5LMR Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_5LMR_001 | 1/A/12:22 | No text annotation | homologous HL_5J7L_001 NA | |
| HL_5LMR_004 | 1/A/189C:189H | No text annotation | homologous HL_6CZR_075 NA | |
| HL_5LMR_007 | 1/A/296:301 | GNRA | homologous HL_4LFB_007 HL_34789.1 | |
| HL_5LMR_008 | 1/A/320:333 | No text annotation | homologous HL_4LFB_008 HL_39665.1 | |
| HL_5LMR_013 | 1/A/522:527 | No text annotation | geometric HL_4WF9_003 HL_75660.6 | |
| HL_5LMR_014 | 1/A/617:623 | GNRA-like with tWH | homologous HL_4LFB_014 HL_92337.1 | |
| HL_5LMR_016 | 1/A/726:731 | GNRA | homologous HL_4LFB_016 HL_34789.1 | |
| HL_5LMR_017 | 1/A/786:796 | No text annotation | homologous HL_5J7L_017 NA | |
| HL_5LMR_019 | 1/A/862:867 | GNRA | homologous HL_5J7L_019 NA | |
| HL_5LMR_021 | 1/A/963:972 | No text annotation | homologous HL_4LFB_021 HL_97521.1 | |
| HL_5LMR_025 | 1/A/1089:1096 | T-loop related | homologous HL_4LFB_025 HL_63894.1 | |
| HL_5LMR_032 | 1/A/1515:1520 | GNRA | homologous HL_4LFB_032 HL_34789.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_5LMR_002 | No text annotation | ||
| HL_5LMR_003 | GNRA | ||
| HL_5LMR_005 | Mini UNCG | ||
| HL_5LMR_006 | GNRA related | ||
| HL_5LMR_009 | UNCG | ||
| HL_5LMR_010 | GNRA | ||
| HL_5LMR_011 | UNCG | ||
| HL_5LMR_012 | GNRA | ||
| HL_5LMR_015 | No text annotation | ||
| HL_5LMR_018 | Mini UNCG | ||
| HL_5LMR_020 | GNRA | ||
| HL_5LMR_022 | GNRA | ||
| HL_5LMR_023 | No text annotation | ||
| HL_5LMR_024 | GNRA | ||
| HL_5LMR_026 | No text annotation | ||
| HL_5LMR_027 | GNRA | ||
| HL_5LMR_028 | GNRA | ||
| HL_5LMR_029 | T-loop with 3 stacked bulged bases | ||
| HL_5LMR_030 | No text annotation | ||
| HL_5LMR_031 | UNCG | ||
| HL_5LMR_033 | tRNA D-loop | ||
| HL_5LMR_034 | tRNA anticodon loop | ||
| HL_5LMR_035 | T-loop with 2 stacked bulged bases |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_5LMR_001 | 1/A/30:32, 1/A/552:553 | Single bulged G | homologous IL_5J7L_001 NA | |
| IL_5LMR_002 | 1/A/44:45, 1/A/396:398 | Single bulged A | homologous IL_4LFB_002 IL_14190.1 | |
| IL_5LMR_005 | 1/A/63:66, 1/A/103:104 | Multiple bulged bases | homologous IL_4LFB_005 IL_71421.1 | |
| IL_5LMR_006 | 1/A/67:69, 1/A/100:102 | Isolated non-canonical cWW pair | homologous IL_4LFB_006 IL_01003.1 | |
| IL_5LMR_008 | 1/A/132:136, 1/A/227:230 | No text annotation | homologous IL_4LFB_008 IL_60988.1 | |
| IL_5LMR_009 | 1/A/148:153, 1/A/168:174 | tWH-tWH-tHW-tHW | homologous IL_4LFB_009 IL_00680.1 | |
| IL_5LMR_011 | 1/A/242:247, 1/A/277:284 | Kink-turn with non-sequential stacking | homologous IL_5J7L_014 NA | |
| IL_5LMR_020 | 1/A/504:511, 1/A/540:541 | SSU/LSU pseudoknot | homologous IL_5J7L_024 NA | |
| IL_5LMR_021 | 1/A/515:521, 1/A/528:536 | Kink-turn related | geometric IL_4V88_415 NA | |
| IL_5LMR_022 | 1/A/569:575, 1/A/880:881 | No text annotation | homologous IL_4LFB_022 IL_20847.1 | |
| IL_5LMR_023 | 1/A/580:584, 1/A/757:761 | tSH-tHW-tHS | homologous IL_4LFB_023 IL_05821.1 | |
| IL_5LMR_029 | 1/A/662:666, 1/A/740:743 | Tandem non-canonical cWW pairs | homologous IL_4LFB_029 IL_15225.1 | |
| IL_5LMR_032 | 1/A/774:778, 1/A/804:805 | Left turn | homologous IL_4LFB_032 IL_29346.3 | |
| IL_5LMR_033 | 1/A/779:783, 1/A/799:803 | tSH-tHW-tHS | homologous IL_4LFB_033 IL_05821.1 | |
| IL_5LMR_034 | 1/A/887:894, 1/A/905:910 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_4LFB_034 IL_84044.1 | |
| IL_5LMR_035 | 1/A/922:923, 1/A/1393:1395 | Single bulged A | homologous IL_6CZR_147 NA | |
| IL_5LMR_037 | 1/A/933:935, 1/A/1380:1384 | Minor groove platform | homologous IL_5J7L_041 NA | |
| IL_5LMR_038 | 1/A/953:954, 1/A/1226:1228 | Minor groove platform | homologous IL_4LFB_038 IL_34520.1 | |
| IL_5LMR_040 | 1/A/1052:1056, 1/A/1204:1206 | Isolated cWS basepair | homologous IL_4LFB_044 IL_82453.1 | |
| IL_5LMR_043 | 1/A/1061:1063, 1/A/1193:1195 | Isolated non-canonical cWW pair | geometric IL_4LFB_047 IL_68118.1 | |
| IL_5LMR_048 | 1/A/1247:1253, 1/A/1284:1290 | No text annotation | homologous IL_4LFB_051 IL_12056.1 | |
| IL_5LMR_049 | 1/A/1255:1258, 1/A/1277:1282 | 180 degree turn | homologous IL_4LFB_052 IL_08849.1 | |
| IL_5LMR_052 | 1/A/1399:1401, 1/A/1501:1504 | No text annotation | homologous IL_4LFB_056 IL_18228.1 | |
| IL_5LMR_053 | 1/A/1401:1404, 1/A/1497:1501 | No text annotation | geometric IL_4V88_464 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_5LMR_003 | No text annotation | ||
| IL_5LMR_004 | Minor groove platform | ||
| IL_5LMR_007 | Multiple bulged bases | ||
| IL_5LMR_010 | Isolated non-canonical cWW pair | ||
| IL_5LMR_012 | No text annotation | ||
| IL_5LMR_013 | C-loop | ||
| IL_5LMR_014 | Single bulged U | ||
| IL_5LMR_015 | C-loop | ||
| IL_5LMR_016 | Single bulged G | ||
| IL_5LMR_017 | No text annotation | ||
| IL_5LMR_018 | 6x5 Sarcin-Ricin; G-bulge | ||
| IL_5LMR_019 | No text annotation | ||
| IL_5LMR_024 | Major groove platform | ||
| IL_5LMR_025 | Major groove minor groove platform; mini C-loop | ||
| IL_5LMR_026 | No text annotation | ||
| IL_5LMR_027 | Major groove platform; stack outside cWW | ||
| IL_5LMR_028 | Major groove platform | ||
| IL_5LMR_061 | Triple non-canonical cWW pairs | ||
| IL_5LMR_030 | No text annotation | ||
| IL_5LMR_031 | Kink-turn | ||
| IL_5LMR_036 | Single bulged G | ||
| IL_5LMR_039 | Single bulged U | ||
| IL_5LMR_041 | Minor groove platform | ||
| IL_5LMR_042 | Single bulged U | ||
| IL_5LMR_044 | No text annotation | ||
| IL_5LMR_062 | No text annotation | ||
| IL_5LMR_045 | Single stack bend | ||
| IL_5LMR_046 | Minor groove platform | ||
| IL_5LMR_047 | No text annotation | ||
| IL_5LMR_050 | Double sheared | ||
| IL_5LMR_051 | No text annotation | ||
| IL_5LMR_054 | Isolated non-canonical cWW pair | ||
| IL_5LMR_055 | Not an internal loop | ||
| IL_5LMR_063 | Isolated non-canonical cWW pair | ||
| IL_5LMR_056 | Tandem non-canonical cWW pairs | ||
| IL_5LMR_057 | Double sheared | ||
| IL_5LMR_058 | UAA/GAN variation | ||
| IL_5LMR_059 | Isolated non-canonical cWW pair | ||
| IL_5LMR_060 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_5LMR_002 | 1/A/586:588, 1/A/651:654, 1/A/754:755 | No text annotation | geometric J3_6CZR_016 NA | |
| J3_5LMR_016 | 1/A/586:588, 1/A/651:655, 1/A/751:755 | No text annotation | homologous J3_4LFB_015 J3_17385.5 | |
| J3_5LMR_004 | 1/A/826:829, 1/A/857:861, 1/A/868:874 | No text annotation | homologous J3_6CZR_018 NA | |
| J3_5LMR_018 | 1/A/936:939, 1/A/1344:1350, 1/A/1372:1379 | No text annotation | homologous J3_4LFB_002 J3_85722.1 | |
| J3_5LMR_007 | 1/A/955:962, 1/A/973:984, 1/A/1221:1225 | No text annotation | homologous J3_4LFB_004 J3_88451.1 | |
| J3_5LMR_010 | 1/A/1063:1068, 1/A/1107:1113, 1/A/1187:1193 | No text annotation | homologous J3_5J7L_008 NA | |
| J3_5LMR_013 | 1/A/1237:1241, 1/A/1296:1303, 1/A/1334:1337 | No text annotation | homologous J3_4LFB_009 J3_03192.1 | |
| J4_5LMR_001 | 1/A/115:122, 1/A/239:240, 1/A/286:289, 1/A/311:312 | No text annotation | homologous J4_4LFB_001 J4_90044.1 | |
| J4_5LMR_003 | 1/A/575:577, 1/A/764:769, 1/A/810:821, 1/A/879:880 | No text annotation | homologous J4_4LFB_003 J4_14595.1 | |
| J5_5LMR_001 | 1/A/36:39, 1/A/403:406, 1/A/436:442, 1/A/492:500, 1/A/545:548 | No text annotation | homologous J5_4LFB_001 J5_70703.1 | |
| J5_5LMR_002 | 1/A/58:61, 1/A/106:113, 1/A/314:316, 1/A/337:339, 1/A/350:354 | No text annotation | homologous J5_4LFB_002 J5_58574.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_5LMR_001 | No text annotation | ||
| J3_5LMR_014 | No text annotation | ||
| J3_5LMR_015 | No text annotation | ||
| J3_5LMR_003 | No text annotation | ||
| J3_5LMR_005 | No text annotation | ||
| J3_5LMR_006 | No text annotation | ||
| J3_5LMR_008 | No text annotation | ||
| J3_5LMR_009 | No text annotation | ||
| J3_5LMR_011 | No text annotation | ||
| J3_5LMR_012 | No text annotation | ||
| J3_5LMR_017 | No text annotation | ||
| J4_5LMR_002 | No text annotation | ||
| J4_5LMR_004 | tRNA junction |
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