Skip to main content

Advertisement

Table 2 Motifs predicted from a region 50 bp upstream to 150 bp downstream of TSS

From: Development of a novel prediction method of cis-elements to hypothesize collaborative functions of cis-element pairs in iron-deficient rice

Motif name Sscore P-value* Annotations
CTATATAT 2.08 1.03E-69 TATA-box motif
AGCTAGCT 2.05 1.71E-86 DCEp1 motif
TATAAGTA 2.00 3.56E-05  
CTTAATTA 1.99 3.68E-25  
TGATCATG 1.99 2.57E-12  
GCCTATAA 1.97 9.44E-08 BRE U -TATA motif 2
TATACACA 1.96 3.47E-15  
TATAAAAG 1.95 1.19E-05  
TAACTAGT 1.95 4.19E-10  
GTCCTGTA 1.95 2.09E-08  
CAACTATA 1.95 2.56E-07  
CACTTAGT 1.94 6.14E-06  
ACTGAAGT 1.93 6.06E-05  
CATCAAGC 1.93 2.22E-08  
GTACTACG 1.93 1.74E-07  
ACATACCA 1.93 7.81E-09  
AGTTGCAG 1.93 1.93E-11  
GTACGTTC 1.93 7.25E-10  
GCTATAGC 1.92 3.32E-08  
CTAAGCTA 1.92 2.17E-09  
  1. * P-values were calculated using a binominal test. Using 500 bp of upstream sequence from the TSS, the number of motifs in regulated genes and the number of every 8-bp sequence in regulated genes were compared from the number of motifs in all genes and the number of every 8-bp sequence in all genes. This P-value was not used to predict cis-acting motifs. These numbers used to calculate P-values and annotations using PLACE and TRANSFAC are shown in Additional file 5.