6FT6 Internal, Hairpin and 3-way Junction Loop Motifs
Valid loops
| # | loop id | location | annotation (mapped to, source) | motif group (similar to) |
|---|---|---|---|---|
| 1/1/38:45 | homologous HL_5TBW_001 | NA HL_23481.5* | ||
| 1/1/69:74 | homologous HL_5TBW_002 | NA HL_96776.3* | ||
| 1/1/90:96 | homologous HL_5TBW_003 | NA HL_67216.5* | ||
| 1/1/132:136 | homologous HL_5TBW_004 | NA HL_36982.3* | ||
| 1/1/194:201 | T-loop with 1 bulged base homologous HL_5TBW_005 | NA HL_68493.6* | ||
| 1/1/208:212 | homologous HL_5TBW_006 | NA HL_98557.5* | ||
| 1/1/216:224 | homologous HL_5TBW_007 | NA HL_08002.6* | ||
| 1/1/278:287 | homologous HL_5TBW_008 | NA HL_54035.7* | ||
| 1/1/357:362 | Other HL homologous HL_5TBW_010 | NA HL_43074.18* | ||
| 1/1/382:387 | GNRA homologous HL_5TBW_011 | NA HL_43074.18* | ||
| 1/1/543:548 | homologous HL_5TBW_012 | NA HL_94386.1* | ||
| 1/1/599:604 | GNRA homologous HL_5TBW_013 | NA HL_43074.18* | ||
| 1/1/640:649 | NA | NA | ||
| 1/1/686:694 | homologous HL_5TBW_015 | NA HL_80105.3* | ||
| 1/1/707:712 | GNRA homologous HL_5TBW_016 | NA HL_43074.18* | ||
| 1/1/732:737 | GNRA homologous HL_5TBW_017 | NA HL_43074.18* | ||
| 1/1/958:963 | homologous HL_5TBW_022 | NA HL_15942.5* | ||
| 1/1/1126:1132 | geometric HL_4V9F_003 | NA HL_94352.4* | ||
| 1/1/1148:1155 | homologous HL_5TBW_026 | NA HL_72451.5* | ||
| 1/1/1403:1408 | GNRA homologous HL_5TBW_030 | NA HL_43074.18* | ||
| 1/1/2840:2848 | Other HL geometric HL_1P6V_001 | NA HL_79299.11* | ||
| 1/1/2896:2905 | NA | NA | ||
| 1/1/2920:2926 | geometric HL_5TBW_022 | NA HL_15942.5* | ||
| 1/1/3025:3030 | GNRA homologous HL_5TBW_065 | NA HL_43074.18* | ||
| 1/1/3068:3073 | Ribsomal LSU H95 homologous HL_5TBW_066 | NA HL_67719.1* | ||
| 1/1/3110:3124 | homologous HL_5TBW_067 | NA HL_56677.5* | ||
| 1/1/3194:3197 | homologous HL_5TBW_068 | NA HL_46546.1* | ||
| 1/1/3240:3247 | homologous HL_5TBW_069 | NA HL_27757.1* | ||
| 1/1/3303:3311 | homologous HL_5TBW_070 | NA HL_05018.6* | ||
| 1/1/3350:3353 | homologous HL_5TBW_071 | NA HL_69353.7* | ||
| 1/2/69:89 | NA | NA | ||
| 1/2/108:114 | homologous HL_5TBW_075 | NA HL_06569.2* | ||
| 1/2/124:129 | homologous HL_5TBW_076 | NA HL_60357.1* | ||
| 1/3/36:41 | NA | NA | ||
| 1/3/88:93 | NA | NA |
Problematic loops
Valid loops
| # | loop id | location | annotation (mapped to, source) | motif group (similar to) |
|---|---|---|---|---|
| 1/1/7:8, 1/2/150:152 | Single bulged C homologous IL_5TBW_002 | NA IL_61258.10* | ||
| 1/1/12:15, 1/2/144:146 | geometric IL_3LA5_001 | NA IL_01312.13* | ||
| 1/1/27:28, 1/1/56:58 | Single stack bend homologous IL_5TBW_004 | NA IL_04038.4* | ||
| 1/1/31:38, 1/1/45:53 | tSH-tHW-tHH-tHS geometric IL_5TBW_005 | NA IL_22863.1* | ||
| 1/1/82:89, 1/1/97:103 | homologous IL_5TBW_006 | NA IL_29509.1* | ||
| 1/1/123:124, 1/1/144:149 | homologous IL_5TBW_007 | NA IL_19724.1* | ||
| 1/1/125:127, 1/1/141:143 | homologous IL_5TBW_008 | NA IL_01312.13* | ||
| 1/1/163:165, 1/1/257:258 | Single stack bend homologous IL_5TBW_009 | NA IL_04038.4* | ||
| 1/1/168:170, 1/1/248:254 | NA | NA | ||
| 1/1/177:178, 1/1/238:241 | Major groove platform geometric IL_7A0S_073 | NA IL_80663.10* | ||
| 1/1/189:191, 1/1/204:205 | Single bulged U homologous IL_5TBW_012 | NA IL_83039.11* | ||
| 1/1/272:274, 1/1/291:293 | Isolated cWH basepair geometric IL_4KQ0_004 | NA IL_42589.6* | ||
| 1/1/337:339, 1/2/25:26 | Single bulged A homologous IL_5TBW_013 | NA IL_80007.16* | ||
| 1/1/376:379, 1/1/390:403 | geometric IL_5TBW_014 | NA IL_60992.5* | ||
| 1/1/404:410, 1/2/13:19 | Triple sheared with non-canonical cWW geometric IL_5TBW_015 | NA IL_66414.5* | ||
| 1/1/429:431, 1/1/628:630 | homologous IL_5TBW_016 | NA IL_01312.13* | ||
| 1/1/512:513, 1/1/577:579 | Single bulged A homologous IL_5TBW_018 | NA IL_40508.4* | ||
| 1/1/517:525, 1/1/567:573 | homologous IL_5TBW_019 | NA IL_41593.1* | ||
| 1/1/531:538, 1/1/553:561 | homologous IL_5TBW_020 | NA IL_94501.1* | ||
| 1/1/668:670, 1/1/792:794 | homologous IL_5TBW_021 | NA IL_01312.13* | ||
| 1/1/680:684, 1/1/696:700 | homologous IL_5TBW_022 | NA IL_92343.1* | ||
| 1/1/725:728, 1/1/741:745 | UAA/GAN homologous IL_5TBW_023 | NA IL_53523.5* | ||
| 1/1/752:753, 1/1/779:781 | Single bulged A homologous IL_5TBW_024 | NA IL_80007.16* | ||
| 1/1/755:757, 1/1/774:777 | geometric IL_4N0T_004 | NA IL_87332.1* | ||
| 1/1/803:805, 1/1/938:940 | homologous IL_5TBW_027 | NA IL_01312.13* | ||
| 1/1/805:809, 1/1/931:938 | NA | NA | ||
| 1/1/969:972, 1/1/1110:1113 | NA | NA | ||
| 1/1/972:981, 1/1/1102:1110 | NA | NA | ||
| 1/1/983:985, 1/1/1099:1100 | Single bulged G homologous IL_5TBW_037 | NA IL_59137.10* | ||
| 1/1/1120:1122, 1/1/1136:1138 | homologous IL_5TBW_046 | NA IL_01312.13* | ||
| 1/1/1167:1171, 1/1/1328:1332 | UAA/GAN homologous IL_5TBW_048 | NA IL_53523.5* | ||
| 1/1/1173:1180, 1/1/1325:1326 | SSU/LSU pseudoknot geometric IL_5TBW_049 | NA IL_15861.6* | ||
| 1/1/1180:1182, 1/1/1324:1325 | Single bulged U homologous IL_5TBW_050 | NA IL_83039.11* | ||
| 1/1/1186:1194, 1/1/1314:1320 | NA | NA | ||
| 1/1/1194:1206, 1/1/1298:1314 | NA | NA | ||
| 1/1/1207:1209, 1/1/1296:1297 | Single bulged U homologous IL_5TBW_053 | NA IL_83039.11* | ||
| 1/1/1218:1226, 1/1/1283:1287 | Kink-turn homologous IL_5TBW_054 | NA IL_90538.3* | ||
| 1/1/1376:1378, 1/1/1428:1431 | Isolated cWS basepair homologous IL_5TBW_057 | NA IL_01312.13* | ||
| 1/1/1385:1387, 1/1/1420:1421 | Single bulged A homologous IL_5TBW_058 | NA IL_80007.16* | ||
| 1/1/1388:1395, 1/1/1415:1419 | Kink-turn homologous IL_5TBW_059 | NA IL_29549.9* | ||
| 1/1/1398:1400, 1/1/1411:1412 | Single bulged A homologous IL_5TBW_060 | NA IL_80007.16* | ||
| 1/1/1444:1451, 1/1/2353:2359 | 8x7 Sarcin-Ricin with CC bifurcated pair; G-bulge geometric IL_4V9F_012 | NA IL_59724.1* | ||
| 1/1/2391:2394, 1/1/2986:2988 | Major groove platform with extra pair homologous IL_5TBW_091 | NA IL_87630.5* | ||
| 1/1/2835:2839, 1/1/2849:2853 | Triple sheared homologous IL_5TBW_106 | NA IL_56467.6* | ||
| 1/1/2879:2882, 1/1/2940:2947 | NA | NA | ||
| 1/1/2889:2891, 1/1/2912:2914 | homologous IL_5TBW_110 | NA IL_01312.13* | ||
| 1/1/2891:2892, 1/1/2909:2912 | Minor groove platform with intercalation geometric IL_7RQB_099 | NA IL_95601.1* | ||
| 1/1/2918:2920, 1/1/2926:2928 | geometric IL_1U9S_007 | NA IL_01312.13* | ||
| 1/1/3004:3007, 1/1/3139:3144 | Double sheared homologous IL_5TBW_114 | NA IL_09705.7* | ||
| 1/1/3012:3014, 1/1/3040:3042 | homologous IL_5TBW_115 | NA IL_01312.13* | ||
| 1/1/3018:3025, 1/1/3030:3036 | 8x7 Sarcin-Ricin; G-bulge geometric IL_5TBW_116 | NA IL_04346.5* | ||
| 1/1/3047:3051, 1/1/3091:3094 | Major groove minor groove platform with tHH homologous IL_5TBW_117 | NA IL_28060.3* | ||
| 1/1/3054:3059, 1/1/3084:3088 | UAA/GAN related homologous IL_5TBW_118 | NA IL_53523.5* | ||
| 1/1/3063:3064, 1/1/3077:3080 | Multiple bulged bases homologous IL_5TBW_119 | NA IL_13730.12* | ||
| 1/1/3103:3107, 1/1/3127:3131 | UAA/GAN homologous IL_5TBW_120 | NA IL_53523.5* | ||
| 1/1/3177:3179, 1/1/3210:3211 | Single bulged A homologous IL_5TBW_123 | NA IL_80007.16* | ||
| 1/1/3179:3188, 1/1/3204:3210 | geometric IL_5TBW_124 | NA IL_56867.1* | ||
| 1/1/3193:3194, 1/1/3197:3199 | Single bulged U geometric IL_5TBW_125 | NA IL_83039.11* | ||
| 1/1/3225:3229, 1/1/3258:3260 | homologous IL_5TBW_126 | NA IL_50789.1* | ||
| 1/1/3233:3235, 1/1/3252:3254 | homologous IL_5TBW_127 | NA IL_01312.13* | ||
| 1/1/3235:3238, 1/1/3249:3252 | Tandem non-canonical cWW pairs geometric IL_6MWN_005 | NA IL_85877.10* | ||
| 1/1/3300:3303, 1/1/3311:3314 | Tandem non-canonical cWW pairs geometric IL_5TBW_129 | NA IL_85877.10* | ||
| 1/1/3318:3320, 1/1/3387:3388 | Single bulged U geometric IL_5TBW_130 | NA IL_83039.11* | ||
| 1/1/3324:3325, 1/1/3381:3383 | Single bulged U homologous IL_5TBW_131 | NA IL_21340.1* | ||
| 1/1/3328:3330, 1/1/3373:3378 | Isolated non-canonical cWW with bulges homologous IL_5TBW_132 | NA IL_55456.1* | ||
| 1/1/3332:3337, 1/1/3367:3371 | homologous IL_5TBW_133 | NA IL_47002.1* | ||
| 1/1/3340:3342, 1/1/3363:3364 | NA | NA | ||
| 1/1/3342:3345, 1/1/3360:3363 | tWS-tSW homologous IL_5TBW_135 | NA IL_09705.7* | ||
| 1/1/3349:3350, 1/1/3353:3356 | Multiple bulged bases geometric IL_7V9E_001 | NA IL_13730.12* | ||
| 1/2/43:64, 1/2/96:101 | NA | NA | ||
| 1/2/64:66, 1/2/93:96 | Isolated non-canonical cWW with bulges homologous IL_5TBW_145 | NA IL_55456.1* | ||
| 1/2/68:69, 1/2/89:91 | Single bulged U homologous IL_5TBW_146 | NA IL_83039.11* | ||
| 1/3/15:16, 1/3/63:65 | NA | NA | ||
| 1/3/21:27, 1/3/53:58 | NA | NA | ||
| 1/3/28:29, 1/3/49:52 | NA | NA | ||
| 1/3/29:30, 1/3/47:49 | NA | NA | ||
| 1/3/32:36, 1/3/41:45 | NA | NA | ||
| 1/3/72:80, 1/3/100:106 | NA | NA | ||
| 1/3/81:87, 1/3/94:99 | NA | NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_6FT6_017 | NA | ||
| IL_6FT6_026 | geometric IL_5TBW_026 | ||
| IL_6FT6_029 | Single bulged G geometric IL_5TBW_029 | ||
| IL_6FT6_030 | Triple sheared homologous IL_5TBW_030 | ||
| IL_6FT6_031 | Major groove platform with extra cWW homologous IL_5TBW_031 | ||
| IL_6FT6_032 | Single bulged U geometric IL_7RQB_080 | ||
| IL_6FT6_033 | Multiple bulged bases homologous IL_5TBW_033 | ||
| IL_6FT6_037 | homologous IL_5TBW_044 | ||
| IL_6FT6_046 | geometric IL_4V9F_043 | ||
| IL_6FT6_047 | Major groove platform with extra cWW homologous IL_5TBW_056 | ||
| IL_6FT6_053 | homologous IL_5TBW_062 | ||
| IL_6FT6_054 | UAA/GAN homologous IL_5TBW_063 | ||
| IL_6FT6_055 | Other IL homologous IL_5TBW_064 | ||
| IL_6FT6_056 | Isolated non-canonical cWW with bulges geometric IL_5TBW_145 | ||
| IL_6FT6_057 | NA | ||
| IL_6FT6_058 | homologous IL_5TBW_068 | ||
| IL_6FT6_059 | Single bulged C homologous IL_5TBW_069 | ||
| IL_6FT6_060 | Single stack bend geometric IL_5TBW_070 | ||
| IL_6FT6_061 | homologous IL_5TBW_071 | ||
| IL_6FT6_062 | homologous IL_5TBW_072 | ||
| IL_6FT6_063 | Kink-turn homologous IL_5TBW_073 | ||
| IL_6FT6_064 | homologous IL_5TBW_074 | ||
| IL_6FT6_065 | Isolated tWW turn homologous IL_5TBW_075 | ||
| IL_6FT6_066 | Major groove platform; stack outside cWW geometric IL_5TBW_076 | ||
| IL_6FT6_067 | Intercalated tWH homologous IL_5TBW_077 | ||
| IL_6FT6_068 | tSH-tSH-tHH-tHS homologous IL_5TBW_078 | ||
| IL_6FT6_069 | homologous IL_5TBW_079 | ||
| IL_6FT6_070 | homologous IL_5TBW_080 | ||
| IL_6FT6_071 | Single bulged A homologous IL_5TBW_082 | ||
| IL_6FT6_072 | Kink-turn related homologous IL_5TBW_083 | ||
| IL_6FT6_073 | Single bulged U homologous IL_5TBW_086 | ||
| IL_6FT6_074 | Major groove platform with extra pair geometric IL_5TBW_087 | ||
| IL_6FT6_075 | homologous IL_5TBW_088 | ||
| IL_6FT6_077 | Major groove platform geometric IL_4WF9_078 | ||
| IL_6FT6_078 | NA | ||
| IL_6FT6_079 | Minor groove platform homologous IL_5TBW_094 | ||
| IL_6FT6_080 | Isolated tHS basepair with bulges homologous IL_5TBW_095 | ||
| IL_6FT6_081 | homologous IL_5TBW_096 | ||
| IL_6FT6_082 | geometric IL_4V84_070 | ||
| IL_6FT6_083 | geometric IL_5TBW_110 | ||
| IL_6FT6_084 | NA | ||
| IL_6FT6_085 | NA | ||
| IL_6FT6_086 | geometric IL_4N0T_004 | ||
| IL_6FT6_087 | Multiple bulged bases geometric IL_4V88_392 | ||
| IL_6FT6_093 | geometric IL_4V88_470 |
Valid loops
| # | loop id | location | annotation (mapped to, source) | motif group (similar to) |
|---|---|---|---|---|
| 1/1/113:123, 1/1/149:158, 1/1/263:267 | NA | NA | ||
| 1/1/369:376, 1/1/403:404, 1/2/19:20 | homologous J3_5TBW_002 | NA | ||
| 1/1/502:503, 1/1/588:597, 1/1/606:611 | homologous J3_5TBW_003 | NA | ||
| 1/1/2886:2889, 1/1/2914:2916, 1/1/2930:2936 | NA | NA | ||
| 1/1/3298:3300, 1/1/3314:3318, 1/1/3388:3390 | NA | NA | ||
| 1/3/9:14, 1/3/66:67, 1/3/111:112 | NA | NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_6FT6_004 | NA | ||
| J3_6FT6_005 | homologous J3_5TBW_005 | ||
| J3_6FT6_006 | NA | ||
| J3_6FT6_007 | homologous J3_5TBW_008 | ||
| J3_6FT6_008 | homologous J3_5TBW_009 | ||
| J3_6FT6_009 | homologous J3_5TBW_010 | ||
| J3_6FT6_010 | NA | ||
| J3_6FT6_011 | homologous J3_5TBW_012 | ||
| J3_6FT6_012 | NA |
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