3J7A Internal, Hairpin and 3-way Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_3J7A_001 | 1/A/7:17 | No text annotation Not in a motif group | homologous HL_4V88_186 HL_89881.2 | |
| HL_3J7A_002 | 1/A/152:158 | No text annotation Not in a motif group | geometric HL_7RQB_047 NA | |
| HL_3J7A_004 | 1/A/245:252 | T-loop with 1 bulged base Not in a motif group | geometric HL_4V88_191 HL_56241.2 | |
| HL_3J7A_006 | 1/A/336:344 | No text annotation Not in a motif group | homologous HL_4V88_193 HL_69023.3 | |
| HL_3J7A_007 | 1/A/374:379 | GNRA Not in a motif group | geometric HL_3RG5_007 HL_85603.1 | |
| HL_3J7A_008 | 1/A/399:410 | No text annotation Not in a motif group | homologous HL_4V88_195 HL_84288.1 | |
| HL_3J7A_009 | 1/A/420:425 | UNCG Not in a motif group | homologous HL_4V88_196 HL_29960.1 | |
| HL_3J7A_010 | 1/A/456:462 | No text annotation Not in a motif group | homologous HL_4V88_197 HL_26380.1 | |
| HL_3J7A_012 | 1/A/528:538 | No text annotation Not in a motif group | geometric HL_4UYK_001 HL_36684.1 | |
| HL_3J7A_013 | 1/A/576:581 | Other HL Not in a motif group | homologous HL_4V88_200 HL_53845.3 | |
| HL_3J7A_015 | 1/A/814:822 | No text annotation Not in a motif group | homologous HL_4V88_203 HL_46766.2 | |
| HL_3J7A_018 | 1/A/969:978 | No text annotation Not in a motif group | homologous HL_4V88_206 HL_12326.2 | |
| HL_3J7A_019 | 1/A/1006:1011 | Other HL Not in a motif group | homologous HL_4V88_207 HL_87030.3 | |
| HL_3J7A_020 | 1/A/1066:1076 | No text annotation Not in a motif group | homologous HL_4V88_208 HL_12326.2 | |
| HL_3J7A_021 | 1/A/1185:1190 | Other HL Not in a motif group | homologous HL_4V88_210 HL_85603.1 | |
| HL_3J7A_022 | 1/A/1222:1227 | GNRA Not in a motif group | homologous HL_4V88_211 HL_85603.1 | |
| HL_3J7A_023 | 1/A/1289:1298 | No text annotation Not in a motif group | homologous HL_4V88_212 HL_73530.2 | |
| HL_3J7A_026 | 1/A/1411:1418 | No text annotation Not in a motif group | homologous HL_4V88_215 HL_71554.2 | |
| HL_3J7A_028 | 1/A/1642:1648 | No text annotation Not in a motif group | homologous HL_4V88_217 HL_85603.1 | |
| HL_3J7A_030 | 1/A/1797:1802 | GNRA Not in a motif group | homologous HL_4V88_218 HL_85603.1 | |
| HL_3J7A_031 | 1/A/1847:1858 | No text annotation Not in a motif group | homologous HL_4V88_219 HL_75768.1 | |
| HL_3J7A_032 | 1/A/1891:1899 | No text annotation Not in a motif group | homologous HL_4V88_220 HL_75828.1 | |
| HL_3J7A_034 | 1/A/2070:2075 | Other HL Not in a motif group | homologous HL_4V88_222 HL_16173.1 | |
| HL_3J7A_035 | 1/7/11:23 | No text annotation Not in a motif group | homologous HL_4WT8_218 NA | |
| HL_3J7A_036 | 1/7/27:40 | No text annotation Not in a motif group | ||
| HL_3J7A_037 | 1/7/50:60 | No text annotation Not in a motif group | homologous HL_4WQ1_225 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_3J7A_003 | No text annotation | ||
| HL_3J7A_005 | No text annotation | ||
| HL_3J7A_011 | No text annotation | ||
| HL_3J7A_014 | No text annotation | ||
| HL_3J7A_016 | No text annotation | ||
| HL_3J7A_017 | No text annotation | ||
| HL_3J7A_024 | No text annotation | ||
| HL_3J7A_025 | No text annotation | ||
| HL_3J7A_027 | No text annotation | ||
| HL_3J7A_029 | No text annotation | ||
| HL_3J7A_033 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_3J7A_001 | 1/A/24:26, 1/A/607:608 | Single bulged C Not in a motif group | homologous IL_4V88_384 IL_61258.13 | |
| IL_3J7A_002 | 1/A/37:41, 1/A/472:477 | No text annotation Not in a motif group | homologous IL_4V88_386 IL_41507.1 | |
| IL_3J7A_003 | 1/A/42:48, 1/A/437:439 | No text annotation Not in a motif group | homologous IL_4V88_387 IL_33912.1 | |
| IL_3J7A_004 | 1/A/50:52, 1/A/434:435 | Minor groove platform Not in a motif group | homologous IL_4V88_388 IL_80097.2 | |
| IL_3J7A_005 | 1/A/58:63, 1/A/89:91 | No text annotation Not in a motif group | ||
| IL_3J7A_006 | 1/A/64:68, 1/A/84:88 | No text annotation Not in a motif group | homologous IL_4V88_390 IL_77691.2 | |
| IL_3J7A_008 | 1/A/111:114, 1/A/308:311 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_4V88_391 IL_30621.4 | |
| IL_3J7A_009 | 1/A/115:118, 1/A/306:307 | Multiple bulged bases Not in a motif group | homologous IL_4V88_392 IL_44546.2 | |
| IL_3J7A_010 | 1/A/119:123, 1/A/302:305 | UAA/GAN variation Not in a motif group | geometric IL_3LOA_001 IL_58764.4 | |
| IL_3J7A_011 | 1/A/141:147, 1/A/163:170 | tWH-tWH-tHW-tHW Not in a motif group | homologous IL_4V88_394 IL_80604.2 | |
| IL_3J7A_014 | 1/A/266:268, 1/A/294:295 | Single bulged A Not in a motif group | homologous IL_4V88_399 IL_37497.7 | |
| IL_3J7A_015 | 1/A/270:272, 1/A/291:292 | No text annotation Not in a motif group | ||
| IL_3J7A_016 | 1/A/317:322, 1/A/354:361 | Kink-turn with non-sequential stacking Not in a motif group | homologous IL_4V88_402 IL_45067.3 | |
| IL_3J7A_017 | 1/A/324:329, 1/A/351:352 | No text annotation Not in a motif group | geometric IL_5Y58_001 IL_48100.2 | |
| IL_3J7A_018 | 1/A/369:371, 1/A/382:387 | No text annotation Not in a motif group | homologous IL_4V88_404 IL_11347.1 | |
| IL_3J7A_019 | 1/A/395:397, 1/A/412:414 | Isolated cWH basepair Not in a motif group | homologous IL_4V88_405 IL_70707.3 | |
| IL_3J7A_020 | 1/A/417:419, 1/A/426:428 | Isolated near basepair Not in a motif group | homologous IL_4V88_406 IL_52767.5 | |
| IL_3J7A_021 | 1/A/445:447, 1/A/469:470 | Single bulged U Not in a motif group | homologous IL_4V88_407 IL_83039.17 | |
| IL_3J7A_022 | 1/A/449:454, 1/A/464:467 | C-loop with extra cWW pair Not in a motif group | homologous IL_4V88_408 IL_93630.2 | |
| IL_3J7A_023 | 1/A/521:524, 1/A/542:550 | No text annotation Not in a motif group | ||
| IL_3J7A_024 | 1/A/557:564, 1/A/594:595 | SSU/LSU pseudoknot Not in a motif group | homologous IL_4V88_413 IL_15861.8 | |
| IL_3J7A_025 | 1/A/564:566, 1/A/593:594 | Single bulged U Not in a motif group | geometric IL_4V88_407 IL_83039.17 | |
| IL_3J7A_026 | 1/A/569:575, 1/A/582:590 | No text annotation Not in a motif group | homologous IL_4V88_415 IL_55871.1 | |
| IL_3J7A_027 | 1/A/623:629, 1/A/1205:1206 | No text annotation Not in a motif group | homologous IL_4V88_416 IL_38186.1 | |
| IL_3J7A_028 | 1/A/631:633, 1/A/1042:1044 | No text annotation Not in a motif group | homologous IL_4V88_417 IL_86319.3 | |
| IL_3J7A_029 | 1/A/634:638, 1/A/1037:1041 | tSH-tHW-tHS Not in a motif group | homologous IL_4V88_418 IL_17136.2 | |
| IL_3J7A_031 | 1/A/796:797, 1/A/865:868 | Minor groove platform Not in a motif group | geometric IL_7RQB_073 NA | |
| IL_3J7A_032 | 1/A/798:800, 1/A/862:864 | No text annotation Not in a motif group | homologous IL_4V88_424 IL_86319.3 | |
| IL_3J7A_033 | 1/A/801:809, 1/A/854:861 | No text annotation Not in a motif group | homologous IL_4V88_425 IL_69091.1 | |
| IL_3J7A_034 | 1/A/827:835, 1/A/845:846 | No text annotation Not in a motif group | ||
| IL_3J7A_035 | 1/A/877:880, 1/A/922:926 | No text annotation Not in a motif group | ||
| IL_3J7A_036 | 1/A/881:883, 1/A/919:921 | No text annotation Not in a motif group | geometric IL_5TBW_008 IL_86319.3 | |
| IL_3J7A_037 | 1/A/883:886, 1/A/916:919 | Tandem non-canonical cWW pairs Not in a motif group | geometric IL_1D4R_001 IL_30621.4 | |
| IL_3J7A_038 | 1/A/886:888, 1/A/914:916 | No text annotation Not in a motif group | geometric IL_5UNE_001 IL_76273.2 | |
| IL_3J7A_039 | 1/A/890:892, 1/A/910:912 | No text annotation Not in a motif group | geometric IL_6OL3_002 IL_86319.3 | |
| IL_3J7A_040 | 1/A/933:934, 1/A/1031:1034 | Major groove platform; stack outside cWW Not in a motif group | homologous IL_4V88_428 IL_50694.3 | |
| IL_3J7A_041 | 1/A/936:937, 1/A/1027:1029 | Single bulged U Not in a motif group | geometric IL_6UFH_004 IL_83039.17 | |
| IL_3J7A_042 | 1/A/939:942, 1/A/1023:1025 | No text annotation Not in a motif group | geometric IL_5MSF_001 IL_86319.3 | |
| IL_3J7A_043 | 1/A/943:946, 1/A/1020:1022 | Isolated non-canonical cWW with bulges Not in a motif group | geometric IL_3TD0_005 IL_43275.2 | |
| IL_3J7A_044 | 1/A/954:957, 1/A/993:996 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_4V88_432 IL_30621.4 | |
| IL_3J7A_045 | 1/A/962:968, 1/A/979:988 | No text annotation Not in a motif group | homologous IL_8C3A_440 IL_22252.1 | |
| IL_3J7A_046 | 1/A/1054:1058, 1/A/1084:1085 | Left turn Not in a motif group | geometric IL_5J7L_036 IL_29346.1 | |
| IL_3J7A_047 | 1/A/1059:1063, 1/A/1079:1083 | tSH-tHW-tHS Not in a motif group | homologous IL_4V88_436 IL_17136.2 | |
| IL_3J7A_048 | 1/A/1103:1105, 1/A/1196:1202 | No text annotation Not in a motif group | homologous IL_4V88_437 IL_19557.3 | |
| IL_3J7A_049 | 1/A/1117:1119, 1/A/1169:1171 | No text annotation Not in a motif group | geometric IL_3SZX_002 IL_86319.3 | |
| IL_3J7A_050 | 1/A/1212:1219, 1/A/1230:1235 | 8x6 Sarcin-Ricin with inserted Y; G-bulge Not in a motif group | homologous IL_4V88_440 IL_24606.2 | |
| IL_3J7A_051 | 1/A/1247:1248, 1/A/1927:1929 | Single bulged A Not in a motif group | homologous IL_4V88_441 IL_37497.7 | |
| IL_3J7A_052 | 1/A/1250:1252, 1/A/1924:1925 | Single bulged G Not in a motif group | homologous IL_4V88_442 IL_00225.4 | |
| IL_3J7A_053 | 1/A/1258:1261, 1/A/1914:1918 | C-loop Not in a motif group | homologous IL_4V88_443 IL_63596.7 | |
| IL_3J7A_054 | 1/A/1274:1276, 1/A/1710:1712 | No text annotation Not in a motif group | homologous IL_4V88_444 IL_86319.3 | |
| IL_3J7A_055 | 1/A/1279:1280, 1/A/1705:1707 | Minor groove platform Not in a motif group | homologous IL_4V88_445 IL_42622.5 | |
| IL_3J7A_056 | 1/A/1369:1371, 1/A/1686:1687 | Single bulged U Not in a motif group | homologous IL_4V88_449 IL_83039.17 | |
| IL_3J7A_057 | 1/A/1373:1377, 1/A/1682:1684 | Isolated cWS basepair Not in a motif group | geometric IL_4LFB_044 IL_76319.2 | |
| IL_3J7A_058 | 1/A/1377:1379, 1/A/1676:1682 | Minor groove platform with extra cWW Not in a motif group | homologous IL_4V88_451 IL_92788.3 | |
| IL_3J7A_059 | 1/A/1381:1382, 1/A/1672:1674 | Single bulged A Not in a motif group | homologous IL_4V88_452 IL_37497.7 | |
| IL_3J7A_060 | 1/A/1408:1410, 1/A/1419:1420 | Minor groove platform Not in a motif group | homologous IL_4V88_454 IL_80097.2 | |
| IL_3J7A_061 | 1/A/1440:1445, 1/A/1628:1632 | No text annotation Not in a motif group | ||
| IL_3J7A_062 | 1/A/1447:1450, 1/A/1623:1626 | No text annotation Not in a motif group | ||
| IL_3J7A_063 | 1/A/1451:1454, 1/A/1609:1622 | No text annotation Not in a motif group | ||
| IL_3J7A_064 | 1/A/1455:1458, 1/A/1605:1608 | No text annotation Not in a motif group | ||
| IL_3J7A_065 | 1/A/1635:1637, 1/A/1653:1658 | No text annotation Not in a motif group | homologous IL_8C3A_465 IL_58032.1 | |
| IL_3J7A_066 | 1/A/1743:1745, 1/A/1784:1786 | No text annotation Not in a motif group | geometric IL_5CCB_001 IL_86319.3 | |
| IL_3J7A_067 | 1/A/1791:1794, 1/A/1805:1808 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_4V88_461 IL_30621.4 | |
| IL_3J7A_068 | 1/A/1837:1842, 1/A/1863:1868 | No text annotation Not in a motif group | geometric IL_4V88_462 IL_19954.2 | |
| IL_3J7A_070 | 1/A/1933:1935, 1/A/2056:2059 | No text annotation Not in a motif group | geometric IL_5J7L_058 IL_36143.3 | |
| IL_3J7A_071 | 1/A/1935:1938, 1/A/2052:2056 | No text annotation Not in a motif group | homologous IL_4V88_464 IL_99670.1 | |
| IL_3J7A_072 | 1/A/1939:1941, 1/A/2049:2051 | No text annotation Not in a motif group | geometric IL_4V88_465 IL_86319.3 | |
| IL_3J7A_073 | 1/A/1941:1943, 1/A/2046:2049 | Isolated non-canonical cWW with bulges Not in a motif group | geometric IL_5J7L_009 IL_43275.2 | |
| IL_3J7A_074 | 1/A/1947:1949, 1/A/2040:2042 | AA cWW Not in a motif group | homologous IL_4V88_467 IL_86319.3 | |
| IL_3J7A_075 | 1/A/1950:1953, 1/A/2036:2039 | Double sheared Not in a motif group | homologous IL_4V88_468 IL_09705.11 | |
| IL_3J7A_076 | 1/A/1953:1955, 1/A/2035:2036 | Single bulged U Not in a motif group | geometric IL_4V88_469 IL_83039.17 | |
| IL_3J7A_077 | 1/A/1962:1964, 1/A/2026:2028 | No text annotation Not in a motif group | homologous IL_4V88_470 IL_70707.3 | |
| IL_3J7A_078 | 1/A/1966:1969, 1/A/2021:2024 | Double sheared Not in a motif group | homologous IL_4V88_471 IL_09705.11 | |
| IL_3J7A_079 | 1/A/1970:1972, 1/A/2018:2020 | No text annotation Not in a motif group | geometric IL_7A0S_107 IL_70707.3 | |
| IL_3J7A_080 | 1/A/1975:1979, 1/A/2011:2015 | Triple sheared Not in a motif group | homologous IL_4V88_474 IL_56467.9 | |
| IL_3J7A_081 | 1/A/1979:1983, 1/A/2007:2011 | No text annotation Not in a motif group | geometric IL_5TBW_121 IL_05145.3 | |
| IL_3J7A_082 | 1/A/1983:1984, 1/A/2005:2007 | Single stack bend Not in a motif group | geometric IL_4LFB_041 IL_76488.5 | |
| IL_3J7A_083 | 1/7/25:27, 1/7/40:42 | No text annotation Not in a motif group | geometric IL_4ZC7_001 IL_86319.3 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_3J7A_007 | No text annotation | ||
| IL_3J7A_012 | No text annotation | ||
| IL_3J7A_013 | No text annotation | ||
| IL_3J7A_030 | Tandem non-canonical cWW pairs | ||
| IL_3J7A_069 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_3J7A_001 | 1/A/810:813, 1/A/823:825, 1/A/848:853 | No text annotation Not in a motif group | homologous J3_4V88_032 NA | |
| J3_3J7A_002 | 1/A/950:953, 1/A/997:1005, 1/A/1012:1016 | No text annotation Not in a motif group | homologous J3_4V88_033 NA | |
| J3_3J7A_003 | 1/A/1106:1108, 1/A/1180:1184, 1/A/1191:1195 | No text annotation Not in a motif group | ||
| J3_3J7A_004 | 1/A/1262:1265, 1/A/1878:1884, 1/A/1906:1913 | No text annotation Not in a motif group | homologous J3_4V88_035 NA | |
| J3_3J7A_005 | 1/A/1269:1272, 1/A/1714:1716, 1/A/1871:1874 | No text annotation Not in a motif group | homologous J3_4V88_036 NA | |
| J3_3J7A_006 | 1/A/1281:1288, 1/A/1299:1310, 1/A/1700:1704 | No text annotation Not in a motif group | ||
| J3_3J7A_007 | 1/A/1316:1321, 1/A/1364:1368, 1/A/1688:1694 | No text annotation Not in a motif group | homologous J3_4V88_038 NA | |
| J3_3J7A_008 | 1/A/1384:1389, 1/A/1429:1435, 1/A/1664:1670 | No text annotation Not in a motif group | ||
| J3_3J7A_009 | 1/A/1438:1440, 1/A/1632:1635, 1/A/1658:1661 | No text annotation Not in a motif group | homologous J3_4V88_040 NA | |
| J3_3J7A_010 | 1/A/1716:1720, 1/A/1830:1837, 1/A/1868:1871 | No text annotation Not in a motif group | homologous J3_4V88_041 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_3J7A_011 | No text annotation |
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