Multiple alignments in combination with multiTF were used to analyze the transcription factor binding site distribution of functionally characterized sites
230 kb PAX6 | 155 kb NKX2.5 | 150 kb Pax9/Nkx2.9 | |||
|---|---|---|---|---|---|
| Kleinjan DA, 2004 | Brown CO, 2004 | Santagati F, 2003 | |||
| TFBS | PAX6 | SMAD | GATA | Gli | |
| human | 209 | 2027 | 1834 | 652 | |
| + mouse | 15 | 60 | 82 | 84 | |
| + rat | 15 | 59 | 63 | 61 | |
| + chicken | 3 | 3 | 10 | 5 | |
| + frog | 1 + 1 | 1 + 2 | 2 + 3 | 1 + 1 | |
| + fish* | 1 | 0 | 0 | 1 | |
With each additional species, the number of predicted sites was reduced. The addition of frog and fish mostly identified only the functionally known sites (in bold).
* Fugu rupripes, Fugu tetraodon or zebrafish sequences were used interchangeably based on coverage