Motif IL_13959.4 Version IL_13959.4 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 | 8 | 1-8 | 2-7 | 3-6 | 4-5 | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | IL_2O3V_002 | 2O3V | 0.8733 | 1 | Decoding loop related | A+B | RNA (23-mer) | C | 7 | G | 8 | C | 9 | U | 10 | * | A | 38 | A | 39 | A | 41 | G | 42 | cWW | cWWa | cWW | |
2 | IL_2IL9_002 | 2IL9 | 0.7139 | 0 | M | Ribosomal Binding Domain of the IRES RNA | A | 6058 | A | 6059 | U | 6060 | A | 6061 | * | U | 6018 | A | 6019 | U | 6020 | U | 6021 | cWW | ncWW | cWW | ||
3 | IL_2QBG_017 | 2QBG | 0.2409 | 0 | B | 23S rRNA | G | 536 | G | 537 | A | 538 | G | 539 | * | U | 554 | G | 555 | A | 556 | C | 557 | cWW | tSH | tHS | cWW | |
4 | IL_4BPP_087 | 4BPP | 0.1762 | 0 | A | 18S RRNA | U | 1682 | A | 1683 | A | 1684 | A | 1685 | * | U | 1640 | G | 1641 | A | 1642 | A | 1643 | cWW | tSH | tHS | cWW | |
5 | IL_3U5F_088 | 3U5F | 0.2281 | 0 | 6 | 18S rRNA | C | 1729 | A | 1730 | A | 1731 | A | 1732 | * | U | 1669 | G | 1670 | A | 1671 | G | 1672 | cWW | tSH | tHS | cWW | |
6 | IL_3U5H_120 | 3U5H | 0.2586 | 2 | 5 | 25S rRNA | C | 3004 | A | 3005 | A | 3006 | U | 3007 | * | A | 3139 | G | 3140 | A | 3141 | G | 3144 | cWW | tSH | tHS | cWW | |
7 | IL_4A1B_117 | 4A1B | 0.2511 | 2 | 1 | 26S RRNA | C | 2993 | G | 2994 | A | 2995 | C | 2996 | * | G | 3128 | G | 3129 | A | 3131 | G | 3133 | cWW | tSH | tHS | cWW | |
8 | IL_4BPP_003 | 4BPP | 0.2419 | 1 | A | 18S RRNA | U | 37 | A | 38 | A | 39 | A | 40 | * | U | 458 | G | 459 | C | 461 | A | 462 | cWW | tSH | tHS | cWW | |
9 | IL_4IOA_083 | 4IOA | 0.1426 | 0 | Double sheared | X | LSU rRNA | C | 2343 | G | 2344 | A | 2345 | G | 2346 | * | C | 2329 | G | 2330 | A | 2331 | G | 2332 | cWW | tSH | tHS | cWW |
10 | IL_3V2F_086 | 3V2F | 0.1176 | 0 | A | 23S Ribosomal RNA | C | 2364 | G | 2365 | A | 2366 | G | 2367 | * | C | 2350 | G | 2351 | A | 2352 | G | 2353 | cWW | tSH | tHS | cWW | |
11 | IL_2QBG_088 | 2QBG | 0.1321 | 0 | B | 23S rRNA | C | 2364 | G | 2365 | A | 2366 | G | 2367 | * | C | 2350 | G | 2351 | A | 2352 | G | 2353 | cWW | tSH | tHS | cWW | |
12 | IL_1SAQ_002 | 1SAQ | 0.0000 | 0 | Double sheared | B+A | RNA (8-mer) | C | 111 | G | 112 | A | 113 | G | 114 | * | C | 103 | G | 104 | A | 105 | G | 106 | cWW | tSH | tHS | cWW |
13 | IL_1SA9_001 | 1SA9 | 0.1049 | 0 | B+A | RNA (8-mer) | C | 111 | G | 112 | A | 113 | G | 114 | * | C | 103 | G | 104 | A | 105 | G | 106 | cWW | tSH | tHS | cWW | |
14 | IL_3D0U_002 | 3D0U | 0.1695 | 0 | Double sheared | A | Lysine Riboswitch RNA | C | 67 | G | 68 | A | 69 | G | 70 | * | C | 16 | G | 17 | A | 18 | G | 19 | cWW | tSH | tHS | cWW |
15 | IL_4A1B_007 | 4A1B | 0.2366 | 0 | 1 | 26S RRNA | C | 162 | A | 163 | A | 164 | C | 165 | * | G | 254 | G | 255 | A | 256 | G | 257 | cWW | tSH | ntHS | cWW | |
16 | IL_4BPP_085 | 4BPP | 0.2264 | 0 | A | 18S RRNA | U | 1625 | A | 1626 | A | 1627 | C | 1628 | * | G | 1697 | G | 1698 | A | 1699 | A | 1700 | cWW | tSH | tHS | cWW | |
17 | IL_1FJG_059 | 1FJG | 0.2804 | 0 | Double sheared (H) | A | SSU rRNA | U | 1481 | G | 1482 | A | 1483 | C | 1484 | * | G | 1416 | G | 1417 | A | 1418 | G | 1419 | cWW | tSH | tHS | cWW |
18 | IL_4A1B_005 | 4A1B | 0.2883 | 0 | 1 | 26S RRNA | C | 138 | A | 139 | A | 140 | C | 141 | * | G | 125 | A | 126 | A | 127 | G | 128 | cWW | tSH | cWW | ||
19 | IL_3U5F_013 | 3U5F | 0.2827 | 0 | 6 | 18S rRNA | C | 186 | G | 187 | A | 188 | C | 189 | * | G | 196 | A | 197 | A | 198 | G | 199 | cWW | tSH | tHS | cWW | |
20 | IL_4IOA_058 | 4IOA | 0.2882 | 0 | Double sheared | X | LSU rRNA | U | 1530 | C | 1531 | A | 1532 | G | 1533 | * | C | 1491 | A | 1492 | A | 1493 | G | 1494 | cWW | tHS | cWW | |
21 | IL_1S72_098 | 1S72 | 0.3625 | 0 | 0 | LSU rRNA | C | 2873 | G | 2874 | A | 2875 | G | 2876 | * | C | 2881 | G | 2882 | A | 2883 | G | 2884 | cWW | tSH | tHS | cWW | |
22 | IL_4A1B_132 | 4A1B | 0.3705 | 0 | 1 | 26S RRNA | C | 3316 | G | 3317 | A | 3318 | U | 3319 | * | A | 3300 | G | 3301 | A | 3302 | G | 3303 | cWW | tSH | tHS | cWW | |
23 | IL_3U5F_085 | 3U5F | 0.3596 | 0 | 6 | 18S rRNA | C | 1653 | G | 1654 | A | 1655 | U | 1656 | * | A | 1744 | G | 1745 | A | 1746 | G | 1747 | cWW | tSH | tHS | cWW | |
24 | IL_3DIR_002 | 3DIR | 0.4369 | 0 | A | RNA (174-MER) | C | 70 | G | 71 | A | 72 | G | 73 | * | C | 19 | G | 20 | A | 21 | G | 22 | cWW | tSH | tHS | cWW | |
25 | IL_2AW7_065 | 2AW7 | 0.4639 | 0 | A | 16S ribosomal RNA | U | 1481 | G | 1482 | A | 1483 | C | 1484 | * | G | 1416 | G | 1417 | A | 1418 | G | 1419 | cWW | tSH | tHS | cWW | |
26 | IL_3U5H_141 | 3U5H | 0.5328 | 0 | 5 | 25S rRNA | C | 3360 | G | 3361 | A | 3362 | U | 3363 | * | A | 3342 | G | 3343 | A | 3344 | G | 3345 | cWW | tSH | ntSs | cWW |
3D structures
Complete motif including flanking bases
Sequence | Counts |
---|---|
CGAG*CGAG | 8 |
CGAU*AGAG | 3 |
UGAC*GGAG | 2 |
CGCU*AAAAG | 1 |
AAUA*UAUU | 1 |
GGAG*UGAC | 1 |
UAAA*UGAA | 1 |
CAAA*UGAG | 1 |
CAAU*AGAACG | 1 |
CGAC*GGAAAG | 1 |
UAAA*UGACA | 1 |
CAAC*GGAG | 1 |
UAAC*GGAA | 1 |
CAAC*GAAG | 1 |
CGAC*GAAG | 1 |
UCAG*CAAG | 1 |
Non-Watson-Crick part of the motif
Sequence | Counts |
---|---|
GA*GA | 14 |
AA*GA | 4 |
GC*AAA | 1 |
AU*AU | 1 |
AA*GAAC | 1 |
GA*GAAA | 1 |
AA*GAC | 1 |
AA*AA | 1 |
GA*AA | 1 |
CA*AA | 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, 2 parents | Exact match | Exact match | Exact match | Exact match | Exact match | Exact match | Exact match | Exact match |
Parent motifs
Children motifs
Child motif | Common motif instances | Only in IL_13959.4 | Only in the child motif |
---|---|---|---|
IL_13959.5 Compare | IL_4BPP_003, IL_4IOA_058, IL_1SAQ_002, IL_2QBG_088, IL_3U5F_085, IL_4A1B_117, IL_4A1B_132, IL_3U5H_141, IL_3U5H_120, IL_3U5F_088, IL_2O3V_002, IL_3D0U_002, IL_4IOA_083, IL_4A1B_005, IL_1FJG_059, IL_4A1B_007, IL_1S72_098, IL_3DIR_002, IL_2QBG_017, IL_3U5F_013, IL_2IL9_002, IL_4BPP_087, IL_4BPP_085, IL_1SA9_001, IL_2AW7_065 | IL_3V2F_086 | IL_1VW3_072, IL_4NVV_085 |
- Annotations
-
- (20)
- Double sheared (4)
- Double sheared (H) (1)
- Decoding loop related (1)
- Basepair signature
- cWW-tSH-tHS-cWW
- Heat map statistics
- Min 0.07 | Avg 0.39 | Max 0.95
Coloring options: