Legend for Supplementary Figure S1
Conserved Su(H), proneural, bHLH repressor and MatInspector identified
transcription factor binding site sequences upstream of the E(spl) genes. Multispecies Conserved Sequence (MCS) were identified in EvoPrint outputs representing nine
Drosophila species (D. melanogaster, D. simulans, D. yakuba, D. erecta, D. ananasse, D.
pseuodoobscura, D. virilis, D. mojavensis and D. grimshawi) and scanned for consensus
sites. Capital letters represent sequences conserved in all nine species. Specific
sequences for sites are underlined and are presented in the context of the MCS where
they are located. MCS numbers are based on the distance upstream from the putative
transcription start sites (NELLESEN et al. 1999). Sites containing a modification from the
consensus sequence are denoted with an asterisk. Su(H) paired sites are designated SPS.
Sites are color-coded: Su(H) sites are orange, proneural sites are red, bHLH repressor
sites are blue and MatInspector identified transcription factor binding sites are all in
green.
Supplementary Figure S1
m1
Paired
Class B Ebox
Su(H)1
-1198 GCGGCCTTCGcGTGCGTGACgaGCATtCGCTTAGCGGTCATTGATTGGCC-1147
-1198 GCGGCCTTCGcGTGCGTGACgaGCATtCGCTTAGCGGTCATTGATTGGCC -1147
-1115 AGGGCGCCGtcAGCAACAAGTGTGT*GAACACcATTAAaCGGTGaTTAG-1071
1
GTGT*GAA site is a modified consensus site (* indicates T versus G), however Nellesen et al
determined that Su(H) binds the site with high affinity. This site is categorized as a partial consensus high
affinity site (Hpc) in Table 2 of the manuscript. This site is present in all species examined except D.
grimshawi.
m2
Chorion factor
Su(H)1 high affinity
Broad Complex Z2
Proneural Ac/Sc
Su(H) high affinity
Proneural Atonal
E74A
Snail
Su(H)1 high affinity
Doublesex
Dorsal
Su(H) low affinity
N box
Su(H)2 low affinity
Zeste
CF2-II
Crocodile
-1326 AGGTCAcGGCCTCATTA -1309
-1221 GGAGCGTGT*GAa -1209
-1138 GAGCCTGATTATAAATGACAACAAACAGGCcAACAAGTAGCAAtAACAGCTGCTC -1083
-1138 GAGCCTGATTATAAATGACAACAAACAGGCcAACAAGTAGCAAtAACAGCTGCTC -1083
-1025 AACAACAAtAATagtgccccgaaAAAAgCCGAAAAcCCAAGTGAAATTCTTATAAGCCCTTTCCCACACTCG -953
-833 AAgGGAACAGGTGCt -818
-874 CCAGGACGGAAAT -861
-833 AAgGGAACAGGTGCt -818
-693 GGGTACCGTGT*GAATGTgAAAACAAAGTCAGTCGTGCATAAATGACG -676
-693 GGGTACCGTGTGAATGTgAAAACAAAGTCAGTCGTGCATAAATGACG -676
-693 GGGTACCGTGTGAATGTgAAAACAAAGTCAGTCGTGCATAAATGACG -676
-351 CATCTACCTGCAGCCaAAACTCATCAAgCGGCCCTTGTCGATTGTACGTGCATGGGAAAAGTACACACA -282
-270 GCTTGTgGATTCCTGTTGGAATTTATTTGGGAAATACGCGCACATAAAA -221
-144 g*TGAGAGTGCACTCAAATTTCGTACgGTGCT -113
-144 gTGAGAGTGCACTCAAATTTCGTACgGTGCT -113
-38 GcCTCATATATAAATATGAGCG -16
-38 GcCTCATATATAAATATGAGCG -16
GTGT*GAA site is a modified consensus site (* indicates T versus G), however NELLESEN et al. (1999)
determined that Su(H) binds the site with high affinity. This site is categorized as a partial consensus high
affinity site (Hpc) in Table 2 of the manuscript.
1
2
The low affinity consensus site is completely conserved in D. yakuba, D. erecta, D. anannase, D.
pseudoobscura, and D. grimshawi, but is modified to a partial consensus site (G to T designated with an
asterisk) in D. mojavensis and D. virilis.
HLHm3
Hunchback
Caudal
Paired
Ftz
Adf-1
SPS
-1783 AAAAAacAGGCAACATTTTaTACAC -1758
-1783 AAAAAacAGGCAACATTTTaTACAC -1758
-1547 AATCGATAcgCTtcAACGAAA -1526
-1547 AATCGATAcgCTtcAACGAAA -1526
-1138 CAGCAAcAACATTTCAGCAATCCATCGGATCGCATCACAATCCAGCCATCCGTCCAACG
TGTGGGAAACACACGACAAATCTGTTTCCCACGGTCTCGTAAAGTAGGCACaccgCACACAC -1017
-1138 CAGCAAcAACATTTCAGCAATCCATCGGATCGCATCACAATCCAGCCATCCGTCCAACG
TGTGGGAAACACACGACAAATCTGTTTCCCACGGTCTCGTAAAGTAGGCACaccgCACACAC -1017
m4
Snail
Ftz
Croc
Paired
Krueppel
Ftz
Class C Ebox-Hairy
Ftz
Ftz
Ftz
Deformed
Dead ringer
Ftz
Snail
Su(H) low affinity
Class B E box
BRCZ1
Caudal
Snail
Escargot
SPS
Proneural Ac/Sc
Su(H) high affinity
-1235 atCTGtTAACGCCAGCCTACAacTTCTCACC -1206
-1196 CTTAATTTGTC -1185
-1168 AAATATTTAT -1157
-1141 CAATCCATTAAGtAC -1126
-1141 CAATCCATTAAGtAC -1126
-1141 CAATCCATTAAGtAC -1126
-1032 CGCCTCACGCGCCATCA -1015
-895 CTGCTAATTGT -884
-868 AAATTAAAAGCAACTCCTTC -848
-779 AaTTTgATAAATTTcAAATTACAGCGCATTAAat -747
-636 CATTAATTGTT -625
-636 CATTAATTGTT -625
-636 CATTAATTGTT -625
-574 TGCACACGTGTTC -561
-571 GTTCgAGCGTTGAAAATTGAAAATaTTCTCCCACGT -532
-524 TGCACACGTGTTC -511
-475 ATAAAAACCAAAAGTGATC -456
-475 ATAAAAACCAAAAGTGATC -456
-334 ttcaaCAGGTGcgAG -319 check
-334 ttcaaCAGGTGcgAG -319 check
-340 ACTGTGGGAACTGgTaGAAAGTCTCGtTTCTCACGATCCTG -295
-184 AAACACACCTGCCGTTTTT -161
-114 CACGTATCCTTGTAgTTTCCCACACTCG -82
HLHm5
Ftz
Su(H) low affinity
c-rel
Deformed
Ftz
Proneural-Ac/Sc
Class C Ebox/Hairy
SPS
Paired
1
-1413 TTCAATTAGCcCATGTCGTAAAGTACAAATAACTATTGCGtACA -1369
-1258 CGACAAGAGtGaAAAACTAAAGTAAAGCAG -1228
-1258 CGACAAGAGtGaAAAACTAAAGTAAAGCAG -1228
-1258 CGACAAGAGtGaAAAACTAAAGTAAAGCAGgcAGtAATCAGT -1216
-946 TGTAATCGtAACCATATAAGCGtCTTAAATGGCAGGTGTGCACATCGCGTGGGAAACACACGACG -881
-946 TGTAATCGtAACCATATAAGCGtCTTAAATGGCAGGTGTGCACATCGCGTGGGAAACACACGACG -881
-946 TGTAATCGtAACCATATAAGCGtCTTAAATGGCAGGTGTGCACATCGCGTGGGAAACACACGACG -881
-946 TGTAATCGtAACCATATAAGCGtCTTAAATGGCAGGTGTGCACATCGCGTGGGAA
ACACACGACGcgtCtcGAGCgGTTCTCACGATATGAAAATCGAGCAA -844
-875 GAGCgGtTCTCACGATATGAAAATCGAGCAA -844
The consensus site is conserved in all species examined except for D. ananassae, which contains a partial
consensus with two modifications.
m6
Ftz
-468 GGGCTGTGGCCTAAATTGCAAaCAGCTGCCACTCGAACCGTGGGATActTTTtCCCCTA -409
Zeste
-468 GGGCTGTGGCCTAAATTGCAAaCAGCTGCCACTCGAACCGTGGGATActTTTtCCCCTA -409
Proneural Ac/Sc
-468 GGGCTGTGGCCTAAATTGCAAaCAGCTGCCACTCGAACCGTGGGATActTTTtCCCCTA -409
Dorsal
-468 GGGCTGTGGCCTAAATTGCAAaCAGCTGCCACTCGAACCGTGGGATActTTTtCCCCTA -409
Su(H) low affinity
-354 CGAACCTTATCCATGGGAACCACAACTGCTCaACGCTCTCAATATTTAtT -304
Trithorax-like (GAGA)
Croc
Class B Ebox
Snail
-354 CGAACCTTATCCATGGGAACCACAACTGCTCaACGCTCTCAATATTTAtT -304
-354 CGAACCTTATCCATGGGAACCACAACTGCTCaACGCTCTCAATATTTAtT -304
-217 GATTATCCTGCACGTGTTGAGCTTGCT -190
-217 GATTATCCTGCACGTGTTGAGCTTGCT -190
The majority of m6 bHLH repressor sites are found outside of MCSs, consequently the sites reported here
do not represent all of the consensus sites found in multiple species (see Table 4 for the total number of
sites).
1
The conserved Ac/Sc proneural site is a partial consensus site in D. melanogaster, D. simulans, D.
yakuba, D. erecta, D. ananassae, D. pseudoobscura, and D. persimillis, however it is a consensus site in D.
virilis, D. mojavensis and D. grimshawi.
HLHm7
Dorsal
N box
SPS
Class B Ebox
-709 CGATTATAACTTATAACACCAACgAGCGAGAAAATCTTGTGGGAAACTTGAGGGCA
AAGTGTTTCCCACGATTCGAA -631
-709 CGATTATAACTTATAACACCAACgAGCGAGAAAATCTTGTGGGAAACTTGAGGGCA
AAGTGTTTCCCACGATTCGAA -631
-709 CGATTATAACTTATAACACCAACgAGCGAGAAAATCTTGTGGGAAACTTGAGGGCA
AAGTGTTTCCCACGATTCGAA -631
-43 GGCACGTGCAGCTATAAAAGCaGcgGTAACcGGAGA -7
All species examined contain at least one consensus Ac/Sc proneural site, however the site(s) are not
present in MCSs and are thus not represented here (See Table 3 for the total number of sites).
HLHm8
Ftz
Dorsal
Dorsal
SPS
-394 CGACAGGATGAGGCAgTGAAGTATGCATTAAGGATAATAACACCGG -348
-257 AGCGAAGCATGTGGCCAAAAgGgAAAACAAACGAGAAAAAATTGTGTGAGAAACTTACTTTCAGcTC -190
-257 AGCGAAGCATGTGGCCAAAAgGgAAAACAAACGAGAAAAAATTGTGTGAGAAACTTACTTTCAGcTC -190
-324 AGCGAAGCATGTGGCCAAAAgGgAAAACAAACGAGAAAAAATTGTGTGAGAA
ACTTACTTTCAGcTCGGTTCCCACGCCACGAGCCACAAGGATTGT-160
N box
-324 AGCGAAGCATGTGGCCAAAAgGgAAAACAAACGAGAAAAAATTGTGTGAGAA
ACTTACTTTCAGcTCGGTTCCCACGCCACGAGCCACAAGGATTGT-160
-324 AGCGAAGCATGTGGCCAAAAgGgAAAACAAACGAGAAAAAATTGTGTGAGAA
ACTTACTTTCAGcTCGGTTCCCACGCCACGAGCCACAAGGATTGT-160
-144 TTGCAGCTGTTCC -131
N box
Proneural Ac/Sc
m
Deformed
Deformed
PAX6 P3
Su(H) high affinity
Su(H) high affinity
Su(H) high affinity
Proneural- Ac/Sc
Dorsal
- 898 AATTAATTAAAATATCTatA -878
- 898 AATTAATTAAAATATCTatA -878
- 898 AATTAATTAAAATATCTatA -878
-759 TGTGGGAAAGTT -747
-632 TgTGGgAATGCGTGGGAAT -613
-482 CGTGAGAAATTTTACcAAGGAACACCTGCC -452
-482 CGTGAGAAATTTTACcAAGGAACACCTGCC -452
-348 CgAAAAATTGTTTCCCACACT -327
Su(H) high affinity
-348 CgAAAAATTGTTTCCCACACT -327
HLHm
Ftz
Paired
Heat shock factor
Paired
Paired
Paired
Su(H) high affinity
Adf-1
N box
-826 CAATCAAGAATAATCATGTAAACGAAAAGCGTAATGCT -788
-826 CAATCAAGAATAATCATGTAAACGAAAAGCGTAATGCT -788
-826 CAATCAAGAATAATCATGTAAACGAAAAGCGTAATGCT -788
-826 CAATCAAGAATAATCATGTAAACGAAAAGCGTAATGCT -788
-766 CCACGATCCAATCAATGATCCATAAAGCGcTaacAAAAAA -726
-766 CCACGATCCAATCAATGATCCATAAAGCGcTaacAAAAAA -726
-322 CGTCGTGGAAAtcGGCTGCGAAACAGTTTCCCACGGTATAACAATCACA -273
-96 GCAGCAGGCcGCGCACGAGGCAAAAtGaGtgTCcCgCTCGCACTC -61
-96 GCAGCAGGCcGCGCACGAGGCAAAAtGaGtgTCcCgCTCGCACTC -61
HLHm
Ftz
N box
Su(H) high Affinity
Proneural Ac/Sc
E74A
BCZ1
Su(H) low affinity
Proneural Ac/Sc
SPS
Ttk69
Knirps
E74A
-709 gcATTAAGCgCACTCGaCGCACACGAGCAATGTTCCCACAGGAtCAT -662
-707ATTAAGCgCACTCGaCGCACACGAGCAATGTTCCCACAGGAtCAT -662
-707ATTAAGCgCACTCGaCGCACACGAGCAATGTTCCCACAGGAtCAT -662
-410 CAAATCATAacACAcaAATCTAGAAAcGGCAGCTG -375
-571 AAACAGGAAGT -560
-410 CAAATCATAacACAcaAATCTAGAAAcGGCAGCTG -375
-365 AAATTCCCAT -355
-318 GCAGGTGAGC -308
-301 TGTGAGAAACCgAGtagGAAaGtGtTTCCCACGATcCTgGCAGCGaTCCTGCTCCCT -244
-301 TGTGAGAAACCgAGtagGAAaGtGtTTCCCACGATcCTgGCAGCGaTCCTGCTCCCT -244
-216 ACAATAAGAAatCGccCgAACAATAAG -189
-175 AGCGGAAGG -166
HLHm
Proneural Ac/Sc1
N box
SPS
N box
Class B E box
N box
1
-1418 GCGCCAAACAAGTGtCA*CAGCTGACC -1392
-1350 ATCCCAATACTTGTGGGAATGtcTccAGTAcACTTTCTCACGATG -1305
-1350 ATCCCAATACTTGTGGGAATGtcTccAGTAcACTTTCTCACGATG -1305
-603 GCACGAG -596
-185 TGCACACGTGCA -173
-159 TTGCCaCAAgCAGAG -149
The partial consensus site for Ac/Sc (A versus G designated with an asterisk) is conserved in all eight
species examined.