Table III. Intramotif SNP density for 20 selected cis-element motifs from AGRIS, Athena, and PLACE.
The top- and bottom-10 nonredundant cis-motifs, which were found at least 1,000 times in the sequence interval between −500 nt and the TSS with respect to the TSS, were selected according to their intramotif SNP density. Functional associations were taken from the ProFITS database (Ling et al., 2010). Motifs were required to not contain any ambiguity codes in their motif definitions, to ensure that detected intramotif SNPs correspond to true deviations from the motif and are not merely predefined acceptable variations of the same motif. For example, the motif CARGCW8GAT, sequence CWWWWWWWWG, was found with high SNP density likely caused by the loosely defined motif sequence alone. The motifs are listed with their motif sequences, including ambiguity codes, motif and SNP counts, and intramotif SNP density (i.e. the number of SNPs in a specific motif divided by the number of mappings of this motif times its length).
| SNP Status | Motif Name | Motif Sequence | Length | Motif Hits | No. of SNPs | SNP Density | ProFITS Annotation |
|---|---|---|---|---|---|---|---|
| SNP poor | G-box promoter motif | CACGTG | 6 | 3,675 | 248 | 0.011 | Fos-related oncoproteins |
| TELO-box promoter motif | AAACCCTAA | 9 | 2,020 | 249 | 0.014 | Activation of expression in root primordia | |
| UP2ATMSD | AAACCCTA | 8 | 3,473 | 391 | 0.014 | Axillary bud outgrowth | |
| GADOWNAT | ACGTGTC | 7 | 2,073 | 232 | 0.016 | GA-down-regulated genes found in Arabidopsis seed germination | |
| ANAERO3CONSENSUS | TCATCAC | 7 | 2,735 | 316 | 0.017 | Anaerobically induced transcription | |
| AtMYC2 BS in RD22 | CACATG | 6 | 7,315 | 729 | 0.017 | Dehydration-responsive gene; ABA induction, water stress | |
| MYCATERD1 | CATGTG | 6 | 7,315 | 729 | 0.017 | Water stress | |
| SORLIP5 | GAGTGAG | 7 | 1,523 | 179 | 0.017 | Light-Induced transcription | |
| LTRE promoter motif | ACCGACA | 7 | 899 | 114 | 0.018 | Putative low-temperature-responsive element | |
| AtMYB2 BS in RD22 | CTAACCA | 7 | 2,081 | 266 | 0.018 | Dehydration-responsive gene; ABA induction, water stress | |
| SNP rich | TATA-box motif | TATAAA | 6 | 42,104 | 5,663 | 0.022 | Process of transcription by RNA polymerase |
| T-box promoter motif | ACTTTG | 6 | 12,852 | 1788 | 0.023 | Light-activated transcription | |
| ANAERO2CONSENSUS | AGCAGC | 6 | 2,554 | 369 | 0.024 | Anaerobically induced transcription | |
| ASF1MOTIFCAMV | TGACG | 5 | 13,173 | 1,606 | 0.024 | Involved in transcriptional activation of several genes by auxin and/or salicylic acid; may be relevant to light regulation | |
| Bellringer BS1 IN AG | AAATTAAA | 8 | 8,137 | 1,620 | 0.025 | Floral meristem, carpel, and stamen development | |
| RAV1-B binding site motif | CACCTG | 6 | 1,975 | 299 | 0.025 | Auxin- and salicylic acid-induced transcription; light-regulated transcription | |
| LEAFYATAG | CCAATGT | 7 | 1,623 | 290 | 0.026 | Floral meristem development | |
| LTRECOREATCOR15 | CCGAC | 5 | 8,606 | 1,207 | 0.028 | ABA, cold, and drought stress-induced transcription | |
| MYB2AT | TAACTG | 6 | 5,479 | 991 | 0.030 | Water stress | |
| Hexamer promoter motif | CCGTCG | 6 | 1,855 | 370 | 0.033 | Mersitem development, histone regulation |