Motif HL_39895.5 Version HL_39895.5 of this group appears in releases 1.2 to 1.4
| #S | Loop id | PDB | Disc | #Non-core | Annotation | Chain(s) | Standardized name | 1 | 2 | 3 | 4 | 5 | 1-5 | 2-4 | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | HL_2QBG_006 | 2QBG | 0.7219 | 1 | B | 23S rRNA | U | 137 | U | 138 | C | 140 | G | 141 | A | 142 | cWW | tSW | |
| 2 | HL_3U5F_005 | 3U5F | 0.6612 | 1 | 6 | 18S rRNA | C | 230 | U | 231 | C | 233 | G | 234 | G | 235 | ncWW | ||
| 3 | HL_2AW7_023 | 2AW7 | 0.3851 | 1 | A | 16S ribosomal RNA | C | 1028 | U | 1029 | C | 1031 | G | 1032 | G | 1033 | cWW | ||
| 4 | HL_2AW7_005 | 2AW7 | 0.3311 | 1 | A | 16S ribosomal RNA | C | 207 | U | 208 | C | 210 | G | 211 | G | 212 | cWW | ntSW | |
| 5 | HL_1YKV_002 | 1YKV | 0.1795 | 1 | D | Diels-Alder ribozyme | C | 220 | U | 221 | C | 223 | G | 224 | G | 225 | ncWW | tSW | |
| 6 | HL_1F7Y_002 | 1F7Y | 0.2237 | 1 | B | 16S RIBOSOMAL RNA FRAGMENT | C | 32 | U | 33 | C | 35 | G | 36 | G | 37 | cWW | tSW | |
| 7 | HL_1FJG_009 | 1FJG | 0.1660 | 1 | UNCG (H) | A | SSU rRNA | C | 342 | U | 343 | C | 345 | G | 346 | G | 347 | cWW | tSW |
| 8 | HL_1FJG_031 | 1FJG | 0.1679 | 1 | UNCG (H) | A | SSU rRNA | C | 1449 | U | 1450 | C | 1452 | G | 1453 | G | 1454 | cWW | tSW |
| 9 | HL_1F7Y_001 | 1F7Y | 0.1539 | 1 | B | 16S RIBOSOMAL RNA FRAGMENT | C | 8 | U | 9 | C | 11 | G | 12 | G | 13 | cWW | tSW | |
| 10 | HL_1S72_044 | 1S72 | 0.1243 | 1 | UNCG (H) | 0 | LSU rRNA | C | 1769 | U | 1770 | C | 1772 | G | 1773 | G | 1774 | cWW | tSW |
| 11 | HL_2AW7_009 | 2AW7 | 0.1384 | 1 | A | 16S ribosomal RNA | C | 342 | U | 343 | C | 345 | G | 346 | G | 347 | cWW | tSW | |
| 12 | HL_1FJG_011 | 1FJG | 0.1350 | 1 | UNCG (H) | A | SSU rRNA | C | 419 | U | 420 | C | 422 | G | 423 | G | 424 | cWW | tSW |
| 13 | HL_1UN6_003 | 1UN6 | 0.1242 | 1 | UNCG | F | 5S RIBOSOMAL RNA | C | 15 | U | 16 | C | 18 | G | 19 | G | 64 | cWW | tSW |
| 14 | HL_4AY2_001 | 4AY2 | 0.1251 | 1 | UNCG | C | 5'-R-PPP(GP*GP*CP*GP*CP*GP*GP*CP*UP*UP*CP*GP*GP*CP *CP*GP*CP*GP*CP*C)-3' | C | 8 | U | 9 | C | 11 | G | 12 | G | 13 | cWW | tSW |
| 15 | HL_4JF2_003 | 4JF2 | 0.0973 | 1 | UNCG | A | PreQ1-II Riboswitch | C | 60 | U | 61 | C | 63 | G | 64 | G | 65 | cWW | tSW |
| 16 | HL_2QBG_044 | 2QBG | 0.0883 | 1 | B | 23S rRNA | C | 1691 | U | 1692 | C | 1694 | G | 1695 | G | 1696 | cWW | tSW | |
| 17 | HL_1I6U_002 | 1I6U | 0.0000 | 1 | D | 16S RRNA FRAGMENT | C | 16 | U | 17 | C | 19 | G | 20 | G | 21 | cWW | tSW | |
| 18 | HL_3V2F_040 | 3V2F | 0.0874 | 1 | A | 23S Ribosomal RNA | C | 1691 | U | 1692 | C | 1694 | G | 1695 | G | 1696 | cWW | tSW | |
| 19 | HL_3U5H_043 | 3U5H | 0.1424 | 1 | 5 | 25S rRNA | C | 1923 | U | 1924 | C | 1926 | G | 1927 | G | 1928 | cWW | tSW | |
| 20 | HL_4A1B_042 | 4A1B | 0.1374 | 1 | 1 | 26S RRNA | C | 1947 | U | 1948 | C | 1950 | G | 1951 | G | 1952 | cWW | tSW | |
| 21 | HL_4IOA_041 | 4IOA | 0.1525 | 1 | UNCG | X | LSU rRNA | C | 1708 | U | 1709 | C | 1711 | G | 1712 | G | 1713 | cWW | tSW |
| 22 | HL_3U5F_011 | 3U5F | 0.1327 | 1 | 6 | 18S rRNA | C | 414 | C | 415 | A | 417 | G | 418 | G | 419 | cWW | tSW | |
| 23 | HL_2HW8_001 | 2HW8 | 0.0973 | 1 | UNCG | B | 36-MER | C | 15 | U | 16 | C | 18 | G | 19 | G | 20 | cWW | tSW |
| 24 | HL_3UMY_001 | 3UMY | 0.1529 | 1 | UNCG (H) | B | LSU rRNA | C | 2143 | U | 2144 | C | 2146 | G | 2147 | G | 2148 | cWW | tSW |
| 25 | HL_2QBG_040 | 2QBG | 0.2072 | 1 | B | 23S rRNA | C | 1533 | U | 1534 | C | 1536 | G | 1537 | G | 1538 | cWW | tSW | |
| 26 | HL_2AW7_011 | 2AW7 | 0.1776 | 1 | A | 16S ribosomal RNA | C | 419 | U | 420 | C | 422 | G | 423 | G | 424 | cWW | tSW | |
| 27 | HL_2AW7_031 | 2AW7 | 0.1420 | 1 | A | 16S ribosomal RNA | C | 1449 | U | 1450 | C | 1452 | G | 1453 | G | 1454 | cWW | tSW | |
| 28 | HL_1NBS_006 | 1NBS | 0.1825 | 1 | UNCG | B | RNase P class B | C | 152 | U | 153 | C | 155 | G | 156 | G | 157 | cWW | tSW |
| 29 | HL_2XZM_011 | 2XZM | 0.2649 | 1 | A | 18S RRNA | C | 405 | U | 406 | C | 408 | G | 409 | G | 410 | cWW | tSW | |
| 30 | HL_4FAW_008 | 4FAW | 0.3509 | 1 | A | Group II catalytic intron D1-D4-3 | G | 338 | U | 339 | C | 341 | G | 342 | C | 343 | ncWW | tSW | |
| 31 | HL_3V7E_005 | 3V7E | 0.4203 | 1 | UNCG variation (H) | D | SAM-I riboswitch | C | 265 | U | 266 | C | 268 | G | 269 | G | 270 | cWW | |
| 32 | HL_3U5H_012 | 3U5H | 0.6856 | 1 | 5 | 25S rRNA | C | 543 | C | 544 | C | 546 | G | 547 | G | 548 | cWW | ||
| 33 | HL_2NUE_001 | 2NUE | 0.6279 | 1 | GNRA related | C | 46-MER | C | 21 | G | 22 | A | 24 | A | 25 | G | 26 | cWW | ncSW |
| 34 | HL_4A1B_014 | 4A1B | 0.6048 | 1 | 1 | 26S RRNA | C | 626 | U | 627 | A | 629 | G | 630 | G | 631 | cWW | ncWW | |
| 35 | HL_3V2F_049 | 3V2F | 0.8163 | 1 | A | 23S Ribosomal RNA | C | 2143 | U | 2144 | C | 2146 | G | 2147 | G | 2148 | ncWW |
3D structures
Complete motif including flanking bases
| Sequence | Counts |
|---|---|
| CUUCGG | 21 |
| CUACGG | 6 |
| CUCCGG | 2 |
| UUUCGA | 1 |
| CCAAGG | 1 |
| GUUCGC | 1 |
| CCUCGG | 1 |
| CGCAAG | 1 |
| CUAAGG | 1 |
Non-Watson-Crick part of the motif
| Sequence | Counts |
|---|---|
| UUCG | 23 |
| UACG | 6 |
| UCCG | 2 |
| CAAG | 1 |
| CUCG | 1 |
| GCAA | 1 |
| UAAG | 1 |
Release history
Parent motifs
| Parent motif | Common motif instances | Only in HL_39895.5 | Only in the parent motif |
|---|---|---|---|
| HL_39895.4 Compare | HL_1UN6_003, HL_4A1B_014, HL_2HW8_001, HL_1FJG_009, HL_1F7Y_001, HL_1F7Y_002, HL_3V7E_005, HL_2NUE_001, HL_3U5H_012, HL_1FJG_011, HL_1NBS_006, HL_1FJG_031, HL_2AW7_009, HL_2AW7_005, HL_1YKV_002, HL_4IOA_041, HL_1I6U_002, HL_3V2F_049, HL_3V2F_040, HL_3U5F_011, HL_2XZM_011, HL_3UMY_001, HL_3U5H_043, HL_4A1B_042, HL_2AW7_023, HL_3U5F_005, HL_1S72_044, HL_4AY2_001, HL_2QBG_006, HL_4FAW_008, HL_2QBG_040, HL_2QBG_044, HL_2AW7_011, HL_2AW7_031 | HL_4JF2_003 |
Children motifs
| Child motif | Common motif instances | Only in HL_39895.5 | Only in the child motif |
|---|---|---|---|
| HL_39895.6 Compare | HL_1UN6_003, HL_4A1B_014, HL_2HW8_001, HL_1FJG_009, HL_1F7Y_001, HL_1F7Y_002, HL_3V7E_005, HL_2NUE_001, HL_3U5H_012, HL_1FJG_011, HL_1NBS_006, HL_1FJG_031, HL_2AW7_009, HL_2AW7_005, HL_1YKV_002, HL_4IOA_041, HL_1I6U_002, HL_3V2F_049, HL_3V2F_040, HL_3U5F_011, HL_3UMY_001, HL_3U5H_043, HL_4A1B_042, HL_2AW7_023, HL_3U5F_005, HL_1S72_044, HL_4AY2_001, HL_2QBG_006, HL_4FAW_008, HL_4JF2_003, HL_2QBG_040, HL_2QBG_044, HL_2AW7_011, HL_2AW7_031 | HL_2XZM_011 | HL_4BPP_011 |
- Annotations
-
- (22)
- UNCG (6)
- UNCG (H) (5)
- GNRA related (1)
- UNCG variation (H) (1)
- Basepair signature
- cWW-tSW-R
- Heat map statistics
- Min 0.04 | Avg 0.38 | Max 1.01
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