9H3V Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_9H3V_001 | 1/A/59:68 | No text annotation | homologous HL_5J7L_134 NA | |
| HL_9H3V_002 | 1/A/87:95 | No text annotation | homologous HL_5J7L_135 NA | |
| HL_9H3V_003 | 1/A/123:128 | No text annotation | homologous HL_5J7L_136 NA | |
| HL_9H3V_007 | 1/A/246:252 | No text annotation | homologous HL_4WF9_008 HL_76371.1 | |
| HL_9H3V_008 | 1/A/305:312 | T-loop with 2 stacked bulged bases | homologous HL_4WF9_010 HL_13999.1 | |
| HL_9H3V_010 | 1/A/327:335 | T-loop with unstacked turn | homologous HL_5J7L_144 NA | |
| HL_9H3V_013 | 1/A/462:467 | GNRA | homologous HL_4WF9_015 HL_34789.1 | |
| HL_9H3V_014 | 1/A/487:493 | GNRA | homologous HL_9DFE_015 HL_34789.1 | |
| HL_9H3V_021 | 1/A/744:753 | No text annotation | homologous HL_7A0S_022 HL_50204.1 | |
| HL_9H3V_022 | 1/A/779:785 | UNCG variation | geometric HL_1P6V_001 NA | |
| HL_9H3V_025 | 1/A/978:985 | No text annotation | homologous HL_9DFE_026 HL_47171.1 | |
| HL_9H3V_027 | 1/A/1222:1227 | GNRA | homologous HL_5J7L_164 NA | |
| HL_9H3V_028 | 1/A/1281:1289 | T-loop with 2 stacked bulged bases | homologous HL_5J7L_165 NA | |
| HL_9H3V_029 | 1/A/1324:1330 | Pseudoknot geometry with 3' bulge | homologous HL_5J7L_166 NA | |
| HL_9H3V_030 | 1/A/1363:1368 | GNRA | homologous HL_5J7L_167 NA | |
| HL_9H3V_031 | 1/A/1389:1398 | No text annotation | homologous HL_5J7L_168 NA | |
| HL_9H3V_032 | 1/A/1451:1459 | Mini UNCG with extended bulge | homologous HL_5J7L_169 NA | |
| HL_9H3V_035 | 1/A/1565:1568 | Mini UNCG | homologous HL_5J7L_172 NA | |
| HL_9H3V_036 | 1/A/1612:1619 | No text annotation | homologous HL_4WF9_038 HL_28592.1 | |
| HL_9H3V_037 | 1/A/1630:1636 | GNRA | homologous HL_5J7L_174 NA | |
| HL_9H3V_041 | 1/A/1777:1787 | No text annotation | homologous HL_4WF9_043 HL_87681.1 | |
| HL_9H3V_042 | 1/A/1806:1811 | GNRA related | homologous HL_5J7L_179 NA | |
| HL_9H3V_043 | 1/A/2027:2036 | No text annotation | homologous HL_5J7L_183 NA | |
| HL_9H3V_045 | 1/A/2209:2215 | No text annotation | homologous HL_5J7L_185 NA | |
| HL_9H3V_047 | 1/A/2264:2276 | No text annotation | homologous HL_5J7L_187 NA | |
| HL_9H3V_056 | 1/A/2819:2827 | No text annotation | homologous HL_5J7L_201 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_9H3V_004 | No text annotation | ||
| HL_9H3V_005 | No text annotation | ||
| HL_9H3V_006 | No text annotation | ||
| HL_9H3V_009 | No text annotation | ||
| HL_9H3V_011 | No text annotation | ||
| HL_9H3V_012 | Pseudoknot geometry | ||
| HL_9H3V_015 | No text annotation | ||
| HL_9H3V_016 | T-loop with 2 stacked bulged bases | ||
| HL_9H3V_017 | No text annotation | ||
| HL_9H3V_018 | GNRA | ||
| HL_9H3V_019 | GNRA | ||
| HL_9H3V_020 | GNRA wlth tandem sheared | ||
| HL_9H3V_023 | No text annotation | ||
| HL_9H3V_024 | GNRA | ||
| HL_9H3V_026 | No text annotation | ||
| HL_9H3V_033 | Pseudoknot geometry with 3' bulge | ||
| HL_9H3V_034 | UNCG | ||
| HL_9H3V_038 | UNCG | ||
| HL_9H3V_039 | No text annotation | ||
| HL_9H3V_040 | No text annotation | ||
| HL_9H3V_044 | No text annotation | ||
| HL_9H3V_046 | Externally structured | ||
| HL_9H3V_048 | No text annotation | ||
| HL_9H3V_049 | GNRA | ||
| HL_9H3V_050 | GNRA | ||
| HL_9H3V_051 | No text annotation | ||
| HL_9H3V_052 | GNRA | ||
| HL_9H3V_053 | Ribsomal LSU H95 | ||
| HL_9H3V_054 | No text annotation | ||
| HL_9H3V_055 | No text annotation | ||
| HL_9H3V_057 | GNRA | ||
| HL_9H3V_058 | No text annotation | ||
| HL_9H3V_059 | Mini UNCG |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_9H3V_001 | 1/A/24:30, 1/A/510:516 | Triple sheared with non-canonical cWW | homologous IL_5J7L_245 NA | |
| IL_9H3V_002 | 1/A/36:37, 1/A/442:444 | Single bulged A | homologous IL_7A0S_002 IL_14190.1 | |
| IL_9H3V_006 | 1/A/188:194, 1/A/201:208 | 8x7 Sarcin-Ricin; G-bulge | homologous IL_7A0S_006 IL_62167.1 | |
| IL_9H3V_007 | 1/A/239:245, 1/A/253:258 | 7x6 Sarcin-Ricin; G-bulge | homologous IL_5J7L_251 NA | |
| IL_9H3V_010 | 1/A/293:295, 1/A/343:347 | No text annotation | homologous IL_5J7L_254 NA | |
| IL_9H3V_011 | 1/A/378:381, 1/A/394:396 | No text annotation | ||
| IL_9H3V_012 | 1/A/481:484, 1/A/496:509 | No text annotation | homologous IL_5J7L_255 NA | |
| IL_9H3V_013 | 1/A/536:539, 1/A/554:557 | Double sheared | homologous IL_5J7L_256 NA | |
| IL_9H3V_016 | 1/A/672:674, 1/A/806:808 | Isolated non-canonical cWW pair | homologous IL_7A0S_014 IL_01003.1 | |
| IL_9H3V_017 | 1/A/674:678, 1/A/799:806 | No text annotation | homologous IL_9DFE_016 IL_73855.1 | |
| IL_9H3V_018 | 1/A/697:698, 1/A/763:765 | Single bulged A | homologous IL_5J7L_261 NA | |
| IL_9H3V_019 | 1/A/702:703, 1/A/728:730 | Single bulged G | homologous IL_7A0S_017 IL_28408.1 | |
| IL_9H3V_022 | 1/A/775:777, 1/A/787:791 | Multiple bulged bases | geometric IL_5J7L_265 NA | |
| IL_9H3V_023 | 1/A/844:847, 1/A/933:934 | 90 degree turn | geometric IL_5J7L_267 NA | |
| IL_9H3V_024 | 1/A/844:848, 1/A/930:934 | No text annotation | homologous IL_5J7L_399 NA | |
| IL_9H3V_025 | 1/A/847:848, 1/A/930:933 | Stack outside cWW | homologous IL_5J7L_268 NA | |
| IL_9H3V_026 | 1/A/850:851, 1/A/926:928 | Single stack bend | homologous IL_5J7L_269 NA | |
| IL_9H3V_027 | 1/A/856:862, 1/A/915:921 | 7x7 Sarcin-Ricin with intercalated A; G-bulge | homologous IL_5J7L_270 NA | |
| IL_9H3V_031 | 1/A/994:996, 1/A/1159:1160 | Single bulged C | homologous IL_4WF9_035 IL_05642.1 | |
| IL_9H3V_032 | 1/A/998:1002, 1/A/1153:1157 | UAA/GAN | homologous IL_7A0S_033 IL_08938.1 | |
| IL_9H3V_033 | 1/A/1004:1011, 1/A/1150:1151 | SSU/LSU pseudoknot | homologous IL_5J7L_278 NA | |
| IL_9H3V_034 | 1/A/1011:1013, 1/A/1149:1150 | Single bulged U | homologous IL_5J7L_279 NA | |
| IL_9H3V_035 | 1/A/1018:1024, 1/A/1140:1144 | Kink-turn related | homologous IL_4WF9_039 IL_57188.6 | |
| IL_9H3V_036 | 1/A/1024:1030, 1/A/1124:1140 | No text annotation | ||
| IL_9H3V_039 | 1/A/1196:1198, 1/A/1247:1250 | Isolated cWS basepair | homologous IL_7A0S_041 IL_42997.4 | |
| IL_9H3V_040 | 1/A/1202:1206, 1/A/1240:1243 | No text annotation | homologous IL_5J7L_287 NA | |
| IL_9H3V_041 | 1/A/1208:1215, 1/A/1234:1238 | Kink-turn | homologous IL_5J7L_288 NA | |
| IL_9H3V_042 | 1/A/1262:1269, 1/A/2011:2017 | 8x7 Sarcin-Ricin; G-bulge | homologous IL_5J7L_289 NA | |
| IL_9H3V_043 | 1/A/1310:1313, 1/A/1603:1604 | Major groove platform; stack outside cWW | geometric IL_4V9F_008 IL_74641.1 | |
| IL_9H3V_044 | 1/A/1319:1323, 1/A/1331:1333 | Major groove minor groove platform with tHH | homologous IL_4WF9_050 IL_06671.1 | |
| IL_9H3V_045 | 1/A/1351:1355, 1/A/1376:1380 | UAA/GAN | homologous IL_7A0S_048 IL_89021.3 | |
| IL_9H3V_046 | 1/A/1357:1361, 1/A/1370:1374 | tSH-tHW-tHS | homologous IL_4WF9_052 IL_05821.1 | |
| IL_9H3V_049 | 1/A/1432:1435, 1/A/1557:1561 | Tandem non-canonical cWW pairs | homologous IL_5J7L_296 NA | |
| IL_9H3V_052 | 1/A/1468:1471, 1/A/1520:1524 | No text annotation | homologous IL_5J7L_299 NA | |
| IL_9H3V_053 | 1/A/1474:1478, 1/A/1513:1517 | tSH-tHW-tHS | homologous IL_5J7L_300 NA | |
| IL_9H3V_055 | 1/A/1489:1491, 1/A/1499:1500 | Single bulged A | homologous IL_5J7L_302 NA | |
| IL_9H3V_056 | 1/A/1526:1529, 1/A/1542:1546 | UAA/GAN variation | homologous IL_5J7L_303 NA | |
| IL_9H3V_057 | 1/A/1651:1656, 1/A/2004:2006 | No text annotation | homologous IL_7A0S_059 IL_12566.5 | |
| IL_9H3V_058 | 1/A/1663:1665, 1/A/1995:1997 | Isolated tWW turn | homologous IL_4WF9_063 IL_10432.1 | |
| IL_9H3V_059 | 1/A/1666:1669, 1/A/1993:1994 | Major groove platform; stack outside cWW | geometric IL_8C3A_082 NA | |
| IL_9H3V_060 | 1/A/1666:1674, 1/A/1990:1994 | No text annotation | geometric IL_8C3A_484 NA | |
| IL_9H3V_061 | 1/A/1669:1674, 1/A/1990:1993 | Intercalated tWH | homologous IL_4WF9_065 IL_28217.1 | |
| IL_9H3V_065 | 1/A/1770:1771, 1/A/1980:1982 | Single bulged A | homologous IL_4WF9_068 IL_14190.1 | |
| IL_9H3V_066 | 1/A/1798:1804, 1/A/1813:1821 | Kink-turn related | homologous IL_7A0S_065 IL_17069.6 | |
| IL_9H3V_068 | 1/A/2054:2056, 1/A/2612:2615 | No text annotation | ||
| IL_9H3V_079 | 1/A/2350:2353, 1/A/2364:2367 | Double sheared | homologous IL_4WF9_087 IL_58355.1 | |
| IL_9H3V_081 | 1/A/2636:2640, 1/A/2774:2782 | tSH-tHS-tHW | homologous IL_7A0S_093 IL_04638.4 | |
| IL_9H3V_084 | 1/A/2680:2684, 1/A/2725:2727 | C-loop | homologous IL_5J7L_347 NA | |
| IL_9H3V_085 | 1/A/2687:2691, 1/A/2718:2722 | UAA/GAN related, with intercalation | homologous IL_5J7L_348 NA | |
| IL_9H3V_086 | 1/A/2695:2696, 1/A/2711:2714 | Multiple bulged bases | homologous IL_5J7L_349 NA | |
| IL_9H3V_089 | 1/A/2806:2811, 1/A/2889:2892 | No text annotation | homologous IL_5J7L_351 NA | |
| IL_9H3V_090 | 1/A/2838:2839, 1/A/2878:2880 | Major groove intercalation | homologous IL_4WF9_106 IL_78536.1 | |
| IL_9H3V_091 | 1/A/2843:2846, 1/A/2870:2874 | Multiple bulged bases with non-canonical cWW | homologous IL_5J7L_353 NA | |
| IL_9H3V_097 | 1/B/71:79, 1/B/97:105 | Bacterial 5S Loop E | homologous IL_5J7L_359 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_9H3V_003 | Minor groove platform | ||
| IL_9H3V_004 | Kink-turn | ||
| IL_9H3V_005 | Single stack bend | ||
| IL_9H3V_008 | No text annotation | ||
| IL_9H3V_009 | No text annotation | ||
| IL_9H3V_014 | Isolated non-canonical cWW pair | ||
| IL_9H3V_015 | AAA cross-strand stack | ||
| IL_9H3V_020 | Triple sheared | ||
| IL_9H3V_021 | Major groove platform | ||
| IL_9H3V_028 | Single bulged G | ||
| IL_9H3V_029 | C-loop with bulged stacked A's | ||
| IL_9H3V_030 | Isolated non-canonical cWW pair | ||
| IL_9H3V_037 | Isolated non-canonical cWW pair | ||
| IL_9H3V_038 | Tandem non-canonical cWW pairs | ||
| IL_9H3V_047 | No text annotation | ||
| IL_9H3V_048 | UAA/GAN | ||
| IL_9H3V_050 | tSH-tHW | ||
| IL_9H3V_051 | Single bulged U | ||
| IL_9H3V_054 | 180 degree turn | ||
| IL_9H3V_062 | tSH-tSH-tHH-tHS | ||
| IL_9H3V_063 | 6x5 Sarcin-Ricin; G-bulge | ||
| IL_9H3V_064 | Triple sheared | ||
| IL_9H3V_067 | Major groove platform | ||
| IL_9H3V_069 | No text annotation | ||
| IL_9H3V_070 | Isolated non-canonical cWW pair | ||
| IL_9H3V_071 | No text annotation | ||
| IL_9H3V_072 | No text annotation | ||
| IL_9H3V_073 | No text annotation | ||
| IL_9H3V_074 | Kink-turn related | ||
| IL_9H3V_075 | No text annotation | ||
| IL_9H3V_076 | Single bulged U | ||
| IL_9H3V_077 | No text annotation | ||
| IL_9H3V_078 | No text annotation | ||
| IL_9H3V_080 | No text annotation | ||
| IL_9H3V_082 | Single stack bend | ||
| IL_9H3V_083 | Sarcin-Ricin target in LSU H95; G-bulge | ||
| IL_9H3V_087 | UAA/GAN with extra cWW | ||
| IL_9H3V_088 | Single bulged A | ||
| IL_9H3V_092 | tHS double platform | ||
| IL_9H3V_093 | Major groove intercalation | ||
| IL_9H3V_094 | No text annotation | ||
| IL_9H3V_095 | No text annotation | ||
| IL_9H3V_096 | Symmetric double minor groove platform |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_9H3V_001 | 1/A/30:31, 1/A/474:481, 1/A/509:510 | No text annotation | homologous J3_4WF9_010 J3_68715.1 | |
| J3_9H3V_002 | 1/A/32:35, 1/A/445:461, 1/A/468:473 | No text annotation | homologous J3_5J7L_067 NA | |
| J3_9H3V_003 | 1/A/56:57, 1/A/70:76, 1/A/110:114 | No text annotation | homologous J3_5J7L_037 NA | |
| J3_9H3V_004 | 1/A/297:301, 1/A/316:325, 1/A/337:341 | No text annotation | homologous J3_5J7L_068 NA | |
| J3_9H3V_005 | 1/A/683:689, 1/A/773:775, 1/A/791:794 | No text annotation | homologous J3_5J7L_038 NA | |
| J3_9H3V_006 | 1/A/698:700, 1/A/732:736, 1/A/760:763 | No text annotation | homologous J3_9DFE_008 J3_69816.1 | |
| J3_9H3V_007 | 1/A/1298:1303, 1/A/1625:1627, 1/A/1639:1642 | No text annotation | homologous J3_5J7L_041 NA | |
| J3_9H3V_008 | 1/A/1306:1309, 1/A/1605:1611, 1/A/1620:1622 | No text annotation | homologous J3_7A0S_007 J3_47341.1 | |
| J3_9H3V_009 | 1/A/1344:1349, 1/A/1382:1385, 1/A/1402:1403 | No text annotation | homologous J3_5J7L_043 NA | |
| J3_9H3V_010 | 1/A/1424:1429, 1/A/1564:1565, 1/A/1568:1574 | No text annotation | homologous J3_7A0S_019 J3_34864.3 | |
| J3_9H3V_012 | 1/A/2330:2347, 1/A/2370:2372, 1/A/2381:2385 | No text annotation | ||
| J3_9H3V_014 | 1/A/2812:2815, 1/A/2831:2836, 1/A/2882:2888 | No text annotation | homologous J3_5J7L_048 NA | |
| J4_9H3V_001 | 1/A/268:269, 1/A/370:375, 1/A/399:406, 1/A/421:424 | No text annotation | homologous J4_5J7L_018 NA | |
| J4_9H3V_002 | 1/A/297:301, 1/A/316:319, 1/A/323:325, 1/A/337:341 | No text annotation | homologous J4_5J7L_019 NA | |
| J4_9H3V_003 | 1/A/601:604, 1/A/624:628, 1/A/635:638, 1/A/650:656 | No text annotation | homologous J4_5J7L_020 NA | |
| J4_9H3V_004 | 1/A/1270:1276, 1/A/1294:1295, 1/A/1645:1648, 1/A/2009:2010 | No text annotation | homologous J4_5J7L_021 NA | |
| J4_9H3V_005 | 1/A/1310:1314, 1/A/1338:1343, 1/A/1404:1405, 1/A/1597:1604 | No text annotation | homologous J4_5J7L_022 NA | |
| J4_9H3V_006 | 1/A/1313:1314, 1/A/1338:1343, 1/A/1404:1405, 1/A/1597:1603 | No text annotation | homologous J4_5J7L_023 NA | |
| J4_9H3V_008 | 1/A/1772:1776, 1/A/1788:1792, 1/A/1827:1830, 1/A/1975:1979 | No text annotation | homologous J4_5J7L_025 NA | |
| J5_9H3V_001 | 1/A/47:54, 1/A/116:121, 1/A/130:131, 1/A/148:151, 1/A/175:178 | No text annotation | ||
| J5_9H3V_002 | 1/A/531:533, 1/A/560:564, 1/A/577:579, 1/A/1261:1262, 1/A/2017:2018 | No text annotation | homologous J5_5J7L_014 NA | |
| J5_9H3V_003 | 1/A/584:589, 1/A/668:671, 1/A/809:812, 1/A/1195:1196, 1/A/1250:1256 | No text annotation | homologous J5_5J7L_015 NA | |
| J5_9H3V_004 | 1/A/1674:1682, 1/A/1706:1707, 1/A/1751:1752, 1/A/1756:1764, 1/A/1988:1990 | No text annotation | homologous J5_5J7L_016 NA | |
| J6_9H3V_001 | 1/A/45:46, 1/A/179:183, 1/A/214:224, 1/A/231:235, 1/A/262:266, 1/A/426:433 | No text annotation | ||
| J7_9H3V_001 | 1/A/8:15, 1/A/525:531, 1/A/2018:2023, 1/A/2040:2043, 1/A/2625:2630, 1/A/2788:2789, 1/A/2894:2895 | No text annotation | ||
| J7_9H3V_002 | 1/A/817:822, 1/A/835:838, 1/A/940:946, 1/A/971:976, 1/A/987:991, 1/A/1163:1164, 1/A/1185:1190 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_9H3V_011 | Kink-turn 3-way junction | ||
| J3_9H3V_013 | No text annotation | ||
| J3_9H3V_015 | No text annotation | ||
| J4_9H3V_007 | No text annotation | ||
| J4_9H3V_009 | No text annotation | ||
| J4_9H3V_010 | No text annotation | ||
| J5_9H3V_005 | No text annotation |
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