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Table 5 Verification of prediction by experimental analysis

From: Prediction of transcriptional regulatory elements for plant hormone responses based on microarray data

AGI code Position from TSS1 RARf Predicted cis-element REG Prediction assessment Reference4 Response Element name MEME Gibbs Sampler
   Drought2 SA3         
AT5G52310
(RD29A)
-231 3.12   ATACCGACATCA   Positive Yamaguchi-Shinozaki, 1994 Drought DRE No detect. No detect.
  -175 3.94   ACTACCGACATGAG   Positive Narusaka, 2003 Drought DRE No detect. No detect.
  -137 4.22   AAGCCGACACA   Positive Narusaka, 2003 Drought DRE-core No detect. No detect.
  -125 3.76   ACACGCGTAGA AtREG536 ?5 Narusaka, 2003 Drought   No detect. 7 No detect.
  -82 3.44   ACAGACGC   False positive Yamaguchi-Shinozaki, 1994 Drought   No detect No detect
  -71 5.01   ATACGTGTCCCT AtREG557,472 Positive Narusaka, 2003 Drought ABRE No detect. No detect.7
AT5G52300
(RD29B)
-163 3.16   CGTACGTGTCA AtREG450 False positive Uno, 2000 Drought   No detect No detect7
  -137 *     Absent 7 Uno, 2000 Drought ABRE No detect. No detect.7
  -112 3.21   GTACGTGTCA AtREG557, 389 Positive Uno, 2000 Drought ABRE No detect. No detect. 7
AT2G14610
(PR1)
-669   3.82 ACGTCACT   Positive Pape, 2010 INA6/SA LS5 No detect. No detect.
  -657   6.38 TACTTACGTCAT   Positive Lebel, 1998; Pape, 2010 INA6/SA LS7 No detect. No detect.
  -607   3.65 TAGGCAAG   False positive Lebel, 1998 INA6/SA   No detect No detect
  1. 1Position from major TSS data from ppdb. 21 h-treatment. 3See Table 3 for experimental conditions. 4Source of functional analysis. *RARf for ABA response is 3.7. 5Lack of the corresponding functional data. 6INA: 2,6-dichloro isonicotinic acid, a SA analog. 7Detected with the promoter set of ABA response. For analysis of RD29B by MEME and Gibbs Sampler, it was included to the applied promoter set. Promoter scan for prediction was achieved for the regions where linker scan or intensive functional analyses were achieved, and peaks with RARf > 3.0 were selected as prediction. Utilized RARf tables are shown in the table.