Motif HL_00828.1 Version HL_00828.1 of this group appears in releases 3.88 to 3.88
#S | Loop id | PDB | Disc | #Non-core | Annotation | Chain(s) | Standardized name | 1 | 2 | 3 | 4 | 5 | 6 | 1-6 | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | HL_3R4F_005 | 3R4F | 0.4339 | 0 | Pseudoknot geometry | A | pRNA | U | 52 | G | 53 | G | 54 | U | 55 | U | 56 | G | 57 | ncWW |
2 | HL_1U6B_002 | 1U6B | 0.3822 | 0 | Pseudoknot geometry | B | 197-MER | C | 70 | G | 71 | C | 72 | C | 73 | C | 74 | G | 75 | cWW |
3 | HL_5U30_002 | 5U30 | 0.4031 | 1 | Pseudoknot geometry | B | sgRNA | U | 43 | U | 45 | C | 46 | C | 47 | A | 48 | G | 49 | cWW |
4 | HL_6UFM_005 | 6UFM | 0.2346 | 0 | Pseudoknot geometry | B | RNA (98-MER) | G | 50 | G | 51 | A | 52 | A | 53 | A | 54 | C | 55 | cWW |
5 | HL_4V9F_067 | 4V9F | 0.1939 | 0 | Ribsomal LSU H95 | 0 | LSU rRNA | C | 2737 | G | 2738 | A | 2739 | G | 2740 | A | 2741 | G | 2742 | cWW |
6 | HL_8C3A_067 | 8C3A | 0.1958 | 0 | Ribsomal LSU H95 | 1 | LSU rRNA | U | 3040 | G | 3041 | A | 3042 | U | 3043 | C | 3044 | A | 3045 | cWW |
7 | HL_5TBW_066 | 5TBW | 0.2096 | 0 | Ribsomal LSU H95 | 1 | LSU rRNA | U | 3068 | G | 3069 | A | 3070 | U | 3071 | C | 3072 | A | 3073 | cWW |
8 | HL_7A0S_064 | 7A0S | 0.0000 | 0 | Ribsomal LSU H95 | X | LSU rRNA | U | 2680 | A | 2681 | C | 2682 | C | 2683 | A | 2684 | A | 2685 | cWW |
9 | HL_5J7L_198 | 5J7L | 0.0956 | 0 | Ribsomal LSU H95 | DA | LSU rRNA | U | 2701 | G | 2702 | C | 2703 | C | 2704 | A | 2705 | A | 2706 | cWW |
10 | HL_4WF9_061 | 4WF9 | 0.1430 | 0 | Ribsomal LSU H95 | X | LSU rRNA | U | 2728 | G | 2729 | C | 2730 | C | 2731 | A | 2732 | A | 2733 | cWW |
11 | HL_4PQV_002 | 4PQV | 0.4043 | 1 | Pseudoknot geometry | A | Flavivirus 3' UTR stem loop IV | C | 28 | G | 29 | C | 30 | C | 31 | G | 32 | G | 34 | cWW |
12 | HL_3V7E_001 | 3V7E | 0.5200 | 1 | Pseudoknot geometry | C | SAM-I riboswitch | G | 23 | C | 25 | U | 26 | G | 27 | G | 28 | C | 29 | cWW |
13 | HL_6MWN_004 | 6MWN | 0.3923 | 1 | Pseudoknot geometry | B | IRES | G | 650 | U | 652 | G | 653 | G | 654 | A | 655 | C | 656 | cWW |
14 | HL_5FJC_001 | 5FJC | 0.4233 | 1 | Pseudoknot geometry | A | SAM-I riboswitch | G | 23 | C | 25 | U | 26 | G | 27 | G | 28 | C | 29 | cWW |
15 | HL_4AOB_001 | 4AOB | 0.4273 | 1 | Pseudoknot geometry | A | SAM-I riboswitch | G | 23 | C | 25 | U | 26 | G | 27 | G | 28 | C | 29 | cWW |
16 | HL_4KQY_001 | 4KQY | 0.3781 | 1 | Pseudoknot geometry | A | SAM-I riboswitch | G | 23 | C | 25 | U | 26 | G | 27 | G | 28 | C | 29 | cWW |
17 | HL_6VMY_003 | 6VMY | 0.4532 | 1 | Pseudoknot geometry | A | Cobalamin riboswitch | G | 268 | C | 270 | C | 271 | C | 272 | G | 273 | C | 274 | cWW |
18 | HL_7YSE_002 | 7YSE | 0.7093 | 1 | Pseudoknot geometry | E | tRNA | U | 32 | G | 34 | C | 35 | C | 36 | A | 37 | A | 38 | cWW |
19 | HL_6UFM_004 | 6UFM | 0.8326 | 2 | Pseudoknot geometry | B | RNA (98-MER) | G | 13 | A | 16 | U | 17 | C | 18 | A | 19 | C | 20 | cWW |
3D structures
Complete motif including flanking bases
Sequence | Counts |
---|---|
GACUGGC | 4 |
UGAUCA | 2 |
UGCCAA | 2 |
UGGUUG | 1 |
CGCCCG | 1 |
UUUCCAG | 1 |
GGAAAC | 1 |
CGAGAG | 1 |
UACCAA | 1 |
CGCCGAG | 1 |
GCUGGAC | 1 |
GUCCCGC | 1 |
UUGCCAA | 1 |
GCCAUCAC | 1 |
Non-Watson-Crick part of the motif
Sequence | Counts |
---|---|
ACUGG | 4 |
GAUC | 2 |
GCCA | 2 |
GGUU | 1 |
GCCC | 1 |
UUCCA | 1 |
GAAA | 1 |
GAGA | 1 |
ACCA | 1 |
GCCGA | 1 |
CUGGA | 1 |
UCCCG | 1 |
UGCCA | 1 |
CCAUCA | 1 |
Release history
Release | 3.88 |
---|---|
Date | 2024-09-11 |
Status | New id, > 2 parents |
Parent motifs
This motif has no parent motifs.
Children motifs
This motif has no children motifs.- Annotations
-
- Pseudoknot geometry (13)
- Ribsomal LSU H95 (6)
- Basepair signature
- cWW-F-F-F-F
- Heat map statistics
- Min 0.08 | Avg 0.44 | Max 0.97
Coloring options: