Motif IL_28947.3 Version IL_28947.3 of this group appears in releases 1.14 to 1.14
| #S | Loop id | PDB | Disc | #Non-core | Annotation | Chain(s) | Standardized name for chain | 1 | 2 | break | 3 | 4 | 1-4 | 2-3 | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | IL_4NVV_107 | 4NVV | 0.1986 | 1 | B | 5S rRNA | C | 17 | G | 18 | * | C | 65 | G | 67 | cWW | cWW | |
| 2 | IL_1S72_099 | 1S72 | 0.1734 | 1 | Major groove intercalation (H) | 9 | 5S rRNA | C | 15 | G | 16 | * | C | 64 | G | 66 | cWW | cWW |
| 3 | IL_1S72_022 | 1S72 | 0.0982 | 2 | Multiple bulged bases (H) | 0 | LSU rRNA | C | 726 | G | 727 | * | C | 699 | G | 702 | cWW | cWW |
| 4 | IL_2QBG_060 | 2QBG | 0.0000 | 1 | B | LSU rRNA | C | 1499 | G | 1500 | * | C | 1489 | G | 1491 | cWW | cWW | |
| 5 | IL_2AW7_005 | 2AW7 | 0.0913 | 2 | A | SSU rRNA | U | 103 | G | 104 | * | C | 63 | A | 66 | cWW | cWW | |
| 6 | IL_1FJG_005 | 1FJG | 0.1120 | 2 | Multiple bulged bases (H) | A | SSU rRNA | C | 103 | G | 104 | * | C | 63 | G | 66 | cWW | cWW |
| 7 | IL_2NZ4_007 | 2NZ4 | 0.1531 | 1 | R+G | glmS ribozyme | C | 52 | G | 53 | * | C | 5 | G | 7 | cWW | cWW | |
| 8 | IL_3U5H_137 | 3U5H | 0.2393 | 1 | 5 | LSU rRNA | C | 3324 | G | 3325 | * | U | 3381 | G | 3383 | cWW | cWW | |
| 9 | IL_4NVV_061 | 4NVV | 0.2324 | 1 | A | LSU rRNA | C | 1545 | G | 1546 | * | U | 1535 | G | 1537 | cWW | cWW | |
| 10 | IL_2QBG_086 | 2QBG | 0.3005 | 1 | B | LSU rRNA | U | 2220 | G | 2221 | * | U | 2202 | G | 2204 | cWW | cWW | |
| 11 | IL_4A1B_063 | 4A1B | 0.2761 | 1 | 1 | LSU rRNA | U | 1437 | A | 1438 | * | U | 1424 | G | 1426 | cWW | cWW | |
| 12 | IL_1S72_042 | 1S72 | 0.2313 | 1 | Single bulged G (H) | 0 | LSU rRNA | C | 1225 | G | 1226 | * | U | 1136 | G | 1138 | cWW | cWW |
| 13 | IL_4NVV_072 | 4NVV | 0.3324 | 2 | A | LSU rRNA | U | 1872 | G | 1873 | * | U | 1920 | A | 1923 | cWW | cWW | |
| 14 | IL_4IOA_067 | 4IOA | 0.3955 | 2 | Multiple bulged bases | X | LSU rRNA | U | 1833 | G | 1834 | * | U | 1881 | A | 1884 | cWW | cWW |
| 15 | IL_4NVV_034 | 4NVV | 0.4685 | 1 | A | LSU rRNA | G | 927 | G | 928 | * | U | 941 | C | 943 | cWW | ||
| 16 | IL_1XOK_001 | 1XOK | 0.4239 | 2 | Major groove intercalation | A | alfalfa mosaic virus RNA 3' UTR | C | 846 | U | 847 | * | A | 864 | G | 867 | cWW | cWW |
| 17 | IL_1XOK_002 | 1XOK | 0.5122 | 2 | Major groove intercalation | A+B | alfalfa mosaic virus RNA 3' UTR | C | 868 | C | 869 | * | G | 877 | G | 880 | cWW | cWW |
| 18 | IL_387D_001 | 387D | 0.5905 | 2 | Multiple bulged bases | A | RNA Pseudoknot | U | 1 | C | 2 | * | G | 15 | A | 18 | cWW | cWW |
| 19 | IL_1U9S_008 | 1U9S | 0.7593 | 1 | Stack outside cWW | A | RNase P class A | G | 195 | C | 196 | * | G | 217 | C | 219 | cWW | cWW |
| 20 | IL_4FAW_014 | 4FAW | 0.7955 | 2 | A | Group II catalytic intron D1-D4-3 | U | 365 | A | 366 | * | U | 375 | G | 378 | cWW | cWW | |
| 21 | IL_4C7O_003 | 4C7O | 0.8595 | 1 | Single bulged C | E | SRP RNA | C | 12 | G | 13 | * | C | 31 | G | 33 | cWW | cWW |
| 22 | IL_3U5H_063 | 3U5H | 0.8187 | 1 | 5 | LSU rRNA | C | 1420 | G | 1421 | * | C | 1385 | G | 1387 | cWW | cWW | |
| 23 | IL_1KXK_003 | 1KXK | 0.8472 | 2 | Multiple bulged bases | A | Group II catalytic intron | U | 28 | G | 29 | * | C | 42 | G | 45 | cWW | cWW |
| 24 | IL_3U5H_019 | 3U5H | 0.5476 | 1 | 5 | LSU rRNA | U | 512 | G | 513 | * | C | 577 | G | 579 | cWW | cWW |
3D structures
Complete motif including flanking bases
| Sequence | Counts |
|---|---|
| CG*CAG | 5 |
| UG*UGAA | 2 |
| CG*CAUG | 1 |
| UG*CGAA | 1 |
| CG*CGUG | 1 |
| CG*UUG | 1 |
| CG*UAG | 1 |
| UG*UUG | 1 |
| UA*UUG | 1 |
| CG*UGG | 1 |
| GG*UAC | 1 |
| CU*AAUG | 1 |
| CC*GAUG | 1 |
| UC*GGAA | 1 |
| GC*GGC | 1 |
| UA*UACG | 1 |
| CG*CCG | 1 |
| UG*CACG | 1 |
| UG*CAG | 1 |
Non-Watson-Crick part of the motif
| Sequence | Counts |
|---|---|
| *A | 8 |
| *GA | 4 |
| *AU | 3 |
| *U | 3 |
| *G | 2 |
| *AC | 2 |
| *GU | 1 |
| *C | 1 |
Release history
| Release | 1.14 |
|---|---|
| Date | 2014-04-27 |
| Status | Updated, 1 parent |
Parent motifs
| Parent motif | Common motif instances | Only in IL_28947.3 | Only in the parent motif |
|---|---|---|---|
| IL_28947.2 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_4NVV_034, IL_4NVV_107, IL_4NVV_061, IL_4NVV_072 | IL_3V2F_069, IL_3V2F_059 |
Children motifs
| Child motif | Common motif instances | Only in IL_28947.3 | Only in the child motif |
|---|---|---|---|
| IL_04465.1 Compare | IL_2QBG_086, IL_2NZ4_007, IL_1S72_042, IL_3U5H_063, IL_4A1B_063, IL_2QBG_060, IL_4NVV_034, IL_3U5H_137, IL_4NVV_061, IL_4C7O_003, IL_1S72_022, IL_1FJG_005, IL_4NVV_107, IL_3U5H_019, IL_1S72_099, IL_2AW7_005, IL_4FAW_014 | IL_387D_001, IL_4IOA_067, IL_1U9S_008, IL_1KXK_003, IL_4NVV_072, IL_1XOK_001, IL_1XOK_002 | IL_2QBG_107, IL_1U9S_006, IL_1S72_045, IL_4CUV_143, IL_3D0U_005, IL_3U5F_033, IL_1FJG_022, IL_4CUX_033, IL_4CUV_067, IL_4BPP_033, IL_2AW7_029, IL_4IOA_101, IL_4CUV_108, IL_4IOA_024 |
| IL_84950.1 Compare | IL_387D_001, IL_1U9S_008, IL_1XOK_001, IL_1KXK_003, IL_4NVV_072, IL_4IOA_067, IL_1XOK_002 | IL_2QBG_086, IL_2NZ4_007, IL_1S72_042, IL_3U5H_063, IL_4A1B_063, IL_2QBG_060, IL_4NVV_034, IL_3U5H_137, IL_4NVV_061, IL_4C7O_003, IL_1S72_022, IL_1FJG_005, IL_4NVV_107, IL_3U5H_019, IL_1S72_099, IL_2AW7_005, IL_4FAW_014 | IL_3U5F_086, IL_4CUX_087 |
- Annotations
-
- (13)
- Multiple bulged bases (3)
- Multiple bulged bases (H) (2)
- Major groove intercalation (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
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