Motif HL_46680.2 Version HL_46680.2 of this group appears in releases 3.87 to 3.87
| #S | Loop id | PDB | Disc | #Non-core | Annotation | Chain(s) | Standardized name | 1 | 2 | 3 | 4 | 5 | 1-5 | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | HL_6MWN_004 | 6MWN | 0.4358 | 2 | Pseudoknot geometry | B | IRES | G | 650 | G | 653 | G | 654 | A | 655 | C | 656 | cWW |
| 2 | HL_5FJC_001 | 5FJC | 0.4547 | 2 | Pseudoknot geometry | A | SAM-I riboswitch | G | 23 | U | 26 | G | 27 | G | 28 | C | 29 | cWW |
| 3 | HL_4AOB_001 | 4AOB | 0.4374 | 2 | Pseudoknot geometry | A | SAM-I riboswitch | G | 23 | U | 26 | G | 27 | G | 28 | C | 29 | cWW |
| 4 | HL_4KQY_001 | 4KQY | 0.3823 | 2 | Pseudoknot geometry | A | SAM-I riboswitch | G | 23 | U | 26 | G | 27 | G | 28 | C | 29 | cWW |
| 5 | HL_6VMY_003 | 6VMY | 0.4494 | 2 | Pseudoknot geometry | A | Cobalamin riboswitch | G | 268 | C | 271 | C | 272 | G | 273 | C | 274 | cWW |
| 6 | HL_5U30_002 | 5U30 | 0.4146 | 2 | Pseudoknot geometry | B | sgRNA | U | 43 | C | 46 | C | 47 | A | 48 | G | 49 | cWW |
| 7 | HL_1U6B_002 | 1U6B | 0.3415 | 1 | Pseudoknot geometry | B | 197-MER | C | 70 | C | 72 | C | 73 | C | 74 | G | 75 | cWW |
| 8 | HL_5TBW_066 | 5TBW | 0.0000 | 1 | Ribsomal LSU H95 | 1 | LSU rRNA | U | 3068 | A | 3070 | U | 3071 | C | 3072 | A | 3073 | cWW |
| 9 | HL_8C3A_067 | 8C3A | 0.0844 | 1 | Ribsomal LSU H95 | 1 | LSU rRNA | U | 3040 | A | 3042 | U | 3043 | C | 3044 | A | 3045 | cWW |
| 10 | HL_4V9F_067 | 4V9F | 0.1787 | 1 | Ribsomal LSU H95 | 0 | LSU rRNA | C | 2737 | A | 2739 | G | 2740 | A | 2741 | G | 2742 | cWW |
| 11 | HL_6UFM_005 | 6UFM | 0.2338 | 1 | Pseudoknot geometry | B | RNA (98-MER) | G | 50 | A | 52 | A | 53 | A | 54 | C | 55 | cWW |
| 12 | HL_5J7L_198 | 5J7L | 0.2291 | 1 | Ribsomal LSU H95 | DA | LSU rRNA | U | 2701 | C | 2703 | C | 2704 | A | 2705 | A | 2706 | cWW |
| 13 | HL_7A0S_064 | 7A0S | 0.2096 | 1 | Ribsomal LSU H95 | X | LSU rRNA | U | 2680 | C | 2682 | C | 2683 | A | 2684 | A | 2685 | cWW |
| 14 | HL_4WF9_061 | 4WF9 | 0.2513 | 1 | Ribsomal LSU H95 | X | LSU rRNA | U | 2728 | C | 2730 | C | 2731 | A | 2732 | A | 2733 | cWW |
| 15 | HL_4PQV_002 | 4PQV | 0.4069 | 2 | Pseudoknot geometry | A | Flavivirus 3' UTR stem loop IV | C | 28 | C | 30 | C | 31 | G | 32 | G | 34 | cWW |
| 16 | HL_7A0S_037 | 7A0S | 0.6545 | 2 | X | LSU rRNA | G | 1508 | A | 1510 | A | 1511 | A | 1512 | C | 1514 | ncWW | |
| 17 | HL_4OQU_002 | 4OQU | 0.7559 | 4 | Pseudoknot geometry | A | SAM-I/IV riboswitch | G | 32 | G | 36 | A | 37 | C | 38 | C | 40 | cWW |
| 18 | HL_8VTW_037 | 8VTW | 0.6771 | 2 | Pseudoknot geometry with 3' bulge | 1A | LSU rRNA | G | 1492 | A | 1494 | A | 1495 | A | 1496 | C | 1498 | cWW |
| 19 | HL_5J7L_170 | 5J7L | 0.7045 | 2 | Pseudoknot geometry with 3' bulge | DA | LSU rRNA | G | 1492 | A | 1494 | A | 1495 | A | 1496 | C | 1498 | cWW |
| 20 | HL_5TBW_032 | 5TBW | 0.8300 | 2 | Pseudoknot geometry with 3' bulge | 1 | LSU rRNA | A | 1506 | C | 1508 | A | 1509 | G | 1510 | U | 1512 | cWW |
| 21 | HL_8C3A_032 | 8C3A | 0.8449 | 2 | Pseudoknot geometry with 3' bulge | 1 | LSU rRNA | A | 1502 | C | 1504 | A | 1505 | G | 1506 | U | 1508 | cWW |
| 22 | HL_7A0S_033 | 7A0S | 0.7562 | 2 | Pseudoknot geometry with 3' bulge | X | LSU rRNA | G | 1337 | U | 1339 | C | 1340 | G | 1341 | C | 1343 | cWW |
| 23 | HL_8VTW_033 | 8VTW | 0.7345 | 2 | Pseudoknot geometry with 3' bulge | 1A | LSU rRNA | G | 1324 | U | 1326 | C | 1327 | G | 1328 | C | 1330 | cWW |
| 24 | HL_4WF9_033 | 4WF9 | 0.6768 | 2 | Pseudoknot geometry with 3' bulge | X | LSU rRNA | G | 1361 | U | 1363 | C | 1364 | G | 1365 | C | 1367 | cWW |
| 25 | HL_4V9F_035 | 4V9F | 0.6774 | 2 | Pseudoknot geometry with 3' bulge | 0 | LSU rRNA | G | 1430 | U | 1432 | G | 1433 | A | 1434 | C | 1436 | cWW |
| 26 | HL_5J7L_166 | 5J7L | 0.7189 | 2 | Pseudoknot geometry with 3' bulge | DA | LSU rRNA | G | 1324 | U | 1326 | A | 1327 | A | 1328 | C | 1330 | cWW |
| 27 | HL_5VJ9_003 | 5VJ9 | 0.7192 | 1 | Pseudoknot geometry with 3' bulge | C | RNA (16-mer) | G | 6 | C | 8 | G | 9 | A | 10 | C | 11 | cWW |
| 28 | HL_5NDH_001 | 5NDH | 0.7194 | 1 | Pseudoknot geometry with 3' bulge | A | RNA (16-mer) | G | 6 | C | 8 | G | 9 | A | 10 | C | 11 | cWW |
| 29 | HL_5NDI_002 | 5NDI | 0.7219 | 1 | Pseudoknot geometry with 3' bulge | B | RNA (20-mer) | G | 8 | A | 9 | C | 10 | G | 11 | C | 13 | cWW |
| 30 | HL_8VTW_040 | 8VTW | 0.6868 | 1 | Pseudoknot geometry with 3' bulge | 1A | LSU rRNA | C | 1631 | A | 1631|||A | A | 1632 | G | 1633 | G | 1635 | cWW |
3D structures
Complete motif including flanking bases
| Sequence | Counts |
|---|---|
| GACUGGC | 3 |
| GACGAC | 3 |
| UGAUCA | 2 |
| UGCCAA | 2 |
| GCAAAUC | 2 |
| AGCAGUU | 2 |
| GGUCGUC | 2 |
| GCUGGAC | 1 |
| GUCCCGC | 1 |
| UUUCCAG | 1 |
| CGCCCG | 1 |
| CGAGAG | 1 |
| GGAAAC | 1 |
| UACCAA | 1 |
| CGCCGAG | 1 |
| GAAAAUC | 1 |
| GACGGACAC | 1 |
| GCUCGUC | 1 |
| GCUGAUC | 1 |
| GUUAAUC | 1 |
| CAAGAG | 1 |
Non-Watson-Crick part of the motif
| Sequence | Counts |
|---|---|
| ACUGG | 3 |
| ACGA | 3 |
| GAUC | 2 |
| GCCA | 2 |
| CAAAU | 2 |
| GCAGU | 2 |
| GUCGU | 2 |
| CUGGA | 1 |
| UCCCG | 1 |
| UUCCA | 1 |
| GCCC | 1 |
| GAGA | 1 |
| GAAA | 1 |
| ACCA | 1 |
| GCCGA | 1 |
| AAAAU | 1 |
| ACGGACA | 1 |
| CUCGU | 1 |
| CUGAU | 1 |
| UUAAU | 1 |
| AAGA | 1 |
Release history
| Release | 3.87 |
|---|---|
| Date | 2024-08-14 |
| Status | Updated, 2 parents |
Parent motifs
This motif has no parent motifs.
Children motifs
This motif has no children motifs.- Annotations
-
- Pseudoknot geometry with 3' bulge (13)
- Pseudoknot geometry (10)
- Ribsomal LSU H95 (6)
- (1)
- Basepair signature
- cWW-F-F-F
- Heat map statistics
- Min 0.06 | Avg 0.56 | Max 0.98
Coloring options: