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Table 2 Conservation of CRE and TATA elements in light-induced genes

From: Identification of novel light-induced genes in the suprachiasmatic nucleus

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
  1. * 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.