
 >EG:25E8 .3
>Diff : B+
>CG2924|FBan0002924|CT42120|FBan0002924  last_updated:000321 
 >EG:25E8 .2
>Diff : A+ C-
>CG2918|FBan0002918|CT9894|FBan0002918  last_updated:000321 
 >EG:25E8 .1
>Diff : 0
>CG2879|FBan0002879|CT9868|FBan0002879  last_updated:000321 
 >EG:25E8 .6
>Diff : D
\##### Note:  EG:25E8 . 6:235-283  matches  CG2879:1-49 .
\#
\#Comments:
\#
\# EG:25E8 .6 is a small gene predicted by both Genefinder and Genscan with
\#marginally good scores. It contains small repeats, thus i am not sure
\#about its true existence.
\#There are no other supportive evidence for this gene (the protein
\#similarity hits are not convincing, as it is written in XDrosDB).
\#The start of CG2879 matches the end of  EG:25E8 .6. If CG2879 extends
\#further down, it should match gene  EG:25E8 .1.
\#
\#CONCLUSION: Ambigious.
\#
>CG2865|FBan0002865|CT9798|FBan0002865  last_updated:000321 
 >EG:25E8 .4
>Diff : 0
>CG2845|FBan0002845|CT9736|FBan0002845  last_updated:000321 
 >EG:BACH48C10 .3|FBgn0003079;phl
>Diff : B+
\##### WARNING: Known gene \!
>CG7952|FBan0007952|CT23972|FBan0007952  last_updated:000321 
 >EG:BACH7M4 .5
>Diff : 0
>CG7925|FBan0007925|CT23896|FBan0007925  last_updated:000321 
 >EG:BACH59J11 .1|FBgn0003714;tko
>Diff : 0
>CG7803|FBan0007803|CT23694|FBan0007803  last_updated:000321 
 >EG:BACH59J11 .3|FBgn0004050;z
>Diff : 0
>CG9659|FBan0009659|CT27300|FBan0009659  last_updated:000321 
 >EG:BACR25B3 .8|FBgn0001404;egh
>Diff : 0
>CG8590|FBan0008590|CT24639|FBan0008590  last_updated:000321 
 >EG:BACR25B3 .9
>Diff : 0
>CG9900|FBan0009900|CT25082|FBan0009900  last_updated:000321 
 >EG:BACR7C10 .3|FBgn0004643;mit(1)15
>Diff : 0
\##### NOTE: 100% match on the first 260 a.a. only!
\##### WARNING: Known gene \!
\#
\#Comments:
\#This was a partial version of the gene (splitted between two clones). The
\#complete version sent to Melanie on 4-Sep-2000. Coparison with CG9900
\#showed (almost) 100% a.a. identity over the whole 721 a.a.
\#
>CG2621|FBan0002621|CT8875|FBan0002621  last_updated:000321 
 >EG:155E2 .3|FBgn0003371;sgg (/partial; this is the 3' terminus)
>Diff : A+
\#
\#Comments:
\#This was a partial version of the gene. The complete version sent to
\#Melanie on 4-Sep-2000. Comparison with CG9900 showed (almost) 100%
\#a.a. identity over the whole 721 a.a.
\#
\#After checking, i found that  EG:155E2 .3 is practically identical to Q27605
\#'PROTEIN KINASE SHAGGY, SGG46 ISOFORM (EC 2.7.1.-) (PROTEIN ZESTE-WHITE 3)
\#(SGG46).'
\#
>CG2655|FBan0002655|CT8939|FBan0002655  last_updated:000321 
 >EG:155E2 .2|FBgn0011276;HLH3B
>Diff : 0
>CG2652|FBan0002652|CT8935|FBan0002652  last_updated:000321 
 >EG:155E2 .5
>Diff : 0
>CG2647|FBan0002647|CT8963|FBan0002647  last_updated:000321 
 >EG:155E2 .4|FBgn0003068;per
>Diff : A- B+
\##### WARNING: Known gene \!
\#
\#Comments:
\#
\#There are four alternatively splice per genes reported by EDGP.
\#
\#CONCLUSION: No differences really.
\#
>CG2650|FBan0002650|CT8975|FBan0002650  last_updated:000321 
 >EG:155E2 .1|FBgn0000092;anon-3B1.2
>Diff : B-
>CG2658|FBan0002658|CT8999|FBan0002658  last_updated:000321 
 >EG:100G10 .7
>Diff : 0
>CG2662|FBan0002662|CT9011|FBan0002662  last_updated:000321 
 >EG:100G10 .6
>Diff : 0
>CG2675|FBan0002675|CT9063|FBan0002675  last_updated:000321 
 >EG:100G10 .5
>Diff : A+
>CG2677|FBan0002677|CT9073|FBan0002677  last_updated:000321 
 >EG:100G10 .3
>Diff : 0
>CG2680|FBan0002680|CT9081|FBan0002680  last_updated:000321 
 >EG:100G10 .4
>Diff : B+
>CG2681|FBan0002681|CT9087|FBan0002681  last_updated:000321 
 >EG:100G10 .2
>Diff : B-
>CG2685|FBan0002685|CT9103|FBan0002685  last_updated:000321 
 >EG:100G10 .1
>Diff : 0
>CG2694|FBan0002694|CT9121|FBan0002694  last_updated:000321 
 >EG:100G10 .8
>Diff : 0
>CG2701|FBan0002701|CT9167|FBan0002701  last_updated:000321 
 >EG:95B7 .9
>Diff : 0
>CG2706|FBan0002706|CT9201|FBan0002706  last_updated:000321 
 >EG:95B7 .8|FBgn0000928;fs(1)Yb
>Diff : 0
>CG2707|FBan0002707|CT9213|FBan0002707  last_updated:000321 
 >EG:95B7 .4|FBgn0000927;fs(1)Ya
>Diff : A-
>CG2709|FBan0002709|CT9223|FBan0002709  last_updated:000321 
 >EG:95B7 .5
>Diff : 0
>CG2711|FBan0002711|CT9225|FBan0002711  last_updated:000321 
 >EG:95B7 .6
>Diff : 0
>CG2713|FBan0002713|CT9227|FBan0002713  last_updated:000321 
 >EG:95B7 .3
>Diff : 0
>CG2712|FBan0002712|CT9229|FBan0002712  last_updated:000321 
 >EG:95B7 .7
>Diff : 0
>CG2714|FBan0002714|CT9231|FBan0002714  last_updated:000321 
 >EG:95B7 .2|FBgn0000376;crm
>Diff : 0
>CG2715|FBan0002715|CT9233|FBan0002715  last_updated:000321 
 >EG:95B7 .11
>Diff : 0
>CG2759|FBan0002759|CT9359|FBan0002759  last_updated:000321 
 >EG:BACN33B1 .1|FBgn0003996;w
>Diff : 0
 >EG:BACR43E12 .6
>CG14417|FBan0014417|CT34074|FBan0014417  last_updated:000321 
>Diff : 0
 >EG:BACR43E12 .5
>CG14418|FBan0014418|CT34075|FBan0014418  last_updated:000321 
>Diff : B+
>CG3591|FBan0003591|CT12085|FBan0003591  last_updated:000321 
 >EG:100G7 .2|FBgn0014097;anon-3Cb
>Diff : 0
>CG3598|FBan0003598|CT12109|FBan0003598  last_updated:000321 
 >EG:100G7 .3
>Diff : 0
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