7OHV Internal, Hairpin and 3-way Junction Loop Motifs
Valid loops
| # | loop id | location | annotation (mapped to, source) | motif group (similar to) |
|---|---|---|---|---|
| 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* | ||
| 1/1/599:604 | GNRA homologous HL_5TBW_013 | NA HL_43074.18* | ||
| 1/1/3194:3197 | homologous HL_5TBW_068 | NA HL_46546.1* | ||
| 1/6/11:17 | NA | NA | ||
| 1/6/36:43 | NA | NA |
Problematic loops
Valid loops
| # | loop id | location | annotation (mapped to, source) | motif group (similar to) |
|---|---|---|---|---|
| 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* | ||
| 1/1/404:411, 1/2/12:19 | NA | NA | ||
| 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* | ||
| 1/1/680:684, 1/1/696:700 | homologous IL_5TBW_022 | NA IL_92343.1* | ||
| 1/1/969:970, 1/1/1111:1113 | Single stack bend homologous IL_5TBW_035 | NA IL_04038.4* | ||
| 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 homologous IL_5TBW_049 | NA IL_15861.6* | ||
| 1/1/1180:1182, 1/1/1324:1325 | Single bulged U geometric IL_7A0S_035 | NA IL_83039.11* | ||
| 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* | ||
| 1/1/3164:3166, 1/1/3284:3286 | geometric IL_7A0S_026 | NA IL_01312.13* | ||
| 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* | ||
| 1/6/26:27, 1/6/51:54 | NA | NA | ||
| 1/6/30:34, 1/6/45:48 | NA | NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_7OHV_001 | Single bulged C homologous IL_5TBW_002 | ||
| IL_7OHV_002 | Single bulged U homologous IL_5TBW_003 | ||
| IL_7OHV_003 | Single stack bend homologous IL_5TBW_004 | ||
| IL_7OHV_004 | tSH-tHW-tHH-tHS geometric IL_5TBW_005 | ||
| IL_7OHV_005 | homologous IL_5TBW_006 | ||
| IL_7OHV_006 | homologous IL_5TBW_007 | ||
| IL_7OHV_007 | homologous IL_5TBW_008 | ||
| IL_7OHV_008 | Single bulged A geometric IL_7RQB_059 | ||
| IL_7OHV_009 | NA | ||
| IL_7OHV_010 | Major groove platform geometric IL_4WF9_026 | ||
| IL_7OHV_011 | Single bulged U homologous IL_5TBW_012 | ||
| IL_7OHV_015 | homologous IL_5TBW_016 | ||
| IL_7OHV_016 | NA | ||
| IL_7OHV_020 | homologous IL_5TBW_021 | ||
| IL_7OHV_022 | UAA/GAN homologous IL_5TBW_023 | ||
| IL_7OHV_023 | Single bulged A geometric IL_3MJA_001 | ||
| IL_7OHV_024 | NA | ||
| IL_7OHV_025 | geometric IL_3RW6_004 | ||
| IL_7OHV_026 | NA | ||
| IL_7OHV_028 | NA | ||
| IL_7OHV_034 | NA | ||
| IL_7OHV_035 | NA | ||
| IL_7OHV_036 | Single bulged U homologous IL_5TBW_053 | ||
| IL_7OHV_037 | NA | ||
| IL_7OHV_038 | geometric IL_4V9F_043 | ||
| IL_7OHV_039 | Major groove platform with extra cWW homologous IL_5TBW_056 | ||
| IL_7OHV_042 | Kink-turn homologous IL_5TBW_059 | ||
| IL_7OHV_043 | Single bulged A homologous IL_5TBW_060 | ||
| IL_7OHV_044 | 7x6 Sarcin-Ricin; G-bulge homologous IL_5TBW_061 | ||
| IL_7OHV_045 | NA | ||
| IL_7OHV_046 | C-loop geometric IL_4MGN_001 | ||
| IL_7OHV_047 | UAA/GAN homologous IL_5TBW_063 | ||
| IL_7OHV_048 | Other IL homologous IL_5TBW_064 | ||
| IL_7OHV_049 | Isolated tHS basepair with bulges geometric IL_4V9F_076 | ||
| IL_7OHV_050 | NA | ||
| IL_7OHV_051 | Triple sheared homologous IL_5TBW_067 | ||
| IL_7OHV_052 | homologous IL_5TBW_068 | ||
| IL_7OHV_053 | Major groove platform geometric IL_4WF9_078 | ||
| IL_7OHV_054 | homologous IL_5TBW_071 | ||
| IL_7OHV_055 | homologous IL_5TBW_072 | ||
| IL_7OHV_056 | NA | ||
| IL_7OHV_057 | homologous IL_5TBW_074 | ||
| IL_7OHV_058 | NA | ||
| IL_7OHV_059 | NA | ||
| IL_7OHV_060 | Triple sheared homologous IL_5TBW_106 | ||
| IL_7OHV_061 | geometric IL_4YHW_001 | ||
| IL_7OHV_062 | Minor groove platform with intercalation geometric IL_5J7L_342 | ||
| IL_7OHV_063 | Double sheared homologous IL_5TBW_114 | ||
| IL_7OHV_064 | homologous IL_5TBW_115 | ||
| IL_7OHV_065 | 8x7 Sarcin-Ricin; G-bulge geometric IL_5TBW_116 | ||
| IL_7OHV_066 | Major groove minor groove platform with tHH homologous IL_5TBW_117 | ||
| IL_7OHV_067 | NA | ||
| IL_7OHV_068 | Multiple bulged bases homologous IL_5TBW_119 | ||
| IL_7OHV_069 | geometric IL_3ICQ_003 | ||
| IL_7OHV_070 | UAA/GAN homologous IL_5TBW_120 | ||
| IL_7OHV_071 | Isolated cWS basepair geometric IL_4TS2_003 | ||
| IL_7OHV_073 | Tandem non-canonical cWW pairs geometric IL_1D4R_001 | ||
| IL_7OHV_077 | homologous IL_5TBW_126 | ||
| IL_7OHV_078 | homologous IL_5TBW_127 | ||
| IL_7OHV_079 | Tandem non-canonical cWW pairs geometric IL_5C5W_003 | ||
| IL_7OHV_080 | Tandem non-canonical cWW pairs geometric IL_5EW4_002 | ||
| IL_7OHV_081 | Single bulged U geometric IL_3TZR_002 | ||
| IL_7OHV_082 | NA | ||
| IL_7OHV_083 | Isolated non-canonical cWW with bulges homologous IL_5TBW_132 | ||
| IL_7OHV_084 | homologous IL_5TBW_133 | ||
| IL_7OHV_085 | Single bulged U geometric IL_1ET4_002 | ||
| IL_7OHV_086 | tWS-tSW homologous IL_5TBW_135 | ||
| IL_7OHV_087 | Isolated non-canonical cWW with bulges homologous IL_5TBW_145 |
Valid loops
| # | loop id | location | annotation (mapped to, source) | motif group (similar to) |
|---|---|---|---|---|
| 1/1/502:503, 1/1/588:597, 1/1/606:611 | homologous J3_5TBW_003 | NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_7OHV_001 | NA | ||
| J3_7OHV_002 | homologous J3_5TBW_002 | ||
| J3_7OHV_004 | NA | ||
| J3_7OHV_005 | NA | ||
| J3_7OHV_006 | homologous J3_5TBW_010 | ||
| J3_7OHV_007 | NA | ||
| J3_7OHV_008 | homologous J3_5TBW_015 | ||
| J3_7OHV_009 | NA |
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