Table I.
The putative HY5 binding sites predicted by RBSS from genes involved in hormone signaling
Genes implicated in auxin or cytokinin pathways are arranged according to Cluis et al. (2004).
| Gene Namea | Gene Identificationb | HBACGTVDc | In Vivo HY5 Targetd | Sequence and Locationf | Classificationg | |
|---|---|---|---|---|---|---|
| Auxin-related genes | ||||||
| Auxin carriers | ||||||
| AUX1 | At1g77690 | Yesc | 1 e | 134 AGACACGTGTGG 145 | G-box | |
| EIR1/PIN2 | At5g57090 | Yes | 1 | 66 AATCACGTGGCG 77 | G-box | |
| PID | At2g34650 | Yes | Yes | 2 | 790 TCACACGTGTCA 801 | G-box |
| 806 TCTTACGTCATC 817 | C/A-box | |||||
| PIN1 | At1g73590 | Yes | Yes | 1 | 813 CTACACGTAAAC 824 | G/A-box |
| REH1/PIN3 | At1g70940 | Yes | Yes | 1 | 949 GGTCACGTATTT 960 | G/A-box |
| PIN4 | At2g01420 | Yes | 1 | 850 TGCCACGTGTCC 861 | G-box | |
| Auxin response factors | ||||||
| ARF4 | At5g60450 | Yes | 2 | 605 GGTTACGTCAAT 616 | C/A-box | |
| 716 TTTGACGTATTT 727 | C/A-box | |||||
| ARF6 | At1g30330 | Yes | Yes | 1 | 94 AAACACGTATAT 105 | G/A-box |
| ARF18 | At1g23750 | Yes | Yes | 2 | 771 TTTTACGTAAGA 782 | A-box |
| 926 GTACACGTGTTA 937 | G-box | |||||
| ARF11 | At2g46530 | Yes | 2 | 480 TAACACGTGAAA 491 | G-box | |
| 937 CGACACGTAGTT 948 | G/A-box | |||||
| ARF19 | At1g19220 | Yes | Yes | 2 | 73 GCATACGTAGAG 84 | A-box |
| 826 TGCCACGTCAGA 837 | C/G-box | |||||
| MP/ARF5 | At1g19850 | Yes | Yes | 2 | 605 GATTACGTGTGC 616 | G/A-box |
| 637 TTTGACGTAAAC 648 | C/A-box | |||||
| IAA genes | ||||||
| IAA3/SHY2 | At1g04240 | Yes | Yes | 4 | 54 TTACACGTATAA 65 | G/A-box |
| 201 AAAGACGTAAAC 212 | C/A-box | |||||
| 436 ATATACGTGTGT 425 | G/A-box | |||||
| 530 TGTCACGTAGGC 541 | G/A-box | |||||
| IAA5 | At1g15580 | Yes | 4 | 389 GATTACGTATGA 400 | A-box | |
| 504 TGTTACGTGTAG 515 | G/A-box | |||||
| 567 TAACACGTGTTC 556 | G-box | |||||
| 586 ATATACGTAGAT 597 | A-box | |||||
| IAA6/SHY1 | At1g52830 | Yes | 1 | 443 ATAGACGTGTCC 454 | C/G-box | |
| IAA7/AXR2 | At3g23050 | Yes | 3 | 88 TACTACGTCAGA 99 | C/A-box | |
| 573 TACCACGTAACT 584 | G/A-box | |||||
| 914 GCCCACGTGTCA 903 | G-box | |||||
| IAA8 | At2g22670 | Yes | Yes | 1 | 467 CGATACGTGGTC 478 | G/A-box |
| IAA9 | At5g65670 | Yes | 1 | 228 CGTGACGTAACC 239 | C/A-box | |
| IAA10 | At1g04100 | Yes | 1 | 203 CAACACGTCTGC 214 | C/G-box | |
| IAA14/SLR | At4g14550 | Yes | 2 | 441 TGATACGTGAAG 452 | G/A-box | |
| 784 GGCCACGTGTTG 795 | G-box | |||||
| IAA15 | At1g80390 | Yes | 1 | 542 CGTGACGTGGGA 553 | C/G-box | |
| IAA17/AXR3 | At1g04250 | Yes | Yes | 1 | 933 ATCCACGTGTCT 944 | G-box |
| IAA19/MSG2 | At3g15540 | Yes | 1 | 905 CTCCACGTGTCG 916 | G-box | |
| IAA20 | At2g46990 | Yes | 1 | 744 TGACACGTGTTT 755 | G-box | |
| IAA27/PAP2 | At4g29080 | Yes | 1 | 864 AATTACGTATAC 875 | A-box | |
| IAA28 | At5g25890 | Yes | 2 | 571 GGACACGTCTAG 582 | C/G-box | |
| 863 ATACACGTATGT 874 | G/A-box | |||||
| IAA30 | At3g62100 | Yes | 4 | 90 AGCGACGTGGAT 101 | C/G-box | |
| 149 GTCCACGTAGAC 160 | G/A-box | |||||
| 230 TGAGACGTGTTT 219 | C/G-box | |||||
| 794 TGACACGTGTAT 805 | G-box | |||||
| Other auxin signaling genes | ||||||
| AXR6/CUL1 | At4g02570 | Yes | 1 | 102 ATATACGTAATT 113 | A-box | |
| NAC1 | At1g56010 | Yes | Yes | 3 | 282 GTCCACGTCTTT 293 | C/G-box |
| 398 GACTACGTCGAC 409 | C/A-box | |||||
| 560 AGACACGTAAAA 549 | G/A-box | |||||
| SAUR-AC1-like | At3g60690 | Yes | Yes | 2 | 604 TGCCACGTGGGT 615 | G-box |
| 617 TCACACGTGTGA 628 | G-box | |||||
| SAUR-AC1-like | At3g61900 | Yes | 2 | 127 CCATACGTGGGC 138 | G/A-box | |
| 255 TTCCACGTATCA 266 | G/A-box | |||||
| SAUR-AC1-like | At4g09530 | Yes | 2 | 55 GCATACGTAATG 66 | A-box | |
| 153 AGCTACGTGATC 164 | G/A-box | |||||
| SAUR-AC1-like | At4g38810 | Yes | Yes | 2 | 105 TGACACGTCATC 116 | C/G-box |
| 363 TAATACGTCATG 374 | C/A-box | |||||
| TIR1 | At1g12820 | Yes | 2 | 424 ACATACGTATTT 435 | A-box | |
| 614 TTATACGTAATC 625 | A-box | |||||
| Cytokinin-related genes | ||||||
| Cytokinin biosynthesis | ||||||
| ACS1 | At3g61510 | Yes | 1 | 115 TTTCACGTGATT 126 | G-box | |
| ACS2 | At1g01480 | Yes | 1 | 30 AATCACGTAGAG 41 | G/A-box | |
| ACS6 | At4g11280 | Yes | 1 | 346 TTCTACGTAAAA 357 | A-box | |
| ACS9 | At3g49700 | Yes | 1 | 802 AGCTACGTGACG 813 | G/A-box | |
| AtIPT1 | At1g68460 | Yes | 2 | 461 TCCCACGTGGCA 472 | G-box | |
| 818 TTTCACGTCTAT 829 | C/G-box | |||||
| AtIPT2 | At2g27760 | Yes | 1 | 871 TAACACGTATTG 882 | G/A-box | |
| AtIPT7 | At3g23630 | Yes | 2 | 44 TAATACGTATGC 55 | A-box | |
| 230 ACACACGTGTTC 241 | G-box | |||||
| Cytokinin oxidases | ||||||
| CKX2 | At2g19500 | Yes | 1 | 403 ACCTACGTATAT 414 | A-box | |
| CKX5/6 | At1g75450 | Yes | Yes | 8 | 216 CACCACGTGAAC 227 | G-box |
| 303 ACACACGTGTGA 314 | G-box | |||||
| 336 TCCCACGTGAAT 325 | G-box | |||||
| 337 ATCCACGTGGCG 348 | G-box | |||||
| 703 CTTGACGTATAC 714 | C/A-box | |||||
| 779 ACATACGTGTGT 790 | G/A-box | |||||
| 859 TGACACGTAGAT 870 | G/A-box | |||||
| 923 TATGACGTGATC 934 | C/G-box | |||||
| Cytokinin + ethylene receptor | ||||||
| ERS1 | At2g40940 | Yes | 1 | 560 TATCACGTAATA 571 | G/A-box | |
| ERS2 | At1g04310 | Yes | 1 | 780 GTCCACGTAGGT 791 | G/A-box | |
| ETR1 | At1g66340 | Yes | 2 | 845 CATTACGTCATT 856 | C/A-box | |
| 963 AATGACGTCGAA 974 | C-box | |||||
| Phosphorelay proteins | ||||||
| AHK1 | At2g17820 | Yes | 1 | 217 GTTGACGTAAAG 228 | C/A-box | |
| AHP1 | At3g21510 | Yes | 1 | 95 TGTTACGTAAAA 106 | A-box | |
| AHP3 | At5g39340 | Yes | 1 | 177 CAAGACGTGTGG 188 | C/G-box | |
| Response regulators | ||||||
| ARR5 | At3g48100 | Yes | 1 | 118 TCTCACGTGTGG 129 | C-box | |
| ARR6 | At5g62920 | Yes | 1 | 555 TTCTACGTAGAT 566 | A-box | |
| ARR7 | At1g19050 | Yes | 2 | 338 ACTGACGTAAAG 349 | C/A-box | |
| 490 AATCACGTGTAT 501 | G-box | |||||
| ARR8 | At2g41310 | Yes | Yes | 1 | 294 AAACACGTCACA 305 | C/G-box |
| ARR9 | At3g57040 | Yes | Yes | 4 | 104 TTTGACGTGTGA 115 | C-box |
| 127 AGACACGTATCG 138 | G/A-box | |||||
| 316 ATTTACGTATTA 305 | A-box | |||||
| 387 GATGACGTCATC 398 | C-box | |||||
| ARR11 | At1g67710 | Yes | 2 | 720 ATTTACGTATAA 731 | A-box | |
| 878 AGAGACGTCAAC 889 | C-box | |||||
| ARR16 | At2g40670 | Yes | 1 | 14 TTCGACGTAGAT 25 | C/A-box | |
| ARR22 | At3g04280 | Yes | 1 | 490 AAATACGTAATG 501 | A-box | |
| Other (putative) cytokinin signaling genes | ||||||
| SOB2/DRNL | At1g24590 | Yes | 2 | 44 ATCCACGTGACT 55 | G-box | |
| 896 AAATACGTAATC 907 | A-box | |||||
| At1g28160 | Yes | 1 | 426 GAAGACGTAGAA 437 | C/A-box | ||
| AtERF11 | At1g28370 | Yes | 2 | 655 CAACACGTGTCA 666 | G-box | |
| 893 AGCCACGTAATA 904 | G/A-box | |||||
| AtERF12 | At1g28360 | Yes | Yes | 3 | 154 GATTACGTCAGC 165 | C/A-box |
| 718 ACCCACGTGTAA 729 | G-box | |||||
| 881 TATTACGTATAG 870 | A-box | |||||
| PEP | At5g10480 | Yes | 1 | 141 ACTGACGTGGAA 152 | C/G-box | |
a
Gene name.
b
Arabidopsis Genome Initiative identification number.
c
The presence of the HY5 binding motif (HBACGTVD) in the −1,000 bp upstream of first amino acid (Met).
d
The presence of in vivo HY5 target site according to Lee et al. (2007).
e
Number of HY5 binding ACEs in the promoter region (−1,000 bp upstream).
f
Locations and sequences of the HY5 binding sites in the reported genes. Number denotes base from the first ATG.
g
ACE types are classified according to the half-site nomenclature. The half-site is named according to the base at +2.