Motif IL_65553.3 Version IL_65553.3 of this group appears in releases 0.9 to 0.9
#S | Loop id | PDB | Disc | #Non-core | Annotation | Chain(s) | Standardized name | 1 | 2 | 3 | 4 | 5 | break | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 1-12 | 2-10 | 2-11 | 3-4 | 3-10 | 3-11 | 4-7 | 4-9 | 5-6 | 5-10 | 6-10 | 7-8 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | IL_3NPB_003 | 3NPB | 0.4019 | 1 | A | TL5 RNA | C | 17 | A | 18 | G | 19 | A | 20 | G | 21 | * | C | 31 | G | 32 | A | 33 | G | 35 | A | 36 | A | 37 | G | 38 | cWW | ncSH | tSs | cWW | |||||||||
2 | IL_4A1B_062 | 4A1B | 0.3345 | 1 | 1 | 26S RRNA | U | 1441 | G | 1442 | G | 1443 | A | 1444 | G | 1445 | * | C | 1414 | C | 1415 | U | 1416 | G | 1418 | A | 1419 | A | 1420 | G | 1421 | cWW | tSH | ntSH | ntSs | tHS | cWW | |||||||
3 | IL_1S72_048 | 1S72 | 0.3039 | 1 | 0 | LSU rRNA | U | 1338 | G | 1339 | G | 1340 | A | 1341 | C | 1342 | * | G | 1312 | A | 1313 | U | 1314 | G | 1316 | A | 1317 | A | 1318 | G | 1319 | cWW | tSH | tSH | ntSs | tHS | cWW | |||||||
4 | IL_2ZJR_043 | 2ZJR | 0.3133 | 1 | X | LSU rRNA | U | 1247 | G | 1248 | G | 1249 | A | 1250 | G | 1251 | * | C | 1221 | G | 1222 | G | 1223 | G | 1225 | A | 1226 | A | 1227 | G | 1228 | cWW | tSH | tSH | tHS | cWW | ||||||||
5 | IL_2QBG_047 | 2QBG | 0.3196 | 1 | B | 23S rRNA | U | 1234 | G | 1235 | G | 1236 | A | 1237 | G | 1238 | * | C | 1208 | U | 1209 | G | 1210 | G | 1212 | A | 1213 | A | 1214 | G | 1215 | cWW | tSH | ntSH | ntHS | cWW | ||||||||
6 | IL_3U5H_064 | 3U5H | 0.2195 | 1 | 5 | 25S rRNA | U | 1415 | C | 1416 | G | 1417 | A | 1418 | A | 1419 | * | U | 1388 | G | 1389 | A | 1390 | G | 1392 | A | 1393 | A | 1394 | G | 1395 | cWW | tSH | tSH | tSs | tHS | cWW | |||||||
7 | IL_3V2F_044 | 3V2F | 0.1550 | 1 | A | 23S Ribosomal RNA | U | 1234 | G | 1235 | G | 1236 | A | 1237 | G | 1238 | * | C | 1208 | G | 1209 | A | 1210 | G | 1212 | A | 1213 | A | 1214 | G | 1215 | cWW | tSH | tSH | tHS | cWW | ||||||||
8 | IL_3GX5_002 | 3GX5 | 0.0000 | 1 | A | RNA (94-MER) | U | 17 | G | 18 | G | 19 | A | 20 | G | 21 | * | C | 31 | G | 32 | A | 33 | G | 35 | A | 36 | A | 37 | A | 38 | cWW | tSH | tSH | tSs | tHS | cWW | |||||||
9 | IL_3V7E_006 | 3V7E | 0.1496 | 1 | D | SAM-I riboswitch | U | 217 | G | 218 | G | 219 | A | 220 | G | 221 | * | C | 231 | G | 232 | A | 233 | G | 235 | A | 236 | A | 237 | A | 238 | cWW | tSH | ntSs | tHS | cWW | ||||||||
10 | IL_3U4M_004 | 3U4M | 0.1736 | 1 | Kink-turn | B | LSU rRNA | G | 2155 | G | 2156 | G | 2157 | A | 2158 | G | 2159 | * | C | 2129 | U | 2130 | G | 2131 | G | 2133 | A | 2134 | A | 2135 | C | 2136 | cWW | tSH | tSH | tSs | tHS | cWW | ||||||
11 | IL_4AOB_002 | 4AOB | 0.3364 | 1 | Kink-turn | A | SAM-I riboswitch | G | 17 | C | 18 | A | 19 | A | 20 | G | 21 | * | U | 31 | G | 32 | A | 33 | G | 35 | A | 36 | C | 37 | C | 38 | cWW | cWB | tSs | tHS | cWW | |||||||
12 | IL_1S72_004 | 1S72 | 0.3515 | 1 | 0 | LSU rRNA | G | 77 | G | 78 | G | 79 | A | 80 | G | 81 | * | C | 93 | G | 94 | A | 95 | G | 97 | A | 98 | A | 99 | C | 100 | cWW | tSH | ntSH | ntSs | tHS | cWW | ntsS | ||||||
13 | IL_3V2F_004 | 3V2F | 0.3883 | 1 | A | 23S Ribosomal RNA | G | 81 | G | 82 | G | 83 | A | 84 | G | 85 | * | C | 97 | G | 98 | U | 99 | G | 102 | A | 103 | U | 104 | C | 105 | cWW | tSH | ntSs | tHS | cWW | ntsS | |||||||
14 | IL_4GXY_005 | 4GXY | 0.3524 | 1 | Kink-turn | A | Adenosylcobalamin riboswitch | G | 82 | G | 83 | G | 84 | A | 85 | G | 86 | * | C | 139 | G | 140 | A | 141 | G | 143 | A | 144 | U | 145 | C | 146 | cWW | tSH | ntSs | tHS | cWW | ncsS | ||||||
15 | IL_1T0K_001 | 1T0K | 0.3471 | 1 | Kink-turn | C+D | RNA (13-mer) + RNA (16-mer) | C | 9 | G | 10 | G | 11 | A | 12 | G | 13 | * | C | 54 | A | 55 | G | 56 | G | 58 | A | 59 | U | 60 | G | 61 | cWW | ntSH | tSs | ntHS | cWW | |||||||
16 | IL_4GMA_003 | 4GMA | 0.4696 | 1 | Kink-turn | Z | Adenosylcobalamin riboswitch | A | 93 | G | 94 | G | 95 | A | 96 | C | 97 | * | G | 143 | G | 144 | A | 145 | G | 147 | A | 148 | G | 149 | U | 150 | ncWW | tSH | ntSs | tHS | cWW | ntsS | ncsS | |||||
17 | IL_3U5F_051 | 3U5F | 0.4959 | 1 | 6 | 18S rRNA | G | 895 | U | 896 | C | 897 | A | 898 | G | 899 | * | C | 910 | U | 911 | U | 912 | G | 914 | A | 915 | U | 916 | U | 917 | ncWW | ntSs | tHS | cWW | tsS | ncsS | |||||||
18 | IL_2ZJR_004 | 2ZJR | 0.4942 | 1 | X | LSU rRNA | A | 80 | C | 81 | G | 82 | A | 83 | G | 84 | * | C | 96 | U | 97 | U | 98 | G | 100 | A | 101 | C | 102 | U | 103 | cWW | ncWB | tSs | ntHS | cWW | ntsS | |||||||
19 | IL_1S72_032 | 1S72 | 0.5483 | 2 | 0 | LSU rRNA | C | 936 | C | 937 | G | 938 | A | 939 | G | 940 | * | C | 1026 | G | 1027 | U | 1028 | G | 1031 | A | 1032 | C | 1033 | G | 1034 | cWW | cWB | ntSs | tHS | ncWW | ||||||||
20 | IL_2AW7_014 | 2AW7 | 0.6943 | 2 | A | 16S ribosomal RNA | G | 242 | A | 243 | U | 245 | A | 246 | G | 247 | * | C | 277 | G | 278 | A | 279 | G | 281 | A | 282 | U | 283 | C | 284 | cWW | tWH | cwW | tHS | cWW | ncsS | ncSH | ||||||
21 | IL_2XZM_017 | 2XZM | 0.7245 | 2 | A | 18S RRNA | U | 302 | A | 303 | C | 305 | A | 306 | G | 307 | * | C | 339 | A | 340 | G | 341 | C | 343 | A | 344 | C | 345 | G | 346 | ncWW | ncWB | cWw | ntSs | cWW | ||||||||
22 | IL_3U5F_019 | 3U5F | 0.7169 | 2 | 6 | 18S rRNA | U | 311 | A | 312 | C | 314 | A | 315 | A | 316 | * | U | 348 | U | 349 | U | 350 | A | 352 | A | 353 | C | 354 | G | 355 | cWW | tWH | cWw | tSs | ntHS | cWW | ncsS | ||||||
23 | IL_3RW6_002 | 3RW6 | 0.6179 | 4 | Kink-turn with non-sequential stacking | H | constitutive transport element(CTE)of Mason-Pfizer monkey virus RNA | U | 11 | A | 12 | C | 16 | A | 17 | G | 18 | * | C | 43 | A | 44 | A | 45 | G | 47 | A | 48 | C | 49 | G | 50 | cWW | tWH | cWw | tSs | tHS | cWW | ncsS |
3D structures
Complete motif including flanking bases
Sequence | Counts |
---|---|
CAGAG*CGACGAAG | 1 |
UGGAG*CCUAGAAG | 1 |
UGGAC*GAUGGAAG | 1 |
UGGAG*CGGAGAAG | 1 |
UGGAG*CUGCGAAG | 1 |
UCGAA*UGACGAAG | 1 |
CGAUGAAG*UGGAG | 1 |
UGGAG*CGACGAAA | 1 |
UGGAG*CGAUGAAA | 1 |
GGGAG*CUGUGAAC | 1 |
GCAAG*UGAUGACC | 1 |
GGGAG*CGAAGAAC | 1 |
GGGAG*CGUGGAUC | 1 |
GGGAG*CGAGGAUC | 1 |
CGGAG*CAGAGAUG | 1 |
AGGAC*GGAUGAGU | 1 |
GUCAG*CUUGGAUU | 1 |
ACGAG*CUUUGACU | 1 |
CCGAG*CGUUUGACG | 1 |
GAUUAG*CGACGAUC | 1 |
UAUCAG*CAGUCACG | 1 |
UAUCAA*UUUCAACG | 1 |
UAAGACAG*CAAUGACG | 1 |
Non-Watson-Crick part of the motif
Sequence | Counts |
---|---|
AGA*GACGAA | 1 |
GGA*CUAGAA | 1 |
GGA*AUGGAA | 1 |
GGA*GGAGAA | 1 |
GGA*UGCGAA | 1 |
CGA*GACGAA | 1 |
GAUGAA*GGA | 1 |
GGA*GACGAA | 1 |
GGA*GAUGAA | 1 |
GGA*UGUGAA | 1 |
CAA*GAUGAC | 1 |
GGA*GAAGAA | 1 |
GGA*GUGGAU | 1 |
GGA*GAGGAU | 1 |
GGA*AGAGAU | 1 |
GGA*GAUGAG | 1 |
UCA*UUGGAU | 1 |
CGA*UUUGAC | 1 |
CGA*GUUUGAC | 1 |
AUUA*GACGAU | 1 |
AUCA*AGUCAC | 1 |
AUCA*UUCAAC | 1 |
AAGACA*AAUGAC | 1 |
Release history
Release | 0.9 |
---|---|
Date | 2013-02-17 |
Status | Updated, 1 parent |
Parent motifs
Parent motif | Common motif instances | Only in IL_65553.3 | Only in the parent motif |
---|---|---|---|
IL_65553.2 Compare | IL_1S72_032, IL_3U5H_064, IL_3U4M_004, IL_3V7E_006, IL_2QBG_047, IL_3U5F_019, IL_2ZJR_004, IL_1S72_048, IL_4A1B_062, IL_3GX5_002, IL_2ZJR_043, IL_3V2F_044, IL_1S72_004, IL_2AW7_014, IL_1T0K_001, IL_4AOB_002, IL_3NPB_003, IL_3U5F_051, IL_2XZM_017, IL_3RW6_002, IL_3V2F_004 | IL_4GMA_003, IL_4GXY_005 |
Children motifs
Child motif | Common motif instances | Only in IL_65553.3 | Only in the child motif |
---|---|---|---|
IL_65553.4 Compare | IL_4GXY_005, IL_3V2F_044, IL_2AW7_014, IL_1S72_048, IL_2XZM_017, IL_3V2F_004, IL_3U5H_064, IL_2QBG_047, IL_1S72_004, IL_3GX5_002, IL_2ZJR_043, IL_3V7E_006, IL_2ZJR_004, IL_4A1B_062, IL_3RW6_002, IL_3U5F_051, IL_1S72_032, IL_1T0K_001, IL_4GMA_003, IL_3U5F_019, IL_4AOB_002, IL_3NPB_003 | IL_3U4M_004 |
- Annotations
-
- Kink-turn (5)
- Kink-turn with non-sequential stacking (1)
- Basepair signature
- cWW-tSH-tWH-cWW-tSH-tHS-tSS-tSS-R-cWW
- Heat map statistics
- Min 0.15 | Avg 0.46 | Max 0.87
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