TABLE 2.
Conservation of putative Su(H) binding sites
| Gene | Site | D. melanogaster | D. simulans | D. yakuba | D. erecta | D. ananassae | D. pseudoobsc. | D. virilis | D. mojavensis | D. grimshawi | aAll 8 species |
|---|---|---|---|---|---|---|---|---|---|---|---|
| m1 | Hpc | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | — | — |
| Lc | 6 | 5 | 5 | 5 | — | — | — | — | — | — | |
| Lpc | — | 1 | 1 | 1 | — | — | — | — | — | — | |
| m2 | Hc | 2 | —b | 2 | 2 | 1 | 2 | 2 | 2 | 2 | 1b |
| Hpc | 2c | —b | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | |
| Lc | 5 | —b | 4 | 4 | 2 | 3 | 1 | 2 | 2 | 1b | |
| Lpc | — | —b | — | — | 1 | — | 1 | — | — | —b | |
| HLHm3 | Hc | 3 | 3 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 |
| Hpc | — | — | — | 1 | — | — | — | — | — | — | |
| Lc | 3 | 3 | 3 | 2 | 1 | — | — | — | — | — | |
| Lpc | — | — | — | 1 | — | — | — | — | — | — | |
| m4 | Hc | 3 | 3 | 3 | 3 | 3 | 3 | 3 | 3 | 3 | 3 |
| Lc | 2 | 1 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 1 | |
| HLHm5 | Hc | 4 | 4 | 4 | 4 | 4 | 4 | 4 | 2 | 3 | 2 |
| Hpc | — | — | — | — | — | — | — | 1 | — | — | |
| Lc | 1 | 1 | 1 | 1 | — | 1 | 1 | 1 | 1 | — | |
| Lpc | 1 | ||||||||||
| m6 | Lc | 3 | 2 | 2 | 2 | 2 | 1 | 1 | 1 | 1 | 1 |
| Lpc | — | 1 | — | — | — | — | — | — | — | — | |
| HLHm7 | Hc | 4 | 4 | 4 | 4 | 2 | 4 | 4 | 4 | 4 | 2 |
| Lc | 2 | — | — | — | 1 | 1 | — | — | — | — | |
| Lpc | — | 1 | 1 | 1 | — | — | — | — | — | — | |
| HLHm8 | Hc | 3 | 3 | 3 | 3 | 3 | 3 | 2 | 2 | 2 | 2 |
| Lc | 3 | 3 | 3 | 3 | 1 | — | — | — | — | — | |
| mα | Hc | 5 | 5 | 5 | 5 | 5 | 5 | 5 | 4 | 4 | 4 |
| Hpc | — | — | — | — | — | — | — | 1 | 1 | — | |
| Lc | 1 | 1 | 1 | 1 | — | — | — | — | — | — | |
| HLHmβ | Hc | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| HLHmγ | Hc | 4 | 4 | 4 | 4 | 4 | 4 | 3 | 3 | 3 | 3 |
| Lc | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | |
| HLHmδ | Hc | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 |
| Lc | 2 | 1 | 1 | 1 | 2 | 1 | — | 1 | — | — |
Su(H) binding sites identified in D. melanogaster (Bailey and Posakony 1995; Eastman et al. 1997; Nellesen et al. 1999) are displayed in italics. Conservation of these sites was analyzed for each of eight other species from BLAT outputs and was checked with individual sequences for each species. Non-italic numbers correspond to the quantity of D. melanogaster sites conserved in each species and dashes represent the lack of sites. H, high-affinity sites, YGTGRGAA; L, low-affinity site, RTGRGAR. Sites that conform perfectly to the consensus are designated c and sites that vary from the consensus at 1 or 2 bases are designated pc for partial consensus. Consensus sequences that vary between species, but still maintain conformation to the consensus site are included in the rows designated “c.”
The number of D. melanogaster sites conserved in all eight other species analyzed.
Publicly available D. simulans m2 sequence data are incomplete and thus are not included in this analysis.
Partial consensus sites with the sequence CGTGTGAA, where the underlined T alters from the consensus, have been determined to be bound by Su(H) with high affinity (Nellesen et al. 1999).