6W7M Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_6W7M_001 | 1/A/12:22 | No text annotation | homologous HL_5J7L_001 HL_89881.5 | |
| HL_6W7M_002 | 1/A/80:89 | No text annotation | ||
| HL_6W7M_003 | 1/A/158:163 | GNRA | homologous HL_4LFB_003 HL_37824.7 | |
| HL_6W7M_004 | 1/A/186:191 | GNRA | homologous HL_5J7L_004 HL_37824.7 | |
| HL_6W7M_005 | 1/A/206:213 | No text annotation | ||
| HL_6W7M_006 | 1/A/259:267 | GNRA related | homologous HL_5J7L_006 HL_84299.4 | |
| HL_6W7M_007 | 1/A/296:301 | GNRA | homologous HL_5J7L_007 HL_37824.7 | |
| HL_6W7M_008 | 1/A/320:333 | No text annotation | homologous HL_5J7L_008 HL_81205.3 | |
| HL_6W7M_009 | 1/A/342:347 | UNCG | homologous HL_5J7L_009 HL_34617.5 | |
| HL_6W7M_010 | 1/A/379:384 | GNRA | homologous HL_5J7L_010 HL_37824.7 | |
| HL_6W7M_011 | 1/A/419:424 | UNCG | homologous HL_5J7L_011 HL_34617.5 | |
| HL_6W7M_012 | 1/A/462:470 | GNRA related | homologous HL_5J7L_012 HL_81538.2 | |
| HL_6W7M_013 | 1/A/522:527 | No text annotation | geometric HL_4WF9_003 HL_75660.5 | |
| HL_6W7M_014 | 1/A/617:623 | No text annotation | homologous HL_4LFB_014 HL_10453.3 | |
| HL_6W7M_015 | 1/A/689:698 | No text annotation | homologous HL_4LFB_015 HL_75293.5 | |
| HL_6W7M_016 | 1/A/726:731 | GNRA | homologous HL_5J7L_016 HL_37824.7 | |
| HL_6W7M_033 | 1/A/783:799 | No text annotation | ||
| HL_6W7M_017 | 1/A/786:796 | No text annotation | ||
| HL_6W7M_018 | 1/A/840:846 | No text annotation | ||
| HL_6W7M_019 | 1/A/862:867 | GNRA | homologous HL_4LFB_019 HL_37824.7 | |
| HL_6W7M_020 | 1/A/897:902 | GNRA | homologous HL_4LFB_020 HL_37824.7 | |
| HL_6W7M_021 | 1/A/963:972 | No text annotation | homologous HL_4LFB_021 HL_50779.4 | |
| HL_6W7M_022 | 1/A/1012:1017 | No text annotation | geometric HL_4WF9_011 HL_75660.5 | |
| HL_6W7M_023 | 1/A/1028:1033 | No text annotation | geometric HL_4V88_198 NA | |
| HL_6W7M_024 | 1/A/1076:1081 | GNRA | homologous HL_5J7L_023 HL_37824.7 | |
| HL_6W7M_034 | 1/A/1089:1096 | T-loop related | homologous HL_4LFB_025 HL_77436.5 | |
| HL_6W7M_026 | 1/A/1134:1140 | No text annotation | homologous HL_6CZR_097 NA | |
| HL_6W7M_027 | 1/A/1165:1171 | GNRA | homologous HL_4LFB_027 HL_37824.7 | |
| HL_6W7M_028 | 1/A/1265:1270 | GNRA | homologous HL_4LFB_028 HL_37824.7 | |
| HL_6W7M_029 | 1/A/1314:1323 | T-loop with 3 stacked bulged bases | homologous HL_5J7L_028 HL_02887.3 | |
| HL_6W7M_030 | 1/A/1356:1366 | No text annotation | homologous HL_4LFB_030 HL_06226.4 | |
| HL_6W7M_031 | 1/A/1449:1454 | UNCG | homologous HL_5J7L_030 HL_34617.5 | |
| HL_6W7M_035 | 1/A/1514:1521 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_6W7M_025 | No text annotation | ||
| HL_6W7M_032 | tRNA anticodon loop |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_6W7M_001 | 1/A/30:32, 1/A/552:553 | Single bulged G | homologous IL_5J7L_001 IL_00225.13 | |
| IL_6W7M_002 | 1/A/44:45, 1/A/396:398 | Single bulged A | homologous IL_5J7L_002 IL_31462.6 | |
| IL_6W7M_003 | 1/A/47:52, 1/A/359:361 | No text annotation | homologous IL_5J7L_003 IL_14177.2 | |
| IL_6W7M_004 | 1/A/54:56, 1/A/356:357 | Minor groove platform | homologous IL_5J7L_004 IL_51454.3 | |
| IL_6W7M_005 | 1/A/63:66, 1/A/103:104 | Multiple bulged bases | homologous IL_6CZR_117 NA | |
| IL_6W7M_006 | 1/A/67:69, 1/A/99:102 | Minor groove platform with extra cWW | homologous IL_5J7L_006 IL_90351.1 | |
| IL_6W7M_007 | 1/A/70:73, 1/A/97:98 | Minor groove platform | homologous IL_5J7L_007 IL_15052.4 | |
| IL_6W7M_008 | 1/A/75:76, 1/A/93:95 | Stack outside cWW | geometric IL_1U9S_008 IL_66635.5 | |
| IL_6W7M_009 | 1/A/128:131, 1/A/231:233 | Isolated non-canonical cWW pair | homologous IL_5J7L_009 IL_57744.1 | |
| IL_6W7M_010 | 1/A/132:136, 1/A/227:230 | Minor groove platform related | homologous IL_6CZR_120 NA | |
| IL_6W7M_011 | 1/A/144:146, 1/A/176:178 | Isolated cWH basepair | homologous IL_5J7L_011 IL_10167.6 | |
| IL_6W7M_012 | 1/A/147:153, 1/A/168:175 | tWH-tWH-tHW-tHW | homologous IL_5J7L_012 IL_80604.6 | |
| IL_6W7M_013 | 1/A/203:206, 1/A/213:214 | Minor groove platform | geometric IL_3MXH_005 IL_15052.4 | |
| IL_6W7M_014 | 1/A/242:247, 1/A/277:284 | Kink-turn with non-sequential stacking | geometric IL_4V88_402 NA | |
| IL_6W7M_015 | 1/A/249:252, 1/A/274:275 | No text annotation | homologous IL_5J7L_015 IL_47074.2 | |
| IL_6W7M_016 | 1/A/292:293, 1/A/304:308 | C-loop | homologous IL_4LFB_013 IL_03109.3 | |
| IL_6W7M_017 | 1/A/367:369, 1/A/392:393 | Single bulged U | homologous IL_5J7L_017 IL_89505.4 | |
| IL_6W7M_018 | 1/A/371:375, 1/A/389:390 | C-loop | geometric IL_6CZR_127 NA | |
| IL_6W7M_059 | 1/A/375:376, 1/A/387:389 | Single bulged G | homologous IL_5J7L_019 IL_00225.13 | |
| IL_6W7M_020 | 1/A/409:416, 1/A/427:433 | No text annotation | homologous IL_5J7L_020 IL_28026.3 | |
| IL_6W7M_021 | 1/A/440:442, 1/A/492:497 | No text annotation | homologous IL_5J7L_021 IL_33323.1 | |
| IL_6W7M_022 | 1/A/446:450, 1/A/483:488 | tSH-tHW-tWW | homologous IL_5J7L_022 IL_88269.4 | |
| IL_6W7M_023 | 1/A/450:455, 1/A/477:483 | No text annotation | geometric IL_5J7L_023 IL_70801.1 | |
| IL_6W7M_024 | 1/A/504:511, 1/A/540:541 | SSU/LSU pseudoknot | homologous IL_5J7L_024 IL_41203.4 | |
| IL_6W7M_025 | 1/A/515:521, 1/A/528:536 | Kink-turn related | geometric IL_4V88_415 NA | |
| IL_6W7M_026 | 1/A/569:575, 1/A/880:881 | No text annotation | homologous IL_6CZR_134 NA | |
| IL_6W7M_027 | 1/A/580:584, 1/A/757:761 | tSH-tHW-tHS | homologous IL_5J7L_027 IL_17136.7 | |
| IL_6W7M_028 | 1/A/594:596, 1/A/644:645 | Major groove platform | homologous IL_4LFB_024 IL_48076.6 | |
| IL_6W7M_029 | 1/A/597:598, 1/A/640:643 | Major groove minor groove platform; mini C-loop | homologous IL_5J7L_029 IL_68140.4 | |
| IL_6W7M_030 | 1/A/605:612, 1/A/628:633 | No text annotation | homologous IL_5J7L_030 IL_78349.3 | |
| IL_6W7M_031 | 1/A/654:655, 1/A/751:754 | Major groove platform; stack outside cWW | homologous IL_4LFB_027 IL_50694.7 | |
| IL_6W7M_032 | 1/A/658:659, 1/A/746:748 | Single stack bend | homologous IL_5J7L_032 IL_26793.1 | |
| IL_6W7M_065 | 1/A/662:666, 1/A/740:743 | Tandem non-canonical cWW pairs | homologous IL_4LFB_029 IL_85033.2 | |
| IL_6W7M_066 | 1/A/673:677, 1/A/713:717 | Triple non-canonical cWW pairs | homologous IL_4LFB_065 IL_49751.4 | |
| IL_6W7M_035 | 1/A/682:688, 1/A/699:708 | Kink-turn related | geometric IL_8C3A_440 NA | |
| IL_6W7M_061 | 1/A/774:778, 1/A/804:805 | Left turn | homologous IL_5J7L_036 IL_29346.2 | |
| IL_6W7M_037 | 1/A/779:783, 1/A/799:803 | tSH-tHW-tHS | homologous IL_6CZR_145 NA | |
| IL_6W7M_038 | 1/A/887:895, 1/A/904:910 | 9x7 Sarcin-Ricin with inserted C; G-bulge | homologous IL_6CZR_146 NA | |
| IL_6W7M_039 | 1/A/933:935, 1/A/1380:1384 | Minor groove platform | homologous IL_5J7L_041 IL_47078.3 | |
| IL_6W7M_040 | 1/A/953:954, 1/A/1226:1228 | Minor groove platform | homologous IL_4LFB_038 IL_51454.3 | |
| IL_6W7M_041 | 1/A/993:997, 1/A/1044:1045 | Minor groove platform | geometric IL_4LFB_039 IL_47078.3 | |
| IL_6W7M_042 | 1/A/998:999, 1/A/1041:1043 | Single stack bend | homologous IL_5J7L_044 IL_26793.1 | |
| IL_6W7M_043 | 1/A/1048:1050, 1/A/1208:1209 | Single bulged U | homologous IL_4LFB_042 IL_89505.4 | |
| IL_6W7M_044 | 1/A/1051:1056, 1/A/1204:1207 | Tandem non-canonical cWW pairs | geometric IL_4V88_473 NA | |
| IL_6W7M_045 | 1/A/1057:1058, 1/A/1199:1203 | Minor groove platform | homologous IL_4LFB_045 IL_95583.2 | |
| IL_6W7M_046 | 1/A/1060:1061, 1/A/1195:1197 | Single bulged U | homologous IL_4LFB_046 IL_89505.4 | |
| IL_6W7M_047 | 1/A/1061:1063, 1/A/1193:1195 | Isolated non-canonical cWW pair | geometric IL_5J7L_050 IL_28037.2 | |
| IL_6W7M_048 | 1/A/1124:1128, 1/A/1144:1149 | No text annotation | homologous IL_5J7L_051 IL_06691.1 | |
| IL_6W7M_049 | 1/A/1129:1132, 1/A/1142:1143 | Minor groove platform | homologous IL_5J7L_052 IL_15052.4 | |
| IL_6W7M_050 | 1/A/1247:1253, 1/A/1284:1290 | No text annotation | homologous IL_5J7L_054 IL_09129.2 | |
| IL_6W7M_051 | 1/A/1255:1258, 1/A/1277:1282 | 180 degree turn | homologous IL_4LFB_052 IL_11344.2 | |
| IL_6W7M_052 | 1/A/1259:1263, 1/A/1272:1276 | Triple sheared | homologous IL_5J7L_056 IL_17948.2 | |
| IL_6W7M_053 | 1/A/1303:1309, 1/A/1328:1334 | No text annotation | ||
| IL_6W7M_054 | 1/A/1412:1414, 1/A/1486:1488 | No text annotation | ||
| IL_6W7M_063 | 1/A/1416:1419, 1/A/1481:1484 | Double sheared | homologous IL_4LFB_060 IL_09705.15 | |
| IL_6W7M_064 | 1/A/1429:1435, 1/A/1466:1471 | No text annotation | ||
| IL_6W7M_056 | 1/A/1430:1435, 1/A/1466:1470 | Triple sheared related | homologous IL_5J7L_063 IL_80231.1 | |
| IL_6W7M_057 | 1/A/1440:1442, 1/A/1460:1461 | Single bulged A | homologous IL_5J7L_064 IL_31462.6 | |
| IL_6W7M_058 | 1/A/1445:1448, 1/A/1455:1457 | No text annotation | homologous IL_5J7L_065 IL_31531.3 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_6W7M_019 | Single bulged G, near cWW | ||
| IL_6W7M_060 | No text annotation | ||
| IL_6W7M_033 | No text annotation | ||
| IL_6W7M_034 | No text annotation | ||
| IL_6W7M_036 | Other IL | ||
| IL_6W7M_062 | No text annotation | ||
| IL_6W7M_055 | Triple sheared |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_6W7M_001 | 1/A/46:47, 1/A/361:367, 1/A/393:395 | No text annotation | homologous J3_5J7L_001 J3_67856.4 | |
| J3_6W7M_002 | 1/A/586:588, 1/A/651:654, 1/A/754:755 | No text annotation | homologous J3_6CZR_016 NA | |
| J3_6W7M_014 | 1/A/586:588, 1/A/651:655, 1/A/751:755 | No text annotation | homologous J3_4LFB_015 J3_17385.4 | |
| J3_6W7M_003 | 1/A/672:673, 1/A/717:725, 1/A/732:734 | No text annotation | homologous J3_5J7L_003 J3_11934.4 | |
| J3_6W7M_004 | 1/A/826:829, 1/A/857:861, 1/A/868:874 | No text annotation | homologous J3_5J7L_004 J3_85054.4 | |
| J3_6W7M_005 | 1/A/936:939, 1/A/1344:1350, 1/A/1372:1379 | No text annotation | homologous J3_4LFB_002 J3_25303.4 | |
| J3_6W7M_006 | 1/A/943:946, 1/A/1235:1237, 1/A/1337:1340 | No text annotation | homologous J3_6CZR_019 NA | |
| J3_6W7M_007 | 1/A/955:962, 1/A/973:984, 1/A/1221:1225 | No text annotation | homologous J3_5J7L_006 J3_83516.4 | |
| J3_6W7M_008 | 1/A/990:993, 1/A/1045:1047, 1/A/1210:1215 | No text annotation | homologous J3_5J7L_007 J3_82572.1 | |
| J3_6W7M_015 | 1/A/990:997, 1/A/1044:1047, 1/A/1210:1215 | No text annotation | homologous J3_5J7L_053 J3_76475.2 | |
| J3_6W7M_016 | 1/A/1003:1006, 1/A/1023:1027, 1/A/1034:1037 | No text annotation | ||
| J3_6W7M_010 | 1/A/1063:1068, 1/A/1107:1113, 1/A/1187:1193 | No text annotation | homologous J3_5J7L_008 J3_08394.3 | |
| J3_6W7M_011 | 1/A/1073:1075, 1/A/1082:1087, 1/A/1098:1102 | No text annotation | ||
| J3_6W7M_017 | 1/A/1116:1118, 1/A/1155:1161, 1/A/1175:1184 | No text annotation | ||
| J3_6W7M_013 | 1/A/1237:1241, 1/A/1296:1303, 1/A/1334:1337 | No text annotation | ||
| J4_6W7M_001 | 1/A/115:122, 1/A/239:240, 1/A/286:289, 1/A/311:312 | No text annotation | homologous J4_5J7L_001 J4_35578.3 | |
| J4_6W7M_004 | 1/A/141:144, 1/A/178:184, 1/A/193:198, 1/A/219:222 | No text annotation | ||
| J4_6W7M_005 | 1/A/575:577, 1/A/764:769, 1/A/810:821, 1/A/879:880 | No text annotation | homologous J4_5J7L_003 J4_61885.6 | |
| J5_6W7M_001 | 1/A/36:39, 1/A/403:406, 1/A/436:440, 1/A/497:500, 1/A/545:548 | No text annotation | homologous J5_5J7L_001 J5_92941.1 | |
| J5_6W7M_002 | 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_5J7L_002 J5_67416.1 | |
| J5_6W7M_003 | 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_59910.6 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_6W7M_009 | No text annotation | ||
| J3_6W7M_012 | No text annotation | ||
| J4_6W7M_002 | No text annotation | ||
| J4_6W7M_003 | No text annotation |
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