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Figure 3 | BMC Genomics

Figure 3

From: Biocomputational prediction of non-coding RNAs in model cyanobacteria

Figure 3

Types of predicted elements. A. The genomic location of predicted RNA element in cluster 80 and synteny around this element is shown. This element is slightly more likely to be transcribed from the forward strand as indicated by the direction of the arrow within the IGR. The length of the intergenic spacer is given in nt and homologous genes are colour-coded. In Synechococcus 6301 an ftrC gene has been inserted into this region relative to the other. The predicted consensus structure of the RNA element (bottom) consists of two stem-loops separated by a 17 nt single-stranded region. The degree of sequence conservation is colour-coded. B. Four of the five sequences in cluster 62 are located upstream of the groES operon. This region is known to contain the palindromic CIRCE element and indeed, this element constitutes a critical part of the conserved sequence and structure. The initiation site of transcription of the groES mRNA was mapped by 5' RACE to occur from the first G within the nine nt loop that is part of the CIRCE element (bold arrow). The fifth sequence has no CIRCE element but has been clustered into cluster 62 based on other sequence features. At the bottom right, the perfect conservation of the CIRCE element in the four compared cyanobacteria is shown.

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