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Rice
Figure 2 | Rice

Figure 2

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

Figure 2

Characterization of motifs predicted using data from rice roots subjected to iron (Fe) deficiency. A, Logo represents aligned sequences included in the CATGCATG motif (IDEF1BS motif). Heights of A/C/G/T in the logo represent the frequency of bases at that position. B, Cover ratio (CR) of the IDEF1BS motif in the 500-bp upstream regions. C, Distribution of the IDEF1BS motif. Numbers of IDEF1BS motifs were counted at a region from 3,000 bp upstream to 2,000 bp downstream of the TSS. The blue line represents the frequency of IDEF1BS in all genes. The number of IDEF1BS motifs in a 50-bp window in genes upregulated by Fe deficiency (red) or all genes (blue) divided by the number of upregulated (N(UP) = 895) or all genes (N = 31,348); next, the frequency was normalized by the average frequency of all genes from 3,000 bp upstream to 2,000 bp downstream of the TSS. D, Logo of the CTATATAT motif (TATA-box motif). E, Cover ratio of the TATA-box motif. F, Distribution of the TATA-box motif. G, Logo of the AGCTAGCT motif (DCEp1 motif). H, Cover ratio of the DCEp1 motif in the 500-bp upstream regions. I, Distribution of the DCEp1 motif.

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