3OW2 Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
3D | Loop id | Location | Annotation; motif group | Mapped info |
---|---|---|---|---|
HL_3OW2_002 | 1/0/83:91 | Pseudoknot geometry | homologous HL_4V9F_002 HL_93324.4 | |
HL_3OW2_006 | 1/0/164:171 | No text annotation | homologous HL_4V9F_006 HL_30068.2 | |
HL_3OW2_007 | 1/0/195:201 | No text annotation | homologous HL_4V9F_007 HL_04783.2 | |
HL_3OW2_011 | 1/0/326:330 | No text annotation | homologous HL_4V9F_011 HL_75660.5 | |
HL_3OW2_014 | 1/0/416:424 | Pseudoknot geometry | homologous HL_4V9F_014 HL_93324.4 | |
HL_3OW2_018 | 1/0/623:632 | No text annotation | geometric HL_7RQB_018 NA | |
HL_3OW2_028 | 1/0/1054:1060 | GNRA | homologous HL_4V9F_028 HL_37824.7 | |
HL_3OW2_029 | 1/0/1076:1083 | No text annotation | homologous HL_4V9F_029 HL_42998.2 | |
HL_3OW2_032 | 1/0/1274:1282 | Anticodon loop related | homologous HL_4V9F_032 HL_77082.1 | |
HL_3OW2_036 | 1/0/1468:1474 | GNRA | homologous HL_4V9F_036 HL_37824.7 | |
HL_3OW2_059 | 1/0/2389:2399 | No text annotation | homologous HL_4V9F_059 HL_91939.2 | |
HL_3OW2_061 | 1/0/2442:2450 | Pseudoknot geometry | homologous HL_4V9F_061 HL_93324.4 | |
HL_3OW2_074 | 1/0/2586:2592 | No text annotation | homologous HL_4V9F_073 HL_30068.2 | |
HL_3OW2_068 | 1/0/2780:2794 | No text annotation | homologous HL_4V9F_068 HL_74055.2 | |
HL_3OW2_069 | 1/0/2836:2844 | No text annotation | homologous HL_4V9F_069 HL_64690.6 |
Problematic loops
# | loop id | Problem | Sequence |
---|---|---|---|
HL_3OW2_001 | Pseudoknot with intercalation | ||
HL_3OW2_003 | No text annotation | ||
HL_3OW2_004 | Mini UNCG related | ||
HL_3OW2_005 | No text annotation | ||
HL_3OW2_008 | No text annotation | ||
HL_3OW2_009 | GNRA | ||
HL_3OW2_010 | T-loop with 2 stacked bulged bases | ||
HL_3OW2_012 | T-loop with unstacked turn | ||
HL_3OW2_013 | No text annotation | ||
HL_3OW2_015 | GNRA | ||
HL_3OW2_016 | GNRA | ||
HL_3OW2_017 | GNRA | ||
HL_3OW2_019 | No text annotation | ||
HL_3OW2_020 | GNRA | ||
HL_3OW2_021 | Mini UNCG | ||
HL_3OW2_022 | GNRA | ||
HL_3OW2_023 | GNRA | ||
HL_3OW2_024 | No text annotation | ||
HL_3OW2_025 | No text annotation | ||
HL_3OW2_026 | No text annotation | ||
HL_3OW2_027 | No text annotation | ||
HL_3OW2_030 | No text annotation | ||
HL_3OW2_073 | No text annotation | ||
HL_3OW2_031 | GNRA wlth tandem sheared | ||
HL_3OW2_033 | GNRA | ||
HL_3OW2_034 | T-loop with 2 stacked bulged bases | ||
HL_3OW2_035 | Pseudoknot geometry with 3' bulge | ||
HL_3OW2_037 | No text annotation | ||
HL_3OW2_038 | No text annotation | ||
HL_3OW2_039 | Other HL | ||
HL_3OW2_040 | GNRA | ||
HL_3OW2_041 | Mini UNCG | ||
HL_3OW2_042 | No text annotation | ||
HL_3OW2_043 | GNRA wlth tandem sheared | ||
HL_3OW2_044 | UNCG | ||
HL_3OW2_045 | GNRA | ||
HL_3OW2_046 | No text annotation | ||
HL_3OW2_047 | No text annotation | ||
HL_3OW2_048 | GNRA | ||
HL_3OW2_049 | GNRA related | ||
HL_3OW2_050 | No text annotation | ||
HL_3OW2_051 | No text annotation | ||
HL_3OW2_052 | No text annotation | ||
HL_3OW2_053 | No text annotation | ||
HL_3OW2_054 | GNRA | ||
HL_3OW2_055 | No text annotation | ||
HL_3OW2_056 | No text annotation | ||
HL_3OW2_057 | No text annotation | ||
HL_3OW2_058 | Pseudoknot geometry | ||
HL_3OW2_060 | GNRA | ||
HL_3OW2_062 | No text annotation | ||
HL_3OW2_063 | No text annotation | ||
HL_3OW2_064 | No text annotation | ||
HL_3OW2_065 | GNRA | ||
HL_3OW2_066 | GNRA | ||
HL_3OW2_067 | Ribsomal LSU H95 | ||
HL_3OW2_070 | GNRA | ||
HL_3OW2_075 | No text annotation | ||
HL_3OW2_071 | No text annotation | ||
HL_3OW2_072 | GNRA |
Valid loops
3D | Loop id | Location | Annotation; motif group | Mapped info |
---|---|---|---|---|
IL_3OW2_004 | 1/0/77:81, 1/0/93:100 | Kink-turn | homologous IL_4V9F_004 IL_01488.3 | |
IL_3OW2_006 | 1/0/158:164, 1/0/171:178 | 8x7 Sarcin-Ricin; G-bulge | geometric IL_4V9F_006 IL_04346.10 | |
IL_3OW2_012 | 1/0/287:290, 1/0/362:365 | Tandem non-canonical cWW pairs | geometric IL_6JDV_002 IL_85033.2 | |
IL_3OW2_015 | 1/0/487:491, 1/0/501:515 | No text annotation | geometric IL_4V9F_014 IL_31504.1 | |
IL_3OW2_016 | 1/0/548:553, 1/0/606:608 | No text annotation | homologous IL_4V9F_015 IL_59302.1 | |
IL_3OW2_018 | 1/0/558:561, 1/0/596:599 | Tandem non-canonical cWW pairs | geometric IL_1JID_002 IL_85033.2 | |
IL_3OW2_019 | 1/0/562:567, 1/0/591:595 | Triple sheared related | homologous IL_4V9F_018 IL_97631.1 | |
IL_3OW2_020 | 1/0/567:572, 1/0/585:591 | 7x6 Sarcin-Ricin; G-bulge | geometric IL_4V9F_019 IL_16458.4 | |
IL_3OW2_021 | 1/0/663:667, 1/0/679:683 | AAA cross-strand stack | homologous IL_4V9F_020 IL_66798.2 | |
IL_3OW2_022 | 1/0/699:702, 1/0/726:727 | Multiple bulged bases | homologous IL_4V9F_021 IL_82107.4 | |
IL_3OW2_023 | 1/0/705:709, 1/0/719:723 | tSH-tHW-tHS | homologous IL_4V9F_022 IL_17136.7 | |
IL_3OW2_108 | 1/0/936:940, 1/0/1026:1034 | Kink-turn | homologous IL_4V9F_031 IL_94910.1 | |
IL_3OW2_033 | 1/0/942:944, 1/0/1023:1024 | Single bulged A | homologous IL_4V9F_032 IL_31462.6 | |
IL_3OW2_039 | 1/0/1101:1108, 1/0/1254:1255 | SSU/LSU pseudoknot | geometric IL_4V9F_038 IL_41203.4 | |
IL_3OW2_040 | 1/0/1108:1110, 1/0/1253:1254 | Single bulged U | homologous IL_4V9F_039 IL_89505.4 | |
IL_3OW2_041 | 1/0/1115:1121, 1/0/1243:1248 | Kink-turn related | homologous IL_4V9F_040 IL_57188.5 | |
IL_3OW2_109 | 1/0/1122:1134, 1/0/1228:1242 | No text annotation | homologous IL_4V9F_109 IL_29826.1 | |
IL_3OW2_042 | 1/0/1136:1138, 1/0/1225:1226 | Single bulged G | homologous IL_4V9F_041 IL_00225.13 | |
IL_3OW2_043 | 1/0/1147:1155, 1/0/1212:1216 | Kink-turn | homologous IL_4V9F_042 IL_99692.2 | |
IL_3OW2_046 | 1/0/1269:1270, 1/0/1286:1289 | Bulged stacked bases | homologous IL_4V9F_045 IL_76709.2 | |
IL_3OW2_048 | 1/0/1303:1305, 1/0/1349:1351 | Isolated non-canonical cWW pair | geometric IL_4V9F_047 IL_28037.2 | |
IL_3OW2_050 | 1/0/1367:1373, 1/0/2052:2057 | 7x6 Sarcin-Ricin; G-bulge | homologous IL_4V9F_049 IL_26307.2 | |
IL_3OW2_078 | 1/0/2279:2280, 1/0/2290:2292 | Single bulged A | homologous IL_4V9F_079 IL_31462.6 | |
IL_3OW2_080 | 1/0/2436:2438, 1/0/2454:2455 | Single stack bend | homologous IL_4V9F_081 IL_26793.1 | |
IL_3OW2_082 | 1/0/2489:2490, 1/0/2531:2533 | Major groove platform | homologous IL_4V9F_082 IL_48076.6 | |
IL_3OW2_084 | 1/0/2494:2496, 1/0/2524:2528 | Major groove minor groove platform with extra cWW | geometric IL_4V9F_084 IL_51387.2 | |
IL_3OW2_085 | 1/0/2501:2505, 1/0/2515:2519 | Triple sheared | homologous IL_4V9F_085 IL_17948.2 | |
IL_3OW2_091 | 1/0/2672:2676, 1/0/2809:2817 | tSH-tHS-tHW | geometric IL_5J7L_345 IL_04638.3 | |
IL_3OW2_096 | 1/0/2772:2777, 1/0/2797:2802 | UAA/GAN with extra cWW | homologous IL_4V9F_096 IL_49767.8 | |
IL_3OW2_101 | 1/9/3015:3016, 1/9/3064:3066 | Major groove intercalation | homologous IL_4V9F_101 IL_31462.6 |
Problematic loops
# | loop id | Problem | Sequence |
---|---|---|---|
IL_3OW2_001 | Triple sheared with non-canonical cWW | ||
IL_3OW2_002 | Single bulged A | ||
IL_3OW2_003 | Major groove platform with extra cWW | ||
IL_3OW2_005 | Single stack bend | ||
IL_3OW2_007 | 7x6 Sarcin-Ricin; G-bulge | ||
IL_3OW2_008 | Major groove platform; stack outside cWW | ||
IL_3OW2_107 | Kink-turn with embedded cWW pair | ||
IL_3OW2_009 | No text annotation | ||
IL_3OW2_010 | Single bulged G | ||
IL_3OW2_011 | No text annotation | ||
IL_3OW2_013 | 8x7 Sarcin-Ricin with CC bifurcated pair; G-bulge | ||
IL_3OW2_014 | Single bulged U | ||
IL_3OW2_017 | No text annotation | ||
IL_3OW2_024 | Isolated non-canonical cWW pair | ||
IL_3OW2_025 | tHW-tHW cross-strand stack | ||
IL_3OW2_026 | Single bulged A | ||
IL_3OW2_027 | Single bulged G | ||
IL_3OW2_028 | Triple sheared | ||
IL_3OW2_029 | Major groove platform with extra cWW | ||
IL_3OW2_030 | Single bulged U | ||
IL_3OW2_031 | Multiple bulged bases | ||
IL_3OW2_032 | Kink-turn | ||
IL_3OW2_034 | 5x5 Sarcin-Ricin with intercalated A; G-bulge | ||
IL_3OW2_035 | Minor groove platform | ||
IL_3OW2_036 | No text annotation | ||
IL_3OW2_037 | No text annotation | ||
IL_3OW2_038 | UAA/GAN | ||
IL_3OW2_110 | No text annotation | ||
IL_3OW2_044 | No text annotation | ||
IL_3OW2_045 | Major groove platform | ||
IL_3OW2_047 | Isolated cWS basepair | ||
IL_3OW2_049 | Kink-turn | ||
IL_3OW2_051 | Major groove platform; stack outside cWW | ||
IL_3OW2_052 | C-loop | ||
IL_3OW2_053 | UAA/GAN | ||
IL_3OW2_054 | No text annotation | ||
IL_3OW2_055 | No text annotation | ||
IL_3OW2_056 | tSH-tHW-tHS | ||
IL_3OW2_057 | tSH-tHH-tHS | ||
IL_3OW2_058 | No text annotation | ||
IL_3OW2_059 | Kink-turn | ||
IL_3OW2_060 | No text annotation | ||
IL_3OW2_061 | Isolated tWW turn | ||
IL_3OW2_062 | Major groove platform; stack outside cWW | ||
IL_3OW2_111 | No text annotation | ||
IL_3OW2_063 | Intercalated tWH | ||
IL_3OW2_064 | tSH-tSH-tHH-tHS | ||
IL_3OW2_065 | Single bulged A | ||
IL_3OW2_066 | Kink-turn related | ||
IL_3OW2_067 | Minor groove platform, major groove intercalation | ||
IL_3OW2_068 | Major groove intercalation | ||
IL_3OW2_069 | Major groove minor groove platform; mini C-loop | ||
IL_3OW2_070 | No text annotation | ||
IL_3OW2_071 | Bulged stacked bases | ||
IL_3OW2_072 | No text annotation | ||
IL_3OW2_073 | No text annotation | ||
IL_3OW2_074 | No text annotation | ||
IL_3OW2_075 | Single bulged U | ||
IL_3OW2_076 | Minor groove platform | ||
IL_3OW2_077 | Isolated tHS basepair with bulges | ||
IL_3OW2_079 | Isolated tHS basepair with bulges | ||
IL_3OW2_081 | Single stack bend | ||
IL_3OW2_083 | Major groove platform | ||
IL_3OW2_086 | Major groove platform | ||
IL_3OW2_087 | Isolated non-canonical cWW pair | ||
IL_3OW2_088 | Multiple bulged bases | ||
IL_3OW2_089 | Major groove platform with intercalation | ||
IL_3OW2_090 | Single bulged A | ||
IL_3OW2_092 | Sarcin-Ricin target in LSU H95; G-bulge | ||
IL_3OW2_093 | C-loop | ||
IL_3OW2_094 | UAA/GAN | ||
IL_3OW2_095 | Bulged stacked bases | ||
IL_3OW2_097 | Isolated non-canonical cWW with bulges | ||
IL_3OW2_098 | Single bulged A | ||
IL_3OW2_099 | tHS double platform | ||
IL_3OW2_100 | Double sheared | ||
IL_3OW2_102 | No text annotation | ||
IL_3OW2_103 | Major groove minor groove platform; mini C-loop | ||
IL_3OW2_104 | Symmetric double minor groove platform | ||
IL_3OW2_105 | 7x6 Sarcin-Ricin; G-bulge | ||
IL_3OW2_106 | Single bulged U |
Valid loops
3D | Loop id | Location | Annotation; motif group | Mapped info |
---|---|---|---|---|
J3_3OW2_016 | 1/0/27:28, 1/0/480:491, 1/0/501:516 | No text annotation | homologous J3_4V9F_012 J3_24879.1 | |
J3_3OW2_017 | 1/0/29:32, 1/0/451:467, 1/0/474:479 | No text annotation | homologous J3_4V9F_013 J3_30040.2 | |
J3_3OW2_018 | 1/0/302:307, 1/0/323:332, 1/0/344:349 | No text annotation | homologous J3_4V9F_015 J3_59706.1 | |
J3_3OW2_006 | 1/0/1412:1415, 1/0/1680:1686, 1/0/1695:1697 | No text annotation | homologous J3_4V9F_006 J3_19545.2 | |
J3_3OW2_019 | 1/0/2316:2318, 1/0/2421:2432, 1/0/2459:2464 | No text annotation | homologous J3_4V9F_018 J3_44792.1 | |
J3_3OW2_010 | 1/9/3009:3014, 1/9/3067:3071, 1/9/3110:3114 | 5S rRNA | homologous J3_4V9F_010 J3_89737.1 | |
J4_3OW2_009 | 1/0/2319:2323, 1/0/2377:2381, 1/0/2407:2409, 1/0/2418:2420 | No text annotation | homologous J4_4V9F_009 J4_04930.6 | |
J5_3OW2_003 | 1/0/641:646, 1/0/759:762, 1/0/902:905, 1/0/1300:1301, 1/0/1354:1360 | No text annotation | homologous J5_4V9F_003 J5_56920.1 | |
J5_3OW2_004 | 1/0/658:661, 1/0/685:689, 1/0/696:699, 1/0/727:728, 1/0/743:747 | No text annotation | homologous J5_4V9F_004 J5_87582.1 | |
J5_3OW2_005 | 1/0/658:661, 1/0/685:689, 1/0/696:702, 1/0/726:728, 1/0/743:747 | No text annotation | homologous J5_4V9F_005 J5_26867.1 | |
J6_3OW2_001 | 1/0/41:42, 1/0/149:153, 1/0/184:194, 1/0/202:206, 1/0/233:237, 1/0/433:440 | No text annotation | ||
J6_3OW2_002 | 1/0/2115:2118, 1/0/2276:2279, 1/0/2292:2293, 1/0/2315:2318, 1/0/2421:2432, 1/0/2459:2470 | No text annotation | ||
J7_3OW2_001 | 1/0/910:915, 1/0/928:931, 1/0/1039:1045, 1/0/1069:1074, 1/0/1085:1089, 1/0/1267:1268, 1/0/1290:1295 | No text annotation |
Problematic loops
# | loop id | Problem | Sequence |
---|---|---|---|
J3_3OW2_011 | No text annotation | ||
J3_3OW2_012 | No text annotation | ||
J3_3OW2_001 | No text annotation | ||
J3_3OW2_002 | No text annotation | ||
J3_3OW2_003 | No text annotation | ||
J3_3OW2_004 | No text annotation | ||
J3_3OW2_005 | No text annotation | ||
J3_3OW2_013 | No text annotation | ||
J3_3OW2_014 | No text annotation | ||
J3_3OW2_007 | No text annotation | ||
J3_3OW2_008 | No text annotation | ||
J3_3OW2_009 | No text annotation | ||
J3_3OW2_015 | No text annotation | ||
J4_3OW2_001 | No text annotation | ||
J4_3OW2_002 | No text annotation | ||
J4_3OW2_003 | No text annotation | ||
J4_3OW2_004 | No text annotation | ||
J4_3OW2_005 | No text annotation | ||
J4_3OW2_006 | No text annotation | ||
J4_3OW2_007 | No text annotation | ||
J4_3OW2_008 | No text annotation | ||
J4_3OW2_010 | No text annotation | ||
J5_3OW2_001 | No text annotation | ||
J5_3OW2_002 | No text annotation | ||
J5_3OW2_006 | No text annotation | ||
J5_3OW2_007 | No text annotation | ||
J5_3OW2_008 | No text annotation |
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