Table 2.
Rfam predictions for regulatory regions in C. glutamicum compared to RNAseq data
|
Rfam
predictiona |
|
RNAseq identificationb |
|||||||
|---|---|---|---|---|---|---|---|---|---|
| Name | ID | Start | End | Bit Score | Strand | RNAseq | Start | End | Gene |
| FMN riboswitch |
RF00050 |
66,442 |
66,279 |
111.60 |
- |
observed |
66,438 |
66,198 |
cg0083 |
| cspA mRNA 5′-UTR |
RF01766 |
186,399 |
186,766 |
60.19 |
+ |
observed |
186,328 |
186,508 |
cg0215 (cspA) |
| TPP riboswitch |
RF00059 |
742,654 |
742,547 |
63.54 |
- |
observed |
742,651 |
742,490 |
cg0825 |
| ydaO-yuaA leader |
RF00379 |
870,027 |
869,859 |
69.93 |
- |
observed |
870,047 |
869,853 |
cg0936 (rpf1) |
| TPP riboswitch |
RF00059 |
1,127,774 |
1,127,883 |
51.03 |
+ |
observed |
1,127,765 |
1,127,874 |
cg1227 |
| mini-ykkC RNA motif |
RF01068 |
1,131,047 |
1,131,094 |
33.52 |
+ |
not observed |
- |
- |
- |
| TPP riboswitch |
RF00059 |
1,373,213 |
1,373,103 |
55.87 |
- |
observed |
1,373,210 |
1,373,105 |
cg1476 (thiC) |
| SAM-IV riboswitch |
RF00634 |
1,374,007 |
1,374,123 |
70.47 |
+ |
observed |
1,374,005 |
1,374,139 |
cg1478 |
| TPP riboswitch |
RF00059 |
1,544,490 |
1,544,383 |
52.11 |
- |
observed |
1,544,485 |
1,544,390 |
cg1655 (thiM) |
| yybP-ykoY leader |
RF00080 |
1,550,030 |
1,550,196 |
43.71 |
+ |
not observed |
- |
- |
- |
| yybP-ykoY leader |
RF00080 |
2,043,157 |
2,042,989 |
49.13 |
- |
observed |
2,043,151 |
2,042,955 |
cg2157 (terC) |
| TPP riboswitch |
RF00059 |
2,120,271 |
2,120,383 |
62.55 |
+ |
observed |
2,120,271 |
2,120,384 |
cg2236 (thiE) |
| mraW RNA motif |
RF01746 |
2,267,021 |
2,266,916 |
56.64 |
- |
observed |
2,266,932 |
2,266,800 |
cg2377 (mraW) |
| ydaO-yuaA leader |
RF00379 |
2,292,467 |
2,292,279 |
59.37 |
- |
observed |
2,292,509 |
2,292,267 |
cg2402 |
| msiK RNA motif |
RF01747 |
2,582,375 |
2,582,317 |
52.13 |
- |
observed |
2,582,404 |
2,582,315 |
cg2708 (msiK1) |
| yybP-ykoY leader | RF00080 | 2,649,004 | 2,648,890 | 49.90 | - | not observed | - | - | - |
aName, ID, coordinates, and bit score of predicted regulatory 5′-UTRs for C. glutamicum were taken from the Rfam database [50].
bRefers to detected TSSs and RNAseq ends relate to the last position of the 5′-UTR. The secondary structures of the verified regulatory regions are shown in Additional file 3: Figure S2.