3J2E Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
3D | Loop id | Location | Annotation; motif group | Mapped info |
---|---|---|---|---|
HL_3J2E_001 | 1/N/12:22 | No text annotation | homologous HL_4LFB_001 HL_89881.5 | |
HL_3J2E_002 | 1/N/82:87 | No text annotation | ||
HL_3J2E_003 | 1/N/158:163 | GNRA | homologous HL_4LFB_003 HL_37824.7 | |
HL_3J2E_004 | 1/N/186:191 | GNRA | homologous HL_5J7L_004 HL_37824.7 | |
HL_3J2E_005 | 1/N/207:212 | No text annotation | ||
HL_3J2E_037 | 1/N/259:267 | GNRA related | homologous HL_5J7L_006 HL_84299.4 | |
HL_3J2E_007 | 1/N/296:301 | GNRA | homologous HL_4LFB_007 HL_37824.7 | |
HL_3J2E_008 | 1/N/320:333 | No text annotation | homologous HL_4LFB_008 HL_81205.3 | |
HL_3J2E_009 | 1/N/342:347 | UNCG | homologous HL_6CZR_080 NA | |
HL_3J2E_010 | 1/N/379:384 | GNRA | homologous HL_5J7L_010 HL_37824.7 | |
HL_3J2E_011 | 1/N/419:424 | Externally structured | geometric HL_5TBW_022 NA | |
HL_3J2E_038 | 1/N/459:473 | No text annotation | ||
HL_3J2E_013 | 1/N/522:527 | No text annotation | geometric HL_4WF9_003 HL_75660.5 | |
HL_3J2E_014 | 1/N/617:623 | No text annotation | homologous HL_5J7L_014 HL_10453.3 | |
HL_3J2E_015 | 1/N/689:698 | No text annotation | homologous HL_4LFB_015 HL_75293.5 | |
HL_3J2E_016 | 1/N/726:731 | GNRA | homologous HL_5J7L_016 HL_37824.7 | |
HL_3J2E_034 | 1/N/785:797 | No text annotation | ||
HL_3J2E_017 | 1/N/786:796 | No text annotation | ||
HL_3J2E_018 | 1/N/840:846 | No text annotation | geometric HL_8VM9_005 HL_32346.3 | |
HL_3J2E_019 | 1/N/862:867 | GNRA | homologous HL_4LFB_019 HL_37824.7 | |
HL_3J2E_020 | 1/N/897:902 | GNRA | homologous HL_4LFB_020 HL_37824.7 | |
HL_3J2E_039 | 1/N/963:972 | No text annotation | ||
HL_3J2E_022 | 1/N/1012:1017 | GNRA | homologous HL_4LFB_022 HL_37824.7 | |
HL_3J2E_023 | 1/N/1028:1033 | No text annotation | geometric HL_5U3G_001 HL_75660.5 | |
HL_3J2E_024 | 1/N/1076:1081 | GNRA | homologous HL_6CZR_095 NA | |
HL_3J2E_025 | 1/N/1089:1096 | No text annotation | geometric HL_5TBW_024 NA | |
HL_3J2E_026 | 1/N/1134:1140 | No text annotation | homologous HL_5J7L_025 HL_87954.2 | |
HL_3J2E_027 | 1/N/1165:1171 | GNRA | homologous HL_5J7L_026 HL_93535.1 | |
HL_3J2E_028 | 1/N/1265:1270 | GNRA | geometric HL_6AZ4_001 HL_37824.7 | |
HL_3J2E_029 | 1/N/1314:1323 | T-loop with 3 stacked bulged bases | homologous HL_5J7L_028 HL_02887.3 | |
HL_3J2E_030 | 1/N/1356:1366 | No text annotation | ||
HL_3J2E_031 | 1/N/1449:1454 | UNCG | homologous HL_4LFB_031 HL_34617.5 | |
HL_3J2E_032 | 1/N/1515:1520 | GNRA | homologous HL_4LFB_032 HL_37824.7 |
Problematic loops
# | loop id | Problem | Sequence |
---|---|---|---|
HL_3J2E_006 | No text annotation | ||
HL_3J2E_012 | No text annotation | ||
HL_3J2E_033 | No text annotation | ||
HL_3J2E_035 | GNRA with near cWW | ||
HL_3J2E_021 | No text annotation | ||
HL_3J2E_036 | No text annotation |
Valid loops
3D | Loop id | Location | Annotation; motif group | Mapped info |
---|---|---|---|---|
IL_3J2E_001 | 1/N/30:32, 1/N/552:553 | Single bulged G | homologous IL_6CZR_113 NA | |
IL_3J2E_002 | 1/N/44:45, 1/N/396:398 | Single bulged A | homologous IL_5J7L_002 IL_31462.5 | |
IL_3J2E_003 | 1/N/47:52, 1/N/359:361 | No text annotation | homologous IL_4LFB_003 IL_14177.2 | |
IL_3J2E_004 | 1/N/54:56, 1/N/356:357 | Minor groove platform | homologous IL_5J7L_004 IL_51454.2 | |
IL_3J2E_006 | 1/N/63:66, 1/N/103:104 | Multiple bulged bases | homologous IL_5J7L_005 IL_82107.4 | |
IL_3J2E_007 | 1/N/67:69, 1/N/99:102 | Minor groove platform with extra cWW | homologous IL_5J7L_006 IL_90351.1 | |
IL_3J2E_008 | 1/N/70:73, 1/N/97:98 | Minor groove platform | homologous IL_5J7L_007 IL_15052.4 | |
IL_3J2E_088 | 1/N/75:76, 1/N/93:95 | No text annotation | ||
IL_3J2E_010 | 1/N/128:136, 1/N/227:233 | No text annotation | ||
IL_3J2E_012 | 1/N/144:146, 1/N/176:178 | Isolated cWH basepair | homologous IL_5J7L_011 IL_10167.5 | |
IL_3J2E_013 | 1/N/147:153, 1/N/168:175 | tWH-tWH-tHW-tHW | homologous IL_5J7L_012 IL_80604.6 | |
IL_3J2E_015 | 1/N/202:206, 1/N/213:215 | No text annotation | ||
IL_3J2E_016 | 1/N/242:247, 1/N/277:284 | Kink-turn with non-sequential stacking | homologous IL_5J7L_014 IL_46174.3 | |
IL_3J2E_089 | 1/N/249:252, 1/N/274:275 | No text annotation | homologous IL_5J7L_015 IL_47074.2 | |
IL_3J2E_018 | 1/N/292:293, 1/N/304:308 | No text annotation | ||
IL_3J2E_020 | 1/N/367:369, 1/N/392:393 | Single bulged U | geometric IL_8C3A_068 NA | |
IL_3J2E_079 | 1/N/371:375, 1/N/389:390 | C-loop | homologous IL_5J7L_018 IL_03109.3 | |
IL_3J2E_022 | 1/N/375:376, 1/N/387:389 | Single bulged G | geometric IL_4LFB_016 IL_00225.13 | |
IL_3J2E_080 | 1/N/409:416, 1/N/427:433 | No text annotation | homologous IL_4LFB_017 IL_28026.3 | |
IL_3J2E_025 | 1/N/440:442, 1/N/492:497 | No text annotation | homologous IL_5J7L_021 IL_33323.1 | |
IL_3J2E_026 | 1/N/446:450, 1/N/483:488 | tSH-tHW-tWW | geometric IL_5J7L_022 IL_88269.4 | |
IL_3J2E_027 | 1/N/450:455, 1/N/477:483 | No text annotation | ||
IL_3J2E_029 | 1/N/504:511, 1/N/540:541 | SSU/LSU pseudoknot | homologous IL_5J7L_024 IL_41203.4 | |
IL_3J2E_030 | 1/N/515:521, 1/N/528:536 | No text annotation | ||
IL_3J2E_090 | 1/N/569:575, 1/N/880:881 | No text annotation | homologous IL_6CZR_134 NA | |
IL_3J2E_032 | 1/N/580:584, 1/N/757:761 | tSH-tHW-tHS | homologous IL_5J7L_027 IL_17136.7 | |
IL_3J2E_034 | 1/N/594:596, 1/N/644:645 | Major groove platform | homologous IL_5J7L_028 IL_48076.6 | |
IL_3J2E_035 | 1/N/597:598, 1/N/640:643 | Major groove minor groove platform; mini C-loop | homologous IL_5J7L_029 IL_68140.4 | |
IL_3J2E_037 | 1/N/605:613, 1/N/627:633 | No text annotation | ||
IL_3J2E_038 | 1/N/654:655, 1/N/751:754 | Major groove platform; stack outside cWW | geometric IL_1G1X_001 IL_50694.7 | |
IL_3J2E_039 | 1/N/658:659, 1/N/746:748 | Single stack bend | homologous IL_5J7L_032 IL_26793.1 | |
IL_3J2E_041 | 1/N/662:666, 1/N/740:743 | Tandem non-canonical cWW pairs | homologous IL_5J7L_033 IL_85033.2 | |
IL_3J2E_042 | 1/N/673:677, 1/N/713:717 | Triple non-canonical cWW pairs | homologous IL_5J7L_361 IL_49751.4 | |
IL_3J2E_043 | 1/N/684:688, 1/N/699:706 | Kink-turn | homologous IL_5J7L_035 IL_01488.3 | |
IL_3J2E_044 | 1/N/773:779, 1/N/803:806 | No text annotation | ||
IL_3J2E_082 | 1/N/773:783, 1/N/799:806 | No text annotation | ||
IL_3J2E_045 | 1/N/779:783, 1/N/799:803 | tSH-tHW-tHS | homologous IL_4LFB_033 IL_17136.7 | |
IL_3J2E_047 | 1/N/887:894, 1/N/905:910 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_5J7L_038 IL_41756.4 | |
IL_3J2E_091 | 1/N/921:923, 1/N/1393:1396 | Isolated non-canonical cWW pair | geometric IL_4P3U_007 IL_28037.2 | |
IL_3J2E_048 | 1/N/924:927, 1/N/1390:1392 | No text annotation | geometric IL_4M6D_013 IL_31737.3 | |
IL_3J2E_049 | 1/N/933:935, 1/N/1380:1384 | Minor groove platform | homologous IL_4LFB_037 IL_47078.3 | |
IL_3J2E_050 | 1/N/951:954, 1/N/1226:1230 | Tandem non-canonical cWW pairs | geometric IL_5EW4_002 IL_85033.2 | |
IL_3J2E_051 | 1/N/993:997, 1/N/1044:1045 | Minor groove platform | homologous IL_5J7L_043 IL_47078.3 | |
IL_3J2E_052 | 1/N/998:999, 1/N/1041:1043 | Single stack bend | homologous IL_5J7L_044 IL_26793.1 | |
IL_3J2E_054 | 1/N/1048:1050, 1/N/1208:1209 | Single bulged U | homologous IL_4LFB_042 IL_89505.4 | |
IL_3J2E_055 | 1/N/1052:1056, 1/N/1204:1206 | Isolated cWS basepair | homologous IL_4LFB_044 IL_76319.5 | |
IL_3J2E_056 | 1/N/1057:1058, 1/N/1199:1203 | Minor groove platform | homologous IL_6CZR_155 NA | |
IL_3J2E_057 | 1/N/1060:1061, 1/N/1195:1197 | Single bulged A | homologous IL_5J7L_049 IL_31462.5 | |
IL_3J2E_061 | 1/N/1124:1128, 1/N/1144:1149 | No text annotation | homologous IL_5J7L_051 IL_06691.1 | |
IL_3J2E_062 | 1/N/1129:1132, 1/N/1142:1143 | Minor groove platform | homologous IL_5J7L_052 IL_15052.4 | |
IL_3J2E_063 | 1/N/1158:1162, 1/N/1174:1181 | No text annotation | ||
IL_3J2E_064 | 1/N/1247:1253, 1/N/1284:1290 | No text annotation | homologous IL_5J7L_054 IL_09129.2 | |
IL_3J2E_065 | 1/N/1255:1258, 1/N/1277:1282 | 180 degree turn | homologous IL_5J7L_055 IL_11344.2 | |
IL_3J2E_066 | 1/N/1259:1263, 1/N/1272:1276 | Triple sheared | geometric IL_5J7L_274 IL_17948.2 | |
IL_3J2E_068 | 1/N/1303:1308, 1/N/1329:1334 | No text annotation | homologous IL_5J7L_057 IL_85536.2 | |
IL_3J2E_069 | 1/N/1399:1401, 1/N/1501:1504 | No text annotation | geometric IL_5J7L_058 IL_61438.4 | |
IL_3J2E_070 | 1/N/1401:1404, 1/N/1497:1501 | No text annotation | homologous IL_4LFB_068 IL_65718.4 | |
IL_3J2E_071 | 1/N/1405:1409, 1/N/1491:1496 | Other IL | geometric IL_4WF9_084 NA | |
IL_3J2E_072 | 1/N/1412:1414, 1/N/1486:1488 | Isolated non-canonical cWW pair | homologous IL_4LFB_059 IL_87907.2 | |
IL_3J2E_086 | 1/N/1412:1416, 1/N/1484:1488 | No text annotation | ||
IL_3J2E_074 | 1/N/1416:1419, 1/N/1481:1484 | Double sheared | homologous IL_4LFB_060 IL_09705.15 | |
IL_3J2E_075 | 1/N/1430:1435, 1/N/1466:1470 | Triple sheared related | homologous IL_5J7L_063 IL_80231.1 | |
IL_3J2E_076 | 1/N/1440:1442, 1/N/1460:1461 | Single bulged A | homologous IL_5J7L_064 IL_31462.5 | |
IL_3J2E_092 | 1/N/1445:1448, 1/N/1455:1457 | No text annotation |
Problematic loops
# | loop id | Problem | Sequence |
---|---|---|---|
IL_3J2E_005 | Isolated non-canonical cWW pair | ||
IL_3J2E_078 | No text annotation | ||
IL_3J2E_009 | No text annotation | ||
IL_3J2E_011 | Isolated non-canonical cWW pair | ||
IL_3J2E_014 | Isolated non-canonical cWW pair | ||
IL_3J2E_017 | No text annotation | ||
IL_3J2E_019 | Isolated non-canonical cWW pair | ||
IL_3J2E_021 | No text annotation | ||
IL_3J2E_023 | Isolated cWH basepair | ||
IL_3J2E_024 | No text annotation | ||
IL_3J2E_028 | Isolated non-canonical cWW pair | ||
IL_3J2E_031 | Isolated non-canonical cWW pair | ||
IL_3J2E_036 | Stack and bulge | ||
IL_3J2E_040 | Not an internal loop | ||
IL_3J2E_081 | No text annotation | ||
IL_3J2E_046 | Isolated cWH basepair | ||
IL_3J2E_083 | Tandem non-canonical cWW pairs | ||
IL_3J2E_084 | No text annotation | ||
IL_3J2E_053 | No text annotation | ||
IL_3J2E_058 | Isolated non-canonical cWW pair | ||
IL_3J2E_059 | Isolated non-canonical cWW pair | ||
IL_3J2E_060 | No text annotation | ||
IL_3J2E_085 | No text annotation | ||
IL_3J2E_067 | Isolated non-canonical cWW pair | ||
IL_3J2E_073 | No text annotation | ||
IL_3J2E_087 | No text annotation | ||
IL_3J2E_077 | No text annotation |
Valid loops
3D | Loop id | Location | Annotation; motif group | Mapped info |
---|---|---|---|---|
J3_3J2E_012 | 1/N/46:52, 1/N/359:367, 1/N/393:395 | No text annotation | homologous J3_5J7L_050 J3_46317.4 | |
J3_3J2E_020 | 1/N/586:588, 1/N/651:654, 1/N/754:755 | No text annotation | geometric J3_4LFB_011 J3_56052.5 | |
J3_3J2E_021 | 1/N/586:588, 1/N/651:655, 1/N/751:755 | No text annotation | homologous J3_4LFB_015 J3_17385.4 | |
J3_3J2E_010 | 1/N/672:673, 1/N/717:725, 1/N/732:734 | No text annotation | homologous J3_5J7L_003 J3_11934.4 | |
J3_3J2E_002 | 1/N/826:829, 1/N/857:861, 1/N/868:874 | No text annotation | ||
J3_3J2E_003 | 1/N/936:939, 1/N/1344:1350, 1/N/1372:1379 | No text annotation | homologous J3_4LFB_002 J3_25303.4 | |
J3_3J2E_015 | 1/N/941:946, 1/N/1235:1237, 1/N/1337:1342 | No text annotation | ||
J3_3J2E_022 | 1/N/955:962, 1/N/973:984, 1/N/1221:1225 | No text annotation | homologous J3_5J7L_006 J3_83516.4 | |
J3_3J2E_005 | 1/N/990:993, 1/N/1045:1047, 1/N/1210:1215 | No text annotation | homologous J3_4LFB_005 J3_82572.1 | |
J3_3J2E_023 | 1/N/990:997, 1/N/1044:1047, 1/N/1210:1215 | No text annotation | homologous J3_5J7L_053 J3_76475.2 | |
J3_3J2E_006 | 1/N/1003:1006, 1/N/1023:1027, 1/N/1034:1037 | No text annotation | ||
J3_3J2E_007 | 1/N/1061:1068, 1/N/1107:1114, 1/N/1186:1195 | No text annotation | ||
J3_3J2E_011 | 1/N/1073:1074, 1/N/1083:1087, 1/N/1098:1102 | No text annotation | ||
J3_3J2E_008 | 1/N/1116:1118, 1/N/1155:1158, 1/N/1181:1184 | No text annotation | homologous J3_5J7L_010 J3_82365.4 | |
J3_3J2E_018 | 1/N/1116:1118, 1/N/1155:1162, 1/N/1174:1184 | No text annotation | ||
J3_3J2E_019 | 1/N/1237:1241, 1/N/1296:1303, 1/N/1334:1337 | No text annotation | homologous J3_5J7L_011 J3_37047.6 | |
J4_3J2E_004 | 1/N/115:122, 1/N/239:240, 1/N/286:289, 1/N/311:312 | No text annotation | ||
J4_3J2E_005 | 1/N/142:144, 1/N/178:184, 1/N/193:198, 1/N/219:221 | No text annotation | homologous J4_5J7L_002 J4_01665.1 | |
J4_3J2E_003 | 1/N/575:577, 1/N/764:769, 1/N/810:821, 1/N/879:880 | No text annotation | homologous J4_5J7L_003 J4_61885.6 | |
J5_3J2E_001 | 1/N/36:39, 1/N/403:406, 1/N/436:440, 1/N/497:500, 1/N/545:548 | No text annotation | homologous J5_5J7L_001 J5_92941.1 | |
J5_3J2E_002 | 1/N/36:39, 1/N/403:406, 1/N/436:442, 1/N/492:500, 1/N/545:548 | No text annotation | homologous J5_5J7L_002 J5_67416.1 | |
J5_3J2E_003 | 1/N/58:66, 1/N/103:113, 1/N/314:316, 1/N/337:339, 1/N/350:354 | No text annotation |
Problematic loops
# | loop id | Problem | Sequence |
---|---|---|---|
J3_3J2E_001 | No text annotation | ||
J3_3J2E_013 | No text annotation | ||
J3_3J2E_014 | No text annotation | ||
J3_3J2E_004 | No text annotation | ||
J3_3J2E_016 | No text annotation | ||
J3_3J2E_017 | No text annotation | ||
J4_3J2E_001 | No text annotation | ||
J4_3J2E_002 | No text annotation |
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