Motif IL_83039.5 Version IL_83039.5 of this group appears in releases 3.22 to 3.24
#S | Loop id | PDB | Disc | #Non-core | Annotation | Chain(s) | Standardized name | 1 | 2 | break | 3 | 4 | 1-4 | 2-3 | ||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | IL_3IWN_003 | 3IWN | 0.5894 | 1 | Major groove intercalation | A | C-di-GMP riboswitch | G | 81 | G | 82 | * | C | 42 | C | 44 | cWW | cWW |
2 | IL_3MXH_003 | 3MXH | 0.5257 | 1 | Major groove intercalation | R | c-di-GMP riboswitch | G | 86 | G | 87 | * | C | 52 | C | 54 | cWW | cWW |
3 | IL_1MJI_003 | 1MJI | 0.4169 | 2 | Multiple bulged bases | D | 5S rRNA fragment | C | 30 | C | 31 | * | G | 51 | G | 54 | cWW | cWW |
4 | IL_1ET4_002 | 1ET4 | 0.4012 | 1 | Major groove intercalation | A | RNA APTAMER, 35-MER | C | 218 | C | 219 | * | G | 226 | G | 228 | cWW | cWW |
5 | IL_5TBW_131 | 5TBW | 0.6673 | 1 | Single bulged U | 1 | LSU rRNA | C | 3324 | G | 3325 | * | U | 3381 | G | 3383 | cWW | cWW |
6 | IL_5LYS_008 | 5LYS | 0.5671 | 1 | Single bulged U | B | 7SK RNA | C | 45 | G | 46 | * | C | 62 | G | 64 | cWW | cWW |
7 | IL_5J7L_334 | 5J7L | 0.4810 | 1 | Single bulged U | DA | LSU rRNA | G | 2414 | G | 2415 | * | U | 2401 | C | 2403 | cWW | cWW |
8 | IL_4WF9_088 | 4WF9 | 0.4138 | 1 | Single bulged U | X | LSU rRNA | G | 2441 | G | 2442 | * | U | 2428 | C | 2430 | cWW | cWW |
9 | IL_5TBW_086 | 5TBW | 0.4525 | 1 | Single bulged U | 1 | LSU rRNA | C | 2237 | G | 2238 | * | C | 2204 | G | 2206 | cWW | cWW |
10 | IL_4KZD_001 | 4KZD | 0.3864 | 1 | Single bulged U | R | RNA (84-MER) | C | 10 | G | 11 | * | C | 74 | G | 76 | cWW | cWW |
11 | IL_5J7L_017 | 5J7L | 0.3465 | 1 | Single bulged U | AA | SSU rRNA | C | 392 | A | 393 | * | U | 367 | G | 369 | cWW | cWW |
12 | IL_4V88_439 | 4V88 | 0.3067 | 1 | Single bulged U | A6 | SSU rRNA | C | 1066 | C | 1067 | * | G | 1051 | G | 1053 | cWW | cWW |
13 | IL_5TBW_032 | 5TBW | 0.3432 | 1 | Single bulged U | 1 | LSU rRNA | C | 873 | G | 875 | * | C | 886 | G | 887 | cWW | cWW |
14 | IL_4LFB_046 | 4LFB | 0.3886 | 1 | Single bulged U | A | SSU rRNA | C | 1195 | G | 1197 | * | C | 1060 | G | 1061 | cWW | cWW |
15 | IL_6CZR_156 | 6CZR | 0.4332 | 1 | Single bulged U | 1a | SSU rRNA | C | 1177 | G | 1179 | * | C | 1043 | G | 1044 | cWW | cWW |
16 | IL_4V9F_039 | 4V9F | 0.2333 | 1 | Single bulged U | 0 | LSU rRNA | G | 1108 | G | 1110 | * | C | 1253 | C | 1254 | cWW | cWW |
17 | IL_397D_001 | 397D | 0.2090 | 3 | Multiple bulged bases | A+B | RNA (15-mer) + RNA (12-mer) | A | 22 | G | 26 | * | C | 39 | U | 40 | cWW | cWW |
18 | IL_1S03_005 | 1S03 | 0.2041 | 1 | Single bulged U | B | 47-MER | A | 6 | G | 8 | * | C | 41 | U | 42 | cWW | cWW |
19 | IL_4Y4O_253 | 4Y4O | 0.1843 | 1 | Single bulged U | 2A | LSU rRNA | G | 2067 | G | 2069 | * | C | 2442 | C | 2443 | cWW | cWW |
20 | IL_4IOA_075 | 4IOA | 0.2507 | 1 | Single bulged U | X | LSU rRNA | G | 2050 | G | 2052 | * | C | 2421 | C | 2422 | cWW | cWW |
21 | IL_4WF9_080 | 4WF9 | 0.2305 | 1 | Single bulged U | X | LSU rRNA | G | 2094 | G | 2096 | * | C | 2469 | C | 2470 | cWW | cWW |
22 | IL_4V9F_074 | 4V9F | 0.2769 | 1 | Single bulged U | 0 | LSU rRNA | A | 2108 | G | 2110 | * | C | 2477 | U | 2478 | cWW | cWW |
23 | IL_3NDB_005 | 3NDB | 0.3008 | 1 | Single bulged U | M | SRP RNA | G | 237 | G | 238 | * | C | 139 | C | 141 | cWW | cWW |
24 | IL_4FRG_002 | 4FRG | 0.2513 | 1 | Single bulged U | B | cobalamin riboswitch aptamer domain | G | 23 | G | 25 | * | C | 39 | C | 40 | cWW | cWW |
25 | IL_3TZR_002 | 3TZR | 0.3037 | 1 | Single bulged U | B+A | RNA (16-mer) | G | 105 | G | 107 | * | U | 61 | C | 62 | cWW | cWW |
26 | IL_3MEI_001 | 3MEI | 0.3434 | 1 | Single bulged U | A+B | RNA (23-mer) | C | 7 | G | 8 | * | C | 15 | G | 17 | cWW | cWW |
27 | IL_2ZY6_002 | 2ZY6 | 0.3060 | 1 | Single bulged U | A | phenylalanyl transfer RNA | C | 24 | C | 25 | * | G | 10 | G | 12 | cWW | cWW |
28 | IL_5TBW_053 | 5TBW | 0.3114 | 1 | Single bulged U | 1 | LSU rRNA | C | 1296 | C | 1297 | * | G | 1207 | G | 1209 | cWW | cWW |
29 | IL_2A64_003 | 2A64 | 0.1954 | 1 | Single bulged U | A | ribonuclease P RNA | C | 77 | C | 78 | * | G | 66 | G | 68 | cWW | cWW |
30 | IL_5J7L_046 | 5J7L | 0.1896 | 1 | Single bulged U | AA | SSU rRNA | C | 1208 | C | 1209 | * | G | 1048 | G | 1050 | cWW | cWW |
31 | IL_3W3S_005 | 3W3S | 0.2251 | 1 | Single bulged U | B | Selenocysteine transfer RNA | C | 26||||43_455 | C | 27||||43_455 | * | G | 43||||43_455 | G | 44||||43_455 | cWW | cWW |
32 | IL_3W3S_002 | 3W3S | 0.2251 | 1 | Single bulged U | B | Selenocysteine transfer RNA | C | 26 | C | 27 | * | G | 43 | G | 44 | cWW | cWW |
33 | IL_2PN3_003 | 2PN3 | 0.2541 | 1 | Single bulged U | A+B | RNA (24-mer) + RNA (20-mer) | U | 61 | C | 62 | * | G | 105 | G | 107 | cWW | cWW |
34 | IL_5TBW_134 | 5TBW | 0.2644 | 1 | Single bulged U | 1 | LSU rRNA | U | 3363 | C | 3364 | * | G | 3340 | A | 3342 | cWW | cWW |
35 | IL_4V88_449 | 4V88 | 0.2465 | 1 | Single bulged U | A6 | SSU rRNA | C | 1440 | C | 1441 | * | G | 1268 | G | 1270 | cWW | cWW |
36 | IL_4V9F_107 | 4V9F | 0.2357 | 1 | Single bulged U | 9 | 5S rRNA | C | 95 | C | 96 | * | G | 86 | G | 88 | cWW | cWW |
37 | IL_4LFB_042 | 4LFB | 0.2280 | 1 | Single bulged U | A | SSU rRNA | C | 1208 | C | 1209 | * | G | 1048 | G | 1050 | cWW | cWW |
38 | IL_4V88_407 | 4V88 | 0.1742 | 1 | Single bulged U | A6 | SSU rRNA | U | 463 | A | 464 | * | U | 439 | A | 441 | cWW | cWW |
39 | IL_6CZR_126 | 6CZR | 0.2327 | 1 | Single bulged U | 1a | SSU rRNA | G | 388 | A | 389 | * | U | 363 | C | 365 | cWW | cWW |
40 | IL_2UWM_003 | 2UWM | 0.2313 | 1 | Single bulged U | D | RNA (23-mer) | C | 25 | G | 27 | * | C | 21 | G | 22 | cWW | cWW |
41 | IL_3D2V_001 | 3D2V | 0.1701 | 1 | Single bulged U | A | TPP riboswitch (THI element) | C | 5 | C | 6 | * | G | 73 | G | 75 | cWW | cWW |
42 | IL_3WBM_001 | 3WBM | 0.2074 | 1 | Single bulged U | Y+X | RNA (25-MER) | U | 23 | C | 24 | * | G | 2 | A | 4 | cWW | cWW |
43 | IL_5TBW_093 | 5TBW | 0.1451 | 1 | Single bulged U | 1 | LSU rRNA | G | 2409 | U | 2411 | * | A | 2811 | C | 2812 | cWW | cWW |
44 | IL_4V9F_029 | 4V9F | 0.1588 | 1 | Single bulged U | 0 | LSU rRNA | G | 834 | G | 836 | * | C | 847 | C | 848 | cWW | cWW |
45 | IL_4LFB_014 | 4LFB | 0.0000 | 1 | Single bulged U | A | SSU rRNA | G | 392 | A | 393 | * | U | 367 | C | 369 | cWW | cWW |
46 | IL_4IOA_034 | 4IOA | 0.1629 | 1 | Single bulged U | X | LSU rRNA | A | 1022 | G | 1024 | * | C | 1160 | U | 1161 | cWW | cWW |
47 | IL_1S03_001 | 1S03 | 0.3524 | 1 | Single bulged U | A | 47-MER | A | 6 | G | 8 | * | C | 41 | U | 42 | cWW | cWW |
48 | IL_5TBW_125 | 5TBW | 0.3077 | 1 | Single bulged U | 1 | LSU rRNA | G | 3197 | G | 3199 | * | C | 3193 | C | 3194 | cWW | cWW |
49 | IL_5TBW_050 | 5TBW | 0.2763 | 1 | Single bulged U | 1 | LSU rRNA | A | 1180 | A | 1182 | * | U | 1324 | U | 1325 | cWW | cWW |
50 | IL_4V88_401 | 4V88 | 0.3402 | 1 | Single bulged U | A6 | SSU rRNA | G | 279 | G | 281 | * | C | 275 | C | 276 | cWW | cWW |
51 | IL_5TBW_130 | 5TBW | 0.2954 | 1 | Single bulged U | 1 | LSU rRNA | G | 3318 | A | 3320 | * | U | 3387 | C | 3388 | ncWW | cWW |
52 | IL_5TBW_089 | 5TBW | 0.3045 | 2 | Bulged stacked bases | 1 | LSU rRNA | G | 2276 | C | 2277 | * | G | 2307 | U | 2310 | cWW | cWW |
53 | IL_5J7L_318 | 5J7L | 0.2141 | 2 | Bulged stacked bases | DA | LSU rRNA | G | 1933 | C | 1934 | * | G | 1964 | C | 1967 | cWW | cWW |
54 | IL_4IOA_071 | 4IOA | 0.1792 | 2 | X | LSU rRNA | G | 1916 | C | 1917 | * | G | 1947 | C | 1950 | cWW | cWW | |
55 | IL_5TBW_003 | 5TBW | 0.2051 | 1 | Single bulged U | 1+4 | LSU rRNA + 5.8S rRNA | A | 13 | C | 15 | * | G | 144 | U | 145 | cWW | cWW |
56 | IL_4WF9_038 | 4WF9 | 0.1992 | 1 | Single bulged U | X | LSU rRNA | A | 1055 | A | 1057 | * | U | 1193 | U | 1194 | cWW | cWW |
57 | IL_2OIU_003 | 2OIU | 0.2693 | 1 | Single bulged U | Q | L1 Ribozyme RNA Ligase | A | 41 | C | 42 | * | G | 18 | U | 20 | cWW | cWW |
58 | IL_2PJP_001 | 2PJP | 0.2762 | 1 | Single bulged U | B | SECIS RNA | A | 29 | C | 30 | * | G | 16 | U | 18 | cWW | cWW |
59 | IL_5TBW_012 | 5TBW | 0.2724 | 1 | Single bulged U | 1 | LSU rRNA | A | 204 | C | 205 | * | G | 189 | U | 191 | cWW | cWW |
60 | IL_4V9F_013 | 4V9F | 0.2087 | 1 | Single bulged U | 0 | LSU rRNA | G | 322 | C | 323 | * | G | 307 | C | 309 | cWW | cWW |
61 | IL_4V88_414 | 4V88 | 0.2676 | 1 | Single bulged U | A6 | SSU rRNA | G | 586 | C | 587 | * | G | 557 | C | 559 | cWW | cWW |
62 | IL_5TBW_146 | 5TBW | 0.3082 | 1 | Single bulged U | 4 | 5.8S rRNA | G | 68 | U | 69 | * | A | 89 | C | 91 | cWW | cWW |
63 | IL_4Y4O_215 | 4Y4O | 0.3685 | 1 | Single bulged U | 2A | LSU rRNA | G | 1011 | C | 1013 | * | G | 1149 | C | 1150 | cWW | cWW |
64 | IL_5J7L_279 | 5J7L | 0.3735 | 1 | Single bulged U | DA | LSU rRNA | G | 1011 | C | 1013 | * | G | 1149 | C | 1150 | cWW | cWW |
65 | IL_5J7L_298 | 5J7L | 0.4363 | 1 | Single bulged U | DA | LSU rRNA | G | 1459 | C | 1461 | * | G | 1450 | C | 1451 | cWW | cWW |
66 | IL_4C7O_001 | 4C7O | 0.4103 | 1 | Single bulged U | E | SRP RNA | G | 38 | A | 40 | * | U | 7 | C | 8 | cWW | cWW |
67 | IL_4WF9_030 | 4WF9 | 0.4013 | 1 | Single bulged U | X | LSU rRNA | A | 897 | U | 898 | * | A | 969 | U | 971 | cWW | cWW |
68 | IL_4O26_001 | 4O26 | 0.3834 | 1 | Single bulged U | E | Telomerase TR | G | 193 | C | 194 | * | G | 181 | C | 183 | cWW | cWW |
69 | IL_6JQ6_006 | 6JQ6 | 0.3970 | 1 | Single bulged U | U | RNA (81-MER) | G | 55 | U | 56 | * | A | 38 | C | 40 | cWW | cWW |
70 | IL_6JQ6_003 | 6JQ6 | 0.3970 | 1 | Single bulged U | U | RNA (81-MER) | G | 55||||11_555 | U | 56||||11_555 | * | A | 38||||11_555 | C | 40||||11_555 | cWW | cWW |
71 | IL_6JQ5_003 | 6JQ5 | 0.3871 | 1 | Single bulged U | A | RNA (82-MER) | G | 55 | U | 56 | * | A | 38 | C | 40 | cWW | cWW |
72 | IL_6JQ5_006 | 6JQ5 | 0.4074 | 1 | Single bulged U | B | RNA (82-MER) | G | 55 | U | 56 | * | A | 38 | C | 40 | cWW | cWW |
73 | IL_2A64_002 | 2A64 | 0.3675 | 1 | Single bulged U | A | ribonuclease P RNA | G | 395 | C | 396 | * | G | 51 | C | 53 | cWW | cWW |
74 | IL_2R8S_004 | 2R8S | 0.3074 | 1 | Single bulged U | R | P4-P6 RNA RIBOZYME DOMAIN | A | 192 | C | 193 | * | G | 129 | U | 131 | cWW | cWW |
75 | IL_6MWN_006 | 6MWN | 0.3005 | 1 | Single bulged U | B | IRES | G | 646 | A | 647 | * | U | 659 | C | 661 | cWW | cWW |
76 | IL_5TBW_025 | 5TBW | 0.1840 | 1 | Single bulged U | 1 | LSU rRNA | A | 755 | U | 756 | * | A | 775 | U | 777 | cWW | cWW |
3D structures
Complete motif including flanking bases
Sequence | Counts |
---|---|
CC*GUG | 12 |
GUG*CC | 8 |
GU*AUC | 5 |
CG*CUG | 4 |
CUG*CG | 4 |
AUG*CU | 4 |
AC*GUU | 4 |
GC*GUC | 4 |
GG*CUC | 3 |
GA*UUC | 3 |
GUC*GC | 3 |
GG*UUC | 2 |
UC*GUA | 2 |
AUA*UU | 2 |
GUA*UC | 2 |
GC*GCAC | 2 |
AU*AUU | 2 |
CC*GAAG | 1 |
CG*UUG | 1 |
CA*UUG | 1 |
AUCUG*CU | 1 |
GUG*UC | 1 |
UC*GUG | 1 |
UA*UUA | 1 |
GUU*AC | 1 |
GC*GCAU | 1 |
AUC*GU | 1 |
Non-Watson-Crick part of the motif
Sequence | Counts |
---|---|
*U | 45 |
U* | 26 |
*CA | 3 |
*AA | 1 |
UCU* | 1 |
- Annotations
-
- Single bulged U (68)
- Major groove intercalation (3)
- Multiple bulged bases (2)
- Bulged stacked bases (2)
- (1)
- Basepair signature
- cWW-cWW
- Heat map statistics
- Min 0.05 | Avg 0.39 | Max 0.95
Coloring options: