Motif IL_55938.4 Version IL_55938.4 of this group appears in releases 1.5 to 1.13
#S | Loop id | PDB | Disc | #Non-core | Annotation | Chain(s) | Standardized name | 1 | 2 | 3 | 4 | break | 5 | 6 | 7 | 1-7 | 2-3 | 2-6 | 3-6 | 4-5 | |||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | IL_3U5H_061 | 3U5H | 0.3110 | 1 | 5 | 25S rRNA | G | 1262 | G | 1264 | U | 1265 | G | 1266 | * | C | 1275 | U | 1276 | C | 1277 | cWW | cSH | cWw | cWW | ||
2 | IL_1S72_029 | 1S72 | 0.1744 | 0 | Major groove platform with extra cWW (H) | 0 | LSU rRNA | G | 830 | U | 831 | U | 832 | G | 833 | * | C | 849 | U | 850 | C | 851 | cWW | cSH | cWw | cWW | |
3 | IL_3V2F_022 | 3V2F | 0.1534 | 0 | A | 23S Ribosomal RNA | G | 738 | G | 739 | U | 740 | G | 741 | * | C | 756 | U | 757 | C | 758 | cWW | cSH | cWw | cWW | ||
4 | IL_4IOA_018 | 4IOA | 0.1542 | 0 | X | LSU rRNA | G | 751 | G | 752 | U | 753 | G | 754 | * | C | 769 | U | 770 | C | 771 | cWW | cSH | ntSH | cWw | cWW | |
5 | IL_4A1B_038 | 4A1B | 0.0000 | 0 | 1 | 26S RRNA | G | 894 | A | 895 | U | 896 | A | 897 | * | U | 913 | U | 914 | C | 915 | cWW | cSH | cWw | cWW | ||
6 | IL_3U5F_014 | 3U5F | 0.1919 | 1 | 6 | 18S rRNA | U | 259 | U | 261 | U | 262 | C | 263 | * | G | 204 | U | 205 | A | 206 | cWW | cSH | cWw | cWW | ||
7 | IL_3U5H_033 | 3U5H | 0.1762 | 0 | 5 | 25S rRNA | G | 869 | G | 870 | U | 871 | U | 872 | * | A | 888 | U | 889 | C | 890 | cWW | cSH | cWw | cWW | ||
8 | IL_4BPP_014 | 4BPP | 0.2623 | 1 | A | 18S RRNA | U | 256 | G | 257 | U | 259 | C | 260 | * | G | 199 | U | 200 | A | 201 | cWW | ncSH | cWw | cWW | ||
9 | IL_3V2F_091 | 3V2F | 0.2547 | 1 | A | 23S Ribosomal RNA | G | 2489 | G | 2490 | U | 2492 | U | 2493 | * | A | 2459 | U | 2460 | C | 2461 | cWW | cSH | cWw | cWW | ||
10 | IL_1S72_082 | 1S72 | 0.2382 | 1 | 0 | LSU rRNA | G | 2524 | G | 2525 | U | 2527 | U | 2528 | * | G | 2494 | U | 2495 | C | 2496 | cWW | cSH | cWw | cWW | ||
11 | IL_4A1B_109 | 4A1B | 0.3606 | 1 | 1 | 26S RRNA | U | 2846 | U | 2847 | U | 2849 | U | 2850 | * | G | 2816 | U | 2817 | G | 2818 | cWW | cWw | cWW | |||
12 | IL_3U5H_111 | 3U5H | 0.3840 | 1 | 5 | 25S rRNA | U | 2858 | U | 2859 | U | 2861 | U | 2862 | * | G | 2828 | U | 2829 | G | 2830 | cWW | cWw | cWW | |||
13 | IL_1S72_003 | 1S72 | 0.4285 | 0 | Major groove platform with extra cWW (H) | 0 | LSU rRNA | C | 440 | A | 441 | A | 442 | C | 443 | * | G | 39 | C | 40 | G | 41 | cWW | cSH | cWWa | ncWW | cWW |
14 | IL_2QBZ_004 | 2QBZ | 0.4374 | 0 | X | M-Box RNA, ykoK riboswitch aptamer | C | 33 | U | 34 | C | 35 | C | 36 | * | G | 149 | U | 150 | G | 151 | cWW | cSH | cwW | cWW | ||
15 | IL_3V2F_003 | 3V2F | 0.5397 | 0 | A | 23S Ribosomal RNA | C | 433 | U | 434 | C | 435 | C | 436 | * | G | 42 | A | 43 | G | 44 | cWW | cSH | cWW | cWW | ||
16 | IL_1XJR_001 | 1XJR | 0.7098 | 1 | Isolated basepair with bulged bases | A | s2m RNA | C | 9 | C | 10 | A | 12 | G | 13 | * | C | 39 | A | 40 | G | 41 | cWW | cWW | |||
17 | IL_3P49_009 | 3P49 | 0.6883 | 1 | A | Glycine riboswitch | C | 109 | G | 110 | A | 112 | G | 113 | * | C | 142 | A | 143 | G | 144 | ncWW | ntHS | cWW | |||
18 | IL_3P49_006 | 3P49 | 0.6691 | 1 | A | Glycine riboswitch | C | 34 | G | 35 | A | 37 | G | 38 | * | C | 51 | A | 52 | G | 53 | ncWW | ntHS | ncWW |
3D structures
Complete motif including flanking bases
Sequence | Counts |
---|---|
GGUG*CUC | 2 |
UUUUU*GUG | 2 |
CGAAG*CAG | 2 |
GAGUG*CUC | 1 |
GUUG*CUC | 1 |
GAUA*UUC | 1 |
UUUUC*GUA | 1 |
GGUU*AUC | 1 |
UGAUC*GUA | 1 |
AUC*GGUUU | 1 |
GGCUU*GUC | 1 |
CAAC*GCG | 1 |
CUCC*GUG | 1 |
GAG*CUCC | 1 |
CCGAG*CAG | 1 |
Non-Watson-Crick part of the motif
Sequence | Counts |
---|---|
GU*U | 3 |
UUU*U | 3 |
GAA*A | 2 |
AGU*U | 1 |
UU*U | 1 |
AU*U | 1 |
GAU*U | 1 |
U*GUU | 1 |
GCU*U | 1 |
AA*C | 1 |
UC*U | 1 |
A*UC | 1 |
CGA*A | 1 |
Release history
Release | 1.5 | 1.6 | 1.7 | 1.8 | 1.9 | 1.10 | 1.11 | 1.12 | 1.13 |
---|---|---|---|---|---|---|---|---|---|
Date | 2013-08-03 | 2013-08-31 | 2013-09-28 | 2013-11-05 | 2013-12-07 | 2014-01-04 | 2014-02-01 | 2014-03-01 | 2014-03-29 |
Status | Updated, 1 parent | Exact match | Exact match | Exact match | Exact match | Exact match | Exact match | Exact match | Exact match |
Parent motifs
Parent motif | Common motif instances | Only in IL_55938.4 | Only in the parent motif |
---|---|---|---|
IL_55938.3 Compare | IL_4A1B_038, IL_1XJR_001, IL_1S72_029, IL_3U5F_014, IL_3V2F_091, IL_1S72_003, IL_2QBZ_004, IL_3U5H_061, IL_3U5H_111, IL_1S72_082, IL_4A1B_109, IL_3U5H_033, IL_3P49_006, IL_3V2F_003, IL_3P49_009, IL_4IOA_018, IL_3V2F_022 | IL_4BPP_014 | IL_2XZM_014 |
Children motifs
Child motif | Common motif instances | Only in IL_55938.4 | Only in the child motif |
---|---|---|---|
IL_55938.5 Compare | IL_4A1B_038, IL_1XJR_001, IL_1S72_029, IL_3U5F_014, IL_2QBZ_004, IL_1S72_003, IL_4BPP_014, IL_3U5H_061, IL_3U5H_111, IL_1S72_082, IL_4A1B_109, IL_3U5H_033, IL_3P49_006, IL_3P49_009, IL_4IOA_018 | IL_3V2F_003, IL_3V2F_091, IL_3V2F_022 | IL_1VW3_020, IL_4NVV_024 |
- Annotations
-
- (15)
- Major groove platform with extra cWW (H) (2)
- Isolated basepair with bulged bases (1)
- Basepair signature
- cWW-cSH-cWW-cWW
- Heat map statistics
- Min 0.08 | Avg 0.44 | Max 0.84
Coloring options: