Category 2: genes that are known to be in a region where there are no CG's (often an intron of another gene). Also a few cases where there is a CG in the right place but there's more than one gene to match to it. If no CT/CG match can be made then log it for the time of reannotation. Leyla's method: BLASTP at Berkeley using FASTA from aa_embl.dros or aa_Adh.dros. If no good hits, BLASTN at NCBI using FASTA from na_embl.dros or na_Adh.dros (or FASTA from NCBI accession: e.g. EG:EG0007.5 translation missing from aa_embl.dros due to formatting glitch.) Alignments with SEAN as needed for verification. MATCHES: Bem46 FBgn0025109=CG18642|FBan0018642|CT42330| (adjacent to CG3736 okr) BG:DS00810.3 =CG18456|FBan0018456|CT35228| BG:DS05899.7 (548aa)=CG18095|FBan0018095|CT40625|(442) CG18095 different after aa 416 and truncates at aa 442. BG:DS07473.1 (2190aa)=CG12455|FBan0012455|CT32536|(2172aa) Mostly correct! CG12455 missing 18 aa between aa 84-102 of published CDS. BG:DS07721.3 =CG15282|FBan0015282|CT35230 aa 1-139 of CG15282 match aa 54-192 of BG:DS07721.3 from aa_Adh.dros. (but structure needs to be checked.) SPLIT between genes, to be merged/fixed: BG:DS00180.5: (no CG between BG:DS00180.3 and BG:DS00180.12 ) some of BG:DS00180 (734 aa) is split between CG8855|FBan0008855|CT25428| (832aa) (aa 394-620 align) and CG17988|FBan0017988|CT40163| (792aa) (aa 166-282 align) No good BLASTP match to the rest of the protein. PART OF HYBRID, to be split: BG:DS00180.7: CG16882|FBan0016882|CT37468(1035aa)|CT37470|(917aa) is a hybrid between BG:DS00180.7 (421aa) and BG:DS00180.8 . (448 aa) Note two transcripts associated with CG16882: aa 8-421 of BG:DS00180.7 correspond to aa 504-917 of CT37470 and aa 622-1035 of CT37468 aa 1-448 of BG:DS00180.8 correspond to aa 1-448 of CT37468 aa 119-448 of BG:DS00180.8 correspond to aa 1-330 of CT37470 EG:34F3.2: CG12467|FBan0012467|CT32681| (1376aa) is a hybrid of EG:34F3.2 FBgn0025622 (1014aa) and EG:34F3.1 FBgn0025623 (504 aa) EG:EG0007.4: CG4857|FBan0004857|CT15601| (1911aa) is a hybrid of EG:EG0007.4 FBgn0026082 (911 aa) and EG:EG0007.12 FBgn0026083 (978 aa) ONE gene with 2 transcripts, one transcript corresponds to EG:140G11.3 , the other corresponds to FcpC3!: EG:140G11.3 =G4015|FBan0004015|CT41858| FcpC3=CG4015|FBan0004015|CT13332| TO BE ANNOTATED in the future, but the presence of annotatable sequence has been verified by BLASTN to scaffolds at NCBI: gdl-ORF39 no CG between Z600 and Eip71CD (aligns to AE003530) (end of gdl-ORF is only 68 bp from gdl ATG) l(2)rot no CG within l(2)not (aligns to AE003461) Lcp65Ab1 no CG between Lcp65Aa and Lcp65Ac (aligns to AE003563) Lcp65Ab2 no CG between Lcp65Aa and Lcp65Ac (aligns to AE003563) scw no CG within Lar (aligns to AE003663) ( NB:translation of Lar CG10443|FBan0010443|CT29268| is severely truncated: 2029 aa in CDS set vs 74 aa from CT29268!) (scw should be between exon 4 and 5 of Lar) BG:DS02795.3 only CG12455/CT32536 between PRL-1 and Ca-α1D (aligns to AE003650) BG:DS00810.1 only CG18456/CT35228 between BG:DS07721.6 and BG:DS06874.1 (aligns to AE003645) BG:DS00810.2 only CG18456/CT35228 between BG:DS07721.6 and BG:DS06874.1 (aligns to AE003645) BG:DS00929.15 no CG between vig and vas (aligns to AE003646) BG:DS01514.3 no CG between rk and bgm (aligns to AE003642) BG:DS03192.3 no CG between stc and BG:DS03192.2 (aligns to AE003646) BG:DS03192.4 no CG within BG:DS03192.2 (aligns to AE003646) BG:DS03792.2 no CG within wb aka CG15288/CT35236 (aligns to AE003643) BG:DS05899.6 only CG18095/CT40625 between BG:DS05899.1 and BG:DS05899.3 (aligns to AE003642) BG:DS07295.4 no CG within BG:DS07295.1 (aligns to AE003646) BG:DS07721.1 only CG15282/CT35230 between Adhr and BG:DS07721.6 (aligns to AE003644) BG:DS08249.1 only CG18507/CT42208 (nj) between BG:BACR48E02.4 and BG:DS08249.2 (aligns to AE003641) BG:DS08249.4 no CG between BG:DS08249.3 and BG:DS00797.1 (aligns to AE003641) BG:DS08249.5 no CG between BG:DS08249.3 and BG:DS00797.1 (aligns to AE003641) BG:DS09219.1 only CG15282/CT35230 between Adhr and BG:DS07721.6 (aligns to AE003644) EG:EG0007.5 no CG between EG:EG0007.12 and Fas2 (aligns to AE003430)
