Identification of novel light-induced genes in the suprachiasmatic nucleus

BMC Neuroscience

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.

ISSN: 1471-2202