8C90 Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_8C90_001 | 1/A/59:68 | No text annotation | homologous HL_5J7L_134 NA | |
| HL_8C90_002 | 1/A/87:95 | No text annotation | homologous HL_5J7L_135 NA | |
| HL_8C90_003 | 1/A/123:128 | No text annotation | homologous HL_4WF9_003 HL_75660.7 | |
| HL_8C90_007 | 1/A/225:230 | No text annotation | homologous HL_5J7L_140 NA | |
| HL_8C90_009 | 1/A/305:312 | T-loop with 2 stacked bulged bases | homologous HL_5J7L_142 NA | |
| HL_8C90_010 | 1/A/319:323 | No text annotation | homologous HL_7RQB_011 NA | |
| HL_8C90_011 | 1/A/327:335 | T-loop with unstacked turn | homologous HL_5J7L_144 NA | |
| HL_8C90_014 | 1/A/462:467 | GNRA | homologous HL_4WF9_015 HL_34789.4 | |
| HL_8C90_015 | 1/A/487:493 | GNRA | homologous HL_5J7L_148 NA | |
| HL_8C90_016 | 1/A/542:551 | Externally structured | geometric HL_8C3A_022 NA | |
| HL_8C90_017 | 1/A/566:575 | T-loop with 2 stacked bulged bases | geometric HL_3AMU_003 HL_33597.3 | |
| HL_8C90_018 | 1/A/611:617 | No text annotation | homologous HL_5J7L_151 NA | |
| HL_8C90_019 | 1/A/629:634 | GNRA | homologous HL_4WF9_020 HL_34789.4 | |
| HL_8C90_055 | 1/A/641:647 | No text annotation | homologous HL_5J7L_153 NA | |
| HL_8C90_025 | 1/A/978:985 | No text annotation | homologous HL_5J7L_160 NA | |
| HL_8C90_027 | 1/A/1222:1227 | GNRA | homologous HL_5J7L_164 NA | |
| HL_8C90_028 | 1/A/1281:1289 | T-loop with 2 stacked bulged bases | homologous HL_5J7L_165 NA | |
| HL_8C90_029 | 1/A/1324:1330 | Pseudoknot geometry with 3' bulge | homologous HL_5J7L_166 NA | |
| HL_8C90_031 | 1/A/1389:1398 | No text annotation | homologous HL_5J7L_168 NA | |
| HL_8C90_032 | 1/A/1451:1459 | Mini UNCG with extended bulge | homologous HL_5J7L_169 NA | |
| HL_8C90_036 | 1/A/1612:1619 | No text annotation | geometric HL_4WF9_038 HL_28592.2 | |
| HL_8C90_037 | 1/A/1630:1636 | GNRA | homologous HL_5J7L_174 NA | |
| HL_8C90_039 | 1/A/1752:1756 | No text annotation | homologous HL_7RQB_044 NA | |
| HL_8C90_040 | 1/A/2027:2036 | No text annotation | homologous HL_4WF9_047 HL_78372.1 | |
| HL_8C90_041 | 1/A/2264:2276 | No text annotation | homologous HL_7A0S_053 HL_02042.1 | |
| HL_8C90_044 | 1/A/2356:2361 | GNRA | homologous HL_5J7L_190 NA | |
| HL_8C90_045 | 1/A/2374:2379 | GNRA | homologous HL_5J7L_191 NA | |
| HL_8C90_048 | 1/A/2701:2706 | Ribsomal LSU H95 | homologous HL_7A0S_064 HL_12125.2 | |
| HL_8C90_050 | 1/A/2796:2799 | Mini UNCG | geometric HL_4V88_192 NA | |
| HL_8C90_051 | 1/A/2819:2827 | No text annotation | homologous HL_5J7L_201 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_8C90_004 | No text annotation | ||
| HL_8C90_005 | No text annotation | ||
| HL_8C90_006 | No text annotation | ||
| HL_8C90_008 | No text annotation | ||
| HL_8C90_012 | No text annotation | ||
| HL_8C90_013 | No text annotation | ||
| HL_8C90_057 | Pseudoknot geometry | ||
| HL_8C90_020 | No text annotation | ||
| HL_8C90_021 | No text annotation | ||
| HL_8C90_022 | No text annotation | ||
| HL_8C90_023 | No text annotation | ||
| HL_8C90_024 | No text annotation | ||
| HL_8C90_026 | No text annotation | ||
| HL_8C90_030 | GNRA | ||
| HL_8C90_033 | Pseudoknot geometry with 3' bulge | ||
| HL_8C90_034 | UNCG | ||
| HL_8C90_035 | No text annotation | ||
| HL_8C90_056 | No text annotation | ||
| HL_8C90_038 | No text annotation | ||
| HL_8C90_042 | No text annotation | ||
| HL_8C90_043 | Pseudoknot geometry | ||
| HL_8C90_046 | No text annotation | ||
| HL_8C90_047 | GNRA | ||
| HL_8C90_049 | No text annotation | ||
| HL_8C90_052 | GNRA | ||
| HL_8C90_053 | No text annotation | ||
| HL_8C90_054 | Mini UNCG |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_8C90_001 | 1/A/24:30, 1/A/510:516 | Triple sheared with non-canonical cWW | homologous IL_4WF9_001 IL_22311.1 | |
| IL_8C90_002 | 1/A/36:37, 1/A/442:444 | Single bulged A | homologous IL_5J7L_246 NA | |
| IL_8C90_003 | 1/A/43:44, 1/A/434:436 | Minor groove platform | homologous IL_5J7L_247 NA | |
| IL_8C90_080 | 1/A/82:85, 1/A/97:104 | Kink-turn | geometric IL_1U63_003 IL_24134.1 | |
| IL_8C90_005 | 1/A/183:184, 1/A/212:214 | Single stack bend | homologous IL_7A0S_005 IL_15011.2 | |
| IL_8C90_006 | 1/A/188:194, 1/A/201:208 | 8x7 Sarcin-Ricin; G-bulge | homologous IL_7A0S_006 IL_62167.3 | |
| IL_8C90_007 | 1/A/239:245, 1/A/253:258 | 7x6 Sarcin-Ricin; G-bulge | homologous IL_7RQB_007 NA | |
| IL_8C90_010 | 1/A/293:295, 1/A/343:347 | No text annotation | homologous IL_5J7L_254 NA | |
| IL_8C90_012 | 1/A/481:484, 1/A/496:509 | No text annotation | homologous IL_5J7L_255 NA | |
| IL_8C90_013 | 1/A/536:539, 1/A/554:557 | Double sheared | homologous IL_5J7L_256 NA | |
| IL_8C90_014 | 1/A/564:566, 1/A/575:577 | Isolated non-canonical cWW pair | homologous IL_4WF9_017 IL_71625.3 | |
| IL_8C90_015 | 1/A/606:610, 1/A/618:622 | AAA cross-strand stack | homologous IL_5J7L_258 NA | |
| IL_8C90_016 | 1/A/672:674, 1/A/806:808 | Isolated non-canonical cWW pair | homologous IL_4WF9_020 IL_01003.3 | |
| IL_8C90_017 | 1/A/674:678, 1/A/799:806 | tHW-tHW cross-strand stack | geometric IL_4V9F_024 IL_73855.1 | |
| IL_8C90_018 | 1/A/844:847, 1/A/933:934 | 90 degree turn | homologous IL_5J7L_267 NA | |
| IL_8C90_081 | 1/A/844:848, 1/A/930:934 | No text annotation | homologous IL_5J7L_399 NA | |
| IL_8C90_019 | 1/A/847:848, 1/A/930:933 | Stack outside cWW | geometric IL_5J7L_268 NA | |
| IL_8C90_020 | 1/A/850:851, 1/A/926:928 | Single stack bend | homologous IL_5J7L_269 NA | |
| IL_8C90_021 | 1/A/854:856, 1/A/922:923 | Single stack bend | geometric IL_7A0S_054 IL_15011.2 | |
| IL_8C90_082 | 1/A/855:857, 1/A/921:922 | Single stack bend | geometric IL_8C3A_012 NA | |
| IL_8C90_022 | 1/A/857:862, 1/A/915:921 | No text annotation | ||
| IL_8C90_023 | 1/A/862:863, 1/A/913:915 | Single bulged G | homologous IL_5J7L_271 NA | |
| IL_8C90_024 | 1/A/864:868, 1/A/909:912 | C-loop with bulged stacked A's | homologous IL_5J7L_272 NA | |
| IL_8C90_025 | 1/A/870:873, 1/A/904:907 | No text annotation | ||
| IL_8C90_026 | 1/A/994:996, 1/A/1159:1160 | Single bulged C | homologous IL_4WF9_035 IL_05642.2 | |
| IL_8C90_027 | 1/A/998:1002, 1/A/1153:1157 | UAA/GAN | homologous IL_4WF9_036 IL_08938.1 | |
| IL_8C90_028 | 1/A/1004:1011, 1/A/1150:1151 | SSU/LSU pseudoknot | homologous IL_4WF9_037 IL_11411.1 | |
| IL_8C90_029 | 1/A/1011:1013, 1/A/1149:1150 | Single bulged U | geometric IL_5J7L_279 NA | |
| IL_8C90_030 | 1/A/1018:1024, 1/A/1140:1144 | Kink-turn related | homologous IL_4WF9_039 IL_57188.6 | |
| IL_8C90_031 | 1/A/1024:1030, 1/A/1124:1140 | No text annotation | ||
| IL_8C90_034 | 1/A/1196:1198, 1/A/1247:1250 | Isolated cWS basepair | homologous IL_7A0S_041 IL_42997.5 | |
| IL_8C90_035 | 1/A/1202:1206, 1/A/1240:1243 | No text annotation | homologous IL_5J7L_287 NA | |
| IL_8C90_036 | 1/A/1208:1215, 1/A/1234:1238 | Kink-turn | homologous IL_5J7L_288 NA | |
| IL_8C90_037 | 1/A/1262:1269, 1/A/2011:2017 | 8x7 Sarcin-Ricin; G-bulge | homologous IL_5J7L_289 NA | |
| IL_8C90_038 | 1/A/1310:1313, 1/A/1603:1604 | Major groove platform; stack outside cWW | homologous IL_7RQB_050 NA | |
| IL_8C90_039 | 1/A/1319:1323, 1/A/1331:1333 | Major groove minor groove platform with tHH | homologous IL_4WF9_050 IL_06671.1 | |
| IL_8C90_040 | 1/A/1351:1355, 1/A/1376:1380 | UAA/GAN | homologous IL_7RQB_052 NA | |
| IL_8C90_047 | 1/A/1437:1440, 1/A/1551:1555 | tSH-tHW | homologous IL_5J7L_297 NA | |
| IL_8C90_048 | 1/A/1450:1451, 1/A/1459:1461 | Single bulged U | geometric IL_5J7L_298 NA | |
| IL_8C90_049 | 1/A/1468:1472, 1/A/1519:1524 | No text annotation | geometric IL_3BNN_006 IL_25186.4 | |
| IL_8C90_053 | 1/A/1526:1529, 1/A/1542:1546 | UAA/GAN variation | homologous IL_5J7L_303 NA | |
| IL_8C90_054 | 1/A/1651:1656, 1/A/2004:2006 | No text annotation | homologous IL_7A0S_059 IL_12566.5 | |
| IL_8C90_086 | 1/A/1663:1665, 1/A/1995:1997 | Isolated tWW turn | homologous IL_4WF9_063 IL_10432.1 | |
| IL_8C90_087 | 1/A/1666:1674, 1/A/1990:1994 | No text annotation | homologous IL_4WF9_117 IL_80252.1 | |
| IL_8C90_057 | 1/A/1669:1674, 1/A/1990:1993 | Intercalated tWH | geometric IL_5TBW_077 NA | |
| IL_8C90_058 | 1/A/1712:1718, 1/A/1742:1746 | 6x5 Sarcin-Ricin; G-bulge | homologous IL_5J7L_309 NA | |
| IL_8C90_060 | 1/A/2050:2052, 1/A/2617:2618 | Major groove platform | homologous IL_5J7L_320 NA | |
| IL_8C90_062 | 1/A/2350:2353, 1/A/2364:2367 | Double sheared | homologous IL_5J7L_333 NA | |
| IL_8C90_064 | 1/A/2636:2640, 1/A/2774:2782 | tSH-tHS-tHW | homologous IL_7A0S_093 IL_04638.4 | |
| IL_8C90_066 | 1/A/2680:2684, 1/A/2725:2727 | C-loop | homologous IL_5J7L_347 NA | |
| IL_8C90_067 | 1/A/2687:2691, 1/A/2718:2722 | UAA/GAN related, with intercalation | homologous IL_4WF9_102 IL_82016.1 | |
| IL_8C90_068 | 1/A/2695:2696, 1/A/2711:2714 | Multiple bulged bases | homologous IL_5J7L_349 NA | |
| IL_8C90_070 | 1/A/2795:2796, 1/A/2799:2801 | Single bulged A | geometric IL_7RQB_019 NA | |
| IL_8C90_071 | 1/A/2806:2811, 1/A/2889:2892 | No text annotation | geometric IL_5J7L_351 NA | |
| IL_8C90_072 | 1/A/2838:2839, 1/A/2878:2880 | Major groove intercalation | homologous IL_5J7L_352 NA | |
| IL_8C90_073 | 1/A/2843:2846, 1/A/2870:2874 | Multiple bulged bases with non-canonical cWW | homologous IL_5J7L_353 NA | |
| IL_8C90_074 | 1/A/2847:2853, 1/A/2864:2869 | No text annotation | ||
| IL_8C90_075 | 1/B/17:18, 1/B/65:67 | Major groove intercalation | homologous IL_5J7L_355 NA | |
| IL_8C90_079 | 1/B/71:79, 1/B/97:105 | Bacterial 5S Loop E | homologous IL_5J7L_359 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_8C90_004 | No text annotation | ||
| IL_8C90_008 | No text annotation | ||
| IL_8C90_009 | No text annotation | ||
| IL_8C90_011 | Single stack bend | ||
| IL_8C90_083 | Single stack bend | ||
| IL_8C90_032 | Isolated non-canonical cWW pair | ||
| IL_8C90_033 | Tandem non-canonical cWW pairs | ||
| IL_8C90_041 | tSH-tHW-tHS | ||
| IL_8C90_042 | No text annotation | ||
| IL_8C90_084 | No text annotation | ||
| IL_8C90_043 | UAA/GAN | ||
| IL_8C90_085 | No text annotation | ||
| IL_8C90_044 | Single stack bend | ||
| IL_8C90_045 | Single stack bend | ||
| IL_8C90_046 | No text annotation | ||
| IL_8C90_050 | tSH-tHW-tHS | ||
| IL_8C90_051 | 180 degree turn | ||
| IL_8C90_052 | Single bulged A | ||
| IL_8C90_055 | No text annotation | ||
| IL_8C90_056 | Major groove platform; stack outside cWW | ||
| IL_8C90_059 | No text annotation | ||
| IL_8C90_088 | No text annotation | ||
| IL_8C90_061 | Single stack bend | ||
| IL_8C90_063 | Single bulged U | ||
| IL_8C90_090 | No text annotation | ||
| IL_8C90_089 | No text annotation | ||
| IL_8C90_065 | 7x6 Sarcin-Ricin; G-bulge | ||
| IL_8C90_069 | UAA/GAN with extra cWW | ||
| IL_8C90_076 | No text annotation | ||
| IL_8C90_077 | Single stack bend | ||
| IL_8C90_078 | Symmetric double minor groove platform |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_8C90_001 | 1/A/30:31, 1/A/474:481, 1/A/509:510 | No text annotation | homologous J3_5J7L_036 NA | |
| J3_8C90_010 | 1/A/32:35, 1/A/445:461, 1/A/468:473 | No text annotation | homologous J3_5J7L_067 NA | |
| J3_8C90_002 | 1/A/56:57, 1/A/70:76, 1/A/110:114 | No text annotation | homologous J3_5J7L_037 NA | |
| J3_8C90_011 | 1/A/297:301, 1/A/316:325, 1/A/337:341 | No text annotation | homologous J3_5J7L_068 NA | |
| J3_8C90_003 | 1/A/1298:1303, 1/A/1625:1627, 1/A/1639:1642 | No text annotation | homologous J3_5J7L_041 NA | |
| J3_8C90_004 | 1/A/1306:1309, 1/A/1605:1612, 1/A/1619:1622 | No text annotation | ||
| J3_8C90_005 | 1/A/1344:1349, 1/A/1382:1385, 1/A/1402:1403 | No text annotation | homologous J3_5J7L_043 NA | |
| J3_8C90_006 | 1/A/2295:2299, 1/A/2317:2323, 1/A/2332:2337 | No text annotation | homologous J3_5J7L_071 NA | |
| J3_8C90_007 | 1/A/2789:2791, 1/A/2805:2806, 1/A/2892:2894 | No text annotation | homologous J3_5J7L_047 NA | |
| J3_8C90_008 | 1/A/2812:2815, 1/A/2831:2836, 1/A/2882:2888 | No text annotation | homologous J3_5J7L_048 NA | |
| J3_8C90_009 | 1/B/10:16, 1/B/68:70, 1/B/106:110 | No text annotation | homologous J3_5J7L_049 NA | |
| J4_8C90_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_8C90_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_8C90_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_8C90_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_8C90_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_8C90_011 | 1/A/1444:1445, 1/A/1466:1467, 1/A/1525:1526, 1/A/1546:1547 | No text annotation | homologous J4_5J7L_024 NA | |
| J4_8C90_007 | 1/A/1444:1446, 1/A/1465:1467, 1/A/1525:1526, 1/A/1546:1547 | No text annotation | ||
| J4_8C90_008 | 1/A/2285:2289, 1/A/2343:2347, 1/A/2370:2372, 1/A/2381:2383 | No text annotation | homologous J4_9DFE_009 J4_98139.1 | |
| J4_8C90_009 | 1/A/2643:2646, 1/A/2674:2676, 1/A/2731:2735, 1/A/2769:2771 | No text annotation | homologous J4_5J7L_028 NA | |
| J5_8C90_005 | 1/A/47:54, 1/A/116:121, 1/A/130:131, 1/A/148:150, 1/A/176:178 | No text annotation | homologous J5_5J7L_013 NA | |
| J5_8C90_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_8C90_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_8C90_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_8C90_002 | 1/A/45:46, 1/A/179:183, 1/A/214:224, 1/A/231:235, 1/A/262:267, 1/A/425:433 | No text annotation | ||
| J7_8C90_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_8C90_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_8C90_012 | No text annotation | ||
| J4_8C90_001 | No text annotation | ||
| J4_8C90_010 | No text annotation | ||
| J5_8C90_001 | No text annotation | ||
| J6_8C90_001 | No text annotation |
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