Table 2.
Conservation of CRE and TATA elements in light-induced genes
| Ensembl gene ID | Gene name | Number of conserved CRE elements* | Genomic positions of CRE elements** | Genomic positions of TATA boxes |
| ENSMUSG00000020423 | Btg2 | 2 | -277 to -257 (3) -259 to -239 |
No TATA |
| ENSMUSG00000024190c | Dusp1 | 2 | -349 to -329 -301 to -281 (4) |
-180 to -175*** |
| ENSMUSG00000038418 | Egr1 | 3 | -925 to -905 -424 to -404 -355 to -335 |
-363 to -360 -686 to -682 |
| ENSMUSG00000037868 | Egr2 | 1 | -414 to -394 | -302 to -298 |
| ENSMUSG00000033730 | Egr3 | 2 | -645 to -625 (2) -592 to -572 |
-599 to -596 |
| ENSMUSG00000021250 | Fos | 3 | -500 to -480 -452 to -432 (2) -225 to -205 (2) |
-183 to -178 |
| ENSMUSG00000015312 | Gadd45b | 1 | -925 to -905 | No TATA |
| ENSMUSG00000052684 | Jun | 2 | -1261 to -1241 -1002 to -982 |
-505 to- 502***** |
| ENSMUSG00000003032 | Klf4 | 2 | -1023 to - 1003 -986 to -966 |
-778 to -774 |
| ENSMUSG00000023034 | Nr4a1 | N/A**** | N/A | No TATA |
| ENSMUSG00000020893 | Per1 | 1 | -355 to -335 (2) |
-500 to -497 |
| ENSMUSG00000055866 | Per2 | N/A | N/A | No TATA |
| ENSMUSG00000035828 | Pim3 | 1 | -686 to -666 (2) |
No TATA |
| ENSMUSG00000031880c | Rrad | 1 | -522 to -502 | No TATA |
| ENSMUSG00000034640 | Tiparp | 1 | -1863 to - 1843 |
-1615 to -1610 |
* We defined CRE element as being evolutionary conserved if it was present in at least 3 out of 5 mammalian genomes (Mouse, Rat, Human, Cow and Dog). ** Number in parenthesis indicates how many overlapping CRE elements were identified in the promoter sequence, however, coordinates of only the first of the overlapping elements are given here. *** Mouse and rat promoters have non-canonical CATAAAA variants instead of canonical TATAA in human, cow and dog. However, this non-canonical variant is known to function in a TATA box-like fashion [56,57]. **** N/A = not applicable, because in Nr4a1 and Per2, no conserved CREs were detected within 2 kb of the promoter sequence. ***** In human sequence TATA box was identified within 300 bp downstream of conserved CRE; however, it was not present in other genomes. See additional file 1 for additional notes for this table.