Here are the nc3 category gene matches to CGs (whenever possible) or scaffolds. In a few instances, scaffold coordinates were included to indicate the extent of the annotation changes necessary; the coordinates should be treated as approximate. Leyla κB-Ras CG1669|FBan0001669|CT4492| ζCOP CG3948|FBan0003948|CT13124| 312 CG9166|FBan0009166|CT8251| Aats-trp CG9735|FBan0009735|CT27510| ACXA CG17176|FBan0017176|CT38108| ACXB CG17174|FBan0017174|CT38106| ACXC CG5983|FBan0005983|CT18649| ACXD CG5712|FBan0005712|CT6304| ACXE CG17178|FBan0017178|CT38110| alpha-catenin-related CG2987|FBan0002987|CT10097| anon-69Ag MERGE CG14124|FBan0014124|CT33722| + CG14123|FBan0014123|CT33721| anon-71Aa CG13466|FBan0013466|CT32830| anon-Ryu CG3066|FBan0003066|CT10270| arouser CG4276|FBan0004276|CT37920| and |CT13981| bc10 CG4867|FBan0004867|CT15653| BcDNA:GH02384 matches CG-less sequence on AE003666 No good BLASTP match BcDNA:GH05668 unresolved, to be fixed during reannotation. Third exon of CG3364|FBan0003364|CT11313| overlaps with BcDNA:GH09668 , but the predicted CG3364 CDS falls within an intron of BcDNA:GH05668 , so there is no CDS overlap. BcDNA:LD16071 CG10106|FBan0010106|CT7946| BcDNA:LD22218 matches CG-less sequence on AE003809 No good BLASTP match BcDNA:LD37196 CG7242|FBan0007242|CT22341| best CG6264|FBan0006264|CT19608| BG:DS00004.11 CG2358|FBan0002358|CT7848| BG:DS00180.5 MERGE/SPLIT CG17988|FBan0017988|CT40163| + CG8855|FBan0008855|CT25428| aa 650-766 of CG17988 = aa 166-282 of 734 aa BG:DS00180.5 aa 66-292 of 832 aa CG8855 = aa 394-620 of 734 aa BG:DS00180.5 (aa 431-832 of CG8855 correspond to BG:DS00180.12 ) (no aa correspondence found to first 650 aa of CG17988) BG:DS00180.7 part of CG16882 CG16882 to be SPLIT: aa 8-421 of BG:DS00180.7 correspond to aa 504-917 of CG16882|CT37470 CDS aa 8-421 of BG:DS00180.7 correspond to aa 622-1035 of CG16882|CT37468 CDS aa 1-448 of CG16882 correspond to 448 aa BG:DS00180.8 CDS BG:DS00810.1 matches CG-less sequence on AE003645 No good BLASTP match BG:DS00810.2 matches CG-less sequence on AE003645 No good BLASTP match BG:DS00929.15 matches CG-less sequence on AE003646 No good BLASTP match BG:DS00929.16 matches CG-less sequence on AE003645 and AE003646 No good BLASTP match BG:DS00929.7 matches CG-less sequence on AE003646 No good BLASTP match BG:DS01514.3 matches CG-less sequence on AE003642 No good BLASTP match BG:DS02740.18 matches CG-less sequence on AE003650 No good BLASTP match BG:DS02795.3 matches CG-less sequence on AE003650 No good BLASTP match BG:DS03192.3 matches CG-less sequence on AE003646 No good BLASTP match BG:DS03192.4 matches CG-less sequence on AE003646 No good BLASTP match BG:DS03792.2 matches CG-less sequence on AE003643 No good BLASTP match BG:DS05899.6 matches CG-less sequence on AE003642 No good BLASTP match BG:DS06874.7 matches CG-less sequence on AE003645 No good BLASTP match BG:DS07295.4 matches CG-less sequence on AE003646 No good BLASTP match BG:DS07721.1 matches CG-less sequence on AE003644 No good BLASTP match BG:DS08249.1 matches CG-less sequence on AE003641 No good BLASTP match BG:DS08249.4 matches CG-less sequence on AE003641 No good BLASTP match BG:DS08249.5 matches CG-less sequence on AE003641 No good BLASTP match BG:DS09219.1 matches CG-less sequence on AE003644 No good BLASTP match bon CG5206|FBan0005206|CT16645| Bzd CG13761|FBan0013761|CT33242| c11.1 CG12132|FBan0012132|CT7740| (truncated) c12.1 CG12135|FBan0012135|CT7760| c12.2 CG12149|FBan0012149|CT8343| (truncated) Ca-β CG6320|FBgn0032353|CT19694 (fix) Caps MERGE CG17881 ( BcDNA:GH07283 ) + CG18026 CG17881|FBan0017881|CT39782| (aa 190-910 of Caps) CG18026|FBan0018026|CT40344| (aa 715-1282 of Caps) (these 2 have been annotated as overlapping transcripts: they share all or parts of 3 exons; structure to be fixed) cathD CG1548|FBan0001548|CT3996 Catsup CG10449|FBan0010449|CT29330 ced-6 CG11804|FBan00011804|CT33506 CHORD CG6198|FBan0006198|CT19440 chrw CG3870|FBan0003870|CT12899 cIF2 CG10840|FBan0010840|CT30355 cngl CG9176|FBan0009176|CT26220 COQ7 CG14437|FBan0014437|CT34099 Crg-1 No BLASTP match, no 'CT' matches, but multiple BLASTN matches to contigs, may contain repeat, to be checked at reannotation. Crtp CG13580|FBan0013580|CT32962| dbo CG6224|FBan0006224|CT19492| desert matches CG-less sequence on AE003554 No good BLASTP match Dip1 CG15367|FBan0015367|CT35387| Dip2 CG9771|FBan0009771|CT27623| Dip3 CG12767|FBan0012767|CT30557| disp CG2019|FBan0002019|CT6508| DSH3PX1 CG6757|FBan0006757|CT20989| dynactin-subunit-p25 CG10846|FBan0010846|CT30375| Ef1γ CG11901|FBan0011901|CT5034| EG:140G11.3 CG4015|FBan0004015|CT41858| EG:96G10.8 CG14265|FBan0014265|CT33887| EG:BACR25B3.1 SPLIT CG7981|FBan0007981|CT23996| (corresponds to N-terminus) EG:BACR25B3.10 SPLIT CG7981|FBan0007981|CT23996| (corresponds to C-terminus) EG:BACR25B3.4 CG8310|FBan0008310|CT24372| Important: No CDS (translation) is available for this gene. EG:BACR25B3.9 CG8590|FBan0008590|CT24639| EG:BACR37P7.5 CG12470|FBan0012470|CT32706| EG:BACR43E12.4 CG3526|FBan0003526|CT11880| (extend N-terminus of CG) EG:BACR43E12.5 CG14418|FBan0014418|CT34075| EG:BACR43E12.6 CG14417|FBan0014417|CT34074| EG:BACR7A4.2 CG3713|FBan0003713|CT12463| EG:EG0007.5 matches CG-less sequence on AE003430 No good BLASTP match eIF-3p66 CG10161|FBan0010161|CT28571| epsin-like part of CG13854|FBan0013854|CT33368| + CG13853|FBan0013853|CT33367| MERGE/SPLIT (note: CG13854 is 1370 aa and only the first 448 aa of that matches the published epsin-like mRNA (CDS 642 aa). Rest of epsin-like matches the neighboring CG13853) eso18E CG14233|FBan0014233|CT33849| espinas CG12833|FBan0012833|CT31965| Fad2 CG7923|FBan0007923|CT23928| fbl CG5725|FBan0005725|CT37729| (aa 112-512)(1st exon of CG5725 wrong, coordinates should be 55698-56257 on Acc. AE003591) FKBP59-bp1 CG4535|FBan0004535|CT14666| fne CG4396|FBan0004396|CT7563| (CG missing 2 exons, last exon truncated) FU12 CG9233|FBan0009233|CT26378| Gγ30A CG18511|FBan0018511|CT42246| (intron-exon structure to be fixed, coding exons should be 72488..72600,91049..91154 of AE003624) GCR(ich) CG5812|FBan0005812|CT17997| Glu-RIB CG4481|FBan0004481|CT14586| glycerol-3-phosphate-acyltransferase CG4625|FBan0004625|CT14810| GNBP1 CG6895|FBan0006895|CT21350| GNBP2 (SPLIT?) CG4144|FBan0004144|CT13694| (most of published complete 461 aa CDS contained in the N-terminus of 1189 aa CG4144; CG4144 will probably have to be split.) GNBP3 CG5008|FBan0005008|CT16088| graal MERGE (3-way merge): CG4821 + CG18403 + CG4948 (Tequila) CG4821|FBan0004821|CT15447| aa 1102-1462 of gr= 31-391 of CG4821 (391 aa) CG18403|FBan0018403|CT40927| aa 759-1046 of gr = aa 1-288 of CG18403 (290 aa) CG4948|FBan0004948|CT15880| aa 1-216 of gr = aa 1-216 of CG4948 (516 aa) grau CG3282|FBan0003282|CT11021| (N terminus of CG3282 CDS (1064 aa) corresponds to published grau complete CDS (544 of 570 aa); CG3282 to be split.) Gug CG6964|FBan0006964|CT21511| (small intron-exon differences) Hex CG5443|FBan0005443|CT17278| (all 3 Hex CDSs in here) hgo CG4779|FBan0004779|CT15337| HGTX MERGE CG13475|FBan0013475|CT32840| + CG4745|FBan0004745|CT15114| (1st 139 aa of 238 aa CG4745|CT15114 correspond to the C terminus of HGTX (not clear what the last ~100 aa of CG4745 correspond to) hoip CG3949|FBan0003949|CT13103| icln CG4924|FBan0004924|CT15822| Ilk CG10504|FBan0010504|CT29478| Jafrac1 CG1633|FBan0001633|CT4414| Jafrac2 CG1274|FBan0001274|CT2376| joey CG15736|FBan0015736|CT35978| Kai-RIA CG18039|FBan0018039|CT13538 Important: No CDS (translation) is available for this gene. Currently annotated as: AE003731 complement(join(<126216..126492,126550..126634, 126690..126893,126955..127185,127242..>127405)) correct CDS is: AE003731 complement(join(125064..125234,125299..125448,125508..125620, 125676..125901,125958..126159,126216..126492,126550..126634,126690..126893,126955..127185, 127242..127405,127466..127858,127917..128139,128197..128357,128440..128548)) katanin-60 CG10229|FBan0010229|CT28759| katanin-80 MERGE CG13956|FBan0013956|CT33508| + CG9910|FBan0009910|CT27906| Ku80 CG13241|FBan0013241|CT32491| kurtz-arrestin CG1487|FBan0001487|CT3719|FBan0001487 lack CG4943|FBan0004943|CT15876| larp CG14066|FBan0014066|CT33635| LRP6 CG5912|FBan0005912|CT15575| (missing first 66 aa) mab-2 CG4746|FBan0004746|CT15175| MAP-kinase-phosphatase CG6238|FBan0006238|CT19498| (first 319 aa only, missing rest of 1045 aa protein because of intron-exon annotation problems) CDS annotation on AE003750 reads: complement(join(3645..3843,3907..3972,4265..4656, 4722..4967,5864..5920)) should be: complement(join(1248..1250,1319..3227,3313..3582,3649..3843,3907..3972,4265..4656, 4722..4967,5864..5920)) mary CG13399|FBan0013399|CT32745| Mdh CG5889|FBan0005889|CT18483| mei-217 matches CG-less sequence on AE003504 No good BLASTP match Men CG10120|FBan0010120|CT38328| Menl-1 CG7964|FBan0007964|CT23838| Menl-2 CG7969|FBan0007969|CT23844|F meso18E CG14233|FBan0014233|CT33849| mig CG8367|FBan0008367|CT24629|F miple2 CG18321|FBan18321|CT41577| Mkrn1 CG7184|FBan0007184|CT22183| ms(1)15 CG12157|FBan0012157|CT8493| MTF-1 CG3743|FBan0003743|CT12477| Myo28B1 CG6976|FBan0006976|CT21549| Myt1 CG10569|FBan0010569|CT29656| (CG longer at C terminus than published Myt1 CDS) nerfin-1 CG13906|FBan0013906|CT33443 NHP2 CG5258|FBan0005258|CT16795| nkd MERGE? CG18224|FBan0018224|CT41252| + CG11614|FBan0011614|CT33667 (The exons marked for CG11614|CT33667 belong to nkd, but the CDSs of nkd and CG11614 do not match because of frameshift. nkd coding exons on AE003518 are at coordinates join(155094..155157, 188492..188955,191296..192108, 192628..193004,193559..194627) CG18224|FBan0018224|CT41252| CDS coordinates are 188524..188964 CG11614|FBan0011614|CT33667 exon coordinates are join(<191274..192108,192628..193004,193559..194627)) nmdyn-D7 CG8362|FBan0008362|CT24641| (aa 156-387 of 387 aa CG matches nmdyn-D7 CDS) noe matches CG-less sequence on AE003524 No good BLASTP match NtR CG6698|FBan0006698|CT20794| Ogt CG10392|FBan0010392|CT9123| onecut CG1922|FBan0001922|CT5912| orbit matches CG-less sequence on AE003593 No good BLASTP match p115 CG1422|FBan0001422|CT3352| Pap CG9854|FBan0009854|CT27790| (CG longer at the C terminus than published CDS) PpD14 CG1455|FBan0001455|CT3539| (note: PpD14 is a 73 bp PCR fragment) pins CG5692|FBan0005692|CT17944| pontin CG4003|FBan0004003|CT13291| POSH CG4909|FBan0004909|CT15776| PQBP-1 matches CG-less sequence on AE003678 No good BLASTP match Prosβ5 CG12323|FBan0012323|CT22275| ptr CG2841|FBan0002841|CT9712| Rad CG5692|FBan0005692|CT17944| ran CG1404|FBan0001404|CT3258| raw MERGE CG9321|FBan0009321|CT26527| + CG12437|FBan0012437|CT32326| RecQ4 CG7487|FBan0007487|CT22997| REG CG1591|FBan0001591|CT4191|F reptin CG9750|FBan0009750|CT27557| retinin (SPLIT?) CG13057|FBan0013057|CT32276| (retinin annotated as complete CDS corresponds to aa 395-585 of 585 aa CG13057) Rgl CG8865|FBan0008865|CT25420| (intron-exon boundaries to be fixed) ROC2 CG16988|FBan0016988|CT37703| sbb CG5580|FBan0005580|CT17646| sbr CG1664|FBan0001664|CT4634|F SCAMP CG9195|FBan0009195|CT26276| scro CG18452|FBan0018452|CT38833| corresponds to most of exons 2 and 3 of scro (intron-exon boundaries to be fixed) aligns with AE003199 scylla CG7590|FBan0007590|CT23193| sds22 CG5851|FBan0005851|CT18355| secretory-granule-neuroendocrine-protein CG1168|FBan0001168|CT2051| (CG longer by 10 aa at N terminus than published CDS) sens CG10714|FBan0010714|CT30029 on AE003538 but transcript structure is incorrect CDS on AE003538 annotated as: join(47970..48089,48411..48506) Should be: join(47970..48129,48411..49492,51423..51573,51810..51927,52611..52724) serpin-27A CG11331|FBan0011331|CT31629| SF1 CG5836|FBan0005836|CT18309| (missing one section and too short) SF2 CG6987|FBan0006987|CT21609| sip1 CG7238|FBan0007238|CT22315| SMC1 CG6057|FBan0006057|CT18959| Sox50E CG8404|FBan0008404|CT24693| (1st and last exons to be fixed, aa 19-688 match published CDS) SoxN CG18024|FBan0018024|CT37434| (1st aa to be fixed) SP1029 CG11956|FBan0011956|CT39158| span CG12352|FBan0012352|CT23594| by nucleotide match only Important: No CDS (translation) is available for CG12352 in GadFly or GenBank. sp2 CG8137|FBan0008137|CT24318| (structure to be fixed: missing internal exon and truncated early) SP295 (SPLIT?)CG11326|FBan0011326|CT31613| aa 65-391 of 419 aa SP295 CDS match aa 1-355 of 1024 aa CG11326 (w/ gap) sp3 CG9334|FBan0009334| (extend CG at N-terminus) sp4 CG9453|FBan0009453|CT26788| sp5 CG18525|FBan0018525|CT42292| SP460 matches CG-less sequence on AE003576 No good BLASTP match SP512 CG1200|FBan0001200|CT2130| SP555 CG14041|FBan0014041|CT33600| SP558 CG1155|FBan0001155|CT2019| spag CG13570|FBan0013570|CT32952| Spt5 CG7626|FBan0007626|CT23221| Sr-CII CG8856|FBan0008856|CT25430| (intron-exon boundaries to be fixed) Sr-CIII matches CG-less sequence on AE003577 No good BLASTP match adjacent to Sr-CI (see accession AF221506) Sras CG4852|FBan0004852|CT15587| stich1 CG17100|FBan0017100|CT34464| Sucb CG10622|FBan0010622|CT29754| Sulf1 CG6725|FBan0006725|CT20881| (Sulf1 accession is an incomplete CDS) tantalus CG6586|FBan0006586|CT20496| (extend CG at N-terminus) tara CG6889|FBan0006889|CT19738| thioredoxin CG3864|FBan0003864|CT12877| TO42 matches CG-less sequence on AE002799 and AE003122 (1st 335 bp match CG-less sequence on AE002799, bp 643-1288 match AE003122 and overlap with CG17452|FBan0017452|CT34185| which is on the opposite strand (do NOT merge with CG17452)). Trio CG9208|FBan0009208|CT8909| Tunen CG8805|FBan0008805|CT3034| (CG missing N-terminus) unknown-telomeric-protein-gene matches CG-less sequence on AE003163 No good BLASTP match vanin-like CG3648|FBan0003648|CT12241| (C-terminus to be fixed) vav CG7893|FBan0007893|CT23780| veg CG6657|FBan0006657|CT20658| ventrally-expressed-protein-D matches CG-less sequence on AE003457, No good BLASTP match vhl CG13221|FBan0013221|CT32465| yip2 CG4600|FBan0004600|CT14747| yip3 CG13549|FBan0013549|CT32924| yip6 CG17489|FBan0017489|CT38667| (yip6 partial CDS) yip7 CG6457|FBan0006457|CT19127| (yip7 partial CDS) Zyx102EF matches CG-less sequence on AE003846, No good BLASTP match
