Figure 5

Sequence conservation of the expanded miRNA gene families. A: Sequence alignment of 91 putative mature miRNA coding regions of the PC-5p-67443 family. There are 65 sequences identical to the miRNA identified by deep sequencing, three with a base change from C to T at the last residue, three with a base change from G to A at position 13, three with two base changes from TC to CG at positions 21–22 and C to T at position 8, two with a base change from C to A at the last residue, and 15 with single or double changes at various positions. B: Schematic presentations of sequence conservation of different regions among genes in different families. The black portion of the arrow on the top of the figure represents the approximately 300 base pairs of the sequence flanking the 150 base pairs of a mature miRNA coding region, which is indicated by the white space in the middle of the arrow. The color rectangles indicate various degrees of conservation/divergence among family members with percentages of sequence identity given within each rectangle. Overall, the coding regions and the immediate surrounding sequences are highly conserved (indicated by red), indicating that the genes are likely functional, but the remaining flanking regions are divergent. The family names (numbers) are given on the right side of the figure.