Table 2 In silico predicted sRNA candidates confirmed by strand-specific RNA-seq
sRNA candidate | sRNA class | sRNA type | sRNA start | sRNA end | sRNA length |
|---|---|---|---|---|---|
reg_seq3 | 3′UTR: polA | 28634 | 28755 | 122 | |
reg_seq3b | IGR | spot42 sRNA | 28756 | 28882 | 127 |
reg_seq13 | 3′ UTR: aldA | 139913 | 140154 | 242 | |
reg_seq27 | 3′ UTR: ECA0332 | TPP riboswitch | 380584 | 380826 | 243 |
reg_seq27b | 5′ UTR: icc | isrH (Hfq binding sRNA) | 380825 | 380917 | 93 |
reg_seq31 | 3′ UTR: ECA0449 | 515673 | 515910 | 238 | |
reg_seq34 | 3′ UTR: topB | STAXI sRNA | 601635 | 601862 | 228 |
reg_seq34b | antisense: ECA0527 | STAXI sRNA | 601860 | 602087 | 228 |
reg_seq43 | 3′ UTR: mdh | Glycine riboswitch | 758603 | 758857 | 255 |
reg_seq67 | IGR | 1185902 | 1186147 | 246 | |
reg_seq70 | antisense: ECA1096 | 1225748 | 1226182 | 435 | |
reg_seq76 | 5′ UTR: mend | TPP riboswitch | 1379050 | 1379349 | 300 |
reg_seq109 | antisense: osmB | TPP/ isrH | 2217586 | 2217946 | 361 |
reg_seq129 | IGR | Trp leader | 2602697 | 2602931 | 235 |
reg_seq133 | 5′ UTR: ansA | RtT and TPP | 2651356 | 2651598 | 243 |
reg_seq142 | 3′ UTR: ECA2516 | 2832294 | 2832530 | 237 | |
comp_seq5 | 3′ UTR: glnL | TPP/ isrH | 34992 | 35234 | 243 |
comp_seq11 | 3′ UTR: slmA | isrH | 164026 | 164334 | 309 |
comp_seq16 | 5′UTR: ECA0353 | TPP | 403257 | 403655 | 399 |
comp_seq49 | IGR | TPP | 1218529 | 1218729 | 201 |
comp_seq55 | 5′ UTR: ECA1196 | TPP/ isrH | 1358123 | 1358268 | 146 |
comp_seq111 | IGR | TPP/ isrH | 2881355 | 2881546 | 192 |
comp_seq130 | 3′ UTR: ECA2950 | TPP and RtT | 3295111 | 3295347 | 237 |
comp_seq204 | 5′ UTR: sotB | 4828158 | 4828349 | 192 | |
comp_seq217 | 5′ UTR: ECA4506 | 5046219 | 5046427 | 209 |