Figure 3. The binding sites of miRNA on moss genes.

(A) Three ABI3 genes are annotated with coding regions (CDS) consisting of B3 DNA binding domain, while miR536 targeting sites are downstream to the domain at each genic locus. (B) Base pairings between miR536 (query) and ABI3 (target) are shown in the format of “:” as a canonical match, “ . ” as a wobble match, and blank space as a mismatch. The column of “range” indicates the start and end position of a binding site on a transcript. miR536 sequences with alternative 5′-ends were plotted from 3′ to 5′, and #. Reads are listed for each miR536 isoform. Degradome reads corresponding to miRNA cleavages were highlighted in red. (C) Sequence conservation among the binding sites of ABI3 genes, where * represents a conserved site of the three genes. (D) Base pairings between members of the miR319 family (query) and three MYB genes (target).