Table 1 Predicted cis-regulatory elements in the 5’-UTRs. The predictions were obtained by using Infernal 1.1.2 with the Rfam 12.1 database and compared with the primary 5′-end data set. The list is sorted by Bit Score in descending order. Abbreviation: n.a., not applicable
Infernal prediction with Rfam | RNA-Seq detection | ||||||||
|---|---|---|---|---|---|---|---|---|---|
Name | ID | Start | End | Bit Score | Strand | Status | Start | End | Gene |
Cobalamin riboswitch | RF00174 | 1,066,117 | 1,066,317 | 90.8 | + | observed | 1,066,117 | 1,066,317 | DIP1084 |
Cobalamin riboswitch | RF00174 | 862,214 | 862,414 | 81.8 | + | not observeda | n.a. | n.a. | n.a. |
cspA | RF01766 | 285,506 | 285,923 | 64.8 | + | observed | 285,506 | 285,923 | DIP0320 / cspA |
mraW | RF01746 | 1,640,095 | 1,639,987 | 70.2 | – | observedb | 1,640,095 | 1,639,987 | DIP1606 / mraW |
TPP riboswitch | RF00059 | 924,778 | 924,890 | 60.8 | + | observedc | 924,778 | 924,890 | DIP0953 |
TPP riboswitch | RF00059 | 922,838 | 922,969 | 60.0 | + | observedc | 922,838 | 922,969 | DIP0951 |
msiK | RF01747 | 509,334 | 509,277 | 48.2 | – | observed | 509,334 | 509,277 | DIP0539 |
TPP riboswitch | RF00059 | 27,456 | 27,566 | 57.6 | + | not observeda | n.a. | n.a. | n.a. |