Occurrence of shared motifs in Dorsal target enhancers and false-positive clusters
| . | zen 624 bp . | sog 392 bp . | CG 12443 343 bp . | brk 498 bp . | vnd 348 bp . | rho 299 bp . | vn 497 bp . | sim 631 bp . | Phm 443 bp . | Ady 217 bp . | False positives 6612 bp . |
|---|---|---|---|---|---|---|---|---|---|---|---|
| E-box motifs | |||||||||||
| CANNTG | 3 | 1 | 5 | 4 | 3 | 5 | 3 | 5 | 6 | 1 | 43 |
| CAAATG | 1 | 1 | 2 | 0 | 0 | 1 | 0 | 1 | 0 | 1 | 14 |
| CACATG | 1 | 0 | 0 | 2 | 2 | 1 | 1 | 1 | 1 | 0 | 4 |
| CACTTG | 0 | 0 | 1 | 2 | 0 | 2 | 1 | 0 | 0 | 0 | 8 |
| CAGCTG | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 4 |
| CAGTTG | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 5 |
| CAATTG | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 4 |
| CATATG | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 1 | 2 | 0 | 0 |
| CAGGTG | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 1 |
| CATCTG | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 1 |
| CACGTG | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 |
| CACATGT | 0 | 0 | 0 | 2 | 2 | 1 | 1 | 1 | 1 | 0 | 3 |
| Su(H) motifs | |||||||||||
| CGTGGGAA | 0 | 0 | 0 | 1 | 1 | 1 | 1 | 2 | 0 | 0 | 0 |
| TGTGGGAA | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| CGTGAGAA | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| TGTGAGAA | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| YGTGDGAA | 0 | 0 | 0 | 2 | 1 | 1 | 1 | 5 | 0 | 0 | 0 |
| Clustered motifs | |||||||||||
| CTGNCCY | 0 | 0 | 1 | 4 | 3 | 2 | 3 | 1 | 0 | 0 | 9 |
| CTGWCCY | 0 | 0 | 1 | 3 | 3 | 1 | 2 | 1 | 0 | 0 | 2 |
| . | zen 624 bp . | sog 392 bp . | CG 12443 343 bp . | brk 498 bp . | vnd 348 bp . | rho 299 bp . | vn 497 bp . | sim 631 bp . | Phm 443 bp . | Ady 217 bp . | False positives 6612 bp . |
|---|---|---|---|---|---|---|---|---|---|---|---|
| E-box motifs | |||||||||||
| CANNTG | 3 | 1 | 5 | 4 | 3 | 5 | 3 | 5 | 6 | 1 | 43 |
| CAAATG | 1 | 1 | 2 | 0 | 0 | 1 | 0 | 1 | 0 | 1 | 14 |
| CACATG | 1 | 0 | 0 | 2 | 2 | 1 | 1 | 1 | 1 | 0 | 4 |
| CACTTG | 0 | 0 | 1 | 2 | 0 | 2 | 1 | 0 | 0 | 0 | 8 |
| CAGCTG | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 4 |
| CAGTTG | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 5 |
| CAATTG | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 4 |
| CATATG | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 1 | 2 | 0 | 0 |
| CAGGTG | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 1 |
| CATCTG | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 1 |
| CACGTG | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 |
| CACATGT | 0 | 0 | 0 | 2 | 2 | 1 | 1 | 1 | 1 | 0 | 3 |
| Su(H) motifs | |||||||||||
| CGTGGGAA | 0 | 0 | 0 | 1 | 1 | 1 | 1 | 2 | 0 | 0 | 0 |
| TGTGGGAA | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| CGTGAGAA | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| TGTGAGAA | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| YGTGDGAA | 0 | 0 | 0 | 2 | 1 | 1 | 1 | 5 | 0 | 0 | 0 |
| Clustered motifs | |||||||||||
| CTGNCCY | 0 | 0 | 1 | 4 | 3 | 2 | 3 | 1 | 0 | 0 | 9 |
| CTGWCCY | 0 | 0 | 1 | 3 | 3 | 1 | 2 | 1 | 0 | 0 | 2 |
The frequency of specific sequence motifs belonging to the E-box, Su(H) and CTGWCCY motif families are shown for Dorsal target enhancers, as well as the group of 10 false-positive Dorsal clusters (FP-clusters C1-C10, see supplemental data). The combined presence of sequences matching the E-box motif CACATGT, the Su(H)motif YGTGDGAA, and CTGWCCY (each highlighted in yellow) distinguishes the ventral neurogenic ectoderm enhancers (brk, vnd and rho;shaded in gray) from: mesodermal enhancers (Phm and Ady43A),enhancers responsive to the lowest levels of nuclear Dorsal (zen, sogand CG12443), and from the false-positive clusters of Dorsal-binding sites. As described in the text, a genome-wide search for clusters containing each of these motifs identified enhancers for vn and sim,which, like brk, vnd and rho, are responsive to intermediate levels of the Dorsal gradient and are expressed in the ventral neurogenic ectoderm.