Category 1: genes that we have no clue about - no sign of them in any jam
page, no mention anywhere.  
Leyla's method: BLASTP (at BDGP) of entry in aa_embl_dros against the
Predicted proteins (AA) set. Check match. If any ambiguity, do BLASTN
at NCBI using relevant gene accession against scaffold accessions.
If necessary view pairwise alignments using the SEAN tool (especially 
useful for aligning e.g clusters like and Met75Ca and Met75Cb annotated 
on genomic DNA with scaffold accessions.) 
Genes to which a CG can be assigned:
Amy-p(FBgn0000079)=CG18640|FBan0018640|CT42306|
 BcDNA:GH03186 (FBgn0028502)=CG6446|FBan0006446|CT20096|
Cyt-P450-rBF6-2(FBgn0013773)=CG10240
(invalid gene symbol in GadFly Cyp6a22)
 EG:190E7.1 (FBgn0024368)=CG18091|FBan0018091|CT40606|FBan0018091
 EG:49E4.1 (FBgn0025392)=CG3064|FBan0003064|CT10298|
(intron-exon structure has to be corrected)
Grip75(FBgn0026431)=CG6176|FBan0006176|CT19386|FBan0006176
Gtp-bp(FBgn0010391)=CG2522|FBan0002522|CT3545|FBan0002522
l(2)03659(FBgn0010549)=CG11803|FBan0011803|CT8643|FBan0011803
l(2)k10201 (FBgn0016970) =CG8803|FBan0008803|CT8653|
(translation starts further upstream w/ CTG start than annotated on CG8803)
l(2)tid(FBgn0002174)=CG5504|FBan0005504|CT17450|FBan0005504
(note: CG5504 is erroneously annotated as l(2)dtl in public view of GadFly; 
CG11295 is correctly annotated as l(2)dtl)
Met75Cb(FBgn0028415)=CG18064|FBan0018064|CT40477|FBan0018064
( note:CG18064  is incorrectly identified as Met75Ca; sequence 
corresponding to Met75Ca exists but is unannotated. This is by 
alignment of Acc.AJ249253 (which has both genes) to AE003520.)
msopa (FBgn0004414)=CG14560|FBan0014560|CT34291
(several indels give rise to frameshift in CG protein product.)
Mst98Ca (FBgn0002865)=CG11719|FBan0011719|CT5056|
Mst98Cb (FBgn0004171)=CG18396|FBan0018396|CT41800|
Nckx30C	(FBgn0028704)=CG4106|FBan0004106|CT13634| 
prc (FBgn0028573)=CG5700|FBan0005700|CT17960|FBan0005700 
(intron-exon structure has to be corrected)
Prosα1 (FBgn0026781)=CG18495|FBan0018495|CT42044|CT42048|
(note the 2 transcripts)
Sgs7 (FBgn0003377)=CG18087|FBan0018087|CT40586|
spen (FBgn0016977)=CG18497|FBan0018497|CT36331|CT42170|
(CT36331 translation is very extremely truncated wrt known CDS, Missing 
from GadFly public view)
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Not as good a match as above, but good bet; save for reannotation if you wish:
IM2 (FBgn0025583) is most likely CG18106|FBan0018106|CT40691 despite indel
that causes difference in the middle of protein wrt translation of AF074003. 
This is one of 3 closely related genes close to each other (on AE003799.)
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Genes where there is a sequence match that is not annotated:
 BcDNA:GH02384  (FBgn0027612) 	there is matching sequence but is not annotated
(matches AE003666: 223903(ATG)-222438(TAA) several exons; should be between 
CG11017 and CG2508)
Orf5C (FBgn0011819)		there is matching sequence but is not annotated
(Orf5C is adjacent to Act5C) 
Ste (FBgn0003523)		there is matching sequence but is not annotated 
(it should be in region next to ben (ben correctly annotated as CG18319 but
no neighbors showing in GadFly; note:'Ste locus contains two major size classes 
of a tandemly repeated gene'; the 2 accessions in FlyBase align near each other)  
unknown-telomeric-protein-gene FBgn0027101 there is matching sequence but is not 
annotated 
(AF103941 aligns  with coordinates 42123-42832 of AE003163)
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Ambiguous (no good GadFly BLAST hits, no good uninterrupted BLASTN alignment
to NCBI contigs, should be rechecked when reannotating)
Crg-1 	no CG annotated
	3' end of Crg-1 transcripts align to Acc. AE003327
	(this is a tiny contig)
Dbp80	no CG annotated
	BLAST hits fall on 3 short scaffolds (AE003058, AE002987, AE003078) 
	1 scaffold has annotation for another gene, other 2 have no annotations
Lcp6		no unambiguous matches
(note this from FB and  paper:The  Lcp6 protein may be encoded by an extra 
copy of the 'Lcp-b' gene (Lcp65Ab3) present in the Canton S strain.
i.e. it may not be in all strains.)
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Genes where the symbol has changed (valid symbol already has a CGnumber):
 BcDNA:GH03016  is a synonym of Rh50 CG7499
 BcDNA:GH04413  is a synonym of Appl CG7727
 BcDNA:GH08312  is a synonym of Sap-r CG12070 
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Merges:
Ser5 is probably a fragment of Ser99Da (Ser5 and Ser6 are PCR fragments).
(Will send alignment separately to MA and AG)