Motif IL_87904.5 Version IL_87904.5 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 | 5 | break | 6 | 7 | 8 | 9 | 10 | 1-10 | 2-9 | 3-7 | 3-8 | 4-7 | 5-6 | 7-8 | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | IL_2QWY_001 | 2QWY | 0.5350 | 0 | A | SAM-II riboswitch | C | 16 | G | 17 | U | 18 | A | 19 | U | 20 | * | A | 46 | A | 47 | A | 48 | A | 49 | G | 50 | cWW | tSH | tHS | cWW | ||||
2 | IL_4BPP_028 | 4BPP | 0.5342 | 0 | A | 18S RRNA | G | 509 | A | 510 | A | 511 | C | 512 | A | 513 | * | U | 525 | U | 526 | A | 527 | G | 528 | C | 529 | cWW | cWW | tSH | ntHS | cWW | |||
3 | IL_3U5H_112 | 3U5H | 0.4665 | 0 | 5 | 25S rRNA | U | 2835 | C | 2836 | A | 2837 | A | 2838 | G | 2839 | * | C | 2849 | G | 2850 | A | 2851 | C | 2852 | A | 2853 | cWW | ntSH | tHS | cWW | ||||
4 | IL_2QBG_094 | 2QBG | 0.3912 | 0 | B | 23S rRNA | C | 2466 | C | 2467 | A | 2468 | A | 2469 | G | 2470 | * | C | 2480 | G | 2481 | A | 2482 | C | 2483 | G | 2484 | cWW | ncWB | ntSH | tHS | cWW | |||
5 | IL_4A1B_110 | 4A1B | 0.3828 | 0 | 1 | 26S RRNA | C | 2823 | C | 2824 | A | 2825 | A | 2826 | G | 2827 | * | C | 2837 | G | 2838 | A | 2839 | C | 2840 | G | 2841 | cWW | ncWB | tSH | tHS | cWW | |||
6 | IL_4IOA_089 | 4IOA | 0.4062 | 0 | Triple sheared | X | LSU rRNA | C | 2445 | C | 2446 | G | 2447 | A | 2448 | G | 2449 | * | C | 2459 | G | 2460 | G | 2461 | C | 2462 | G | 2463 | cWW | ncWB | ntSH | tHS | cWW | ||
7 | IL_3V2F_092 | 3V2F | 0.4055 | 0 | A | 23S Ribosomal RNA | C | 2466 | C | 2467 | G | 2468 | A | 2469 | G | 2470 | * | C | 2480 | G | 2481 | G | 2482 | C | 2483 | G | 2484 | cWW | cWB | tHS | cWW | ||||
8 | IL_1U6B_002 | 1U6B | 0.3611 | 0 | Triple sheared | B | 197-MER | G | 84 | C | 85 | A | 86 | A | 87 | C | 88 | * | G | 56 | A | 57 | A | 58 | A | 59 | C | 60 | cWW | ncWW | tSH | tHS | cWW | ||
9 | IL_1S72_083 | 1S72 | 0.3261 | 0 | Triple sheared (H) | 0 | LSU rRNA | G | 2501 | C | 2502 | A | 2503 | A | 2504 | G | 2505 | * | C | 2515 | G | 2516 | A | 2517 | C | 2518 | C | 2519 | cWW | cWB | ntSH | tHS | cWW | ||
10 | IL_2AW7_058 | 2AW7 | 0.4247 | 0 | A | 16S ribosomal RNA | G | 1272 | C | 1273 | A | 1274 | A | 1275 | G | 1276 | * | C | 1259 | G | 1260 | A | 1261 | C | 1262 | C | 1263 | cWW | ncWB | tSH | tHS | cWW | |||
11 | IL_3U5F_091 | 3U5F | 0.3672 | 0 | 6 | 18S rRNA | A | 1678 | G | 1679 | G | 1680 | A | 1681 | U | 1682 | * | A | 1719 | G | 1720 | A | 1721 | A | 1722 | U | 1723 | cWW | tSH | tSH | cWW | ||||
12 | IL_1S72_028 | 1S72 | 0.3553 | 0 | 0 | LSU rRNA | U | 815 | G | 816 | G | 817 | A | 818 | A | 819 | * | U | 794 | G | 795 | A | 796 | A | 797 | G | 798 | cWW | tSH | tSH | tHS | cWW | |||
13 | IL_3U5H_032 | 3U5H | 0.3886 | 0 | 5 | 25S rRNA | U | 855 | G | 856 | G | 857 | A | 858 | G | 859 | * | U | 834 | G | 835 | A | 836 | A | 837 | G | 838 | cWW | tSH | tSH | tHS | cWW | |||
14 | IL_3V2F_021 | 3V2F | 0.3683 | 0 | A | 23S Ribosomal RNA | U | 724 | G | 725 | G | 726 | A | 727 | G | 728 | * | U | 703 | G | 704 | A | 705 | A | 706 | G | 707 | cWW | tSH | tSH | tHS | cWW | |||
15 | IL_2QBG_024 | 2QBG | 0.3566 | 0 | B | 23S rRNA | U | 724 | G | 725 | G | 726 | A | 727 | G | 728 | * | U | 703 | G | 704 | A | 705 | A | 706 | G | 707 | cWW | tSH | tSH | tHS | cWW | |||
16 | IL_2QBG_068 | 2QBG | 0.2995 | 0 | B | 23S rRNA | U | 1736 | G | 1737 | G | 1738 | A | 1739 | G | 1740 | * | U | 1720 | G | 1721 | A | 1722 | G | 1723 | G | 1724 | cWW | ntSH | tSH | tHS | cWW | |||
17 | IL_4BPP_090 | 4BPP | 0.2332 | 0 | A | 18S RRNA | U | 1649 | G | 1650 | G | 1651 | A | 1652 | C | 1653 | * | G | 1672 | A | 1673 | A | 1674 | A | 1675 | A | 1676 | cWW | tSH | tSH | tHS | cWW | |||
18 | IL_2A64_005 | 2A64 | 0.2643 | 0 | Triple sheared | A | ribonuclease P RNA | C | 297 | G | 298 | G | 299 | A | 300 | G | 301 | * | C | 284 | G | 285 | A | 286 | A | 287 | G | 288 | cWW | tSH | ntSH | tHS | cWW | ||
19 | IL_3DHS_004 | 3DHS | 0.2697 | 0 | Triple sheared | A | RNase P RNA | C | 297 | G | 298 | G | 299 | A | 300 | G | 301 | * | C | 284 | G | 285 | A | 286 | A | 287 | G | 288 | cWW | tSH | cWW | ncSH | |||
20 | IL_2A64_006 | 2A64 | 0.2106 | 0 | Triple sheared | A | ribonuclease P RNA | C | 347 | G | 348 | G | 349 | A | 350 | G | 351 | * | C | 378 | G | 379 | A | 380 | A | 381 | G | 382 | cWW | tSH | tSH | cWW | |||
21 | IL_4IOA_070 | 4IOA | 0.1630 | 0 | Triple sheared | X | LSU rRNA | U | 1848 | G | 1849 | G | 1850 | A | 1851 | G | 1852 | * | C | 1865 | G | 1866 | A | 1867 | A | 1868 | A | 1869 | cWW | tSH | tSH | ntHS | cWW | ||
22 | IL_3V2F_072 | 3V2F | 0.0000 | 0 | A | 23S Ribosomal RNA | G | 1856 | G | 1857 | G | 1858 | A | 1859 | G | 1860 | * | C | 1882 | G | 1883 | A | 1884 | A | 1885 | C | 1886 | cWW | tSH | tSH | tHS | cWW | |||
23 | IL_3U5H_075 | 3U5H | 0.1944 | 0 | 5 | 25S rRNA | A | 1806 | G | 1807 | G | 1808 | A | 1809 | A | 1810 | * | U | 1645 | G | 1646 | A | 1647 | A | 1648 | U | 1649 | cWW | tSH | tSH | tHS | cWW | |||
24 | IL_3IWN_002 | 3IWN | 0.2754 | 0 | Triple sheared | A | C-di-GMP riboswitch | G | 31 | G | 32 | A | 33 | C | 34 | G | 35 | * | C | 12 | A | 13 | A | 14 | A | 15 | C | 16 | cWW | tSH | ntHS | cWW | |||
25 | IL_4FAW_002 | 4FAW | 0.2391 | 0 | A | Group II catalytic intron D1-D4-1 | G | 113 | G | 114 | A | 115 | C | 116 | G | 117 | * | C | 70 | U | 71 | A | 72 | A | 73 | C | 74 | cWW | tSH | tHS | cWW | ||||
26 | IL_4A1B_125 | 4A1B | 0.3020 | 0 | 1 | 26S RRNA | G | 3189 | A | 3190 | G | 3191 | C | 3192 | G | 3193 | * | U | 3217 | U | 3218 | A | 3219 | A | 3220 | C | 3221 | cWW | tSH | ntSH | ntHSa | cWW | |||
27 | IL_3UCZ_001 | 3UCZ | 0.3647 | 0 | R | RNA (92-MER) | G | 41 | G | 42 | A | 43 | C | 44 | G | 45 | * | C | 22 | A | 23 | A | 24 | A | 25 | C | 26 | cWW | tSH | ntHS | cWW | ||||
28 | IL_1S72_021 | 1S72 | 0.5210 | 0 | AAA cross-strand stack (H) | 0 | LSU rRNA | G | 679 | G | 680 | G | 681 | A | 682 | G | 683 | * | C | 663 | U | 664 | A | 665 | A | 666 | C | 667 | cWW | tSH | ntHW | cWW | |||
29 | IL_2QBG_019 | 2QBG | 0.5184 | 0 | B | 23S rRNA | G | 618 | G | 619 | G | 620 | A | 621 | G | 622 | * | U | 606 | U | 607 | A | 608 | A | 609 | C | 610 | cWW | tSH | ntHW | cWW | ||||
30 | IL_3V2F_016 | 3V2F | 0.5349 | 0 | A | 23S Ribosomal RNA | C | 618 | G | 619 | G | 620 | A | 621 | G | 622 | * | U | 606 | U | 607 | A | 608 | A | 609 | G | 610 | cWW | tSH | ntHW | cWW | ||||
31 | IL_4IOA_012 | 4IOA | 0.6538 | 0 | AAA cross-strand stack | X | LSU rRNA | C | 629 | G | 630 | G | 631 | A | 632 | G | 633 | * | U | 616 | U | 617 | A | 618 | A | 619 | G | 620 | cWW | tSH | cWW |
3D structures
Complete motif including flanking bases
Sequence | Counts |
---|---|
CGGAG*CGAAG | 3 |
CCAAG*CGACG | 2 |
CCGAG*CGGCG | 2 |
GCAAG*CGACC | 2 |
UGGAG*UGAAG | 2 |
GGACG*CAAAC | 2 |
CGUAU*AAAAG | 1 |
GAACA*UUAGC | 1 |
UCAAG*CGACA | 1 |
GCAAC*GAAAC | 1 |
AGGAU*AGAAU | 1 |
UGGAA*UGAAG | 1 |
UGAAG*UGGAG | 1 |
UGGAG*UGAGG | 1 |
UGGAC*GAAAA | 1 |
UGGAG*CGAAA | 1 |
GGGAG*CGAAC | 1 |
AGGAA*UGAAU | 1 |
GGACG*CUAAC | 1 |
GAGCG*UUAAC | 1 |
GGGAG*CUAAC | 1 |
GGGAG*UUAAC | 1 |
UUAAG*CGGAG | 1 |
CGGAG*UUAAG | 1 |
Non-Watson-Crick part of the motif
Sequence | Counts |
---|---|
GGA*GAA | 10 |
CAA*GAC | 5 |
GGA*UAA | 3 |
CGA*GGC | 2 |
GAC*AAA | 2 |
GUA*AAA | 1 |
AAC*UAG | 1 |
CAA*AAA | 1 |
GAA*GGA | 1 |
GGA*GAG | 1 |
GGA*AAA | 1 |
GAC*UAA | 1 |
AGC*UAA | 1 |
UAA*GGA | 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_87904.5 | Only in the parent motif |
---|---|---|---|
IL_87904.4 Compare | IL_2AW7_058, IL_1S72_083, IL_4A1B_110, IL_4IOA_070, IL_3V2F_021, IL_2QWY_001, IL_2QBG_068, IL_1S72_028, IL_2QBG_019, IL_1S72_021, IL_3IWN_002, IL_2A64_005, IL_2A64_006, IL_2QBG_024, IL_3V2F_092, IL_1U6B_002, IL_2QBG_094, IL_3V2F_072, IL_3U5F_091, IL_4IOA_089, IL_4FAW_002, IL_3U5H_112, IL_3U5H_032, IL_3UCZ_001, IL_4A1B_125, IL_3U5H_075, IL_4IOA_012, IL_3V2F_016, IL_3DHS_004 | IL_4BPP_028, IL_4BPP_090 | IL_2XZM_092, IL_2XZM_027 |
Children motifs
Child motif | Common motif instances | Only in IL_87904.5 | Only in the child motif |
---|---|---|---|
IL_87904.6 Compare | IL_4BPP_028, IL_2AW7_058, IL_4IOA_012, IL_4A1B_110, IL_4IOA_070, IL_2QWY_001, IL_2QBG_068, IL_1S72_028, IL_2QBG_019, IL_1S72_021, IL_3IWN_002, IL_2A64_005, IL_2A64_006, IL_4BPP_090, IL_2QBG_024, IL_1U6B_002, IL_2QBG_094, IL_3U5F_091, IL_4IOA_089, IL_4FAW_002, IL_3U5H_112, IL_3U5H_032, IL_3UCZ_001, IL_4A1B_125, IL_3U5H_075, IL_1S72_083, IL_3DHS_004 | IL_3V2F_072, IL_3V2F_092, IL_3V2F_021, IL_3V2F_016 | IL_1VW3_083, IL_4NVV_075, IL_4NVV_023, IL_4NVV_091, IL_4NVV_017 |
- Annotations
-
- (21)
- Triple sheared (7)
- AAA cross-strand stack (H) (1)
- Triple sheared (H) (1)
- AAA cross-strand stack (1)
- Basepair signature
- cWW-tSH-tSH-tHS-cWW
- Heat map statistics
- Min 0.09 | Avg 0.45 | Max 0.84
Coloring options: