Motif IL_61258.2 Version IL_61258.2 of this group appears in releases 3.7 to 3.11
| #S | Loop id | PDB | Disc | #Non-core | Annotation | Chain(s) | Standardized name | 1 | 2 | break | 3 | 4 | 1-4 | 2-3 | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | IL_4C7O_003 | 4C7O | 0.5701 | 1 | Single bulged C | E | SRP RNA | C | 12 | G | 13 | * | C | 31 | G | 33 | cWW | cWW |
| 2 | IL_4WF9_035 | 4WF9 | 0.3622 | 1 | Single bulged C | X | LSU rRNA | C | 1038 | A | 1040 | * | U | 1203 | G | 1204 | cWW | cWW |
| 3 | IL_5J7L_276 | 5J7L | 0.3857 | 1 | Single bulged C | DA | LSU rRNA | C | 994 | A | 996 | * | U | 1159 | G | 1160 | cWW | cWW |
| 4 | IL_4Y4O_212 | 4Y4O | 0.3397 | 1 | Single bulged C | 2A | LSU rRNA | C | 994 | A | 996 | * | U | 1159 | G | 1160 | cWW | cWW |
| 5 | IL_4IOA_031 | 4IOA | 0.3178 | 1 | Single bulged C | X | LSU rRNA | U | 1005 | A | 1007 | * | U | 1170 | A | 1171 | cWW | cWW |
| 6 | IL_5TBW_049 | 5TBW | 0.2797 | 6 | SSU/LSU pseudoknot | 1 | LSU rRNA | U | 1173 | A | 1180 | * | U | 1325 | A | 1326 | cWW | cWW |
| 7 | IL_4V8P_208 | 4V8P | 0.3489 | 1 | D1 | LSU rRNA | G | 1094 | G | 1096 | * | U | 1117 | C | 1118 | cWW | cWW | |
| 8 | IL_6CK5_003 | 6CK5 | 0.4437 | 1 | Single bulged C | A | Guanidine-I riboswitch | U | 39 | G | 41 | * | C | 21 | A | 22 | cWW | cWW |
| 9 | IL_4Y4O_283 | 4Y4O | 0.4757 | 1 | Single bulged C | 2A | LSU rRNA | U | 2878 | C | 2880 | * | G | 2838 | G | 2839 | cWW | cWW |
| 10 | IL_1KUQ_002 | 1KUQ | 0.3402 | 1 | Single bulged C | B | 16S RIBOSOMAL RNA FRAGMENT | C | 46 | C | 48 | * | G | 21 | G | 22 | cWW | cWW |
| 11 | IL_4V8P_230 | 4V8P | 0.2608 | 1 | Single bulged C (H) | D1 | LSU rRNA | G | 1804 | G | 1806 | * | U | 1693 | C | 1694 | cWW | cWW |
| 12 | IL_4IOA_057 | 4IOA | 0.2102 | 1 | Single bulged C | X | LSU rRNA | G | 1488 | U | 1490 | * | A | 1534 | C | 1535 | cWW | cWW |
| 13 | IL_5TBW_002 | 5TBW | 0.1566 | 1 | Single bulged C | 4+1 | 5.8S rRNA | G | 150 | G | 152 | * | C | 7 | C | 8 | cWW | cWW |
| 14 | IL_4RZD_001 | 4RZD | 0.0000 | 1 | Single bulged C | A | PreQ1-III riboswitch | G | 78 | G | 80 | * | C | 56 | C | 57 | cWW | cWW |
| 15 | IL_5TBW_069 | 5TBW | 0.1141 | 1 | Single bulged C | 1 | LSU rRNA | G | 1778 | G | 1780 | * | C | 1669 | C | 1670 | cWW | cWW |
| 16 | IL_3D0U_001 | 3D0U | 0.2628 | 1 | Single bulged C | A | Lysine Riboswitch RNA | C | 75 | C | 76 | * | G | 9 | G | 11 | cWW | cWW |
| 17 | IL_3DIL_001 | 3DIL | 0.3347 | 1 | Single bulged C | A | RNA (174-MER) | C | 78 | C | 79 | * | G | 12 | G | 14 | cWW | cWW |
| 18 | IL_4V88_384 | 4V88 | 0.2731 | 1 | Single bulged C | A6 | SSU rRNA | U | 24 | A | 26 | * | U | 600 | A | 601 | cWW | cWW |
| 19 | IL_4V8P_234 | 4V8P | 0.3353 | 1 | D1 | LSU rRNA | U | 1758 | G | 1760 | * | C | 1733 | A | 1734 | ncWW | cWW | |
| 20 | IL_4IOA_033 | 4IOA | 0.2973 | 6 | SSU/LSU pseudoknot | X | LSU rRNA | U | 1015 | A | 1022 | * | U | 1161 | A | 1162 | cWW | cWW |
| 21 | IL_3SN2_001 | 3SN2 | 0.2851 | 1 | Single bulged C | B | transferrin receptor iron regulatory element B RNA | C | 24 | A | 25 | * | U | 7 | G | 9 | cWW | cWW |
| 22 | IL_1S03_002 | 1S03 | 0.2613 | 1 | Single bulged C | A | 47-MER | C | 39 | C | 40 | * | G | 9 | G | 11 | cWW | cWW |
| 23 | IL_1DQF_001 | 1DQF | 0.3729 | 1 | Single bulged C | A+B | RNA (9-mer) + RNA (10-mer) | C | 3 | A | 4 | * | U | 15 | G | 17 | cWW | cWW |
| 24 | IL_1DQH_001 | 1DQH | 0.2979 | 1 | Single bulged C | A+B | RNA (9-mer) + RNA (10-mer) | C | 3 | A | 4 | * | U | 15 | G | 17 | cWW | cWW |
| 25 | IL_1S03_006 | 1S03 | 0.2770 | 1 | Single bulged C | B | 47-MER | C | 39 | C | 40 | * | G | 9 | G | 11 | cWW | cWW |
| 26 | IL_3HHN_003 | 3HHN | 0.5228 | 1 | Single bulged C | E | Class I ligase ribozyme, self-ligation product | A | 112 | C | 113 | * | G | 46 | U | 48 | cWW | cWW |
| 27 | IL_3IVK_001 | 3IVK | 0.5963 | 1 | Single bulged C | M | class I ligase product | A | 112 | C | 113 | * | G | 46 | U | 48 | cWW | ncWW |
| 28 | IL_3W3S_001 | 3W3S | 0.4031 | 1 | Single bulged C | B | Selenocysteine transfer RNA | G | 23 | C | 24 | * | G | 11 | C | 12 | cWW | cWW |
| 29 | IL_3SNP_003 | 3SNP | 0.3894 | 1 | Single bulged C | D | ferritin H IRE RNA | A | 24 | C | 25 | * | G | 7 | U | 9 | cWW | cWW |
| 30 | IL_5F5H_002 | 5F5H | 0.3205 | 1 | Single bulged C | D | RNA (21-mer) | G | 18 | U | 20 | * | A | 4 | C | 5 | cWW | cWW |
| 31 | IL_5F5H_001 | 5F5H | 0.2923 | 1 | Single bulged C | C | RNA (21-mer) | G | 18 | U | 20 | * | A | 4 | C | 5 | cWW | cWW |
| 32 | IL_3W3S_004 | 3W3S | 0.3275 | 1 | Single bulged C | B | Selenocysteine transfer RNA | G | 11||||43_455 | C | 12||||43_455 | * | G | 23||||43_455 | C | 24||||43_455 | cWW | cWW |
| 33 | IL_5J7L_311 | 5J7L | 0.4108 | 1 | Single bulged C | DA | LSU rRNA | G | 1731 | G | 1733 | * | C | 1727 | C | 1728 | ncWW | cWW |
| 34 | IL_3SN2_002 | 3SN2 | 0.5859 | 1 | Single bulged C | B | transferrin receptor iron regulatory element B RNA | G | 13 | C | 14 | * | G | 18 | C | 20 | cWW | cWW |
| 35 | IL_2XXA_005 | 2XXA | 0.4884 | 1 | F | SSRP RNA | G | 71 | U | 73 | * | A | 26 | C | 27 | cWW | cWW | |
| 36 | IL_2XXA_003 | 2XXA | 0.3288 | 1 | F | SSRP RNA | G | 82 | C | 84 | * | G | 17 | C | 18 | cWW | cWW | |
| 37 | IL_5KPY_001 | 5KPY | 0.5612 | 1 | Single bulged C | A | 5-hydroxytryptophan RNA aptamer | U | 25 | G | 27 | * | C | 43 | A | 44 | cWW | cWW |
3D structures
Complete motif including flanking bases
| Sequence | Counts |
|---|---|
| GCU*AC | 4 |
| GCG*CC | 4 |
| CC*GCG | 4 |
| CCA*UG | 3 |
| UCG*CA | 3 |
| CA*UCG | 3 |
| AC*GCU | 3 |
| UCA*UA | 2 |
| GCG*UC | 2 |
| GC*GCC | 2 |
| GCC*GC | 2 |
| CG*CCG | 1 |
| UGCCGGAA*UA | 1 |
| UCC*GG | 1 |
| CCC*GG | 1 |
| UCCCUAAA*UA | 1 |
Non-Watson-Crick part of the motif
| Sequence | Counts |
|---|---|
| C* | 22 |
| *C | 13 |
| GCCGGA* | 1 |
| CCCUAA* | 1 |
- Annotations
-
- Single bulged C (30)
- (4)
- SSU/LSU pseudoknot (2)
- Single bulged C (H) (1)
- Basepair signature
- cWW-cWW
- Heat map statistics
- Min 0.06 | Avg 0.45 | Max 1.06
Coloring options: