Figure 4

Examples of sequence profiles and secondary structures of full length trans-encoded sRNAs with common 5'- and 3'-end features. Sequence coverage profile: blue and light grey color denote transcript coverages derived from sample 1 and 2, respectively. Dark grey colored areas represent an overlap of coverages from both samples. y- and x-axis represent coverage and sequence, respectively. Sequence code: blue, A; yellow, C; orange, G; green, U. Grey arrows represent genes flanking or overlapping sRNA genes. Black arrows represent the sRNAs. (a) Trans-encoded sRNA SmelC411, two distinct 5'-ends and one distinct 3'-end; (b) trans-encoded sRNA SmelC111a and cis-encoded mRNA leader SmelB111b; three and two distinct 5'-ends, as well as one distinct and a variable 3'-end, respectively; (c) trans-encoded sRNA SmelA066, one distinct 5'- and a variable 3'-end; (d) type 3 cis-encoded antisense sRNA SmelC520, one distinct 5'-end and a variable 3'-end; (e) type 1 cis-encoded antisense sRNA SmelB062, two distinct 5'- and a variable 3'-end; (f) type 2 and type 1/3 cis-encoded antisense sRNAs: SmelA009, one distinct 5'-end and a variable 3'-end; SmelA010, several 5'- and 3'-ends.