Plant Transcription factor database - Universität Potsdam
version: 3.0

Oryza sativa subsp. indica AP2-EREBP Family

Description

Riechmann & Meyerowitz. 1998: AP2 (APETALA2) and EREBPs (ethylene-responsive element binding proteins) are the prototypic members of a family of transcription factors unique to plants, whose distinguishing characteristic is that they contain the so-called AP2 DNA-binding domain. AP2/ REBP genes form a large multigene family, and they play a variety of roles throughout the plant life cycle: from being key regulators of several developmental processes, like floral organ identity determination or control of leaf epidermal cell identity, to forming part of the mechanisms used by plants to respond to various types of biotic and environmental stress.

Shigyo et al. 2006: AP2/EREBP genes are divided into two subfamilies: AP2 genes with two AP2 domains and EREBP genes with a single AP2/ERF (Ethylene Responsive Element Binding Factor) domain. Expressions of AP2-like genes, including AP2, in Arabidopsis thaliana are regulated by the microRNA miR172. We found that the target site of miR172 is significantly conserved in gymnosperm AP2 homologs, suggesting that regulatory mechanisms of gene expression using microRNA have been conserved over the three hundred million years since the divergence of gymnosperm and flowering plant lineages.

Members of this family
  SHOULD possess AP2 domain

Domain alignments

Benchmark against A. thaliana

The Sensitivity and Positive Predictive Value (PPV) were assessed for this family. The data reported by Feng et al. 2005 for A. thaliana were taken as gold standard.

The gold standard reported 147 members for this family, 146 of which are present in ArabTFDB, giving a PPV of 1.00. One additional member not present in ArabTFDB might be a false negative, giving a Sensitivity of 0.99.

This family is also present in:

References

There are 161 gene models in this family



Gene modelDescriptionDomains
OsIBCD000279 Chr01_447,1050,,,1,1050, AP2 B3
OsIBCD000432 Chr01_678,855,,,1,855, AP2
OsIBCD000785 Chr01_1171,1074,,,1,1074, AP2
OsIBCD001365 Chr01_2016,624,,,1,624, AP2
OsIBCD002794 Chr01_4403,810,,,1,810, AP2
OsIBCD003324 Chr01_5162,630,,,1,630, AP2
OsIBCD003675 Chr01_5670,1281,,,1,1281, AP2
OsIBCD003992 Chr01_6164,1056,,,1,1056, AP2
OsIBCD004191 Chr01_6422,2076,,,1,2076, AP2
OsIBCD005437 Chr02_1046,618,,,1,618, AP2
OsIBCD006527 Chr02_2920,747,,,1,747, AP2
OsIBCD006642 Chr02_3134,783,,,1,783, AP2
OsIBCD006796 Chr02_3395,654,,,1,654, AP2
OsIBCD007202 Chr02_3990,2103,,,1,2103, AP2
OsIBCD007344 Chr02_4204,2427,,,1,2427, AP2 BRO1
OsIBCD007971 Chr02_5120,1182,,,1,1182, AP2
OsIBCD008073 Chr02_5266,639,,,1,639, AP2
OsIBCD008090 Chr02_5287,663,,,1,663, AP2
OsIBCD008179 Chr02_5420,1098,,,1,1098, AP2
OsIBCD008259 Chr02_5532,519,,,1,519, AP2
OsIBCD009032 Chr03_711,1641,,,1,1641, AP2
OsIBCD009072 Chr03_761,939,,,1,939, AP2
OsIBCD009073 Chr03_762,756,,,1,756, AP2
OsIBCD009376 Chr03_1161,1806,,,1,1806, AP2
OsIBCD009902 Chr03_1909,894,,,1,894, AP2
OsIBCD009905 Chr03_1912,1290,,,1,1290, AP2
OsIBCD010105 Chr03_2189,732,,,1,732, AP2
OsIBCD012096 Chr03_5536,1941,,,1,1941, AP2
OsIBCD014186 Chr04_2585,810,,,1,810, AP2
OsIBCD014348 Chr04_2829,588,,,1,588, AP2
OsIBCD014904 Chr04_3598,1872,,,1,1872, AP2
OsIBCD015813 Chr04_4904,504,,,1,504, AP2
OsIBCD015814 Chr04_4905,1569,,,1,1569, AP2
OsIBCD015847 Chr04_4942,1458,,,1,1458, AP2
OsIBCD015857 Chr04_4958,420,,,1,420, AP2
OsIBCD015860 Chr04_4962,420,,,1,420, AP2
OsIBCD016270 Chr05_194,1608,,,1,1608, AP2
OsIBCD017588 Chr05_2568,1263,,,1,1263, AP2
OsIBCD017705 Chr05_2739,597,,,1,597, AP2
OsIBCD017861 Chr05_2998,1002,,,1,1002, AP2
OsIBCD018139 Chr05_3390,1095,,,1,1095, AP2
OsIBCD018341 Chr05_3711,786,,,1,786, AP2
OsIBCD018720 Chr05_4275,1410,,,1,1410, AP2
OsIBCD019394 Chr06_458,1194,,,1,1194, AP2
OsIBCD019626 Chr06_782,537,,,1,537, AP2
OsIBCD019694 Chr06_885,1089,,,1,1089, AP2
OsIBCD019716 Chr06_922,375,,,1,375, AP2
OsIBCD019792 Chr06_1039,813,,,1,813, AP2
OsIBCD021307 Chr06_3710,732,,,1,732, AP2
OsIBCD021511 Chr06_4019,972,,,1,972, AP2
OsIBCD021527 Chr06_4048,1317,,,1,1317, AP2
OsIBCD021528 Chr06_4049,1212,,,1,1212, AP2
OsIBCD021649 Chr06_4226,1341,,,1,1341, AP2
OsIBCD021652 Chr06_4229,1392,,,1,1392, AP2
OsIBCD021653 Chr06_4230,657,,,1,657, AP2
OsIBCD021654 Chr06_4231,792,,,1,792, AP2
OsIBCD022245 Chr07_221,1356,,,1,1356, AP2
OsIBCD022832 Chr07_1171,1311,,,1,1311, AP2
OsIBCD024207 Chr07_3567,1026,,,1,1026, AP2
OsIBCD024574 Chr07_4092,651,,,1,651, AP2
OsIBCD025120 Chr08_636,822,,,1,822, AP2
OsIBCD025131 Chr08_659,690,,,1,690, AP2
OsIBCD026666 Chr08_3390,1257,,,1,1257, AP2
OsIBCD027236 Chr08_4285,2529,,,1,2529, AP2 DUF246
OsIBCD027435 Chr08_4561,912,,,1,912, AP2
OsIBCD028602 Chr09_2049,1545,,,1,1545, AP2
OsIBCD028660 Chr09_2141,1200,,,1,1200, AP2
OsIBCD029466 Chr09_3335,663,,,1,663, AP2
OsIBCD030438 Chr10_1718,894,,,1,894, AP2
OsIBCD031462 Chr10_3270,822,,,1,822, AP2
OsIBCD031721 Chr11_196,1332,,,1,1332, AP2
OsIBCD031962 Chr11_564,957,,,1,957, AP2
OsIBCD032287 Chr11_1095,465,,,1,465, AP2
OsIBCD032531 Chr11_1511,1551,,,1,1551, AP2
OsIBCD033936 Chr12_277,1332,,,1,1332, AP2
OsIBCD034161 Chr12_633,1026,,,1,1026, AP2
OsIBCD035584 Chr12_3047,810,,,1,810, AP2
OsIBCD035867 Chr01_352,1020,,,1,1020, AP2
OsIBCD035889 Chr01_435,951,,,1,951, AP2 B3
OsIBCD035891 Chr01_437,1110,,,1,1110, AP2 B3
OsIBCD036016 Chr01_964,684,,,1,684, AP2
OsIBCD036922 Chr01_5540,708,,,1,708, AP2
OsIBCD037104 Chr01_6309,582,,,1,582, AP2
OsIBCD037252 Chr01_7051,660,,,1,660, AP2
OsIBCD037514 Chr02_1281,600,,,1,600, AP2
OsIBCD037842 Chr02_3123,720,,,1,720, AP2
OsIBCD037906 Chr02_3497,513,,,1,513, AP2
OsIBCD037963 Chr02_3786,1038,,,1,1038, AP2
OsIBCD038091 Chr02_4349,912,,,1,912, AP2
OsIBCD038092 Chr02_4353,1038,,,1,1038, AP2
OsIBCD038137 Chr02_4509,786,,,1,786, AP2
OsIBCD038138 Chr02_4514,675,,,1,675, AP2
OsIBCD038254 Chr02_5158,1017,,,1,1017, AP2
OsIBCD038311 Chr02_5404,594,,,1,594, AP2
OsIBCD038420 Chr03_176,600,,,1,600, AP2
OsIBCD038483 Chr03_495,426,,,1,426, AP2
OsIBCD038515 Chr03_624,1812,,,1,1812, AP2
OsIBCD038536 Chr03_702,948,,,1,948, AP2
OsIBCD038545 Chr03_764,1014,,,1,1014, AP2
OsIBCD038553 Chr03_831,897,,,1,897, AP2
OsIBCD038666 Chr03_1417,777,,,1,777, AP2
OsIBCD039549 Chr03_5959,726,,,1,726, AP2
OsIBCD039611 Chr03_6365,666,,,1,666, AP2
OsIBCD039859 Chr04_1251,393,,,1,393, AP2
OsIBCD040083 Chr04_2598,897,,,1,897, AP2
OsIBCD040327 Chr04_3815,1401,,,1,1401, AP2
OsIBCD040357 Chr04_3978,960,,,1,960, AP2
OsIBCD040360 Chr04_3981,957,,,1,957, AP2
OsIBCD040361 Chr04_3982,987,,,1,987, AP2
OsIBCD040365 Chr04_3997,855,,,1,855, AP2
OsIBCD040366 Chr04_3998,504,,,1,504, AP2
OsIBCD040367 Chr04_4000,654,,,1,654, AP2
OsIBCD040406 Chr04_4185,621,,,1,621, AP2
OsIBCD040407 Chr04_4186,660,,,1,660, AP2
OsIBCD040476 Chr04_4531,669,,,1,669, AP2
OsIBCD040543 Chr04_4902,699,,,1,699, AP2
OsIBCD040579 Chr04_5090,555,,,1,555, AP2
OsIBCD041031 Chr05_2331,837,,,1,837, AP2
OsIBCD041089 Chr05_2627,810,,,1,810, AP2
OsIBCD041208 Chr05_3244,513,,,1,513, AP2
OsIBCD041345 Chr05_3919,570,,,1,570, AP2
OsIBCD041346 Chr05_3920,711,,,1,711, AP2
OsIBCD041439 Chr05_4381,1185,,,1,1185, AP2 B3
OsIBCD041468 Chr05_4513,849,,,1,849, AP2
OsIBCD041489 Chr05_4595,819,,,1,819, AP2
OsIBCD041649 Chr06_435,642,,,1,642, AP2
OsIBCD041691 Chr06_607,1029,,,1,1029, AP2
OsIBCD041703 Chr06_668,555,,,1,555, AP2
OsIBCD041754 Chr06_918,624,,,1,624, AP2
OsIBCD041762 Chr06_941,576,,,1,576, AP2
OsIBCD041764 Chr06_943,624,,,1,624, AP2
OsIBCD041813 Chr06_1160,1092,,,1,1092, AP2
OsIBCD042749 Chr07_894,801,,,1,801, AP2
OsIBCD042907 Chr07_1838,666,,,1,666, AP2
OsIBCD042908 Chr07_1841,720,,,1,720, AP2
OsIBCD043175 Chr07_3224,948,,,1,948, AP2
OsIBCD043335 Chr07_4044,900,,,1,900, AP2
OsIBCD043837 Chr08_2633,906,,,1,906, AP2
OsIBCD043915 Chr08_3055,255,,,1,255, AP2
OsIBCD043927 Chr08_3093,840,,,1,840, AP2
OsIBCD043995 Chr08_3486,729,,,1,729, AP2
OsIBCD044038 Chr08_3681,828,,,1,828, AP2
OsIBCD044150 Chr08_4139,570,,,1,570, AP2
OsIBCD044232 Chr08_4560,411,,,1,411, AP2
OsIBCD044239 Chr08_4576,696,,,1,696, AP2
OsIBCD044240 Chr08_4582,693,,,1,693, AP2
OsIBCD044391 Chr09_923,699,,,1,699, AP2
OsIBCD044420 Chr09_1111,954,,,1,954, AP2
OsIBCD044498 Chr09_1591,876,,,1,876, AP2
OsIBCD044668 Chr09_2372,801,,,1,801, AP2
OsIBCD044783 Chr09_2894,741,,,1,741, AP2
OsIBCD044785 Chr09_2897,681,,,1,681, AP2
OsIBCD044883 Chr09_3338,642,,,1,642, AP2
OsIBCD045171 Chr10_1511,966,,,1,966, AP2
OsIBCD045223 Chr10_1860,684,,,1,684, AP2
OsIBCD045316 Chr10_2233,375,,,1,375, AP2
OsIBCD045569 Chr10_3292,741,,,1,741, AP2
OsIBCD046878 Chr12_2876,1122,,,1,1122, AP2
OsIBCD046905 Chr12_3043,423,,,1,423, AP2
OsIBSD047372 Supscaffold1514_1,816,,,1,816, AP2
OsIBSD048223 Supscaffold1102_4,726,,,1,726, AP2

General references

Gutterson, N; Reuber, TL. 2004. Regulation of disease resistance pathways by AP2/ERF transcription factors. Curr. Opin. Plant Biol. 7(4):465-71 PUBMEDID:15231271
Liu, Y; Zhao, TJ; Liu, JM; Liu, WQ; Liu, Q; Yan, YB; Zhou, HM. 2006. The conserved Ala37 in the ERF/AP2 domain is essential for binding with the DRE element and the GCC box. FEBS Lett. 580(5):1303-8 PUBMEDID:16457823
Magnani, E; Sjölander, K; Hake, S. 2004. From endonucleases to transcription factors: evolution of the AP2 DNA binding domain in plants. Plant Cell 16(9):2265-77 PUBMEDID:15319480
Ohme-Takagi, M; Shinshi, H. 1995. Ethylene-inducible DNA binding proteins that interact with an ethylene-responsive element. Plant Cell 7(2):173-82 PUBMEDID:7756828
Riechmann, JL; Meyerowitz, EM. 1998. The AP2/EREBP family of plant transcription factors. Biol. Chem. 379(6):633-46 PUBMEDID:9687012
Shigyo, M; Hasebe, M; Ito, M. 2006. Molecular evolution of the AP2 subfamily. Gene 366(2):256-65 PUBMEDID:16388920
Shigyo, M; Ito, M. 2004. Analysis of gymnosperm two-AP2-domain-containing genes. Dev. Genes Evol. 214(3):105-14 PUBMEDID:14986134
Weigel, D. 1995. The APETALA2 domain is related to a novel type of DNA binding domain. Plant Cell 7(4):388-9 PUBMEDID:7773013