9J1M Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_9J1M_001 | 1/A/59:68 | Pseudoknot with intercalation | homologous HL_4WF9_067 HL_17803.1 | |
| HL_9J1M_002 | 1/A/87:96 | Pseudoknot geometry | homologous HL_4WF9_002 HL_00911.1 | |
| HL_9J1M_003 | 1/A/123:128 | No text annotation | geometric HL_9DFE_003 HL_82710.3 | |
| HL_9J1M_004 | 1/A/137:144 | GNRA wlth tandem sheared | geometric HL_4WF9_004 HL_98423.1 | |
| HL_9J1M_005 | 1/A/160:170 | No text annotation | geometric HL_5J7L_138 NA | |
| HL_9J1M_006 | 1/A/196:203 | No text annotation | geometric HL_9DFE_005 HL_48677.1 | |
| HL_9J1M_007 | 1/A/227:232 | No text annotation | geometric HL_9BZC_001 HL_89167.1 | |
| HL_9J1M_008 | 1/A/248:254 | No text annotation | geometric HL_9DFE_007 HL_76371.1 | |
| HL_9J1M_011 | 1/A/388:395 | T-loop with 2 stacked bulged bases | geometric HL_5DH6_002 HL_13999.1 | |
| HL_9J1M_012 | 1/A/402:406 | No text annotation | geometric HL_5J7L_143 NA | |
| HL_9J1M_013 | 1/A/410:418 | T-loop with unstacked turn | geometric HL_5J7L_144 NA | |
| HL_9J1M_014 | 1/A/471:481 | No text annotation | geometric HL_5J7L_145 NA | |
| HL_9J1M_015 | 1/A/499:506 | Pseudoknot geometry | geometric HL_5J7L_146 NA | |
| HL_9J1M_016 | 1/A/551:556 | GNRA | geometric HL_9DFE_014 HL_34789.1 | |
| HL_9J1M_017 | 1/A/576:581 | GNRA | geometric HL_9DFE_015 HL_34789.1 | |
| HL_9J1M_018 | 1/A/668:677 | T-loop with 2 stacked bulged bases | geometric HL_9DFE_016 HL_33597.1 | |
| HL_9J1M_019 | 1/A/715:720 | No text annotation | ||
| HL_9J1M_020 | 1/A/733:738 | GNRA | geometric HL_9DFE_018 HL_34789.1 | |
| HL_9J1M_021 | 1/A/745:751 | GNRA | geometric HL_9DFE_019 HL_34789.1 | |
| HL_9J1M_023 | 1/A/841:848 | GNRA wlth tandem sheared | geometric HL_9DFE_020 HL_68642.1 | |
| HL_9J1M_024 | 1/A/872:883 | No text annotation | ||
| HL_9J1M_025 | 1/A/908:914 | No text annotation | geometric HL_5J7L_156 NA | |
| HL_9J1M_026 | 1/A/955:960 | No text annotation | geometric HL_9DFE_023 HL_27530.1 | |
| HL_9J1M_027 | 1/A/1083:1090 | GNRA | geometric HL_9DFE_025 HL_34789.1 | |
| HL_9J1M_028 | 1/A/1107:1114 | No text annotation | geometric HL_4WF9_028 HL_47171.1 | |
| HL_9J1M_032 | 1/A/1353:1358 | GNRA | geometric HL_4WF9_031 HL_34789.1 | |
| HL_9J1M_033 | 1/A/1412:1420 | T-loop with 2 stacked bulged bases | geometric HL_9DFE_031 HL_33597.1 | |
| HL_9J1M_034 | 1/A/1455:1461 | Pseudoknot geometry with 3' bulge | geometric HL_7A0S_033 HL_49081.1 | |
| HL_9J1M_035 | 1/A/1494:1499 | GNRA | geometric HL_9DFE_033 HL_34789.1 | |
| HL_9J1M_036 | 1/A/1520:1529 | No text annotation | geometric HL_9DFE_034 HL_77449.1 | |
| HL_9J1M_037 | 1/A/1688:1699 | Pseudoknot | homologous HL_7A0S_036 HL_00824.1 | |
| HL_9J1M_038 | 1/A/1729:1735 | Pseudoknot geometry with 3' bulge | geometric HL_5J7L_170 NA | |
| HL_9J1M_039 | 1/A/1770:1777 | No text annotation | ||
| HL_9J1M_040 | 1/A/1802:1805 | Mini UNCG | geometric HL_9DFE_037 HL_90436.1 | |
| HL_9J1M_041 | 1/A/1847:1854 | No text annotation | geometric HL_7A0S_040 HL_28592.1 | |
| HL_9J1M_042 | 1/A/1865:1871 | GNRA | geometric HL_5J7L_174 NA | |
| HL_9J1M_043 | 1/A/1926:1931 | UNCG | geometric HL_4JF2_003 NA | |
| HL_9J1M_044 | 1/A/1962:1967 | No text annotation | homologous HL_7A0S_043 NA | |
| HL_9J1M_045 | 1/A/1986:1990 | No text annotation | geometric HL_9DFE_042 HL_80709.4 | |
| HL_9J1M_046 | 1/A/2011:2021 | No text annotation | geometric HL_5J7L_178 NA | |
| HL_9J1M_047 | 1/A/2040:2045 | GNRA | geometric HL_3RW6_001 HL_34789.1 | |
| HL_9J1M_049 | 1/A/2148:2158 | No text annotation | geometric HL_9DFE_046 HL_82185.1 | |
| HL_9J1M_050 | 1/A/2187:2195 | No text annotation | geometric HL_5J7L_182 NA | |
| HL_9J1M_051 | 1/A/2265:2274 | No text annotation | geometric HL_7A0S_049 HL_78372.1 | |
| HL_9J1M_052 | 1/A/2446:2453 | No text annotation | ||
| HL_9J1M_053 | 1/A/2486:2494 | No text annotation | geometric HL_9DFE_051 HL_11974.1 | |
| HL_9J1M_054 | 1/A/2502:2514 | No text annotation | geometric HL_9DFE_052 HL_02042.1 | |
| HL_9J1M_055 | 1/A/2542:2550 | No text annotation | geometric HL_5J7L_219 NA | |
| HL_9J1M_056 | 1/A/2562:2569 | Pseudoknot geometry | geometric HL_5J7L_189 NA | |
| HL_9J1M_057 | 1/A/2593:2600 | GNRA with extra cWW | geometric HL_4WF9_053 HL_45359.1 | |
| HL_9J1M_058 | 1/A/2612:2617 | GNRA | geometric HL_4OQU_003 HL_34789.1 | |
| HL_9J1M_059 | 1/A/2642:2651 | No text annotation | geometric HL_9DFE_057 HL_51853.1 | |
| HL_9J1M_060 | 1/A/2709:2717 | No text annotation | geometric HL_9DFE_058 HL_52011.1 | |
| HL_9J1M_061 | 1/A/2766:2773 | GNRA variation | geometric HL_5J7L_194 NA | |
| HL_9J1M_062 | 1/A/2789:2795 | No text annotation | geometric HL_4WF9_058 HL_48677.1 | |
| HL_9J1M_063 | 1/A/2832:2837 | GNRA | geometric HL_5J7L_196 NA | |
| HL_9J1M_064 | 1/A/2896:2901 | GNRA | geometric HL_8D28_002 HL_34789.1 | |
| HL_9J1M_065 | 1/A/2939:2944 | Ribsomal LSU H95 | geometric HL_5J7L_198 NA | |
| HL_9J1M_066 | 1/A/2983:2997 | No text annotation | geometric HL_5J7L_199 NA | |
| HL_9J1M_068 | 1/A/3054:3062 | No text annotation | geometric HL_9DFE_065 HL_37889.1 | |
| HL_9J1M_069 | 1/A/3091:3096 | GNRA | geometric HL_5J7L_202 NA | |
| HL_9J1M_070 | 1/B/33:47 | No text annotation | geometric HL_5NS3_003 HL_97756.3 | |
| HL_9J1M_071 | 1/B/37:43 | No text annotation | geometric HL_5J7L_203 NA | |
| HL_9J1M_072 | 1/B/83:88 | GNRA | geometric HL_5J7L_167 NA | |
| HL_9J1M_073 | 1/a/15:25 | No text annotation | geometric HL_8C3A_192 NA | |
| HL_9J1M_075 | 1/a/154:159 | GNRA | geometric HL_8P9A_129 HL_34789.1 | |
| HL_9J1M_078 | 1/a/258:266 | GNRA related | geometric HL_5J7L_006 NA | |
| HL_9J1M_079 | 1/a/295:300 | GNRA | geometric HL_5J7L_007 NA | |
| HL_9J1M_080 | 1/a/319:332 | No text annotation | ||
| HL_9J1M_081 | 1/a/341:346 | UNCG | geometric HL_9DFE_040 HL_61337.1 | |
| HL_9J1M_085 | 1/a/513:518 | GNRA variation | geometric HL_5J7L_205 NA | |
| HL_9J1M_086 | 1/a/608:614 | GNRA-like with tWH | geometric HL_4LFB_014 HL_92337.1 | |
| HL_9J1M_087 | 1/a/680:689 | No text annotation | geometric HL_5J7L_015 NA | |
| HL_9J1M_088 | 1/a/717:722 | GNRA | geometric HL_8C3A_212 NA | |
| HL_9J1M_089 | 1/a/777:787 | No text annotation | geometric HL_4LFB_017 HL_38491.1 | |
| HL_9J1M_091 | 1/a/855:860 | GNRA | geometric HL_4LFB_019 HL_34789.1 | |
| HL_9J1M_092 | 1/a/890:895 | GNRA | geometric HL_8C3A_216 NA | |
| HL_9J1M_093 | 1/a/956:965 | No text annotation | geometric HL_5J7L_021 NA | |
| HL_9J1M_095 | 1/a/1067:1072 | GNRA | geometric HL_8C3A_219 NA | |
| HL_9J1M_096 | 1/a/1080:1087 | T-loop related | geometric HL_8C3A_220 NA | |
| HL_9J1M_099 | 1/a/1257:1262 | GNRA | geometric HL_7A0S_070 HL_34789.1 | |
| HL_9J1M_100 | 1/a/1306:1315 | T-loop with 3 stacked bulged bases | geometric HL_4LFB_029 HL_93658.1 | |
| HL_9J1M_101 | 1/a/1348:1359 | No text annotation | geometric HL_5J7L_029 NA | |
| HL_9J1M_103 | 1/a/1508:1513 | GNRA variation | geometric HL_8C3A_227 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_9J1M_009 | Pseudoknot geometry | ||
| HL_9J1M_010 | No text annotation | ||
| HL_9J1M_022 | No text annotation | ||
| HL_9J1M_029 | No text annotation | ||
| HL_9J1M_030 | GNRA with extra cWW | ||
| HL_9J1M_031 | No text annotation | ||
| HL_9J1M_048 | No text annotation | ||
| HL_9J1M_067 | UNCG variation | ||
| HL_9J1M_074 | No text annotation | ||
| HL_9J1M_076 | No text annotation | ||
| HL_9J1M_077 | No text annotation | ||
| HL_9J1M_082 | GNRA | ||
| HL_9J1M_083 | UNCG | ||
| HL_9J1M_084 | No text annotation | ||
| HL_9J1M_090 | No text annotation | ||
| HL_9J1M_094 | GNRA | ||
| HL_9J1M_097 | No text annotation | ||
| HL_9J1M_098 | GNRA | ||
| HL_9J1M_102 | UNCG |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_9J1M_001 | 1/A/24:30, 1/A/598:604 | Triple sheared with non-canonical cWW | geometric IL_4WF9_001 IL_22311.1 | |
| IL_9J1M_002 | 1/A/36:37, 1/A/531:533 | Single bulged A | geometric IL_9DFE_002 IL_14190.1 | |
| IL_9J1M_003 | 1/A/43:44, 1/A/523:525 | Minor groove platform | geometric IL_7A0S_003 IL_34520.1 | |
| IL_9J1M_004 | 1/A/81:85, 1/A/98:105 | Kink-turn | geometric IL_9DFE_004 IL_54465.1 | |
| IL_9J1M_005 | 1/A/185:186, 1/A/214:216 | Single stack bend | geometric IL_4WF9_028 IL_15011.1 | |
| IL_9J1M_006 | 1/A/190:196, 1/A/203:210 | 8x7 Sarcin-Ricin; G-bulge | geometric IL_9DFE_006 IL_62167.1 | |
| IL_9J1M_007 | 1/A/241:247, 1/A/255:260 | 7x6 Sarcin-Ricin; G-bulge | geometric IL_5J7L_251 NA | |
| IL_9J1M_009 | 1/A/323:325, 1/A/451:455 | 8-nt loop receptor | geometric IL_6DME_002 IL_44025.1 | |
| IL_9J1M_010 | 1/A/357:366, 1/A/438:440 | No text annotation | ||
| IL_9J1M_011 | 1/A/370:372, 1/A/433:434 | Single bulged U | geometric IL_8P9A_314 IL_97561.1 | |
| IL_9J1M_012 | 1/A/375:377, 1/A/426:430 | No text annotation | geometric IL_4WF9_014 IL_76658.1 | |
| IL_9J1M_013 | 1/A/383:385, 1/A/398:399 | Single bulged U | geometric IL_3TZR_002 NA | |
| IL_9J1M_014 | 1/A/570:573, 1/A/584:597 | No text annotation | geometric IL_8P9A_243 IL_44923.1 | |
| IL_9J1M_015 | 1/A/624:627, 1/A/656:659 | Double sheared | geometric IL_5J7L_256 NA | |
| IL_9J1M_016 | 1/A/629:631, 1/A/652:654 | Isolated non-canonical cWW pair | geometric IL_2O3Y_004 IL_71625.1 | |
| IL_9J1M_017 | 1/A/666:668, 1/A/677:679 | Isolated non-canonical cWW pair | geometric IL_5J7L_257 NA | |
| IL_9J1M_018 | 1/A/693:695, 1/A/794:795 | Single bulged G | geometric IL_9DFE_018 IL_28408.1 | |
| IL_9J1M_019 | 1/A/709:713, 1/A/722:726 | AAA cross-strand stack | geometric IL_7A0S_013 IL_66798.3 | |
| IL_9J1M_021 | 1/A/801:803, 1/A/935:937 | Isolated non-canonical cWW pair | geometric IL_4WF9_020 IL_01003.1 | |
| IL_9J1M_022 | 1/A/803:807, 1/A/928:935 | No text annotation | geometric IL_9DFE_016 IL_73855.1 | |
| IL_9J1M_023 | 1/A/826:827, 1/A/892:894 | Single bulged A | geometric IL_5J7L_261 NA | |
| IL_9J1M_024 | 1/A/831:832, 1/A/857:859 | Single bulged G | geometric IL_5J7L_262 NA | |
| IL_9J1M_025 | 1/A/832:836, 1/A/853:857 | Triple sheared | geometric IL_9DFE_019 IL_15190.1 | |
| IL_9J1M_026 | 1/A/867:869, 1/A/886:887 | Major groove platform | geometric IL_4WF9_026 IL_48076.7 | |
| IL_9J1M_027 | 1/A/904:906, 1/A/916:920 | No text annotation | geometric IL_9DFE_021 IL_89509.1 | |
| IL_9J1M_028 | 1/A/966:967, 1/A/1068:1070 | Single stack bend | geometric IL_4WF9_028 IL_15011.1 | |
| IL_9J1M_029 | 1/A/973:978, 1/A/1057:1062 | No text annotation | ||
| IL_9J1M_030 | 1/A/985:991, 1/A/1044:1050 | 7x7 Sarcin-Ricin with intercalated A; G-bulge | geometric IL_5J7L_270 NA | |
| IL_9J1M_031 | 1/A/991:992, 1/A/1042:1044 | Minor groove platform | geometric IL_4V9F_034 IL_34520.1 | |
| IL_9J1M_032 | 1/A/993:998, 1/A/1038:1041 | C-loop with bulged stacked A's | geometric IL_9DFE_028 IL_16301.1 | |
| IL_9J1M_033 | 1/A/1000:1002, 1/A/1034:1036 | Isolated non-canonical cWW pair | geometric IL_8C3A_414 NA | |
| IL_9J1M_034 | 1/A/1005:1010, 1/A/1026:1031 | No text annotation | geometric IL_8P9A_410 IL_57885.1 | |
| IL_9J1M_036 | 1/A/1077:1078, 1/A/1095:1097 | Single bulged A | geometric IL_8P9A_399 IL_14190.1 | |
| IL_9J1M_037 | 1/A/1123:1125, 1/A/1289:1290 | Single bulged C | geometric IL_5J7L_276 NA | |
| IL_9J1M_038 | 1/A/1127:1131, 1/A/1283:1287 | UAA/GAN | geometric IL_4WF9_036 IL_08938.1 | |
| IL_9J1M_039 | 1/A/1133:1140, 1/A/1280:1281 | SSU/LSU pseudoknot | geometric IL_4V9F_038 IL_11411.1 | |
| IL_9J1M_040 | 1/A/1140:1142, 1/A/1279:1280 | Single bulged C | geometric IL_3W3S_001 NA | |
| IL_9J1M_041 | 1/A/1147:1153, 1/A/1269:1274 | Kink-turn related | geometric IL_4V9F_040 IL_57188.6 | |
| IL_9J1M_042 | 1/A/1153:1159, 1/A/1253:1269 | No text annotation | geometric IL_5J7L_281 NA | |
| IL_9J1M_043 | 1/A/1160:1163, 1/A/1250:1252 | Isolated non-canonical cWW pair | geometric IL_7A0S_038 IL_30229.1 | |
| IL_9J1M_045 | 1/A/1328:1330, 1/A/1378:1381 | Isolated cWS basepair | geometric IL_4WF9_044 IL_42997.4 | |
| IL_9J1M_046 | 1/A/1339:1346, 1/A/1365:1369 | Kink-turn | geometric IL_5J7L_288 NA | |
| IL_9J1M_047 | 1/A/1393:1400, 1/A/2249:2255 | 8x7 Sarcin-Ricin; G-bulge | geometric IL_9DFE_048 IL_62167.1 | |
| IL_9J1M_048 | 1/A/1450:1454, 1/A/1462:1464 | C-loop | homologous IL_5J7L_291 NA | |
| IL_9J1M_049 | 1/A/1482:1486, 1/A/1507:1511 | UAA/GAN | geometric IL_5J7L_292 NA | |
| IL_9J1M_050 | 1/A/1488:1492, 1/A/1501:1505 | tSH-tHW-tHS | geometric IL_5J7L_293 NA | |
| IL_9J1M_051 | 1/A/1544:1546, 1/A/1822:1824 | Isolated non-canonical cWW pair | geometric IL_3DIL_006 IL_01003.1 | |
| IL_9J1M_052 | 1/A/1655:1659, 1/A/1814:1817 | No text annotation | ||
| IL_9J1M_053 | 1/A/1670:1673, 1/A/1794:1798 | tWW and near cWH | geometric IL_6DLR_005 IL_40706.1 | |
| IL_9J1M_054 | 1/A/1675:1678, 1/A/1788:1792 | No text annotation | geometric IL_9DFE_056 IL_74317.1 | |
| IL_9J1M_055 | 1/A/1706:1709, 1/A/1759:1763 | No text annotation | geometric IL_5J7L_299 NA | |
| IL_9J1M_056 | 1/A/1711:1716, 1/A/1752:1757 | tSH-tHW-tHS-cWW | geometric IL_3LQX_002 IL_35186.1 | |
| IL_9J1M_058 | 1/A/1726:1728, 1/A/1736:1737 | Single bulged A | geometric IL_2OZB_001 NA | |
| IL_9J1M_059 | 1/A/1886:1891, 1/A/2242:2244 | No text annotation | ||
| IL_9J1M_060 | 1/A/1898:1900, 1/A/2233:2235 | No text annotation | geometric IL_9DFE_064 IL_10432.1 | |
| IL_9J1M_061 | 1/A/1901:1904, 1/A/2231:2232 | Major groove platform; stack outside cWW | geometric IL_5J7L_306 NA | |
| IL_9J1M_062 | 1/A/1901:1909, 1/A/2228:2232 | No text annotation | geometric IL_5J7L_386 NA | |
| IL_9J1M_063 | 1/A/1904:1909, 1/A/2228:2231 | Intercalated tWH | geometric IL_5J7L_307 NA | |
| IL_9J1M_064 | 1/A/1921:1926, 1/A/1931:1937 | No text annotation | geometric IL_9DFE_068 IL_20700.1 | |
| IL_9J1M_065 | 1/A/1947:1952, 1/A/1977:1980 | tWW and near cWH | geometric IL_6DLR_005 IL_40706.1 | |
| IL_9J1M_066 | 1/A/1952:1961, 1/A/1968:1977 | No text annotation | ||
| IL_9J1M_067 | 1/A/2004:2005, 1/A/2218:2220 | Single bulged A | geometric IL_9DFE_069 IL_14190.1 | |
| IL_9J1M_068 | 1/A/2032:2038, 1/A/2047:2055 | No text annotation | geometric IL_9DFE_070 IL_17069.6 | |
| IL_9J1M_069 | 1/A/2071:2074, 1/A/2140:2141 | Minor groove platform, major groove intercalation | geometric IL_1U9S_005 NA | |
| IL_9J1M_070 | 1/A/2075:2076, 1/A/2136:2139 | Major groove intercalation | geometric IL_5J7L_315 NA | |
| IL_9J1M_071 | 1/A/2080:2083, 1/A/2131:2132 | Major groove minor groove platform; mini C-loop | geometric IL_4PDB_002 NA | |
| IL_9J1M_072 | 1/A/2085:2089, 1/A/2125:2129 | UAA/GAN with extra stack | geometric IL_9DFE_074 IL_89021.3 | |
| IL_9J1M_073 | 1/A/2090:2095, 1/A/2119:2124 | No text annotation | ||
| IL_9J1M_074 | 1/A/2098:2101, 1/A/2112:2116 | UAA/GAN related | geometric IL_5J7L_317 NA | |
| IL_9J1M_075 | 1/A/2171:2172, 1/A/2202:2205 | No text annotation | geometric IL_9DFE_076 IL_24886.1 | |
| IL_9J1M_076 | 1/A/2172:2183, 1/A/2199:2202 | No text annotation | geometric IL_7A0S_072 IL_04332.3 | |
| IL_9J1M_077 | 1/A/2288:2290, 1/A/2855:2856 | Major groove platform | geometric IL_9DFE_078 IL_48076.7 | |
| IL_9J1M_078 | 1/A/2292:2294, 1/A/2850:2853 | No text annotation | geometric IL_4WF9_079 IL_80025.1 | |
| IL_9J1M_079 | 1/A/2307:2308, 1/A/2676:2679 | Minor groove platform | geometric IL_8P9A_322 IL_34520.1 | |
| IL_9J1M_080 | 1/A/2318:2321, 1/A/2473:2477 | No text annotation | geometric IL_3NPQ_006 IL_93503.1 | |
| IL_9J1M_081 | 1/A/2322:2324, 1/A/2470:2472 | Isolated non-canonical cWW pair | geometric IL_5J7L_326 NA | |
| IL_9J1M_082 | 1/A/2439:2441, 1/A/2458:2459 | Single bulged C | geometric IL_6ZDP_001 NA | |
| IL_9J1M_083 | 1/A/2535:2537, 1/A/2555:2559 | No text annotation | geometric IL_9DFE_088 IL_14250.1 | |
| IL_9J1M_084 | 1/A/2588:2591, 1/A/2602:2605 | Double sheared | geometric IL_5J7L_333 NA | |
| IL_9J1M_085 | 1/A/2639:2641, 1/A/2652:2653 | Major groove platform | geometric IL_5T5A_002 IL_48076.7 | |
| IL_9J1M_086 | 1/A/2691:2692, 1/A/2736:2738 | Single stack bend | geometric IL_4WF9_089 IL_15011.1 | |
| IL_9J1M_087 | 1/A/2692:2693, 1/A/2734:2736 | Major groove platform | geometric IL_9DFE_092 IL_48076.7 | |
| IL_9J1M_088 | 1/A/2695:2697, 1/A/2731:2732 | Major groove platform | geometric IL_9DFE_093 IL_48076.7 | |
| IL_9J1M_089 | 1/A/2697:2699, 1/A/2727:2731 | No text annotation | homologous IL_9DFE_094 IL_36931.1 | |
| IL_9J1M_090 | 1/A/2699:2701, 1/A/2725:2727 | Isolated non-canonical cWW pair | geometric IL_3BNN_005 IL_71625.1 | |
| IL_9J1M_091 | 1/A/2704:2708, 1/A/2718:2722 | Double sheared with non-canonical cWW | geometric IL_5J7L_338 NA | |
| IL_9J1M_092 | 1/A/2745:2746, 1/A/2818:2820 | No text annotation | geometric IL_9DFE_096 IL_46637.1 | |
| IL_9J1M_093 | 1/A/2748:2750, 1/A/2812:2816 | Isolated non-canonical cWW with bulges | geometric IL_9DFE_097 IL_68118.1 | |
| IL_9J1M_094 | 1/A/2750:2751, 1/A/2809:2812 | No text annotation | geometric IL_5J7L_341 NA | |
| IL_9J1M_095 | 1/A/2760:2761, 1/A/2778:2781 | Major groove platform with intercalation | geometric IL_7A0S_091 IL_94991.1 | |
| IL_9J1M_096 | 1/A/2829:2830, 1/A/2839:2841 | Single bulged A | geometric IL_1GID_009 NA | |
| IL_9J1M_097 | 1/A/2874:2878, 1/A/3012:3020 | No text annotation | geometric IL_9DFE_101 IL_04638.4 | |
| IL_9J1M_098 | 1/A/2890:2896, 1/A/2901:2906 | Sarcin-Ricin target in LSU H95; G-bulge | geometric IL_5J7L_346 NA | |
| IL_9J1M_099 | 1/A/2918:2922, 1/A/2963:2965 | C-loop | geometric IL_9DFE_103 IL_63596.12 | |
| IL_9J1M_100 | 1/A/2925:2929, 1/A/2956:2960 | UAA/GAN related, with intercalation | geometric IL_4WF9_102 IL_82016.1 | |
| IL_9J1M_101 | 1/A/2933:2934, 1/A/2949:2952 | Multiple bulged bases | geometric IL_5J7L_349 NA | |
| IL_9J1M_102 | 1/A/2975:2980, 1/A/3000:3005 | UAA/GAN with extra cWW | geometric IL_5J7L_350 NA | |
| IL_9J1M_103 | 1/A/3073:3074, 1/A/3113:3115 | Major groove intercalation | geometric IL_7A0S_099 IL_28408.1 | |
| IL_9J1M_104 | 1/A/3078:3080, 1/A/3106:3109 | Decoding loop related | geometric IL_7A0S_100 IL_05502.1 | |
| IL_9J1M_105 | 1/A/3082:3087, 1/A/3100:3104 | No text annotation | geometric IL_7A0S_101 IL_48489.1 | |
| IL_9J1M_106 | 1/B/2:4, 1/B/111:112 | Single bulged A | geometric IL_5WWT_001 IL_14190.1 | |
| IL_9J1M_107 | 1/B/16:17, 1/B/64:66 | Major groove intercalation | geometric IL_7DLZ_002 NA | |
| IL_9J1M_108 | 1/B/22:28, 1/B/54:59 | No text annotation | ||
| IL_9J1M_109 | 1/B/29:30, 1/B/50:53 | Major groove minor groove platform; mini C-loop | geometric IL_5J7L_357 NA | |
| IL_9J1M_110 | 1/B/33:37, 1/B/43:47 | Symmetric double minor groove platform | geometric IL_5NS3_002 IL_58103.12 | |
| IL_9J1M_111 | 1/B/70:78, 1/B/93:101 | Bacterial 5S Loop E | geometric IL_9DFE_114 IL_71138.1 | |
| IL_9J1M_112 | 1/a/33:35, 1/a/543:544 | Single bulged G | geometric IL_6CZR_113 NA | |
| IL_9J1M_113 | 1/a/47:48, 1/a/395:397 | Single bulged A | geometric IL_4LFB_002 IL_14190.1 | |
| IL_9J1M_114 | 1/a/50:55, 1/a/358:360 | No text annotation | geometric IL_5J7L_003 NA | |
| IL_9J1M_115 | 1/a/57:59, 1/a/355:356 | Minor groove platform | geometric IL_8P9A_377 IL_34520.1 | |
| IL_9J1M_116 | 1/a/66:69, 1/a/98:99 | Multiple bulged bases | geometric IL_4V9F_021 IL_71421.1 | |
| IL_9J1M_118 | 1/a/73:76, 1/a/92:93 | Minor groove platform | geometric IL_3IWN_005 IL_87975.1 | |
| IL_9J1M_120 | 1/a/124:127, 1/a/230:231 | Multiple bulged bases | geometric IL_4LFB_007 IL_75289.1 | |
| IL_9J1M_121 | 1/a/128:132, 1/a/226:229 | No text annotation | geometric IL_4LFB_008 IL_60988.1 | |
| IL_9J1M_122 | 1/a/143:149, 1/a/164:171 | tWH-tWH-tHW-tHW | geometric IL_5J7L_012 NA | |
| IL_9J1M_123 | 1/a/241:246, 1/a/276:283 | Kink-turn with non-sequential stacking | geometric IL_5J7L_014 NA | |
| IL_9J1M_124 | 1/a/248:251, 1/a/273:274 | No text annotation | geometric IL_4LFB_012 IL_22002.1 | |
| IL_9J1M_125 | 1/a/291:292, 1/a/303:307 | C-loop | geometric IL_4LFB_013 IL_06671.1 | |
| IL_9J1M_126 | 1/a/366:368, 1/a/391:392 | Single bulged U | geometric IL_5J7L_017 NA | |
| IL_9J1M_127 | 1/a/370:374, 1/a/388:389 | C-loop | geometric IL_5J7L_018 NA | |
| IL_9J1M_128 | 1/a/374:375, 1/a/386:388 | Single bulged G | geometric IL_5J7L_019 NA | |
| IL_9J1M_131 | 1/a/445:449, 1/a/474:479 | 6x5 Sarcin-Ricin; G-bulge | geometric IL_4LFB_018 IL_82100.1 | |
| IL_9J1M_132 | 1/a/449:452, 1/a/471:474 | No text annotation | ||
| IL_9J1M_134 | 1/a/495:502, 1/a/531:532 | SSU/LSU pseudoknot | geometric IL_5J7L_024 NA | |
| IL_9J1M_136 | 1/a/560:566, 1/a/873:874 | No text annotation | geometric IL_5J7L_026 NA | |
| IL_9J1M_137 | 1/a/571:575, 1/a/748:752 | tSH-tHW-tHS | geometric IL_4LFB_023 IL_05821.1 | |
| IL_9J1M_138 | 1/a/585:587, 1/a/635:636 | Major groove platform | geometric IL_8TSV_001 NA | |
| IL_9J1M_139 | 1/a/588:589, 1/a/631:634 | Major groove minor groove platform; mini C-loop | geometric IL_4LFB_025 IL_73108.1 | |
| IL_9J1M_140 | 1/a/596:602, 1/a/620:624 | No text annotation | geometric IL_8C3A_433 NA | |
| IL_9J1M_141 | 1/a/645:646, 1/a/742:745 | Major groove platform; stack outside cWW | geometric IL_4LFB_027 IL_74641.1 | |
| IL_9J1M_142 | 1/a/648:649, 1/a/738:740 | Major groove platform | geometric IL_5T5A_002 IL_48076.7 | |
| IL_9J1M_143 | 1/a/653:657, 1/a/731:734 | Tandem non-canonical cWW pairs | geometric IL_5J7L_033 NA | |
| IL_9J1M_144 | 1/a/664:668, 1/a/704:708 | Triple non-canonical cWW pairs | geometric IL_4LFB_065 IL_71154.1 | |
| IL_9J1M_145 | 1/a/675:679, 1/a/690:697 | Kink-turn | geometric IL_5J7L_035 NA | |
| IL_9J1M_146 | 1/a/765:769, 1/a/795:796 | Left turn | geometric IL_4LFB_032 IL_29346.3 | |
| IL_9J1M_147 | 1/a/770:774, 1/a/790:794 | tSH-tHW-tHS | geometric IL_5J7L_037 NA | |
| IL_9J1M_148 | 1/a/880:887, 1/a/898:903 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | geometric IL_5J7L_038 NA | |
| IL_9J1M_149 | 1/a/915:916, 1/a/1386:1388 | Single bulged A | geometric IL_4LFB_035 IL_14190.1 | |
| IL_9J1M_150 | 1/a/918:920, 1/a/1383:1384 | Single bulged G | geometric IL_4LFB_036 IL_28408.1 | |
| IL_9J1M_151 | 1/a/926:928, 1/a/1373:1377 | Minor groove platform | geometric IL_5J7L_041 NA | |
| IL_9J1M_152 | 1/a/946:947, 1/a/1218:1220 | Minor groove platform | geometric IL_8C3A_451 NA | |
| IL_9J1M_153 | 1/a/986:990, 1/a/1035:1036 | Minor groove platform | geometric IL_4LFB_039 IL_61370.1 | |
| IL_9J1M_157 | 1/a/1039:1041, 1/a/1200:1201 | Single bulged U | geometric IL_4LFB_042 IL_97561.1 | |
| IL_9J1M_158 | 1/a/1043:1047, 1/a/1196:1198 | Isolated cWS basepair | geometric IL_4LFB_044 IL_82453.1 | |
| IL_9J1M_159 | 1/a/1048:1049, 1/a/1191:1195 | Minor groove platform | geometric IL_5J7L_048 NA | |
| IL_9J1M_160 | 1/a/1051:1052, 1/a/1187:1189 | Single bulged A | geometric IL_5J7L_049 NA | |
| IL_9J1M_161 | 1/a/1052:1054, 1/a/1185:1187 | Isolated non-canonical cWW pair | geometric IL_4LFB_047 IL_68118.1 | |
| IL_9J1M_164 | 1/a/1150:1153, 1/a/1167:1173 | No text annotation | geometric IL_5J7L_053 NA | |
| IL_9J1M_165 | 1/a/1239:1245, 1/a/1276:1282 | No text annotation | geometric IL_4LFB_051 IL_12056.1 | |
| IL_9J1M_168 | 1/a/1295:1300, 1/a/1321:1326 | No text annotation | geometric IL_4LFB_055 IL_57885.1 | |
| IL_9J1M_169 | 1/a/1392:1394, 1/a/1494:1497 | No text annotation | geometric IL_8P9A_452 IL_18228.1 | |
| IL_9J1M_170 | 1/a/1394:1397, 1/a/1490:1494 | No text annotation | geometric IL_8P9A_453 IL_25873.1 | |
| IL_9J1M_171 | 1/a/1398:1400, 1/a/1487:1489 | Isolated non-canonical cWW pair | geometric IL_8C3A_472 NA | |
| IL_9J1M_172 | 1/a/1400:1402, 1/a/1484:1487 | Decoding loop related | geometric IL_3C3Z_002 IL_29925.1 | |
| IL_9J1M_173 | 1/a/1405:1407, 1/a/1479:1481 | Isolated non-canonical cWW pair | geometric IL_5J7L_061 NA | |
| IL_9J1M_174 | 1/a/1409:1412, 1/a/1474:1477 | Double sheared | geometric IL_8P9A_457 IL_58355.1 | |
| IL_9J1M_175 | 1/a/1417:1420, 1/a/1466:1469 | Tandem non-canonical cWW pairs | geometric IL_5LQT_002 NA | |
| IL_9J1M_176 | 1/a/1423:1428, 1/a/1459:1463 | Triple sheared related | geometric IL_5J7L_063 NA | |
| IL_9J1M_177 | 1/a/1428:1430, 1/a/1457:1459 | Isolated non-canonical cWW pair | geometric IL_4LFB_010 IL_01003.1 | |
| IL_9J1M_178 | 1/a/1433:1436, 1/a/1452:1454 | Isolated non-canonical cWW with bulges | geometric IL_7ELQ_002 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_9J1M_008 | No text annotation | ||
| IL_9J1M_020 | Isolated non-canonical cWW pair | ||
| IL_9J1M_035 | No text annotation | ||
| IL_9J1M_044 | Kink-turn | ||
| IL_9J1M_057 | No text annotation | ||
| IL_9J1M_117 | Minor groove platform with extra cWW | ||
| IL_9J1M_119 | No text annotation | ||
| IL_9J1M_129 | No text annotation | ||
| IL_9J1M_130 | No text annotation | ||
| IL_9J1M_133 | No text annotation | ||
| IL_9J1M_135 | No text annotation | ||
| IL_9J1M_154 | No text annotation | ||
| IL_9J1M_155 | Isolated cWH basepair | ||
| IL_9J1M_156 | Isolated non-canonical cWW pair | ||
| IL_9J1M_162 | No text annotation | ||
| IL_9J1M_163 | Minor groove platform | ||
| IL_9J1M_166 | 180 degree turn | ||
| IL_9J1M_167 | Double sheared with non-canonical cWW | ||
| IL_9J1M_179 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_9J1M_001 | 1/A/30:31, 1/A/563:570, 1/A/597:598 | No text annotation | geometric J3_9DFE_001 J3_68715.1 | |
| J3_9J1M_002 | 1/A/30:31, 1/A/563:573, 1/A/584:598 | No text annotation | geometric J3_8P9A_047 J3_17917.1 | |
| J3_9J1M_003 | 1/A/32:35, 1/A/534:550, 1/A/557:562 | No text annotation | geometric J3_4V9F_013 J3_07616.1 | |
| J3_9J1M_004 | 1/A/56:57, 1/A/70:76, 1/A/110:114 | No text annotation | geometric J3_9DFE_004 J3_01004.1 | |
| J3_9J1M_005 | 1/A/318:320, 1/A/458:464, 1/A/488:493 | No text annotation | ||
| J3_9J1M_007 | 1/A/379:383, 1/A/399:408, 1/A/420:424 | No text annotation | geometric J3_4WF9_015 J3_77124.1 | |
| J3_9J1M_008 | 1/A/812:818, 1/A/902:904, 1/A/920:923 | No text annotation | geometric J3_4V9F_002 J3_46658.1 | |
| J3_9J1M_009 | 1/A/827:829, 1/A/861:865, 1/A/889:892 | No text annotation | geometric J3_9DFE_008 J3_69816.1 | |
| J3_9J1M_011 | 1/A/1429:1434, 1/A/1860:1862, 1/A/1874:1877 | No text annotation | geometric J3_9DFE_010 J3_32852.7 | |
| J3_9J1M_012 | 1/A/1437:1440, 1/A/1840:1846, 1/A/1855:1857 | No text annotation | geometric J3_9DFE_011 J3_47341.1 | |
| J3_9J1M_013 | 1/A/1475:1481, 1/A/1512:1516, 1/A/1533:1534 | No text annotation | geometric J3_9DFE_012 J3_94309.1 | |
| J3_9J1M_014 | 1/A/1663:1667, 1/A/1801:1802, 1/A/1805:1810 | No text annotation | geometric J3_4V9F_017 J3_08594.1 | |
| J3_9J1M_015 | 1/A/2328:2330, 1/A/2433:2437, 1/A/2461:2466 | Kink-turn 3-way junction | geometric J3_5J7L_044 NA | |
| J3_9J1M_016 | 1/A/2520:2522, 1/A/2622:2633, 1/A/2659:2665 | No text annotation | geometric J3_5J7L_070 NA | |
| J3_9J1M_017 | 1/A/2533:2535, 1/A/2559:2561, 1/A/2570:2575 | No text annotation | geometric J3_4V9F_008 J3_05327.1 | |
| J3_9J1M_018 | 1/A/2755:2758, 1/A/2783:2785, 1/A/2799:2805 | No text annotation | geometric J3_9DFE_017 J3_32601.6 | |
| J3_9J1M_019 | 1/A/3049:3051, 1/A/3065:3071, 1/A/3117:3121 | No text annotation | ||
| J3_9J1M_020 | 1/B/9:15, 1/B/67:69, 1/B/102:106 | No text annotation | geometric J3_5J7L_049 NA | |
| J3_9J1M_021 | 1/a/49:50, 1/a/360:366, 1/a/392:394 | No text annotation | geometric J3_5J7L_001 NA | |
| J3_9J1M_022 | 1/a/49:55, 1/a/358:366, 1/a/392:394 | No text annotation | geometric J3_5J7L_050 NA | |
| J3_9J1M_023 | 1/a/577:579, 1/a/642:645, 1/a/745:746 | No text annotation | geometric J3_5J7L_002 NA | |
| J3_9J1M_024 | 1/a/577:579, 1/a/642:646, 1/a/742:746 | No text annotation | geometric J3_5J7L_051 NA | |
| J3_9J1M_025 | 1/a/663:664, 1/a/708:716, 1/a/723:725 | No text annotation | geometric J3_4LFB_012 J3_74074.1 | |
| J3_9J1M_026 | 1/a/817:820, 1/a/850:854, 1/a/861:867 | No text annotation | geometric J3_5J7L_004 NA | |
| J3_9J1M_027 | 1/a/929:932, 1/a/1336:1342, 1/a/1365:1372 | No text annotation | geometric J3_5J7L_052 NA | |
| J3_9J1M_028 | 1/a/936:939, 1/a/1227:1229, 1/a/1329:1332 | No text annotation | geometric J3_4LFB_003 J3_44359.1 | |
| J3_9J1M_029 | 1/a/948:955, 1/a/966:977, 1/a/1213:1217 | No text annotation | geometric J3_4LFB_004 J3_88451.1 | |
| J3_9J1M_030 | 1/a/983:986, 1/a/1036:1038, 1/a/1202:1207 | No text annotation | homologous J3_4LFB_005 J3_84394.1 | |
| J3_9J1M_031 | 1/a/983:990, 1/a/1035:1038, 1/a/1202:1207 | No text annotation | geometric J3_6CZR_063 NA | |
| J3_9J1M_032 | 1/a/1054:1059, 1/a/1098:1104, 1/a/1179:1185 | No text annotation | geometric J3_5J7L_008 NA | |
| J3_9J1M_033 | 1/a/1064:1065, 1/a/1074:1078, 1/a/1089:1093 | No text annotation | homologous J3_5J7L_009 NA | |
| J3_9J1M_034 | 1/a/1107:1109, 1/a/1147:1150, 1/a/1173:1176 | No text annotation | geometric J3_5J7L_010 NA | |
| J3_9J1M_035 | 1/a/1107:1109, 1/a/1147:1153, 1/a/1167:1176 | No text annotation | geometric J3_4LFB_018 J3_40706.1 | |
| J3_9J1M_036 | 1/a/1229:1233, 1/a/1288:1295, 1/a/1326:1329 | No text annotation | geometric J3_4LFB_009 J3_03192.1 | |
| J4_9J1M_001 | 1/A/270:275, 1/A/313:318, 1/A/493:495, 1/A/510:513 | No text annotation | ||
| J4_9J1M_002 | 1/A/379:383, 1/A/399:402, 1/A/406:408, 1/A/420:424 | No text annotation | homologous J4_4WF9_002 J4_16174.1 | |
| J4_9J1M_003 | 1/A/1401:1407, 1/A/1425:1426, 1/A/1880:1883, 1/A/2247:2248 | No text annotation | homologous J4_9DFE_003 J4_64571.6 | |
| J4_9J1M_004 | 1/A/1441:1445, 1/A/1469:1474, 1/A/1535:1536, 1/A/1832:1839 | No text annotation | ||
| J4_9J1M_005 | 1/A/1681:1684, 1/A/1703:1705, 1/A/1764:1768, 1/A/1779:1785 | No text annotation | ||
| J4_9J1M_006 | 1/A/2005:2010, 1/A/2022:2026, 1/A/2061:2064, 1/A/2213:2218 | No text annotation | ||
| J4_9J1M_007 | 1/A/2067:2069, 1/A/2143:2144, 1/A/2162:2171, 1/A/2205:2210 | No text annotation | homologous J4_9DFE_008 J4_42306.1 | |
| J4_9J1M_008 | 1/A/2523:2527, 1/A/2581:2585, 1/A/2608:2610, 1/A/2619:2621 | No text annotation | homologous J4_9DFE_009 J4_98139.1 | |
| J4_9J1M_009 | 1/A/2880:2884, 1/A/2912:2914, 1/A/2969:2973, 1/A/3007:3010 | No text annotation | ||
| J4_9J1M_010 | 1/a/110:118, 1/a/237:239, 1/a/285:288, 1/a/310:311 | No text annotation | ||
| J4_9J1M_012 | 1/a/566:568, 1/a/755:760, 1/a/801:812, 1/a/872:873 | No text annotation | homologous J4_5J7L_003 NA | |
| J5_9J1M_001 | 1/A/47:54, 1/A/116:121, 1/A/130:131, 1/A/150:152, 1/A/178:180 | No text annotation | homologous J5_9DFE_001 J5_27223.1 | |
| J5_9J1M_002 | 1/A/619:621, 1/A/662:666, 1/A/679:681, 1/A/1392:1393, 1/A/2255:2256 | No text annotation | homologous J5_9DFE_003 J5_43153.6 | |
| J5_9J1M_003 | 1/A/686:691, 1/A/797:800, 1/A/938:941, 1/A/1327:1328, 1/A/1381:1387 | No text annotation | homologous J5_4WF9_004 J5_74302.6 | |
| J5_9J1M_004 | 1/A/704:707, 1/A/728:733, 1/A/738:742, 1/A/754:760, 1/A/779:785 | No text annotation | ||
| J5_9J1M_005 | 1/A/1909:1917, 1/A/1941:1942, 1/A/1985:1986, 1/A/1990:1998, 1/A/2226:2228 | No text annotation | homologous J5_5J7L_016 NA | |
| J5_9J1M_006 | 1/A/2295:2302, 1/A/2684:2691, 1/A/2738:2745, 1/A/2820:2826, 1/A/2844:2849 | No text annotation | ||
| J5_9J1M_007 | 1/A/2311:2314, 1/A/2481:2484, 1/A/2496:2497, 1/A/2519:2520, 1/A/2665:2673 | No text annotation | homologous J5_9DFE_007 J5_39529.2 | |
| J5_9J1M_008 | 1/a/39:42, 1/a/402:405, 1/a/435:439, 1/a/488:491, 1/a/536:539 | No text annotation | ||
| J5_9J1M_009 | 1/a/39:42, 1/a/402:405, 1/a/435:441, 1/a/483:491, 1/a/536:539 | No text annotation | homologous J5_5J7L_002 NA | |
| J5_9J1M_010 | 1/a/61:64, 1/a/101:108, 1/a/313:315, 1/a/336:338, 1/a/349:353 | No text annotation | homologous J5_4LFB_002 J5_58574.1 | |
| J6_9J1M_001 | 1/A/45:46, 1/A/181:185, 1/A/216:226, 1/A/233:237, 1/A/264:268, 1/A/515:522 | No text annotation | ||
| J6_9J1M_002 | 1/A/2311:2314, 1/A/2481:2484, 1/A/2496:2497, 1/A/2519:2522, 1/A/2622:2633, 1/A/2659:2673 | No text annotation | ||
| J7_9J1M_001 | 1/A/945:951, 1/A/964:965, 1/A/1071:1074, 1/A/1100:1105, 1/A/1116:1120, 1/A/1293:1294, 1/A/1317:1323 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_9J1M_006 | No text annotation | ||
| J3_9J1M_010 | No text annotation | ||
| J4_9J1M_011 | No text annotation |
Coloring options: