Table 2.
Pre-transcriptional motifs
| Name | Motif consensus | MEC | MCS | Region* | Known transcription factor† | Multiplicity score‡ | ImaGO enrichment§ | ImaGO score§ |
|---|---|---|---|---|---|---|---|---|
| ME1 | GTCACGTD | 0.448 | 45.41 | PIG | – | – | – | – |
| ME2 | AWNTGGGTCA | 0.393 | 26.97 | PIG | Hr46 | – | Oesophagus (13–16) | 4.52 |
| ME3 | BCATAAATYA | 0.369 | 36.02 | PCEIG | Caudal | – | Ubiquitous (13–16) | −6.22 |
| ME4 | HAATTAYGCRH | 0.365 | 32.71 | PCE5IG | Engrailed | – | – | – |
| ME5 | STATAWAWR | 0.358 | 24.31 | C | TATA | – | Ventral nerve cord (13–16) | −5.1 |
| ME6 | VATTWGCAT | 0.356 | 44.06 | PE5IG | – | 3.73 | Ubiquitous (11–12) | −7.15 |
| ME7 | BYAATTARH | 0.338 | 15.45 | PCE5IG | Engrailed | 7.08 | Ubiquitous (11–12) | −10.26 |
| ME8 | HRTCAATCA | 0.338 | 42.32 | PIG | – | – | Dorsal pharyngeal muscle PR (11–12) | −4.15 |
| ME9 | TGACANNNNNNTGACA | 0.336 | 9 | G | – | – | – | – |
| ME10 | RCGTGNNNNGCAT | 0.329 | 15.94 | PIG | – | – | – | – |
| ME11 | MATTAAWNATGCR | 0.324 | 12.43 | PIG | acj6 | – | Tracheal PR (11–12) | 4.11 |
| ME12 | TTAATGATG | 0.32 | 20.31 | PG | – | – | – | – |
| ME13 | WTGACANBT | 0.318 | 63.45 | PE5IG | – | 4.14 | Ubiquitous (13–16) | −3.97 |
| ME14 | YGACMTTGA | 0.313 | 27.06 | PIG | – | – | Midgut (13–16) | 4.32 |
| ME15 | AATTRNNNNCAATT | 0.309 | 21.17 | PG | – | – | – | – |
| ME16 | TGACGTCAT | 0.304 | 12.24 | PC5IG | CrebA | – | – | – |
| ME17 | MAATTNAATT | 0.304 | 51.57 | PE5IG | – | – | Ubiquitous (11–12) | −6.66 |
| ME18 | MRYTTCCGYY | 0.304 | 39.04 | PEIG | Dorsal | – | Ubiquitous (11–12) | −4.4 |
| ME19 | MATTRRCACNY | 0.303 | 25.24 | PIG | – | – | – | – |
| ME20 | YTAATGAVS | 0.298 | 44.5 | PEIG | – | – | Foregut PR (11–12) | 4.19 |
| ME21 | TAATTRANNTTNATG | 0.294 | 8.67 | G | – | – | – | – |
| ME22 | WAATGCGCNT | 0.291 | 18.17 | G | – | – | – | – |
| ME23 | MATTWRTCA | 0.288 | 46.25 | PEIG | – | – | Dorsal epidermis PR (11–12) | 4.4 |
| ME24 | YAATTWNRYGC | 0.287 | 30.91 | PG | – | 4.27 | Ubiquitous (11–12) | −4.79 |
| ME25 | TTAYGTAA | 0.283 | 13.06 | 5 | Giant | – | Midgut (13–16) | 5.32 |
| ME26 | YGCGTHAATTR | 0.283 | 13.61 | PEG | – | – | – | – |
| ME27 | AATTRYGWCA | 0.28 | 22.85 | PEIG | – | – | Pericardial cell (13–16) | 4.1 |
| ME28 | GCGCATGH | 0.28 | 30.17 | PCEG | – | – | Ventral nerve cord PR (11–12) | 5.75 |
| ME29 | WAATCARCGC | 0.275 | 13.82 | G | – | – | – | – |
| ME30 | AATTAANNNNNCATNA | 0.271 | 16.44 | G | Antennapedia | – | – | – |
| ME31 | GCGTSAAA | 0.271 | 29.95 | PG | – | – | – | – |
| ME32 | YGCGYRTCAWT | 0.269 | 12.87 | G | – | – | – | – |
| ME33 | GCGTTGAYA | 0.269 | 15.1 | PG | – | – | – | – |
| ME34 | AAATKKCATTA | 0.266 | 14.04 | PG | – | – | – | – |
| ME35 | RACASCTGY | 0.266 | 28.38 | PCEG | Scute | – | Ventral sensory complex SA (11–12) | 4.08 |
| ME36 | TGTCAATTG | 0.265 | 12.65 | PG | – | – | Tracheal system (13–16) | 4.56 |
| ME37 | WAATKNNNNNCRCGY | 0.261 | 23.34 | PEG | – | – | – | – |
| ME38 | CASGTAR | 0.261 | 9.24 | PEG | Single-minded | 4.58 | Ventral epidermis PR (11–12) | 7.41 |
| ME39 | WCACGTGC | 0.26 | 10.54 | PCE5IG | Enhancer of split | – | – | – |
| ME40 | CATTANNNWAATT | 0.259 | 19.02 | G | – | – | – | – |
The top 40 of 145 are shown. MEC, motif excess conservation; MCS, motif conservation score. See Supplementary Table 5c for the full table.
*
Region where the motif was found: P, promoter, C, core promoter; E, enhancers; 5, 5′ UTR; I, intron; G, intergenic genome.
†
The known transcription factor motif matching the consensus sequence.
‡
A multiplicity score is reported for motifs with many repeated occurrences.
§
Tissue where motif is most strongly enriched or depleted, and corresponding score (positive, enrichment; negative, depletion). PR, primordium; SA, specific anlage.