Table 3.
CRE and TATA elements in selected clock genes
| Ensembl gene ID | Gene name | Number of conserved CRE elements within the promoter sequence * | Genomic positions of upstream CRE elements in mouse promoter relative to start codon (ATG starts at position +1) | Genomic positions of TATA boxes if any |
| ENSMUSG00000020038 | Cry1 | 1 | -600 to -580 | No TATA |
| ENSMUSG00000068742 | Cry2 | 1 | -262 to -242 | No TATA |
| ENSMUSG00000029238 | Clock | No CRE *** | N/A | -472 to -469 **** |
| ENSMUSG00000055116 | Bmal1 | No CRE | N/A | No TATA |
| ENSMUSG00000020889 | Rev-erb-alpha (Nr1d1) | No CRE | N/A | No TATA |
| ENSMUSG00000032238 | Ror-alpha (Rora) | No CRE | N/A | No TATA |
| ENSMUSG00000022433 | Casein kinase 1 epsilon (Csnk1e) | No CRE | N/A | No TATA |
| ENSMUSG00000025162 | Casein kinase 1 delta (Csnk1d) | 1 | -330 to -310 (4) ** |
-570 to -567 |
* 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. *** Only mouse and human promoters had predicted CREs; however, these CREs were located in different positions and therefore we did not consider them as being evolutionary conserved. **** Multiple TATA boxes were identified in each species; however, not all of them were evolutionary conserved in all sequences. TATA box shown was shared between four out of five species because dog genomic sequence was not available in that region.