6GC4 Internal, Hairpin and 3-way Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_6GC4_001 | 1/A/59:68 | No text annotation Not in a motif group | homologous HL_5J7L_134 HL_18177.1 | |
| HL_6GC4_002 | 1/A/87:95 | No text annotation Not in a motif group | homologous HL_5J7L_135 HL_84193.1 | |
| HL_6GC4_003 | 1/A/123:128 | No text annotation Not in a motif group | homologous HL_4WF9_003 HL_75407.1 | |
| HL_6GC4_004 | 1/A/136:143 | No text annotation Not in a motif group | ||
| HL_6GC4_005 | 1/A/158:168 | No text annotation Not in a motif group | homologous HL_5J7L_138 HL_81820.1 | |
| HL_6GC4_006 | 1/A/194:201 | No text annotation Not in a motif group | homologous HL_4WF9_006 HL_06192.2 | |
| HL_6GC4_007 | 1/A/225:230 | No text annotation Not in a motif group | homologous HL_5J7L_140 HL_27930.1 | |
| HL_6GC4_008 | 1/A/246:252 | No text annotation Not in a motif group | homologous HL_4WF9_008 HL_67216.7 | |
| HL_6GC4_009 | 1/A/305:312 | T-loop with 1 bulged base Not in a motif group | homologous HL_5J7L_142 HL_89380.2 | |
| HL_6GC4_010 | 1/A/319:323 | No text annotation Not in a motif group | homologous HL_4WF9_011 HL_75407.1 | |
| HL_6GC4_011 | 1/A/327:335 | No text annotation Not in a motif group | homologous HL_5J7L_144 HL_08002.8 | |
| HL_6GC4_012 | 1/A/381:393 | No text annotation Not in a motif group | ||
| HL_6GC4_013 | 1/A/410:417 | No text annotation Not in a motif group | homologous HL_7RQB_014 HL_96598.1 | |
| HL_6GC4_014 | 1/A/462:467 | GNRA Not in a motif group | homologous HL_4WF9_015 HL_42097.1 | |
| HL_6GC4_015 | 1/A/487:493 | No text annotation Not in a motif group | homologous HL_7RQB_016 HL_42097.1 | |
| HL_6GC4_016 | 1/A/542:551 | No text annotation Not in a motif group | homologous HL_7RQB_017 NA | |
| HL_6GC4_017 | 1/A/566:575 | No text annotation Not in a motif group | homologous HL_7RQB_018 HL_89380.2 | |
| HL_6GC4_018 | 1/A/611:617 | No text annotation Not in a motif group | homologous HL_5J7L_151 HL_90617.2 | |
| HL_6GC4_019 | 1/A/629:634 | GNRA Not in a motif group | homologous HL_5J7L_152 HL_42097.1 | |
| HL_6GC4_020 | 1/A/641:647 | No text annotation Not in a motif group | homologous HL_5J7L_153 HL_77805.2 | |
| HL_6GC4_023 | 1/A/779:785 | No text annotation Not in a motif group | geometric HL_7A0S_007 HL_02862.2 | |
| HL_6GC4_024 | 1/A/826:831 | No text annotation Not in a motif group | homologous HL_4WF9_025 HL_64365.1 | |
| HL_6GC4_026 | 1/A/955:962 | No text annotation Not in a motif group | homologous HL_7A0S_026 HL_42097.1 | |
| HL_6GC4_027 | 1/A/978:985 | No text annotation Not in a motif group | homologous HL_7RQB_028 HL_64430.2 | |
| HL_6GC4_028 | 1/A/1168:1181 | No text annotation Not in a motif group | ||
| HL_6GC4_029 | 1/A/1222:1227 | Other HL Not in a motif group | homologous HL_5J7L_164 HL_87030.2 | |
| HL_6GC4_030 | 1/A/1281:1289 | T-loop with 2 stacked bulged bases Not in a motif group | homologous HL_5J7L_165 HL_89380.2 | |
| HL_6GC4_031 | 1/A/1324:1330 | No text annotation Not in a motif group | homologous HL_5J7L_166 HL_46680.1 | |
| HL_6GC4_032 | 1/A/1363:1368 | Other HL Not in a motif group | homologous HL_5J7L_167 HL_87030.2 | |
| HL_6GC4_033 | 1/A/1389:1398 | No text annotation Not in a motif group | homologous HL_5J7L_168 HL_69023.2 | |
| HL_6GC4_034 | 1/A/1451:1459 | No text annotation Not in a motif group | geometric HL_5TBW_004 HL_98426.1 | |
| HL_6GC4_035 | 1/A/1492:1498 | No text annotation Not in a motif group | homologous HL_5J7L_170 HL_46680.1 | |
| HL_6GC4_036 | 1/A/1533:1538 | UNCG Not in a motif group | homologous HL_5J7L_171 HL_03562.2 | |
| HL_6GC4_037 | 1/A/1565:1568 | No text annotation Not in a motif group | homologous HL_5J7L_172 HL_38927.2 | |
| HL_6GC4_038 | 1/A/1612:1619 | No text annotation Not in a motif group | homologous HL_4WF9_038 HL_64430.2 | |
| HL_6GC4_039 | 1/A/1630:1636 | GNRA with one bulged base Not in a motif group | homologous HL_5J7L_174 HL_42097.1 | |
| HL_6GC4_041 | 1/A/1728:1731 | No text annotation Not in a motif group | ||
| HL_6GC4_042 | 1/A/1752:1756 | No text annotation Not in a motif group | homologous HL_5J7L_177 HL_76539.2 | |
| HL_6GC4_047 | 1/A/2027:2036 | No text annotation Not in a motif group | homologous HL_4WF9_047 HL_90642.6 | |
| HL_6GC4_057 | 1/A/2658:2663 | GNRA Not in a motif group | homologous HL_5J7L_197 HL_42097.1 | |
| HL_6GC4_058 | 1/A/2700:2707 | No text annotation Not in a motif group | geometric HL_3R4F_002 HL_35015.1 | |
| HL_6GC4_059 | 1/A/2745:2759 | No text annotation Not in a motif group | homologous HL_7RQB_066 HL_56677.7 | |
| HL_6GC4_060 | 1/A/2796:2799 | No text annotation Not in a motif group | geometric HL_4V88_192 HL_53837.1 | |
| HL_6GC4_061 | 1/A/2819:2827 | No text annotation Not in a motif group | homologous HL_5J7L_201 HL_27930.1 | |
| HL_6GC4_062 | 1/A/2856:2861 | No text annotation Not in a motif group | homologous HL_7A0S_068 HL_42097.1 | |
| HL_6GC4_063 | 1/B/38:44 | No text annotation Not in a motif group | geometric HL_5J7L_203 HL_87939.1 | |
| HL_6GC4_064 | 1/B/86:90 | No text annotation Not in a motif group | homologous HL_5J7L_204 HL_38927.2 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_6GC4_021 | No text annotation | ||
| HL_6GC4_022 | No text annotation | ||
| HL_6GC4_025 | No text annotation | ||
| HL_6GC4_040 | No text annotation | ||
| HL_6GC4_043 | No text annotation | ||
| HL_6GC4_044 | No text annotation | ||
| HL_6GC4_045 | No text annotation | ||
| HL_6GC4_046 | No text annotation | ||
| HL_6GC4_048 | No text annotation | ||
| HL_6GC4_049 | No text annotation | ||
| HL_6GC4_050 | No text annotation | ||
| HL_6GC4_051 | No text annotation | ||
| HL_6GC4_052 | No text annotation | ||
| HL_6GC4_053 | No text annotation | ||
| HL_6GC4_054 | Other HL | ||
| HL_6GC4_055 | GNRA | ||
| HL_6GC4_056 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_6GC4_001 | 1/A/24:30, 1/A/510:516 | Triple sheared with non-canonical cWW Not in a motif group | homologous IL_4WF9_001 IL_66414.6 | |
| IL_6GC4_002 | 1/A/36:37, 1/A/442:444 | Single bulged A Not in a motif group | homologous IL_4WF9_002 IL_37497.2 | |
| IL_6GC4_003 | 1/A/43:44, 1/A/434:436 | Minor groove platform Not in a motif group | homologous IL_5J7L_247 IL_42622.2 | |
| IL_6GC4_004 | 1/A/81:85, 1/A/97:105 | No text annotation Not in a motif group | homologous IL_5J7L_248 IL_93699.1 | |
| IL_6GC4_005 | 1/A/183:184, 1/A/212:214 | Single stack bend Not in a motif group | homologous IL_7A0S_005 IL_76488.2 | |
| IL_6GC4_006 | 1/A/188:194, 1/A/201:208 | 8x7 Sarcin-Ricin; G-bulge Not in a motif group | geometric IL_7A0S_006 IL_04346.7 | |
| IL_6GC4_007 | 1/A/239:245, 1/A/253:258 | 7x6 Sarcin-Ricin; G-bulge Not in a motif group | homologous IL_7RQB_007 IL_76042.2 | |
| IL_6GC4_008 | 1/A/269:271, 1/A/366:370 | No text annotation Not in a motif group | homologous IL_5J7L_252 IL_47972.1 | |
| IL_6GC4_009 | 1/A/274:281, 1/A/359:363 | No text annotation Not in a motif group | homologous IL_5J7L_253 IL_77870.1 | |
| IL_6GC4_010 | 1/A/293:295, 1/A/343:347 | No text annotation Not in a motif group | homologous IL_7RQB_013 IL_69440.1 | |
| IL_6GC4_011 | 1/A/481:484, 1/A/496:509 | No text annotation Not in a motif group | geometric IL_5J7L_255 IL_60992.6 | |
| IL_6GC4_012 | 1/A/536:539, 1/A/554:557 | Double sheared Not in a motif group | homologous IL_5J7L_256 IL_09705.9 | |
| IL_6GC4_013 | 1/A/564:566, 1/A/575:577 | CC cWW Not in a motif group | geometric IL_4E59_001 IL_95997.1 | |
| IL_6GC4_014 | 1/A/606:610, 1/A/618:622 | AAA cross-strand stack Not in a motif group | homologous IL_5J7L_258 IL_17136.1 | |
| IL_6GC4_015 | 1/A/672:674, 1/A/806:808 | No text annotation Not in a motif group | homologous IL_4WF9_020 IL_95997.1 | |
| IL_6GC4_016 | 1/A/674:678, 1/A/799:806 | tHW-tHW cross-strand stack Not in a motif group | geometric IL_5J7L_260 IL_17470.6 | |
| IL_6GC4_022 | 1/A/844:847, 1/A/933:934 | Other IL Not in a motif group | geometric IL_5J7L_267 IL_92001.1 | |
| IL_6GC4_023 | 1/A/847:848, 1/A/930:933 | Stack outside cWW Not in a motif group | homologous IL_5J7L_268 IL_37629.1 | |
| IL_6GC4_024 | 1/A/850:851, 1/A/926:928 | Single stack bend Not in a motif group | homologous IL_5J7L_269 IL_76488.2 | |
| IL_6GC4_025 | 1/A/856:862, 1/A/915:921 | 7x7 Sarcin-Ricin with intercalated A; G-bulge Not in a motif group | homologous IL_5J7L_270 IL_93830.3 | |
| IL_6GC4_026 | 1/A/862:863, 1/A/913:915 | Minor groove platform Not in a motif group | geometric IL_3K0J_002 IL_42622.2 | |
| IL_6GC4_030 | 1/A/994:996, 1/A/1159:1160 | Single bulged C Not in a motif group | homologous IL_4WF9_035 IL_61258.12 | |
| IL_6GC4_031 | 1/A/998:1002, 1/A/1153:1157 | UAA/GAN Not in a motif group | homologous IL_4WF9_036 IL_89002.2 | |
| IL_6GC4_032 | 1/A/1004:1011, 1/A/1150:1151 | SSU/LSU pseudoknot Not in a motif group | homologous IL_5J7L_278 IL_15861.7 | |
| IL_6GC4_033 | 1/A/1011:1013, 1/A/1149:1150 | Single bulged U Not in a motif group | geometric IL_5J7L_279 IL_83039.13 | |
| IL_6GC4_034 | 1/A/1018:1024, 1/A/1140:1144 | No text annotation Not in a motif group | homologous IL_4WF9_039 IL_57188.3 | |
| IL_6GC4_035 | 1/A/1024:1030, 1/A/1124:1140 | No text annotation Not in a motif group | geometric IL_5J7L_281 IL_50715.1 | |
| IL_6GC4_038 | 1/A/1196:1198, 1/A/1247:1250 | Isolated cWS basepair Not in a motif group | homologous IL_4WF9_044 IL_52767.2 | |
| IL_6GC4_039 | 1/A/1202:1206, 1/A/1240:1243 | No text annotation Not in a motif group | homologous IL_5J7L_287 IL_91920.1 | |
| IL_6GC4_040 | 1/A/1208:1215, 1/A/1234:1238 | Kink-turn Not in a motif group | homologous IL_5J7L_288 IL_70923.2 | |
| IL_6GC4_041 | 1/A/1262:1269, 1/A/2011:2017 | 8x7 Sarcin-Ricin; G-bulge Not in a motif group | homologous IL_5J7L_289 IL_04346.7 | |
| IL_6GC4_042 | 1/A/1310:1313, 1/A/1603:1604 | Major groove platform; stack outside cWW Not in a motif group | homologous IL_7RQB_050 IL_50694.2 | |
| IL_6GC4_043 | 1/A/1319:1323, 1/A/1331:1333 | Major groove minor groove platform with tHH Not in a motif group | homologous IL_4WF9_050 IL_37712.2 | |
| IL_6GC4_044 | 1/A/1351:1355, 1/A/1376:1380 | UAA/GAN Not in a motif group | homologous IL_7A0S_048 IL_89002.2 | |
| IL_6GC4_045 | 1/A/1357:1361, 1/A/1370:1374 | tSH-tHW-tHS Not in a motif group | homologous IL_5J7L_293 IL_17136.1 | |
| IL_6GC4_046 | 1/A/1415:1416, 1/A/1582:1587 | No text annotation Not in a motif group | homologous IL_5J7L_294 IL_90348.1 | |
| IL_6GC4_047 | 1/A/1417:1421, 1/A/1577:1581 | UAA/GAN Not in a motif group | homologous IL_5J7L_295 IL_89002.2 | |
| IL_6GC4_048 | 1/A/1432:1435, 1/A/1557:1561 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_5J7L_296 IL_55178.1 | |
| IL_6GC4_049 | 1/A/1437:1440, 1/A/1551:1555 | tSH-tHW Not in a motif group | homologous IL_7A0S_053 IL_04059.1 | |
| IL_6GC4_050 | 1/A/1450:1451, 1/A/1459:1461 | Single bulged U Not in a motif group | homologous IL_5J7L_298 IL_83039.13 | |
| IL_6GC4_051 | 1/A/1468:1471, 1/A/1520:1524 | No text annotation Not in a motif group | homologous IL_5J7L_299 IL_68574.2 | |
| IL_6GC4_052 | 1/A/1474:1479, 1/A/1512:1517 | No text annotation Not in a motif group | ||
| IL_6GC4_053 | 1/A/1481:1482, 1/A/1507:1510 | No text annotation Not in a motif group | homologous IL_5J7L_301 IL_67474.4 | |
| IL_6GC4_054 | 1/A/1489:1491, 1/A/1499:1500 | Single bulged A Not in a motif group | homologous IL_5J7L_302 IL_37497.2 | |
| IL_6GC4_055 | 1/A/1526:1530, 1/A/1541:1546 | Triple sheared related Not in a motif group | geometric IL_4V9F_018 IL_64879.2 | |
| IL_6GC4_056 | 1/A/1651:1656, 1/A/2004:2006 | No text annotation Not in a motif group | homologous IL_5J7L_304 IL_12566.2 | |
| IL_6GC4_057 | 1/A/1663:1665, 1/A/1995:1997 | Isolated tWW turn Not in a motif group | homologous IL_4WF9_063 IL_54997.7 | |
| IL_6GC4_058 | 1/A/1666:1669, 1/A/1993:1994 | Major groove platform; stack outside cWW Not in a motif group | geometric IL_5J7L_306 IL_50694.2 | |
| IL_6GC4_059 | 1/A/1669:1674, 1/A/1990:1993 | Intercalated tWH Not in a motif group | homologous IL_4WF9_065 IL_82842.2 | |
| IL_6GC4_061 | 1/A/1712:1718, 1/A/1742:1746 | 6x5 Sarcin-Ricin; G-bulge Not in a motif group | homologous IL_5J7L_309 IL_88269.3 | |
| IL_6GC4_062 | 1/A/1720:1724, 1/A/1736:1740 | Triple sheared Not in a motif group | homologous IL_5J7L_310 IL_56467.8 | |
| IL_6GC4_063 | 1/A/1727:1728, 1/A/1731:1733 | Single bulged C Not in a motif group | geometric IL_5J7L_311 IL_61258.12 | |
| IL_6GC4_067 | 1/A/2050:2052, 1/A/2617:2618 | Major groove platform Not in a motif group | homologous IL_5J7L_320 IL_27635.1 | |
| IL_6GC4_068 | 1/A/2053:2056, 1/A/2612:2616 | No text annotation Not in a motif group | ||
| IL_6GC4_081 | 1/A/2636:2640, 1/A/2774:2782 | No text annotation Not in a motif group | homologous IL_5J7L_345 IL_04638.1 | |
| IL_6GC4_082 | 1/A/2652:2658, 1/A/2663:2668 | 7x6 Sarcin-Ricin; G-bulge Not in a motif group | geometric IL_4V9F_019 IL_16458.1 | |
| IL_6GC4_083 | 1/A/2680:2684, 1/A/2725:2727 | C-loop Not in a motif group | homologous IL_5J7L_347 IL_63596.6 | |
| IL_6GC4_084 | 1/A/2687:2691, 1/A/2718:2722 | No text annotation Not in a motif group | homologous IL_4WF9_102 IL_08296.3 | |
| IL_6GC4_085 | 1/A/2695:2696, 1/A/2711:2714 | Multiple bulged bases Not in a motif group | homologous IL_5J7L_349 IL_71530.2 | |
| IL_6GC4_086 | 1/A/2737:2742, 1/A/2762:2767 | UAA/GAN with extra cWW Not in a motif group | homologous IL_7A0S_098 IL_49767.5 | |
| IL_6GC4_087 | 1/A/2795:2796, 1/A/2799:2801 | Single bulged A Not in a motif group | geometric IL_7A0S_016 IL_37497.2 | |
| IL_6GC4_088 | 1/A/2806:2811, 1/A/2889:2892 | No text annotation Not in a motif group | homologous IL_5J7L_351 IL_49460.2 | |
| IL_6GC4_089 | 1/A/2838:2839, 1/A/2878:2880 | Major groove intercalation Not in a motif group | homologous IL_4WF9_106 IL_16396.2 | |
| IL_6GC4_090 | 1/A/2843:2846, 1/A/2870:2874 | Multiple bulged bases with non-canonical cWW Not in a motif group | homologous IL_5J7L_353 IL_58764.3 | |
| IL_6GC4_091 | 1/A/2847:2852, 1/A/2865:2869 | No text annotation Not in a motif group | homologous IL_5J7L_354 IL_83162.5 | |
| IL_6GC4_092 | 1/B/17:18, 1/B/65:67 | Major groove intercalation Not in a motif group | homologous IL_4WF9_112 IL_37497.2 | |
| IL_6GC4_093 | 1/B/23:28, 1/B/56:60 | No text annotation Not in a motif group | homologous IL_7RQB_112 NA | |
| IL_6GC4_094 | 1/B/30:31, 1/B/51:54 | Major groove minor groove platform; mini C-loop Not in a motif group | homologous IL_5J7L_357 IL_09061.6 | |
| IL_6GC4_095 | 1/B/34:38, 1/B/44:48 | Symmetric double minor groove platform Not in a motif group | homologous IL_5J7L_358 IL_58103.6 | |
| IL_6GC4_096 | 1/B/71:79, 1/B/97:105 | Bacterial 5S Loop E Not in a motif group | homologous IL_5J7L_359 IL_56455.3 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_6GC4_017 | Single bulged A | ||
| IL_6GC4_018 | Single bulged G | ||
| IL_6GC4_019 | Triple sheared | ||
| IL_6GC4_020 | Major groove platform | ||
| IL_6GC4_021 | Multiple bulged bases | ||
| IL_6GC4_027 | C-loop | ||
| IL_6GC4_028 | No text annotation | ||
| IL_6GC4_029 | No text annotation | ||
| IL_6GC4_036 | Isolated non-canonical cWW with bulges | ||
| IL_6GC4_037 | Tandem non-canonical cWW pairs | ||
| IL_6GC4_060 | tSH-tSH-tHH-tHS | ||
| IL_6GC4_064 | Single bulged A | ||
| IL_6GC4_065 | Kink-turn related | ||
| IL_6GC4_066 | Major groove outside cWW, minor groove, intercalation pocket | ||
| IL_6GC4_069 | Single bulged U | ||
| IL_6GC4_070 | Minor groove platform | ||
| IL_6GC4_071 | Isolated tHS basepair with bulges | ||
| IL_6GC4_072 | No text annotation | ||
| IL_6GC4_073 | No text annotation | ||
| IL_6GC4_074 | No text annotation | ||
| IL_6GC4_075 | No text annotation | ||
| IL_6GC4_076 | No text annotation | ||
| IL_6GC4_077 | No text annotation | ||
| IL_6GC4_078 | Single bulged U | ||
| IL_6GC4_079 | Double sheared | ||
| IL_6GC4_080 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_6GC4_001 | 1/A/30:31, 1/A/474:481, 1/A/509:510 | No text annotation Not in a motif group | ||
| J3_6GC4_002 | 1/A/56:57, 1/A/70:76, 1/A/110:114 | No text annotation Not in a motif group | homologous J3_5J7L_037 NA | |
| J3_6GC4_005 | 1/A/1298:1303, 1/A/1625:1627, 1/A/1639:1642 | No text annotation Not in a motif group | homologous J3_5J7L_041 NA | |
| J3_6GC4_006 | 1/A/1306:1309, 1/A/1605:1611, 1/A/1620:1622 | No text annotation Not in a motif group | homologous J3_5J7L_042 NA | |
| J3_6GC4_007 | 1/A/1344:1349, 1/A/1382:1385, 1/A/1402:1403 | No text annotation Not in a motif group | homologous J3_5J7L_043 NA | |
| J3_6GC4_010 | 1/A/2789:2791, 1/A/2805:2806, 1/A/2892:2894 | No text annotation Not in a motif group | ||
| J3_6GC4_011 | 1/A/2812:2815, 1/A/2831:2836, 1/A/2882:2888 | No text annotation Not in a motif group | homologous J3_5J7L_048 NA | |
| J3_6GC4_012 | 1/B/10:16, 1/B/68:70, 1/B/106:110 | No text annotation Not in a motif group | homologous J3_5J7L_049 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_6GC4_003 | No text annotation | ||
| J3_6GC4_004 | No text annotation | ||
| J3_6GC4_008 | No text annotation | ||
| J3_6GC4_009 | No text annotation |
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