Identification of novel light-induced genes in the suprachiasmatic nucleus

BMC Neuroscience

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.

ISSN: 1471-2202