6YLG Internal, Hairpin and 3-way Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_6YLG_001 | 1/1/38:45 | No text annotation Not in a motif group | ||
| HL_6YLG_002 | 1/1/69:74 | No text annotation Not in a motif group | homologous HL_5TBW_002 HL_96776.3 | |
| HL_6YLG_003 | 1/1/90:96 | No text annotation Not in a motif group | homologous HL_5TBW_003 HL_67216.5 | |
| HL_6YLG_004 | 1/1/132:136 | No text annotation Not in a motif group | homologous HL_5TBW_004 HL_36982.3 | |
| HL_6YLG_005 | 1/1/194:201 | T-loop with 1 bulged base Not in a motif group | homologous HL_5TBW_005 HL_68493.6 | |
| HL_6YLG_006 | 1/1/208:212 | No text annotation Not in a motif group | homologous HL_5TBW_006 HL_98557.5 | |
| HL_6YLG_007 | 1/1/216:224 | No text annotation Not in a motif group | homologous HL_5TBW_007 HL_08002.6 | |
| HL_6YLG_008 | 1/1/278:287 | No text annotation Not in a motif group | homologous HL_5TBW_008 HL_54035.7 | |
| HL_6YLG_010 | 1/1/357:362 | Other HL Not in a motif group | homologous HL_5TBW_010 HL_43074.18 | |
| HL_6YLG_011 | 1/1/382:387 | GNRA Not in a motif group | homologous HL_5TBW_011 HL_43074.18 | |
| HL_6YLG_012 | 1/1/543:548 | No text annotation Not in a motif group | homologous HL_5TBW_012 HL_94386.1 | |
| HL_6YLG_013 | 1/1/599:604 | GNRA Not in a motif group | homologous HL_5TBW_013 HL_43074.18 | |
| HL_6YLG_015 | 1/1/686:694 | No text annotation Not in a motif group | homologous HL_5TBW_015 HL_80105.3 | |
| HL_6YLG_016 | 1/1/707:712 | GNRA Not in a motif group | homologous HL_5TBW_016 HL_43074.18 | |
| HL_6YLG_017 | 1/1/732:737 | GNRA Not in a motif group | homologous HL_5TBW_017 HL_43074.18 | |
| HL_6YLG_022 | 1/1/957:964 | No text annotation Not in a motif group | ||
| HL_6YLG_025 | 1/1/1126:1132 | Other HL Not in a motif group | geometric HL_4V9F_039 HL_68493.6 | |
| HL_6YLG_026 | 1/1/1148:1155 | No text annotation Not in a motif group | homologous HL_5TBW_026 HL_72451.5 | |
| HL_6YLG_030 | 1/1/1403:1408 | GNRA Not in a motif group | homologous HL_5TBW_030 HL_43074.18 | |
| HL_6YLG_059 | 1/1/2840:2848 | No text annotation Not in a motif group | ||
| HL_6YLG_060 | 1/1/2897:2904 | No text annotation Not in a motif group | homologous HL_5TBW_062 HL_92681.5 | |
| HL_6YLG_061 | 1/1/2920:2926 | No text annotation Not in a motif group | geometric HL_4TUW_002 HL_22447.1 | |
| HL_6YLG_063 | 1/1/3025:3030 | GNRA Not in a motif group | homologous HL_5TBW_065 HL_43074.18 | |
| HL_6YLG_064 | 1/1/3068:3073 | Ribsomal LSU H95 Not in a motif group | homologous HL_5TBW_066 HL_67719.1 | |
| HL_6YLG_065 | 1/1/3110:3124 | No text annotation Not in a motif group | homologous HL_5TBW_067 HL_56677.5 | |
| HL_6YLG_066 | 1/1/3194:3197 | No text annotation Not in a motif group | homologous HL_5TBW_068 HL_46546.1 | |
| HL_6YLG_067 | 1/1/3240:3247 | No text annotation Not in a motif group | homologous HL_5TBW_069 HL_27757.1 | |
| HL_6YLG_068 | 1/1/3303:3311 | No text annotation Not in a motif group | homologous HL_5TBW_070 HL_05018.6 | |
| HL_6YLG_071 | 1/2/108:114 | No text annotation Not in a motif group | homologous HL_5TBW_075 HL_06569.2 | |
| HL_6YLG_072 | 1/2/124:129 | No text annotation Not in a motif group | homologous HL_5TBW_076 HL_60357.1 | |
| HL_6YLG_073 | 1/3/36:41 | No text annotation Not in a motif group | homologous HL_5TBW_185 HL_02733.5 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_6YLG_009 | No text annotation | ||
| HL_6YLG_014 | T-loop with 2 stacked bulged bases | ||
| HL_6YLG_018 | No text annotation | ||
| HL_6YLG_019 | GNRA | ||
| HL_6YLG_020 | No text annotation | ||
| HL_6YLG_021 | No text annotation | ||
| HL_6YLG_023 | No text annotation | ||
| HL_6YLG_024 | No text annotation | ||
| HL_6YLG_027 | No text annotation | ||
| HL_6YLG_028 | No text annotation | ||
| HL_6YLG_029 | No text annotation | ||
| HL_6YLG_031 | T-loop with 2 stacked bulged bases | ||
| HL_6YLG_032 | No text annotation | ||
| HL_6YLG_033 | Other HL | ||
| HL_6YLG_034 | No text annotation | ||
| HL_6YLG_035 | No text annotation | ||
| HL_6YLG_036 | GNRA | ||
| HL_6YLG_037 | No text annotation | ||
| HL_6YLG_038 | No text annotation | ||
| HL_6YLG_039 | No text annotation | ||
| HL_6YLG_040 | No text annotation | ||
| HL_6YLG_041 | No text annotation | ||
| HL_6YLG_042 | GNRA with one bulged base | ||
| HL_6YLG_043 | UNCG | ||
| HL_6YLG_044 | No text annotation | ||
| HL_6YLG_045 | No text annotation | ||
| HL_6YLG_046 | No text annotation | ||
| HL_6YLG_047 | GNRA | ||
| HL_6YLG_048 | Other HL | ||
| HL_6YLG_049 | No text annotation | ||
| HL_6YLG_050 | No text annotation | ||
| HL_6YLG_051 | No text annotation | ||
| HL_6YLG_052 | No text annotation | ||
| HL_6YLG_053 | No text annotation | ||
| HL_6YLG_054 | No text annotation | ||
| HL_6YLG_055 | No text annotation | ||
| HL_6YLG_056 | No text annotation | ||
| HL_6YLG_057 | GNRA | ||
| HL_6YLG_058 | No text annotation | ||
| HL_6YLG_062 | GNRA | ||
| HL_6YLG_069 | No text annotation | ||
| HL_6YLG_070 | No text annotation | ||
| HL_6YLG_074 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_6YLG_001 | 1/1/7:8, 1/2/150:152 | Single bulged C Not in a motif group | homologous IL_5TBW_002 IL_61258.10 | |
| IL_6YLG_002 | 1/1/12:15, 1/2/144:146 | No text annotation Not in a motif group | geometric IL_4V9F_105 IL_01312.13 | |
| IL_6YLG_003 | 1/1/27:28, 1/1/56:58 | Single stack bend Not in a motif group | homologous IL_5TBW_004 IL_04038.4 | |
| IL_6YLG_004 | 1/1/31:38, 1/1/45:53 | tSH-tHW-tHH-tHS Not in a motif group | homologous IL_5TBW_005 IL_22863.1 | |
| IL_6YLG_005 | 1/1/82:89, 1/1/97:103 | No text annotation Not in a motif group | homologous IL_5TBW_006 IL_29509.1 | |
| IL_6YLG_006 | 1/1/123:124, 1/1/144:149 | No text annotation Not in a motif group | homologous IL_5TBW_007 IL_19724.1 | |
| IL_6YLG_007 | 1/1/125:127, 1/1/141:143 | No text annotation Not in a motif group | homologous IL_5TBW_008 IL_01312.13 | |
| IL_6YLG_008 | 1/1/163:165, 1/1/257:258 | Single stack bend Not in a motif group | homologous IL_5TBW_009 IL_04038.4 | |
| IL_6YLG_009 | 1/1/169:171, 1/1/247:253 | No text annotation Not in a motif group | ||
| IL_6YLG_010 | 1/1/175:178, 1/1/238:243 | No text annotation Not in a motif group | ||
| IL_6YLG_011 | 1/1/189:191, 1/1/204:205 | Single bulged U Not in a motif group | homologous IL_5TBW_012 IL_83039.11 | |
| IL_6YLG_012 | 1/1/272:274, 1/1/291:293 | Isolated cWH basepair Not in a motif group | geometric IL_4KQ0_002 IL_42589.6 | |
| IL_6YLG_013 | 1/1/337:339, 1/2/25:26 | Single bulged A Not in a motif group | homologous IL_5TBW_013 IL_80007.16 | |
| IL_6YLG_014 | 1/1/376:379, 1/1/390:403 | No text annotation Not in a motif group | homologous IL_5TBW_014 IL_60992.5 | |
| IL_6YLG_015 | 1/1/404:410, 1/2/13:19 | Triple sheared with non-canonical cWW Not in a motif group | homologous IL_5TBW_015 IL_66414.5 | |
| IL_6YLG_016 | 1/1/429:431, 1/1/628:630 | No text annotation Not in a motif group | homologous IL_5TBW_016 IL_01312.13 | |
| IL_6YLG_018 | 1/1/512:513, 1/1/577:579 | Single bulged A Not in a motif group | homologous IL_5TBW_018 IL_40508.4 | |
| IL_6YLG_019 | 1/1/517:525, 1/1/567:573 | No text annotation Not in a motif group | homologous IL_5TBW_019 IL_41593.1 | |
| IL_6YLG_020 | 1/1/531:538, 1/1/553:561 | No text annotation Not in a motif group | homologous IL_5TBW_020 IL_94501.1 | |
| IL_6YLG_021 | 1/1/668:670, 1/1/792:794 | No text annotation Not in a motif group | homologous IL_5TBW_021 IL_01312.13 | |
| IL_6YLG_022 | 1/1/680:684, 1/1/696:700 | No text annotation Not in a motif group | homologous IL_5TBW_022 IL_92343.1 | |
| IL_6YLG_023 | 1/1/725:728, 1/1/741:745 | UAA/GAN Not in a motif group | homologous IL_5TBW_023 IL_53523.5 | |
| IL_6YLG_024 | 1/1/752:753, 1/1/779:781 | Single bulged A Not in a motif group | geometric IL_4R4V_004 IL_80007.16 | |
| IL_6YLG_025 | 1/1/755:756, 1/1/775:777 | Single stack bend Not in a motif group | geometric IL_5J7L_032 IL_04038.4 | |
| IL_6YLG_027 | 1/1/803:805, 1/1/938:940 | No text annotation Not in a motif group | geometric IL_4WF9_020 IL_01312.13 | |
| IL_6YLG_028 | 1/1/805:809, 1/1/931:938 | No text annotation Not in a motif group | ||
| IL_6YLG_034 | 1/1/969:970, 1/1/1111:1113 | Single stack bend Not in a motif group | homologous IL_5TBW_035 IL_04038.4 | |
| IL_6YLG_035 | 1/1/976:981, 1/1/1102:1105 | No text annotation Not in a motif group | ||
| IL_6YLG_036 | 1/1/983:985, 1/1/1099:1100 | Single bulged G Not in a motif group | homologous IL_5TBW_037 IL_59137.10 | |
| IL_6YLG_039 | 1/1/1120:1122, 1/1/1136:1138 | No text annotation Not in a motif group | homologous IL_5TBW_046 IL_01312.13 | |
| IL_6YLG_040 | 1/1/1167:1171, 1/1/1328:1332 | UAA/GAN Not in a motif group | homologous IL_5TBW_048 IL_53523.5 | |
| IL_6YLG_041 | 1/1/1173:1180, 1/1/1325:1326 | SSU/LSU pseudoknot Not in a motif group | geometric IL_5TBW_049 IL_15861.6 | |
| IL_6YLG_042 | 1/1/1180:1182, 1/1/1324:1325 | Single bulged U Not in a motif group | homologous IL_5TBW_050 IL_83039.11 | |
| IL_6YLG_043 | 1/1/1186:1194, 1/1/1314:1320 | No text annotation Not in a motif group | ||
| IL_6YLG_044 | 1/1/1194:1206, 1/1/1298:1314 | No text annotation Not in a motif group | ||
| IL_6YLG_045 | 1/1/1207:1209, 1/1/1296:1297 | Single bulged U Not in a motif group | homologous IL_5TBW_053 IL_83039.11 | |
| IL_6YLG_046 | 1/1/1218:1226, 1/1/1283:1287 | Kink-turn Not in a motif group | homologous IL_5TBW_054 IL_90538.3 | |
| IL_6YLG_049 | 1/1/1376:1378, 1/1/1428:1431 | Isolated cWS basepair Not in a motif group | homologous IL_5TBW_057 IL_01312.13 | |
| IL_6YLG_050 | 1/1/1385:1387, 1/1/1420:1421 | Single bulged A Not in a motif group | homologous IL_5TBW_058 IL_80007.16 | |
| IL_6YLG_051 | 1/1/1388:1395, 1/1/1415:1419 | Kink-turn Not in a motif group | homologous IL_5TBW_059 IL_29549.9 | |
| IL_6YLG_052 | 1/1/1398:1400, 1/1/1411:1412 | Single bulged A Not in a motif group | geometric IL_5WWT_001 IL_80007.16 | |
| IL_6YLG_053 | 1/1/1444:1450, 1/1/2354:2359 | 7x6 Sarcin-Ricin; G-bulge Not in a motif group | homologous IL_5TBW_061 IL_35110.5 | |
| IL_6YLG_081 | 1/1/2391:2394, 1/1/2986:2988 | Major groove platform with extra pair Not in a motif group | homologous IL_5TBW_091 IL_87630.5 | |
| IL_6YLG_091 | 1/1/2835:2839, 1/1/2849:2853 | Triple sheared Not in a motif group | homologous IL_5TBW_106 IL_56467.6 | |
| IL_6YLG_092 | 1/1/2878:2882, 1/1/2940:2948 | No text annotation Not in a motif group | ||
| IL_6YLG_093 | 1/1/2889:2891, 1/1/2912:2914 | No text annotation Not in a motif group | geometric IL_5TBW_110 IL_01312.13 | |
| IL_6YLG_094 | 1/1/2891:2892, 1/1/2909:2912 | Minor groove platform with intercalation Not in a motif group | homologous IL_5TBW_111 IL_95601.1 | |
| IL_6YLG_095 | 1/1/2918:2920, 1/1/2926:2928 | No text annotation Not in a motif group | geometric IL_1Z7F_002 IL_01312.13 | |
| IL_6YLG_097 | 1/1/3004:3007, 1/1/3139:3144 | Double sheared Not in a motif group | homologous IL_5TBW_114 IL_09705.7 | |
| IL_6YLG_098 | 1/1/3012:3014, 1/1/3040:3042 | No text annotation Not in a motif group | homologous IL_5TBW_115 IL_01312.13 | |
| IL_6YLG_099 | 1/1/3018:3025, 1/1/3030:3036 | 8x7 Sarcin-Ricin; G-bulge Not in a motif group | geometric IL_5TBW_116 IL_04346.5 | |
| IL_6YLG_100 | 1/1/3047:3051, 1/1/3091:3094 | Major groove minor groove platform with tHH Not in a motif group | homologous IL_5TBW_117 IL_28060.3 | |
| IL_6YLG_101 | 1/1/3054:3059, 1/1/3084:3088 | UAA/GAN related Not in a motif group | homologous IL_5TBW_118 IL_53523.5 | |
| IL_6YLG_102 | 1/1/3063:3064, 1/1/3077:3080 | Multiple bulged bases Not in a motif group | homologous IL_5TBW_119 IL_13730.12 | |
| IL_6YLG_103 | 1/1/3103:3107, 1/1/3127:3131 | UAA/GAN Not in a motif group | homologous IL_5TBW_120 IL_53523.5 | |
| IL_6YLG_104 | 1/1/3177:3179, 1/1/3210:3211 | Single bulged A Not in a motif group | homologous IL_5TBW_123 IL_80007.16 | |
| IL_6YLG_105 | 1/1/3179:3188, 1/1/3204:3210 | No text annotation Not in a motif group | geometric IL_5TBW_124 IL_56867.1 | |
| IL_6YLG_106 | 1/1/3193:3194, 1/1/3197:3199 | Single bulged U Not in a motif group | geometric IL_5TBW_125 IL_83039.11 | |
| IL_6YLG_107 | 1/1/3225:3229, 1/1/3258:3260 | No text annotation Not in a motif group | homologous IL_5TBW_126 IL_50789.1 | |
| IL_6YLG_108 | 1/1/3233:3235, 1/1/3252:3254 | No text annotation Not in a motif group | homologous IL_5TBW_127 IL_01312.13 | |
| IL_6YLG_109 | 1/1/3235:3238, 1/1/3249:3252 | Tandem non-canonical cWW pairs Not in a motif group | geometric IL_6MWN_005 IL_85877.10 | |
| IL_6YLG_110 | 1/1/3300:3303, 1/1/3311:3314 | Tandem non-canonical cWW pairs Not in a motif group | geometric IL_5TBW_129 IL_85877.10 | |
| IL_6YLG_111 | 1/1/3318:3320, 1/1/3387:3388 | Single bulged U Not in a motif group | homologous IL_5TBW_130 IL_83039.11 | |
| IL_6YLG_112 | 1/1/3324:3325, 1/1/3381:3383 | Single bulged U Not in a motif group | homologous IL_5TBW_131 IL_21340.1 | |
| IL_6YLG_113 | 1/1/3328:3330, 1/1/3373:3378 | Isolated non-canonical cWW with bulges Not in a motif group | homologous IL_5TBW_132 IL_55456.1 | |
| IL_6YLG_114 | 1/1/3332:3337, 1/1/3367:3371 | No text annotation Not in a motif group | homologous IL_5TBW_133 IL_47002.1 | |
| IL_6YLG_115 | 1/1/3340:3345, 1/1/3360:3364 | No text annotation Not in a motif group | ||
| IL_6YLG_116 | 1/2/44:64, 1/2/96:100 | No text annotation Not in a motif group | geometric IL_5TBW_144 IL_23735.1 | |
| IL_6YLG_117 | 1/2/64:66, 1/2/93:96 | Isolated non-canonical cWW with bulges Not in a motif group | homologous IL_5TBW_145 IL_55456.1 | |
| IL_6YLG_118 | 1/2/68:69, 1/2/89:91 | Single bulged U Not in a motif group | geometric IL_5TBW_146 IL_83039.11 | |
| IL_6YLG_119 | 1/3/15:16, 1/3/63:65 | Single bulged A Not in a motif group | homologous IL_5TBW_372 IL_80007.16 | |
| IL_6YLG_120 | 1/3/21:27, 1/3/53:58 | No text annotation Not in a motif group | homologous IL_5TBW_373 IL_05523.1 | |
| IL_6YLG_121 | 1/3/27:29, 1/3/49:53 | No text annotation Not in a motif group | ||
| IL_6YLG_122 | 1/3/29:30, 1/3/47:49 | Single stack bend Not in a motif group | geometric IL_5TBW_375 IL_04038.4 | |
| IL_6YLG_123 | 1/3/32:36, 1/3/41:45 | Symmetric double minor groove platform Not in a motif group | geometric IL_5TBW_376 IL_58103.5 | |
| IL_6YLG_124 | 1/3/72:80, 1/3/100:106 | 8x7 Sarcin-Ricin; G-bulge Not in a motif group | homologous IL_5TBW_377 IL_04346.5 | |
| IL_6YLG_125 | 1/3/84:87, 1/3/94:96 | No text annotation Not in a motif group | geometric IL_5MSF_001 IL_01312.13 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_6YLG_017 | No text annotation | ||
| IL_6YLG_026 | No text annotation | ||
| IL_6YLG_029 | Single bulged G | ||
| IL_6YLG_030 | Triple sheared | ||
| IL_6YLG_031 | Major groove platform with extra cWW | ||
| IL_6YLG_032 | Single bulged U | ||
| IL_6YLG_033 | Multiple bulged bases | ||
| IL_6YLG_037 | No text annotation | ||
| IL_6YLG_038 | Single stack bend | ||
| IL_6YLG_047 | No text annotation | ||
| IL_6YLG_048 | Major groove platform with extra cWW | ||
| IL_6YLG_054 | No text annotation | ||
| IL_6YLG_055 | UAA/GAN | ||
| IL_6YLG_056 | Other IL | ||
| IL_6YLG_057 | Multiple bulged bases | ||
| IL_6YLG_058 | No text annotation | ||
| IL_6YLG_059 | Triple sheared | ||
| IL_6YLG_060 | No text annotation | ||
| IL_6YLG_061 | Single bulged C | ||
| IL_6YLG_062 | Single stack bend | ||
| IL_6YLG_063 | No text annotation | ||
| IL_6YLG_064 | No text annotation | ||
| IL_6YLG_065 | Kink-turn | ||
| IL_6YLG_066 | No text annotation | ||
| IL_6YLG_067 | Isolated tWW turn | ||
| IL_6YLG_068 | Major groove platform; stack outside cWW | ||
| IL_6YLG_069 | Intercalated tWH | ||
| IL_6YLG_070 | tSH-tSH-tHH-tHS | ||
| IL_6YLG_071 | No text annotation | ||
| IL_6YLG_072 | No text annotation | ||
| IL_6YLG_073 | Single bulged A | ||
| IL_6YLG_074 | Kink-turn related | ||
| IL_6YLG_075 | No text annotation | ||
| IL_6YLG_076 | Major groove outside cWW, minor groove, intercalation pocket | ||
| IL_6YLG_077 | Single bulged U | ||
| IL_6YLG_078 | No text annotation | ||
| IL_6YLG_079 | No text annotation | ||
| IL_6YLG_080 | Tandem non-canonical cWW pairs | ||
| IL_6YLG_082 | Single bulged U | ||
| IL_6YLG_083 | Minor groove platform | ||
| IL_6YLG_084 | Isolated tHS basepair with bulges | ||
| IL_6YLG_085 | No text annotation | ||
| IL_6YLG_086 | No text annotation | ||
| IL_6YLG_087 | No text annotation | ||
| IL_6YLG_088 | Isolated tHS basepair with bulges | ||
| IL_6YLG_089 | Tandem non-canonical cWW pairs | ||
| IL_6YLG_090 | Isolated non-canonical cWW with bulges | ||
| IL_6YLG_096 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_6YLG_001 | 1/1/113:123, 1/1/149:158, 1/1/263:267 | No text annotation Not in a motif group | ||
| J3_6YLG_002 | 1/1/369:376, 1/1/403:404, 1/2/19:20 | No text annotation Not in a motif group | ||
| J3_6YLG_003 | 1/1/502:503, 1/1/588:597, 1/1/606:611 | No text annotation Not in a motif group | homologous J3_5TBW_003 NA | |
| J3_6YLG_006 | 1/1/986:987, 1/1/1062:1066, 1/1/1092:1098 | No text annotation Not in a motif group | ||
| J3_6YLG_015 | 1/1/2886:2889, 1/1/2914:2916, 1/1/2930:2936 | No text annotation Not in a motif group | ||
| J3_6YLG_016 | 1/1/3298:3300, 1/1/3314:3318, 1/1/3388:3390 | No text annotation Not in a motif group | ||
| J3_6YLG_017 | 1/3/9:14, 1/3/66:67, 1/3/111:112 | No text annotation Not in a motif group | homologous J3_5TBW_045 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_6YLG_004 | No text annotation | ||
| J3_6YLG_005 | No text annotation | ||
| J3_6YLG_007 | No text annotation | ||
| J3_6YLG_008 | No text annotation | ||
| J3_6YLG_009 | No text annotation | ||
| J3_6YLG_010 | No text annotation | ||
| J3_6YLG_011 | No text annotation | ||
| J3_6YLG_012 | No text annotation | ||
| J3_6YLG_013 | No text annotation | ||
| J3_6YLG_014 | No text annotation |
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