3JAM Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_3JAM_001 | 1/2/7:17 | No text annotation | homologous HL_4V88_186 NA | |
| HL_3JAM_002 | 1/2/70:81 | No text annotation | homologous HL_8C3A_193 NA | |
| HL_3JAM_003 | 1/2/153:159 | GNRA related | homologous HL_4V88_188 NA | |
| HL_3JAM_004 | 1/2/189:194 | No text annotation | homologous HL_8P9A_193 HL_53890.2 | |
| HL_3JAM_005 | 1/2/229:234 | No text annotation | geometric HL_6CZR_075 NA | |
| HL_3JAM_006 | 1/2/242:249 | T-loop with 1 bulged base | homologous HL_4V88_191 NA | |
| HL_3JAM_007 | 1/2/274:280 | No text annotation | geometric HL_6VMY_004 HL_53890.2 | |
| HL_3JAM_008 | 1/2/329:337 | GNRA related | homologous HL_4V88_193 NA | |
| HL_3JAM_009 | 1/2/367:372 | No text annotation | homologous HL_4V88_194 NA | |
| HL_3JAM_010 | 1/2/392:403 | No text annotation | homologous HL_4V88_195 NA | |
| HL_3JAM_011 | 1/2/413:418 | UNCG | homologous HL_4V88_196 NA | |
| HL_3JAM_012 | 1/2/449:455 | No text annotation | homologous HL_4V88_197 NA | |
| HL_3JAM_013 | 1/2/490:495 | No text annotation | ||
| HL_3JAM_014 | 1/2/519:531 | No text annotation | geometric HL_4V88_199 NA | |
| HL_3JAM_015 | 1/2/568:573 | GNRA variation | homologous HL_4V88_200 NA | |
| HL_3JAM_037 | 1/2/703:735 | No text annotation | ||
| HL_3JAM_016 | 1/2/713:725 | No text annotation | ||
| HL_3JAM_017 | 1/2/764:772 | No text annotation | homologous HL_4V88_203 NA | |
| HL_3JAM_018 | 1/2/777:782 | No text annotation | geometric HL_4V9F_003 HL_75660.5 | |
| HL_3JAM_019 | 1/2/828:842 | Pseudoknot geometry | homologous HL_4V88_205 NA | |
| HL_3JAM_020 | 1/2/899:908 | No text annotation | homologous HL_4V88_206 NA | |
| HL_3JAM_021 | 1/2/936:941 | GNRA | homologous HL_4V88_207 NA | |
| HL_3JAM_022 | 1/2/996:1006 | No text annotation | homologous HL_4V88_208 NA | |
| HL_3JAM_038 | 1/2/1054:1063 | No text annotation | ||
| HL_3JAM_024 | 1/2/1083:1088 | GNRA | homologous HL_4V88_210 NA | |
| HL_3JAM_025 | 1/2/1120:1125 | GNRA | homologous HL_4V88_211 NA | |
| HL_3JAM_026 | 1/2/1187:1196 | No text annotation | homologous HL_4V88_212 NA | |
| HL_3JAM_039 | 1/2/1233:1249 | No text annotation | ||
| HL_3JAM_027 | 1/2/1235:1248 | No text annotation | ||
| HL_3JAM_028 | 1/2/1295:1300 | GNRA | homologous HL_4V88_214 NA | |
| HL_3JAM_029 | 1/2/1308:1315 | No text annotation | homologous HL_4V88_215 NA | |
| HL_3JAM_030 | 1/2/1358:1363 | No text annotation | geometric HL_5NFV_001 HL_69752.2 | |
| HL_3JAM_031 | 1/2/1394:1400 | GNRA | homologous HL_4V88_217 NA | |
| HL_3JAM_032 | 1/2/1499:1504 | GNRA | homologous HL_4V88_218 NA | |
| HL_3JAM_033 | 1/2/1548:1559 | No text annotation | homologous HL_4V88_219 NA | |
| HL_3JAM_034 | 1/2/1592:1600 | No text annotation | homologous HL_4V88_220 NA | |
| HL_3JAM_036 | 1/2/1776:1781 | GNRA variation | homologous HL_4V88_222 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_3JAM_023 | No text annotation | ||
| HL_3JAM_035 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_3JAM_001 | 1/2/24:26, 1/2/599:600 | Single bulged C | homologous IL_4V88_384 NA | |
| IL_3JAM_002 | 1/2/35:37, 1/2/470:472 | Isolated non-canonical cWW pair | homologous IL_4V88_385 NA | |
| IL_3JAM_003 | 1/2/37:41, 1/2/465:470 | Triple sheared related | geometric IL_4V88_386 NA | |
| IL_3JAM_004 | 1/2/42:48, 1/2/430:432 | No text annotation | geometric IL_4V88_387 NA | |
| IL_3JAM_005 | 1/2/50:52, 1/2/427:428 | Minor groove platform | homologous IL_4V88_388 NA | |
| IL_3JAM_006 | 1/2/58:63, 1/2/87:89 | No text annotation | homologous IL_4V88_389 NA | |
| IL_3JAM_007 | 1/2/64:69, 1/2/82:86 | No text annotation | homologous IL_4V88_390 NA | |
| IL_3JAM_008 | 1/2/109:112, 1/2/301:304 | Tandem non-canonical cWW pairs | homologous IL_4V88_391 NA | |
| IL_3JAM_087 | 1/2/112:117, 1/2/298:301 | Tandem non-canonical cWW pairs | homologous IL_8C3A_399 NA | |
| IL_3JAM_009 | 1/2/113:117, 1/2/298:300 | Isolated non-canonical cWW pair | geometric IL_6E7L_003 NA | |
| IL_3JAM_091 | 1/2/117:122, 1/2/294:298 | No text annotation | homologous IL_8P9A_382 IL_29223.1 | |
| IL_3JAM_011 | 1/2/123:124, 1/2/291:293 | Single stack bend | geometric IL_4LFB_041 IL_90729.1 | |
| IL_3JAM_012 | 1/2/142:148, 1/2/164:171 | tWH-tWH-tHW-tHW | homologous IL_4V88_394 NA | |
| IL_3JAM_013 | 1/2/149:151, 1/2/161:163 | Isolated non-canonical cWW contact | homologous IL_4V88_395 NA | |
| IL_3JAM_014 | 1/2/185:188, 1/2/195:198 | Double sheared | homologous IL_4V88_396 NA | |
| IL_3JAM_015 | 1/2/203:205, 1/2/258:262 | Major groove platform with extra cWW | homologous IL_4V88_397 NA | |
| IL_3JAM_016 | 1/2/205:206, 1/2/256:258 | Single stack bend | geometric IL_4V83_236 IL_90729.1 | |
| IL_3JAM_017 | 1/2/207:209, 1/2/254:255 | Single stack bend | geometric IL_4LFB_041 IL_90729.1 | |
| IL_3JAM_018 | 1/2/264:266, 1/2/287:288 | Single bulged A | homologous IL_4V88_399 NA | |
| IL_3JAM_019 | 1/2/269:272, 1/2/282:284 | No text annotation | homologous IL_4V88_400 NA | |
| IL_3JAM_020 | 1/2/310:315, 1/2/347:354 | Kink-turn with non-sequential stacking | homologous IL_4V88_402 NA | |
| IL_3JAM_021 | 1/2/317:322, 1/2/344:345 | No text annotation | geometric IL_5Y58_001 IL_59877.1 | |
| IL_3JAM_022 | 1/2/362:364, 1/2/375:380 | No text annotation | homologous IL_4V88_404 NA | |
| IL_3JAM_023 | 1/2/388:390, 1/2/405:407 | Isolated cWH basepair | homologous IL_4V88_405 NA | |
| IL_3JAM_024 | 1/2/410:412, 1/2/419:421 | Isolated near basepair | homologous IL_4V88_406 NA | |
| IL_3JAM_025 | 1/2/438:440, 1/2/462:463 | Single bulged U | geometric IL_4V88_407 NA | |
| IL_3JAM_026 | 1/2/442:446, 1/2/459:460 | C-loop | geometric IL_5J7L_018 IL_03109.3 | |
| IL_3JAM_027 | 1/2/446:447, 1/2/457:459 | Single bulged G | geometric IL_5J7L_019 IL_00225.13 | |
| IL_3JAM_028 | 1/2/479:481, 1/2/504:507 | Isolated non-canonical cWW pair | geometric IL_5MWI_007 NA | |
| IL_3JAM_029 | 1/2/486:490, 1/2/495:499 | No text annotation | ||
| IL_3JAM_030 | 1/2/516:519, 1/2/531:534 | Double sheared | geometric IL_4LFB_060 IL_09705.15 | |
| IL_3JAM_031 | 1/2/549:556, 1/2/586:587 | SSU/LSU pseudoknot | geometric IL_4V88_413 NA | |
| IL_3JAM_032 | 1/2/556:558, 1/2/585:586 | Single bulged U | homologous IL_4V88_414 NA | |
| IL_3JAM_033 | 1/2/561:567, 1/2/574:582 | Kink-turn related | homologous IL_4V88_415 NA | |
| IL_3JAM_034 | 1/2/615:621, 1/2/1103:1104 | No text annotation | homologous IL_4V88_416 NA | |
| IL_3JAM_035 | 1/2/623:625, 1/2/972:974 | Isolated non-canonical cWW pair | homologous IL_4V88_417 NA | |
| IL_3JAM_036 | 1/2/626:630, 1/2/967:971 | tSH-tHW-tHS | geometric IL_7A0S_049 IL_17136.7 | |
| IL_3JAM_037 | 1/2/650:657, 1/2/676:683 | No text annotation | ||
| IL_3JAM_038 | 1/2/746:747, 1/2/801:804 | Major groove minor groove platform; mini C-loop | homologous IL_4V88_423 NA | |
| IL_3JAM_092 | 1/2/748:750, 1/2/798:800 | Isolated non-canonical cWW pair | homologous IL_8P9A_413 IL_28037.2 | |
| IL_3JAM_040 | 1/2/751:759, 1/2/790:797 | No text annotation | homologous IL_4V88_425 NA | |
| IL_3JAM_041 | 1/2/818:821, 1/2/849:851 | Isolated non-canonical cWW pair | homologous IL_4V88_426 NA | |
| IL_3JAM_042 | 1/2/867:869, 1/2/956:959 | Isolated non-canonical cWW pair | geometric IL_1YZ9_001 NA | |
| IL_3JAM_043 | 1/2/870:873, 1/2/952:955 | Tandem non-canonical cWW pairs | geometric IL_4V88_430 NA | |
| IL_3JAM_044 | 1/2/873:877, 1/2/949:952 | Tandem non-canonical cWW pairs | homologous IL_4V88_431 NA | |
| IL_3JAM_045 | 1/2/884:887, 1/2/923:926 | Tandem non-canonical cWW pairs | homologous IL_4V88_432 NA | |
| IL_3JAM_046 | 1/2/892:898, 1/2/909:918 | Kink-turn related | homologous IL_8C3A_440 NA | |
| IL_3JAM_047 | 1/2/983:993, 1/2/1009:1016 | No text annotation | ||
| IL_3JAM_048 | 1/2/1033:1035, 1/2/1094:1100 | No text annotation | homologous IL_4V88_437 NA | |
| IL_3JAM_049 | 1/2/1040:1043, 1/2/1073:1076 | Tandem non-canonical cWW pairs | homologous IL_4V88_438 NA | |
| IL_3JAM_050 | 1/2/1050:1052, 1/2/1065:1066 | Single bulged U | homologous IL_4V88_439 NA | |
| IL_3JAM_051 | 1/2/1110:1117, 1/2/1128:1133 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_4V88_440 NA | |
| IL_3JAM_052 | 1/2/1145:1146, 1/2/1628:1630 | Single bulged A | homologous IL_4V88_441 NA | |
| IL_3JAM_053 | 1/2/1148:1150, 1/2/1625:1626 | Single bulged G | homologous IL_4V88_442 NA | |
| IL_3JAM_054 | 1/2/1156:1159, 1/2/1615:1619 | C-loop | homologous IL_4V88_443 NA | |
| IL_3JAM_055 | 1/2/1172:1174, 1/2/1462:1464 | Isolated non-canonical cWW pair | homologous IL_4V88_444 NA | |
| IL_3JAM_056 | 1/2/1177:1178, 1/2/1457:1459 | Minor groove platform | homologous IL_4V88_445 NA | |
| IL_3JAM_057 | 1/2/1212:1214, 1/2/1446:1448 | Isolated non-canonical cWW pair | geometric IL_4KYY_001 IL_28037.2 | |
| IL_3JAM_093 | 1/2/1223:1232, 1/2/1251:1258 | No text annotation | homologous IL_8P9A_470 IL_28304.1 | |
| IL_3JAM_059 | 1/2/1232:1233, 1/2/1249:1251 | No text annotation | ||
| IL_3JAM_060 | 1/2/1233:1235, 1/2/1248:1249 | Minor groove platform, major groove intercalation | geometric IL_4V9F_066 IL_95583.2 | |
| IL_3JAM_061 | 1/2/1267:1269, 1/2/1438:1439 | Single bulged U | homologous IL_4V88_449 NA | |
| IL_3JAM_062 | 1/2/1271:1275, 1/2/1434:1436 | Isolated cWS basepair | homologous IL_4V88_450 NA | |
| IL_3JAM_089 | 1/2/1271:1277, 1/2/1428:1436 | No text annotation | homologous IL_8P9A_439 IL_86012.1 | |
| IL_3JAM_063 | 1/2/1275:1277, 1/2/1428:1434 | Minor groove platform with extra cWW | geometric IL_4V88_451 NA | |
| IL_3JAM_064 | 1/2/1279:1280, 1/2/1424:1426 | Single bulged A | homologous IL_4V88_452 NA | |
| IL_3JAM_065 | 1/2/1289:1291, 1/2/1322:1324 | Isolated cWH basepair | homologous IL_4V88_453 NA | |
| IL_3JAM_066 | 1/2/1305:1307, 1/2/1316:1317 | Minor groove platform | geometric IL_5ML7_009 IL_51454.2 | |
| IL_3JAM_067 | 1/2/1338:1341, 1/2/1381:1383 | Isolated non-canonical cWW pair | homologous IL_4V88_455 NA | |
| IL_3JAM_068 | 1/2/1343:1347, 1/2/1375:1379 | No text annotation | ||
| IL_3JAM_069 | 1/2/1352:1353, 1/2/1368:1370 | No text annotation | ||
| IL_3JAM_070 | 1/2/1387:1389, 1/2/1405:1410 | No text annotation | homologous IL_8C3A_465 NA | |
| IL_3JAM_071 | 1/2/1478:1485, 1/2/1517:1525 | No text annotation | homologous IL_4V88_459 NA | |
| IL_3JAM_072 | 1/2/1486:1492, 1/2/1511:1516 | 180 degree turn | homologous IL_4V88_460 NA | |
| IL_3JAM_073 | 1/2/1493:1496, 1/2/1507:1510 | Tandem non-canonical cWW pairs | homologous IL_4V88_461 NA | |
| IL_3JAM_094 | 1/2/1538:1543, 1/2/1564:1569 | No text annotation | homologous IL_8P9A_451 IL_85536.2 | |
| IL_3JAM_075 | 1/2/1634:1636, 1/2/1762:1765 | No text annotation | geometric IL_5J7L_058 IL_61438.4 | |
| IL_3JAM_076 | 1/2/1636:1639, 1/2/1758:1762 | No text annotation | homologous IL_4V88_464 NA | |
| IL_3JAM_077 | 1/2/1640:1642, 1/2/1755:1757 | Isolated non-canonical cWW pair | geometric IL_5VCI_002 IL_87907.2 | |
| IL_3JAM_078 | 1/2/1642:1645, 1/2/1751:1755 | No text annotation | ||
| IL_3JAM_079 | 1/2/1648:1650, 1/2/1746:1748 | Isolated non-canonical cWW pair | homologous IL_4V88_467 NA | |
| IL_3JAM_080 | 1/2/1651:1654, 1/2/1742:1745 | Double sheared | homologous IL_4V88_468 NA | |
| IL_3JAM_081 | 1/2/1654:1656, 1/2/1741:1742 | Single bulged U | geometric IL_4V9F_039 IL_89505.4 | |
| IL_3JAM_082 | 1/2/1663:1665, 1/2/1732:1734 | Isolated non-canonical cWW pair | homologous IL_4V88_470 NA | |
| IL_3JAM_083 | 1/2/1667:1670, 1/2/1727:1730 | Double sheared | homologous IL_4V88_471 NA | |
| IL_3JAM_084 | 1/2/1673:1676, 1/2/1721:1724 | Tandem non-canonical cWW pairs | homologous IL_4V88_473 NA | |
| IL_3JAM_085 | 1/2/1676:1680, 1/2/1717:1721 | Triple sheared | geometric IL_4V88_474 NA | |
| IL_3JAM_095 | 1/2/1685:1688, 1/2/1709:1712 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_3JAM_010 | No text annotation | ||
| IL_3JAM_039 | Tandem non-canonical cWW pairs | ||
| IL_3JAM_088 | Isolated non-canonical cWW pair | ||
| IL_3JAM_058 | No text annotation | ||
| IL_3JAM_090 | No text annotation | ||
| IL_3JAM_074 | No text annotation | ||
| IL_3JAM_086 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_3JAM_001 | 1/2/41:42, 1/2/432:438, 1/2/463:465 | No text annotation | geometric J3_4V88_078 NA | |
| J3_3JAM_014 | 1/2/41:48, 1/2/430:438, 1/2/463:465 | No text annotation | homologous J3_8P9A_069 J3_46317.4 | |
| J3_3JAM_015 | 1/2/212:227, 1/2/236:242, 1/2/249:251 | No text annotation | ||
| J3_3JAM_002 | 1/2/632:634, 1/2/860:865, 1/2/961:965 | No text annotation | homologous J3_8C3A_034 NA | |
| J3_3JAM_003 | 1/2/760:763, 1/2/773:775, 1/2/784:789 | No text annotation | homologous J3_4V88_032 NA | |
| J3_3JAM_004 | 1/2/880:883, 1/2/927:935, 1/2/942:946 | No text annotation | homologous J3_4V88_033 NA | |
| J3_3JAM_005 | 1/2/1036:1038, 1/2/1078:1082, 1/2/1089:1093 | No text annotation | homologous J3_4V88_034 NA | |
| J3_3JAM_018 | 1/2/1160:1162, 1/2/1580:1585, 1/2/1607:1614 | No text annotation | ||
| J3_3JAM_007 | 1/2/1167:1170, 1/2/1466:1468, 1/2/1572:1575 | No text annotation | homologous J3_4V88_036 NA | |
| J3_3JAM_008 | 1/2/1179:1186, 1/2/1197:1208, 1/2/1452:1456 | No text annotation | geometric J3_8C3A_040 NA | |
| J3_3JAM_009 | 1/2/1214:1219, 1/2/1262:1266, 1/2/1440:1446 | No text annotation | homologous J3_4V88_038 NA | |
| J3_3JAM_010 | 1/2/1282:1287, 1/2/1326:1331, 1/2/1417:1422 | No text annotation | homologous J3_4V88_039 NA | |
| J3_3JAM_011 | 1/2/1291:1293, 1/2/1302:1305, 1/2/1317:1322 | No text annotation | ||
| J3_3JAM_012 | 1/2/1335:1337, 1/2/1384:1387, 1/2/1410:1413 | No text annotation | homologous J3_8C3A_043 NA | |
| J3_3JAM_017 | 1/2/1335:1337, 1/2/1384:1389, 1/2/1405:1413 | No text annotation | homologous J3_8C3A_086 NA | |
| J3_3JAM_013 | 1/2/1468:1472, 1/2/1531:1538, 1/2/1569:1572 | No text annotation | homologous J3_4V88_041 NA | |
| J4_3JAM_001 | 1/2/99:107, 1/2/306:308, 1/2/356:360, 1/2/382:383 | No text annotation | homologous J4_8P9A_021 J4_15241.1 | |
| J4_3JAM_002 | 1/2/621:623, 1/2/974:979, 1/2/1020:1031, 1/2/1102:1103 | No text annotation | homologous J4_8C3A_022 NA | |
| J5_3JAM_001 | 1/2/31:35, 1/2/472:478, 1/2/508:515, 1/2/535:545, 1/2/591:594 | No text annotation | ||
| J5_3JAM_002 | 1/2/54:57, 1/2/90:97, 1/2/385:387, 1/2/408:410, 1/2/421:425 | No text annotation | homologous J5_8C3A_020 NA | |
| J5_3JAM_003 | 1/2/124:141, 1/2/172:181, 1/2/202:203, 1/2/262:264, 1/2/288:291 | No text annotation | ||
| J5_3JAM_004 | 1/2/124:141, 1/2/172:181, 1/2/202:203, 1/2/262:266, 1/2/287:291 | No text annotation | ||
| J5_3JAM_005 | 1/2/635:640, 1/2/693:698, 1/2/740:744, 1/2/806:816, 1/2/853:859 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_3JAM_006 | No text annotation | ||
| J3_3JAM_016 | No text annotation |
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