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Bayraktaroglu, L. (2000.8.7). Matches of the nc3 class to CGs. 
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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.
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|
        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,
        correct CDS is: AE003731 complement(join(125064..125234,125299..125448,125508..125620,
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
              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
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
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