Category 4: genes that were in the penultimate XML but are now gone and
for which I can't find a replacement in the final xml (but I did no seq
alignment).
Sima checked these by BLASTing protein sequence from aa_embl.dros at the
BDGP against the latest version of aa_gadfly.dros.  Those that did not
match, I tried the nucleic acid sequence from na_embl.dros against
na_gadfly.dros and then against genomic scaffolds at NCBI.
>βggt-II(347aa)
=CG18627|FBan0018627|CT41437|FBan0018627  last_updated:000321 (347aa)
CT10156 == CG3023, gone
>A(225)(711aa)
=CG18255|FBan0018255|CT41348|FBan0018255  last_updated:000321 (1277nt)
(only found as nucleic acid, not as protein)
CG8307 no jam, gone
>Act87E(376aa) 
=CG10067|FBan0010067|CT28343|FBan0010067  last_updated:000321 (376aa)
CT34012 no CG and CT26437 CG9278 gone
>Aprt(182aa)
=CG18315|FBan0018315|CT41563|FBan0018315  last_updated:000321 (182aa)
CG1833 CT5556, gone
>axo(1685aa)
=CG18296|FBan0018296|CT41507|FBan0018296  last_updated:000321 (482aa)
CG7517 CT1277, gone
>Bbbf1(638aa) =no gene in GadFly but matches Celera AE003608 (repeated
many times in this scaffold sequence) 
CT39704 == CG15836, gone
> BG:DS01368.1 (514aa)
=CG18507|FBan0018507|CT42208|FBan0018507  last_updated:000321 (463aa)
CG7153 CT22111 gone
>Eip93F(1221aa)
=CG18389|FBan0018389|CT41792|FBan0018389  last_updated:000321 (1075aa)
CG6505 CT20215, gone
>Gprk1(700aa)
=no gene in GadFly but matches Celera AE002943, AE002613, AE002814,
AE003008, AE003017 (split among many scaffolds)
CT39791 == CG17882 gone
>Optix(60aa)
=CG18455|FBan0018455|CT42028|FBan0018455  last_updated:000321 (218aa)
CG8718 CT9483, gone
>Os9(159aa)
=CG10658|FBan0010658|CT29854|FBan0010658  last_updated:000321 
(only found as nucleic acid, not as protein)
CG10656 CT29836, gone
>Shark(950aa)
=CG18247|FBan0018247|CT41326|FBan0018247  last_updated:000321 (939aa)
CG5801 and CG11991 both gone