Motif HL_13999.2 Version HL_13999.2 of this group appears in releases 4.1 to 4.1
| #S | Loop id | PDB | Disc | #Non-core | Annotation | Chain(s) | Standardized name for chain | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 1-7 | 2-6 | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | HL_2A64_002 | 2A64 | 0.2998 | 1 | T-loop with 2 stacked bulged bases | A | ribonuclease P RNA | C | 69 | U | 70 | G | 71 | A | 72 | G | 73 | A | 74 | G | 76 | cWW | tWH |
| 2 | HL_4WF9_010 | 4WF9 | 0.2030 | 1 | T-loop with 2 stacked bulged bases | X | LSU rRNA | C | 348 | U | 349 | G | 350 | G | 351 | A | 352 | A | 353 | G | 355 | cWW | tWH |
| 3 | HL_9DFE_009 | 9DFE | 0.2377 | 1 | T-loop with 1 bulged base | 1A | LSU rRNA | U | 305 | U | 306 | G | 307 | G | 308 | G | 309 | A | 310 | G | 312 | cWW | tWH |
| 4 | HL_5DH6_002 | 5DH6 | 0.1374 | 1 | T-loop with 2 stacked bulged bases | A | Hammerhead ribozyme (type III) | C | 27 | U | 28 | G | 29 | G | 30 | G | 31 | A | 32 | G | 34 | cWW | tWH |
| 5 | HL_9E6Q_010 | 9E6Q | 0.1052 | 1 | T-loop with 2 stacked bulged bases (H) | 1 | LSU rRNA | C | 333 | U | 334 | G | 335 | G | 336 | A | 337 | A | 338 | G | 340 | cWW | tWH |
| 6 | HL_8B0X_041 | 8B0X | 0.1289 | 1 | T-loop with 2 stacked bulged bases (H) | a | LSU rRNA | C | 305 | U | 306 | G | 307 | G | 308 | A | 309 | A | 310 | G | 312 | cWW | tWH |
| 7 | HL_7A0S_010 | 7A0S | 0.1277 | 1 | T-loop with 1 bulged base | X | LSU rRNA | C | 316 | U | 317 | G | 318 | G | 319 | A | 320 | A | 321 | G | 323 | cWW | tWH |
| 8 | HL_3F2X_001 | 3F2X | 0.0000 | 2 | T-loop with 2 bulged bases not stacked | X | FMN riboswitch | G | 17 | U | 18 | G | 19 | A | 20 | A | 21 | A | 22 | C | 25 | cWW | tWH |
| 9 | HL_6DN2_001 | 6DN2 | 0.0808 | 2 | T-loop with 2 bulged bases not stacked | X | RNA RIBOSWITCH | G | 17 | U | 18 | G | 19 | A | 20 | A | 21 | A | 22 | C | 25 | cWW | tWH |
| 10 | HL_4FRG_001 | 4FRG | 0.1179 | 2 | T-loop with 2 bulged bases not stacked | B | cobalamin riboswitch aptamer domain | G | 28 | U | 29 | G | 30 | A | 31 | A | 32 | A | 33 | C | 36 | cWW | tWH |
| 11 | HL_6DN2_003 | 6DN2 | 0.1097 | 2 | T-loop with 2 bulged bases not stacked | Y | RNA (56-MER) | G | 68 | U | 69 | G | 70 | A | 71 | A | 72 | A | 73 | C | 76 | cWW | tWH |
| 12 | HL_3F2X_004 | 3F2X | 0.1154 | 2 | T-loop with 2 bulged bases not stacked | X | FMN riboswitch | G | 68 | U | 69 | G | 70 | A | 71 | A | 72 | A | 73 | C | 76 | cWW | tWH |
| 13 | HL_8P9A_117 | 8P9A | 0.1622 | 1 | T-loop with 1 bulged base | AR | LSU rRNA | U | 194 | U | 195 | G | 196 | G | 197 | A | 198 | A | 199 | A | 201 | cWW | tWH |
| 14 | HL_8OI5_005 | 8OI5 | 0.1437 | 1 | T-loop with 2 stacked bulged bases (H) | 1 | LSU rRNA | U | 193 | U | 194 | G | 195 | G | 196 | A | 197 | A | 198 | A | 200 | cWW | tWH |
| 15 | HL_9AXU_005 | 9AXU | 0.1538 | 1 | T-loop with 1 bulged base (H) | 2 | LSU rRNA | U | 201 | U | 202 | G | 203 | G | 204 | A | 205 | A | 206 | A | 208 | cWW | tWH |
| 16 | HL_4V9F_010 | 4V9F | 0.1181 | 1 | T-loop with 2 stacked bulged bases | 0 | LSU rRNA | U | 312 | U | 313 | G | 314 | G | 315 | A | 316 | A | 317 | A | 319 | cWW | tWH |
| 17 | HL_8K1E_002 | 8K1E | 0.1923 | 2 | T-loop with 2 stacked bulged bases | A | MALAT1-associated small cytoplasmic RNA/MEN beta RNA | G | 39 | U | 40 | U | 41 | C | 42 | G | 43 | A | 44 | C | 47 | cWW | tWH |
| 18 | HL_4WZD_221 | 4WZD | 0.3721 | 2 | T-loop with 2 stacked bulged bases | 3L | tRNA | G | 62||||P_1 | 5MU | 63||||P_1 | PSU | 64||||P_1 | C | 65||||P_1 | G | 66||||P_1 | A | 67||||P_1 | C | 70||||P_1 | ncWW | tWH |
| 19 | HL_6UGI_001 | 6UGI | 0.3254 | 2 | T-loop with 2 bulged bases not stacked | A | tRNA(Asp) acceptor stem/T stem-loop | G | 12 | U | 13 | U | 14 | C | 15 | G | 16 | A | 17 | C | 20 | cWW | tWH |
| 20 | HL_3VJR_001 | 3VJR | 0.3652 | 2 | T-loop with 2 bulged bases not stacked | B | tRNA CCA-acceptor | G | 13 | U | 14 | U | 15 | C | 16 | G | 17 | A | 18 | C | 21 | cWW | tWH |
| 21 | HL_8GLP_005 | 8GLP | 0.4125 | 1 | T-loop with 2 stacked bulged bases (H) | L5 | LSU rRNA | U | 204 | C | 205 | U | 206 | G | 207 | A | 208 | U | 209 | G | 211 | cWW | |
| 22 | HL_6GSK_219 | 6GSK | 0.7576 | 2 | T-loop related | 3L | tRNA | G | 53 | U | 54 | U | 55 | C | 56 | G | 57 | A | 58 | C | 61 | cWW |
3D structures
Complete motif including flanking bases
| Sequence | Counts |
|---|---|
| GUGAAAUUC | 5 |
| CUGGAAAG | 3 |
| UUGGAACA | 3 |
| GUUCGAGUC | 2 |
| CUGAGAUG | 1 |
| UUGGGAAG | 1 |
| CUGGGAUG | 1 |
| CUGGAAUG | 1 |
| UUGGAAUA | 1 |
| GCGAAUC | 1 |
| GUUCGAUCC | 1 |
| UCUGAUCG | 1 |
| GUUCGAAUC | 1 |
Non-Watson-Crick part of the motif
| Sequence | Counts |
|---|---|
| UGAAAUU | 5 |
| UGGAAA | 3 |
| UGGAAC | 3 |
| UGGAAU | 2 |
| UUCGAGU | 2 |
| UGAGAU | 1 |
| UGGGAA | 1 |
| UGGGAU | 1 |
| (5MU)(PSU)CGAAU | 1 |
| UUCGAUC | 1 |
| CUGAUC | 1 |
| UUCGAAU | 1 |
Release history
| Release | 4.1 |
|---|---|
| Date | 2025-09-10 |
| Status | Updated, 1 parent |
Parent motifs
This motif has no parent motifs.
Children motifs
This motif has no children motifs.- Annotations
-
- T-loop with 2 bulged bases not stacked (7)
- T-loop with 2 stacked bulged bases (6)
- T-loop with 2 stacked bulged bases (H) (4)
- T-loop with 1 bulged base (3)
- T-loop related (1)
- T-loop with 1 bulged base (H) (1)
- Basepair signature
- cWW-tWH-F-F-F
- Heat map statistics
- Min 0.05 | Avg 0.29 | Max 0.90
Coloring options: