Table 2.
Occurrence list of enriched motifs and modules in early and late auxin-inducible promoters from A. thaliana
| combination | ORDER | 0.5 h UP (179) | 1 h UP (250) | 3 h UP (398) | ||
|---|---|---|---|---|---|---|
|
singles |
1 |
AUX2 (134) |
1 |
GRE (172) |
1 |
GRE (273) |
| |
2 |
GRE (123) |
2 |
MYC2 (136) |
2 |
MYC2 (197) |
| |
3 |
AUX1 (93) |
3 |
AUX1 (129) |
3 |
RY (27) |
| |
4 |
MYC2 (91) |
|
.. |
|
.. |
| |
|
.. |
1* |
AUX2 (181) |
|
.. |
|
bipartite |
1 |
GRE-AUX2 (33) |
1 |
GRE-MRE2 (122) |
1 |
GRE-MRE2 (188) |
| |
2 |
GRE-MRE1 (32) |
2 |
GRE-AUX2 (43) |
2 |
MRE1-GRE (65) |
| |
3 |
MYC2-AUX2 (27) |
3 |
AUX2-GRE (39) |
3 |
MYC2-AUX2 (42) |
| |
4 |
AUX2-MYC2 (23) |
4 |
MYC2-AUX2 (34) |
4 |
GRE-MYC2 (37) |
| |
5 |
GRE-AUX1 (21) |
5 |
GRE-AUX1 (32) |
5 |
AUX2-MYC2 (35) |
| |
6 |
AUX1-MYC2 (14) |
6 |
AUX2-MYC2 (28) |
6 |
GRE-AUX1 (31) |
| |
7 |
MYC2-AUX1 (13) |
7 |
AUX1-MYC2 (17) |
7 |
AUX1-MYC2 (20) |
| |
8 |
MRE2-RY (9) |
8/9 |
RY-MRE2 (13) |
8 |
RY-MRE2 (18) |
| |
|
.. |
8/9 |
MYC2-AUX1 (13) |
9 |
MRE2-RY (15) |
| |
|
.. |
10 |
MRE2-RY (11) |
|
.. |
|
tripartite |
1 |
GRE-AUX2-MRE2 (22) |
1 |
GRE-AUX2-MRE2 (27) |
|
.. |
| |
2 |
GRE-AUX1-MRE2 (15) |
2 |
GRE-AUX1-MRE2 (20) |
|
.. |
| |
3 |
MRE2-GRE-AUX1 (13) |
3 |
MRE2-GRE-AUX1 (19) |
|
.. |
| 4 | GRE-AUX2-MRE1 (8) | 4 | GRE-AUX2-MRE1 (9) | .. |
Enrichment of cis-elements in the promoters of significantly (2-fold) auxin-induced genes determined by parameter I. The analysis discriminates between early (0.5 – 1 h) or late (3 h) responding genes. Asterisks indicate enrichment with respect to parameter II. The number of analysed promoters as well as that of promoters containing at least one of the presented motifs or modules is given in parentheses. An extended list of enriched motifs which also considers cis-elements which are present in less than 5% of the analysed promoters can be found in Additional file 3. Presented modules (bipartite, tripartite) exhibit a variable but maximal spacing of 100 bps between each embedded motif. Sequences and abbreviations of cis-elements are given in Table 1.