Motif IL_28947.2 Version IL_28947.2 of this group appears in releases 1.9 to 1.13
#S | Loop id | PDB | Disc | #Non-core | Annotation | Chain(s) | Standardized name | 1 | 2 | break | 3 | 4 | 1-4 | 2-3 | ||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | IL_4FAW_014 | 4FAW | 0.7955 | 2 | A | Group II catalytic intron D1-D4-1 | U | 375 | G | 378 | * | U | 365 | A | 366 | cWW | cWW | |
2 | IL_4C7O_003 | 4C7O | 0.8595 | 1 | Single bulged C | E | SRP RNA | C | 31 | G | 33 | * | C | 12 | G | 13 | cWW | cWW |
3 | IL_3U5H_063 | 3U5H | 0.8187 | 1 | 5 | 25S rRNA | C | 1385 | G | 1387 | * | C | 1420 | G | 1421 | cWW | cWW | |
4 | IL_1KXK_003 | 1KXK | 0.8472 | 2 | Multiple bulged bases | A | ai5g group II Self-splicing intron | C | 42 | G | 45 | * | U | 28 | G | 29 | cWW | cWW |
5 | IL_3U5H_019 | 3U5H | 0.5476 | 1 | 5 | 25S rRNA | C | 577 | G | 579 | * | U | 512 | G | 513 | cWW | cWW | |
6 | IL_1S72_099 | 1S72 | 0.1734 | 1 | Major groove intercalation (H) | 9 | 5S rRNA | C | 64 | G | 66 | * | C | 15 | G | 16 | cWW | cWW |
7 | IL_1S72_022 | 1S72 | 0.0982 | 2 | Multiple bulged bases (H) | 0 | LSU rRNA | C | 699 | G | 702 | * | C | 726 | G | 727 | cWW | cWW |
8 | IL_2QBG_060 | 2QBG | 0.0000 | 1 | B | 23S rRNA | C | 1489 | G | 1491 | * | C | 1499 | G | 1500 | cWW | cWW | |
9 | IL_2AW7_005 | 2AW7 | 0.0913 | 2 | A | 16S ribosomal RNA | C | 63 | A | 66 | * | U | 103 | G | 104 | cWW | cWW | |
10 | IL_1FJG_005 | 1FJG | 0.1120 | 2 | Multiple bulged bases (H) | A | SSU rRNA | C | 63 | G | 66 | * | C | 103 | G | 104 | cWW | cWW |
11 | IL_2NZ4_007 | 2NZ4 | 0.1531 | 1 | G+R | substrate strand RNA 13-mer + GlmS ribozyme | C | 5 | G | 7 | * | C | 52 | G | 53 | cWW | cWW | |
12 | IL_3U5H_137 | 3U5H | 0.2393 | 1 | 5 | 25S rRNA | U | 3381 | G | 3383 | * | C | 3324 | G | 3325 | cWW | cWW | |
13 | IL_3V2F_059 | 3V2F | 0.2568 | 1 | A | 23S Ribosomal RNA | U | 1489 | G | 1491 | * | C | 1499 | G | 1500 | cWW | cWW | |
14 | IL_2QBG_086 | 2QBG | 0.3005 | 1 | B | 23S rRNA | U | 2202 | G | 2204 | * | U | 2220 | G | 2221 | cWW | cWW | |
15 | IL_4A1B_063 | 4A1B | 0.2761 | 1 | 1 | 26S RRNA | U | 1424 | G | 1426 | * | U | 1437 | A | 1438 | cWW | cWW | |
16 | IL_1S72_042 | 1S72 | 0.2313 | 1 | Single bulged G (H) | 0 | LSU rRNA | U | 1136 | G | 1138 | * | C | 1225 | G | 1226 | cWW | cWW |
17 | IL_3V2F_069 | 3V2F | 0.3332 | 2 | A | 23S Ribosomal RNA | U | 1898 | A | 1901 | * | U | 1841 | G | 1842 | cWW | cWW | |
18 | IL_4IOA_067 | 4IOA | 0.3955 | 2 | Multiple bulged bases | X | LSU rRNA | U | 1881 | A | 1884 | * | U | 1833 | G | 1834 | cWW | cWW |
19 | IL_1XOK_001 | 1XOK | 0.4239 | 2 | Basepair outside cWW | A | alfalfa mosaic virus RNA 3' UTR | A | 864 | G | 867 | * | C | 846 | U | 847 | cWW | cWW |
20 | IL_1XOK_002 | 1XOK | 0.5122 | 2 | Basepair outside cWW | B+A | alfalfa mosaic virus RNA 3' UTR | G | 877 | G | 880 | * | C | 868 | C | 869 | cWW | cWW |
21 | IL_387D_001 | 387D | 0.5905 | 2 | Multiple bulged bases | A | RNA Pseudoknot | G | 15 | A | 18 | * | U | 1 | C | 2 | cWW | cWW |
22 | IL_1U9S_008 | 1U9S | 0.7593 | 1 | Stack outside cWW | A | RIBONUCLEASE P | G | 217 | C | 219 | * | G | 195 | C | 196 | cWW | cWW |
3D structures
Complete motif including flanking bases
Sequence | Counts |
---|---|
CAG*CG | 4 |
UACG*UA | 1 |
CCG*CG | 1 |
CACG*UG | 1 |
CAG*UG | 1 |
CAUG*CG | 1 |
CGAA*UG | 1 |
CGUG*CG | 1 |
UUG*CG | 1 |
UAG*CG | 1 |
UUG*UG | 1 |
UUG*UA | 1 |
UGG*CG | 1 |
UG*UGAA | 1 |
UGAA*UG | 1 |
AAUG*CU | 1 |
GAUG*CC | 1 |
GGAA*UC | 1 |
GGC*GC | 1 |
Non-Watson-Crick part of the motif
Sequence | Counts |
---|---|
A* | 6 |
AU* | 3 |
GA* | 3 |
U* | 3 |
AC* | 2 |
G* | 2 |
C* | 1 |
GU* | 1 |
*GA | 1 |
Release history
Release | 1.9 | 1.10 | 1.11 | 1.12 | 1.13 |
---|---|---|---|---|---|
Date | 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 |
Parent motifs
Parent motif | Common motif instances | Only in IL_28947.2 | Only in the parent motif |
---|---|---|---|
IL_28947.1 Compare | IL_2QBG_086, IL_2NZ4_007, IL_4IOA_067, IL_1S72_042, IL_1U9S_008, IL_387D_001, IL_2QBG_060, IL_3U5H_063, IL_1FJG_005, IL_1S72_022, IL_1XOK_001, IL_4A1B_063, IL_1XOK_002, IL_3U5H_019, IL_1S72_099, IL_3U5H_137, IL_4FAW_014, IL_3V2F_069, IL_2AW7_005, IL_3V2F_059 | IL_1KXK_003, IL_4C7O_003 | IL_3V2F_107 |
IL_39674.1 Compare | IL_1KXK_003 | IL_2QBG_086, IL_387D_001, IL_4IOA_067, IL_1S72_042, IL_3U5H_063, IL_2NZ4_007, IL_2QBG_060, IL_4A1B_063, IL_3U5H_137, IL_4C7O_003, IL_1S72_022, IL_1XOK_001, IL_1FJG_005, IL_1XOK_002, IL_3U5H_019, IL_1S72_099, IL_2AW7_005, IL_4FAW_014, IL_3V2F_069, IL_3V2F_059, IL_1U9S_008 | IL_3U5F_086, IL_3V2F_082, IL_1S72_093 |
Children motifs
Child motif | Common motif instances | Only in IL_28947.2 | Only in the child motif |
---|---|---|---|
IL_28947.3 Compare | IL_2QBG_086, IL_387D_001, IL_4IOA_067, IL_1S72_042, IL_3U5H_063, IL_2NZ4_007, IL_2QBG_060, IL_4A1B_063, IL_1KXK_003, IL_3U5H_137, IL_4C7O_003, IL_1S72_022, IL_1XOK_001, IL_1FJG_005, IL_1XOK_002, IL_3U5H_019, IL_1S72_099, IL_2AW7_005, IL_4FAW_014, IL_1U9S_008 | IL_3V2F_069, IL_3V2F_059 | IL_4NVV_034, IL_4NVV_107, IL_4NVV_061, IL_4NVV_072 |
- Annotations
-
- (11)
- Multiple bulged bases (3)
- Multiple bulged bases (H) (2)
- Basepair outside cWW (2)
- Single bulged G (H) (1)
- Major groove intercalation (H) (1)
- Stack outside cWW (1)
- Single bulged C (1)
- Basepair signature
- cWW-cWW
- Heat map statistics
- Min 0.09 | Avg 0.51 | Max 0.97
Coloring options: