Table IV.
Conserved motifs in promoters of Arabidopsis and poplar CYCD genes
Comparisons were made using WeederH as described in the text and “Materials and Methods.” Scores and positions of the sequences relative to the ATG start codon in Arabidopsis CYCD are shown, as well as putative matches to known transcription factor binding sites. The prevalence of the sequence within the Arabidopsis genome is also given.
| CYCD Subgroup | Comparison | Motif | Score | Position | No. of Hits (The Arabidopsis Information Resource) | Putative Binding Site (Plant Care) |
|---|---|---|---|---|---|---|
| CYCD1 | Arabidopsis versus best poplar | TAACCGTCTCTC | 32.4704 | −135 | 5 | Not found |
| GCAACAACACCA | 18.7287 | −113 | 15 | Not found | ||
| ATAAATAAAAAC | 17.525 | −96 | 157 | TATA box element | ||
| CYCD2 | Arabidopsis versus all poplar | TTACTTTG | 15.832 | −948 | 2,478 | DNA-binding protein of sweet potato (Ipomoea batatas) that binds to the SP8a |
| (ACTGTGTA) and SP8b (TACTATT) sequences of sporamin and β-amylase genes | ||||||
| GGTGGTAG | 12.2088 | −645 | 431 | Zinc-finger protein in alfalfa (Medicago sativa) roots, regulates salt tolerance | ||
| ACGTTACC | 11.5886 | −440 | 381 | Trihelix DNA-binding factor GT-3a | ||
| AGGTGTTTAAGA | 11.0741 | −930 | 7 | Not found | ||
| TAATTAACTTAA | 10.8628 | −795 | 45 | SBF-1 | ||
| TGACAAAATATT | 10.1763 | −780 | 45 | Not found | ||
| CYCD3 | Arabidopsis versus all poplar | TTTCACGC | <0.001 | (Consensus) | 465 | E2F class I sites |
| TTTCTCGCGC | <0.001 | (Consensus) | 13 | E2F class I sites | ||
| CYCD5 | Arabidopsis versus best poplar | TTTGGCGGCACC | 56.5282 | −189 | 3 | E2F complex |
| TAACCGCT | 28.5116 | −229 | 362 | MSA, mitosis-specific activator | ||
| CAAATAAAACCT | 15.346 | −278 | 15 | ccaat/tata box like | ||
| AACTAAATGATT | 15.0417 | −926 | 24 | Storekeeper, plant-specific DNA-binding protein important for tuber- specific and Suc- inducible gene expression | ||
| CYCD6 | Arabidopsis versus best poplar | TTAAATAC | 25.571 | −417 | 2,595 | L1-specific homeodomain protein Arabidopsis MERISTEM LAYER1 |
| AAACAACT | 17.3557 | −622 | 2,849 | CA-rich element | ||
| TCTAATAAAAAC | 16.0271 | −665 | 24 | Not found | ||
| TTATGAATATTT | 13.199 | −569 | 54 | Not found | ||
| TTATAAAAACAC | 11.5132 | −493 | 31 | TATA box element | ||
| CYCD7 | Arabidopsis versus poplar | ATTTACCGCGTTTCA TGTGGGACG | 34.1076 | −467 | 1 | Tobacco GT1/rice GT2 AT CAMTA3 AT RAP1 |
| CGACGTCT | 19.0557 | −445 | 257 | OCS-like elements; bZIP transcription factor from Antirrhinum majus | ||
| TTAAAGCT | 15.3937 | −931 | 1,736 | Dof2, single zinc finger transcription factor | ||
| CGTGGACTCACG | 12.6834 | −569 | 2 | Not found | ||
| CACCAGTTTCAT | 11.3275 | −1,000 | 7 | Not found | ||
| CYCD3/6 | With coexpressed genes | TTTCCCGCGC | <0.001 | (Consensus) | E2F binding site |