RNA 3D Hub //

3JBO Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_3JBO_0091/A/270:292UNCG variation
geometric
HL_2CZJ_007
NA
HL_3JBO_0241/A/1066:1076No text annotation
geometric
HL_5J7L_017
NA
HL_3JBO_0391/AA/38:45No text annotation
geometric
HL_4V9F_006
HL_48677.1
HL_3JBO_0411/AA/90:96No text annotation
homologous
HL_8C3A_003
NA
HL_3JBO_0461/AA/285:294No text annotation
homologous
HL_8C3A_008
NA
HL_3JBO_0501/AA/552:576No text annotation
HL_3JBO_0541/AA/764:775No text annotation
homologous
HL_5TBW_015
NA
HL_3JBO_0561/AA/835:859No text annotation
HL_3JBO_0571/AA/883:890UNCG variation
geometric
HL_2CZJ_007
NA
HL_3JBO_0751/AA/1912:1957No text annotation
geometric
HL_4V9F_003
HL_75660.6
HL_3JBO_0781/AA/2111:2118No text annotation
homologous
HL_5TBW_041
NA
HL_3JBO_0821/AA/2403:2407No text annotation
homologous
HL_8C3A_045
NA
HL_3JBO_1121/AA/2829:2926No text annotation
HL_3JBO_0921/AA/3012:3020No text annotation
HL_3JBO_0941/AA/3063:3071No text annotation
homologous
HL_8C3A_059
NA
HL_3JBO_1031/AA/3494:3509No text annotation
HL_3JBO_1091/AC/111:117No text annotation
geometric
HL_5TBW_075
NA

Problematic loops

#loop idProblemSequence
HL_3JBO_001No text annotation
HL_3JBO_002tRNA anticodon loop
HL_3JBO_003T-loop with 2 stacked bulged bases
HL_3JBO_004No text annotation
HL_3JBO_005No text annotation
HL_3JBO_006GNRA
HL_3JBO_007No text annotation
HL_3JBO_008T-loop with 2 stacked bulged bases
HL_3JBO_010GNRA related
HL_3JBO_011No text annotation
HL_3JBO_012No text annotation
HL_3JBO_013UNCG
HL_3JBO_014No text annotation
HL_3JBO_015No text annotation
HL_3JBO_016No text annotation
HL_3JBO_017GNRA variation
HL_3JBO_018No text annotation
HL_3JBO_019No text annotation
HL_3JBO_020No text annotation
HL_3JBO_021No text annotation
HL_3JBO_022No text annotation
HL_3JBO_023GNRA
HL_3JBO_025GNRA
HL_3JBO_026GNRA
HL_3JBO_027No text annotation
HL_3JBO_028Externally structured
HL_3JBO_029No text annotation
HL_3JBO_030T-loop related
HL_3JBO_031No text annotation
HL_3JBO_032UNCG variation
HL_3JBO_033No text annotation
HL_3JBO_034GNRA
HL_3JBO_035No text annotation
HL_3JBO_036No text annotation
HL_3JBO_037No text annotation
HL_3JBO_038No text annotation
HL_3JBO_040No text annotation
HL_3JBO_042No text annotation
HL_3JBO_043T-loop with 2 stacked bulged bases
HL_3JBO_044No text annotation
HL_3JBO_045T-loop with unstacked turn
HL_3JBO_047Pseudoknot geometry
HL_3JBO_048GNRA
HL_3JBO_049GNRA
HL_3JBO_111No text annotation
HL_3JBO_051No text annotation
HL_3JBO_052UNCG variation
HL_3JBO_053T-loop with 2 stacked bulged bases
HL_3JBO_055GNRA
HL_3JBO_058GNRA
HL_3JBO_059No text annotation
HL_3JBO_060No text annotation
HL_3JBO_061Externally structured
HL_3JBO_062No text annotation
HL_3JBO_063GNRA
HL_3JBO_064No text annotation
HL_3JBO_065No text annotation
HL_3JBO_066GNRA
HL_3JBO_067T-loop with 2 stacked bulged bases
HL_3JBO_068No text annotation
HL_3JBO_069GNRA variation
HL_3JBO_070No text annotation
HL_3JBO_071No text annotation
HL_3JBO_072GNRA
HL_3JBO_073No text annotation
HL_3JBO_074No text annotation
HL_3JBO_076No text annotation
HL_3JBO_077Mini UNCG
HL_3JBO_079GNRA
HL_3JBO_080UNCG
HL_3JBO_081No text annotation
HL_3JBO_083No text annotation
HL_3JBO_084GNRA
HL_3JBO_085GNRA with extra cWW
HL_3JBO_086No text annotation
HL_3JBO_087No text annotation
HL_3JBO_088No text annotation
HL_3JBO_089No text annotation
HL_3JBO_090No text annotation
HL_3JBO_091No text annotation
HL_3JBO_093Pseudoknot geometry
HL_3JBO_095No text annotation
HL_3JBO_096No text annotation
HL_3JBO_097No text annotation
HL_3JBO_098No text annotation
HL_3JBO_099No text annotation
HL_3JBO_100GNRA
HL_3JBO_101GNRA
HL_3JBO_102Ribsomal LSU H95
HL_3JBO_113No text annotation
HL_3JBO_104No text annotation
HL_3JBO_105No text annotation
HL_3JBO_114No text annotation
HL_3JBO_106No text annotation
HL_3JBO_107GNRA
HL_3JBO_115Pseudoknot with intercalation
HL_3JBO_108No text annotation
HL_3JBO_110No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_3JBO_2241/A/1373:1379,
1/A/1676:1684		No text annotation
homologous
IL_8P9A_439
IL_99893.1
IL_3JBO_0561/A/1377:1379,
1/A/1676:1682		Minor groove platform with extra cWW
geometric
IL_4V88_451
NA
IL_3JBO_1031/AA/758:762,
1/AA/777:794		No text annotation
IL_3JBO_1161/AA/1095:1104,
1/AA/1228:1233		No text annotation
IL_3JBO_1201/AA/1121:1126,
1/AA/1169:1172		C-loop with bulged stacked A's
homologous
IL_8C3A_043
NA
IL_3JBO_1251/AA/1198:1200,
1/AA/1208:1209		Single bulged A
geometric
IL_7RQB_048
NA
IL_3JBO_1301/AA/1315:1322,
1/AA/1442:1447		No text annotation
geometric
IL_5TBW_051
NA
IL_3JBO_1311/AA/1322:1333,
1/AA/1427:1442		No text annotation
geometric
IL_5TBW_052
NA
IL_3JBO_1331/AA/1475:1481,
1/AA/1499:1506		No text annotation
IL_3JBO_1341/AA/1525:1527,
1/AA/1577:1580		No text annotation
homologous
IL_8C3A_061
NA
IL_3JBO_1491/AA/1868:1874,
1/AA/1884:1890		Kink-turn
homologous
IL_5TBW_073
NA
IL_3JBO_1881/AA/3240:3241,
1/AA/3299:3302		Multiple bulged bases
geometric
IL_5TBW_109
NA
IL_3JBO_1921/AA/3360:3363,
1/AA/3375:3379		No text annotation
IL_3JBO_1981/AA/3448:3449,
1/AA/3462:3465		Multiple bulged bases
homologous
IL_5TBW_119
NA
IL_3JBO_1991/AA/3486:3491,
1/AA/3512:3517		UAA/GAN with extra cWW
geometric
IL_5J7L_350
NA
IL_3JBO_2001/AA/3554:3573,
1/AA/3674:3675		Multiple bulged bases
geometric
IL_1R3E_001
IL_44609.1
IL_3JBO_2081/AA/3716:3717,
1/AA/3773:3775		Single bulged A
geometric
IL_5TBW_123
NA

Problematic loops

#loop idProblemSequence
IL_3JBO_001Single bulged C
IL_3JBO_002Triple sheared related
IL_3JBO_003No text annotation
IL_3JBO_004Minor groove platform
IL_3JBO_005No text annotation
IL_3JBO_006No text annotation
IL_3JBO_007Tandem non-canonical cWW pairs
IL_3JBO_008Major groove intercalation
IL_3JBO_009UAA/GAN related
IL_3JBO_010tWH-tWH-tHW-tHW
IL_3JBO_011No text annotation
IL_3JBO_012Single bulged A
IL_3JBO_013Kink-turn with non-sequential stacking
IL_3JBO_014No text annotation
IL_3JBO_015No text annotation
IL_3JBO_016Isolated cWH basepair
IL_3JBO_017Isolated near basepair
IL_3JBO_018Single bulged U
IL_3JBO_238C-loop
IL_3JBO_019C-loop with extra cWW pair
IL_3JBO_239Single bulged G
IL_3JBO_240No text annotation
IL_3JBO_020No text annotation
IL_3JBO_021SSU/LSU pseudoknot
IL_3JBO_022Single bulged U
IL_3JBO_023Kink-turn related
IL_3JBO_024No text annotation
IL_3JBO_025Isolated non-canonical cWW pair
IL_3JBO_026tSH-tHW-tHS
IL_3JBO_027Isolated non-canonical cWW pair
IL_3JBO_028Tandem non-canonical cWW pairs
IL_3JBO_029Minor groove platform
IL_3JBO_030Isolated non-canonical cWW pair
IL_3JBO_031No text annotation
IL_3JBO_032No text annotation
IL_3JBO_033Single bulged A
IL_3JBO_034Isolated non-canonical cWW pair
IL_3JBO_035Tandem non-canonical cWW pairs
IL_3JBO_036Isolated non-canonical cWW contact
IL_3JBO_037Isolated non-canonical cWW pair
IL_3JBO_038Major groove platform; stack outside cWW
IL_3JBO_039Single bulged U
IL_3JBO_040Isolated non-canonical cWW pair
IL_3JBO_041Isolated non-canonical cWW pair
IL_3JBO_042Isolated non-canonical cWW pair
IL_3JBO_043Kink-turn related
IL_3JBO_044Left turn
IL_3JBO_045tSH-tHW-tHS
IL_3JBO_046No text annotation
IL_3JBO_047Isolated non-canonical cWW pair
IL_3JBO_0488x6 Sarcin-Ricin with inserted Y; G-bulge
IL_3JBO_049Single bulged A
IL_3JBO_050Single bulged G
IL_3JBO_051C-loop
IL_3JBO_052Isolated non-canonical cWW pair
IL_3JBO_053Minor groove platform
IL_3JBO_054Single bulged U
IL_3JBO_055Isolated cWS basepair
IL_3JBO_057Single bulged A
IL_3JBO_058Minor groove platform
IL_3JBO_059Isolated non-canonical cWW pair
IL_3JBO_060Minor groove platform
IL_3JBO_061Major groove platform; stack outside cWW
IL_3JBO_241No text annotation
IL_3JBO_225No text annotation
IL_3JBO_062Tandem non-canonical cWW pairs
IL_3JBO_063No text annotation
IL_3JBO_064No text annotation
IL_3JBO_065No text annotation
IL_3JBO_066Isolated non-canonical cWW pair
IL_3JBO_067No text annotation
IL_3JBO_068Isolated non-canonical cWW pair
IL_3JBO_069Double sheared
IL_3JBO_070Single bulged U
IL_3JBO_071Single stack bend
IL_3JBO_072Single stack bend
IL_3JBO_073Isolated non-canonical cWW pair
IL_3JBO_074Double sheared
IL_3JBO_075Isolated non-canonical cWW pair
IL_3JBO_076Triple sheared
IL_3JBO_077Tandem non-canonical cWW pairs
IL_3JBO_078Single stack bend
IL_3JBO_079Single bulged U
IL_3JBO_080tSH-tHW-tHH-tHS
IL_3JBO_0818x7 Sarcin-Ricin; G-bulge
IL_3JBO_082Multiple bulged bases
IL_3JBO_226No text annotation
IL_3JBO_083No text annotation
IL_3JBO_084Isolated non-canonical cWW pair
IL_3JBO_085Triple non-canonical cWW pairs
IL_3JBO_227No text annotation
IL_3JBO_086Tandem non-canonical cWW pairs
IL_3JBO_087No text annotation
IL_3JBO_088No text annotation
IL_3JBO_089No text annotation
IL_3JBO_228No text annotation
IL_3JBO_090Single bulged U
IL_3JBO_229Isolated cWH basepair
IL_3JBO_230Tandem non-canonical cWW pairs
IL_3JBO_091Single bulged A
IL_3JBO_092No text annotation
IL_3JBO_093Triple sheared with non-canonical cWW
IL_3JBO_094Isolated non-canonical cWW pair
IL_3JBO_095Tandem non-canonical cWW pairs
IL_3JBO_096No text annotation
IL_3JBO_242Tandem non-canonical cWW pairs
IL_3JBO_231Triple non-canonical cWW pairs
IL_3JBO_097Single stack bend
IL_3JBO_098No text annotation
IL_3JBO_099Single bulged C
IL_3JBO_100Stack outside cWW
IL_3JBO_101Tandem non-canonical cWW pairs
IL_3JBO_102No text annotation
IL_3JBO_104No text annotation
IL_3JBO_105Single bulged A
IL_3JBO_106Minor groove platform with extra cWW
IL_3JBO_243Minor groove platform
IL_3JBO_107Isolated non-canonical cWW pair
IL_3JBO_108tHW-tHW cross-strand stack
IL_3JBO_109Single bulged A
IL_3JBO_110Single bulged G
IL_3JBO_111Triple sheared
IL_3JBO_112Major groove platform with extra cWW
IL_3JBO_113Single bulged U
IL_3JBO_114Multiple bulged bases
IL_3JBO_115Single stack bend
IL_3JBO_117Single bulged G
IL_3JBO_1187x7 Sarcin-Ricin with intercalated A; G-bulge
IL_3JBO_119Minor groove platform
IL_3JBO_121Tandem non-canonical cWW pairs
IL_3JBO_122Isolated non-canonical cWW pair
IL_3JBO_232Tandem non-canonical cWW pairs
IL_3JBO_123Isolated non-canonical cWW pair
IL_3JBO_124Isolated non-canonical cWW pair
IL_3JBO_126Isolated non-canonical cWW pair
IL_3JBO_127UAA/GAN with extra cWW
IL_3JBO_128SSU/LSU pseudoknot
IL_3JBO_129Single bulged U
IL_3JBO_132Single bulged U
IL_3JBO_135No text annotation
IL_3JBO_136Kink-turn
IL_3JBO_137Single bulged U
IL_3JBO_1387x6 Sarcin-Ricin; G-bulge
IL_3JBO_139No text annotation
IL_3JBO_140UAA/GAN
IL_3JBO_141No text annotation
IL_3JBO_142Isolated non-canonical cWW pair
IL_3JBO_143Triple sheared
IL_3JBO_144Isolated non-canonical cWW pair
IL_3JBO_145Major groove platform
IL_3JBO_146Tandem non-canonical cWW pairs
IL_3JBO_147No text annotation
IL_3JBO_148Isolated non-canonical cWW pair
IL_3JBO_150Tandem non-canonical cWW pairs
IL_3JBO_151Tandem non-canonical cWW pairs
IL_3JBO_152Isolated non-canonical cWW pair
IL_3JBO_153Double sheared with non-canonical cWW
IL_3JBO_154No text annotation
IL_3JBO_155Isolated tWW turn
IL_3JBO_156Major groove platform; stack outside cWW
IL_3JBO_233No text annotation
IL_3JBO_157Intercalated tWH
IL_3JBO_158tSH-tSH-tHH-tHS
IL_3JBO_159Isolated non-canonical cWW pair
IL_3JBO_160No text annotation
IL_3JBO_161Single bulged A
IL_3JBO_162Kink-turn related
IL_3JBO_163Major groove intercalation
IL_3JBO_164Major groove intercalation
IL_3JBO_165Single stack bend
IL_3JBO_166No text annotation
IL_3JBO_167No text annotation
IL_3JBO_168Bulged stacked bases
IL_3JBO_169No text annotation
IL_3JBO_170Major groove platform with extra pair
IL_3JBO_171No text annotation
IL_3JBO_172Single bulged U
IL_3JBO_173Minor groove platform
IL_3JBO_174No text annotation
IL_3JBO_175Stack outside cWW
IL_3JBO_234Isolated non-canonical cWW with bulges
IL_3JBO_176Tandem non-canonical cWW pairs
IL_3JBO_177Single bulged A
IL_3JBO_178Isolated tHS basepair with bulges
IL_3JBO_179Isolated non-canonical cWW pair
IL_3JBO_235No text annotation
IL_3JBO_180No text annotation
IL_3JBO_181Major groove platform
IL_3JBO_182Isolated non-canonical cWW pair
IL_3JBO_183Major groove platform
IL_3JBO_184Major groove minor groove platform with extra cWW
IL_3JBO_185No text annotation
IL_3JBO_186Major groove platform
IL_3JBO_187Isolated non-canonical cWW with bulges
IL_3JBO_189Major groove platform with intercalation
IL_3JBO_190Isolated non-canonical cWW pair
IL_3JBO_191Single bulged A
IL_3JBO_193Double sheared
IL_3JBO_194Isolated non-canonical cWW pair
IL_3JBO_195Sarcin-Ricin target in LSU H95; G-bulge
IL_3JBO_196Major groove minor groove platform with tHH
IL_3JBO_197UAA/GAN related
IL_3JBO_201Single bulged A
IL_3JBO_202No text annotation
IL_3JBO_236No text annotation
IL_3JBO_203Single stack bend
IL_3JBO_204Tandem non-canonical cWW pairs
IL_3JBO_205No text annotation
IL_3JBO_206Tandem non-canonical cWW pairs
IL_3JBO_207Isolated non-canonical cWW pair
IL_3JBO_209Isolated non-canonical cWW pair
IL_3JBO_210No text annotation
IL_3JBO_211Single bulged U
IL_3JBO_212Double sheared; A in syn
IL_3JBO_213Single bulged A
IL_3JBO_214No text annotation
IL_3JBO_244No text annotation
IL_3JBO_237No text annotation
IL_3JBO_215No text annotation
IL_3JBO_216Major groove minor groove platform; mini C-loop
IL_3JBO_217Symmetric double minor groove platform
IL_3JBO_2188x7 Sarcin-Ricin; G-bulge
IL_3JBO_219Isolated cWH basepair
IL_3JBO_220No text annotation
IL_3JBO_221Isolated non-canonical cWW pair
IL_3JBO_222No text annotation
IL_3JBO_223No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_3JBO_0161/AA/446:454,
1/AA/501:506,
1/AA/692:701		No text annotation
J3_3JBO_0421/AA/446:455,
1/AA/500:506,
1/AA/692:701		No text annotation
J3_3JBO_0241/AA/1675:1680,
1/AA/1734:1738,
1/AA/1755:1756		No text annotation
homologous
J3_5TBW_010
NA
J3_3JBO_0451/AA/3575:3580,
1/AA/3621:3627,
1/AA/3658:3672		No text annotation
J5_3JBO_0151/A/643:648,
1/A/752:755,
1/A/792:793,
1/A/871:877,
1/A/926:928		No text annotation
J5_3JBO_0091/AA/753:756,
1/AA/796:800,
1/AA/807:823,
1/AA/872:873,
1/AA/902:906		No text annotation
J5_3JBO_0121/AA/2692:2699,
1/AA/3174:3182,
1/AA/3226:3235,
1/AA/3310:3316,
1/AA/3334:3339		No text annotation
J6_3JBO_0011/AA/23:28,
1/AA/56:68,
1/AA/75:79,
1/AA/106:110,
1/AA/329:338,
1/AC/37:38		No text annotation

Problematic loops

#loop idProblemSequence
J3_3JBO_001No text annotation
J3_3JBO_035No text annotation
J3_3JBO_002No text annotation
J3_3JBO_036No text annotation
J3_3JBO_003No text annotation
J3_3JBO_004No text annotation
J3_3JBO_005No text annotation
J3_3JBO_006No text annotation
J3_3JBO_007No text annotation
J3_3JBO_008No text annotation
J3_3JBO_009No text annotation
J3_3JBO_010No text annotation
J3_3JBO_011No text annotation
J3_3JBO_012No text annotation
J3_3JBO_037No text annotation
J3_3JBO_013No text annotation
J3_3JBO_038No text annotation
J3_3JBO_014No text annotation
J3_3JBO_039No text annotation
J3_3JBO_040No text annotation
J3_3JBO_015No text annotation
J3_3JBO_041No text annotation
J3_3JBO_017No text annotation
J3_3JBO_018No text annotation
J3_3JBO_043No text annotation
J3_3JBO_019No text annotation
J3_3JBO_020No text annotation
J3_3JBO_021No text annotation
J3_3JBO_022No text annotation
J3_3JBO_023No text annotation
J3_3JBO_025No text annotation
J3_3JBO_026No text annotation
J3_3JBO_027No text annotation
J3_3JBO_044No text annotation
J3_3JBO_028No text annotation
J3_3JBO_029No text annotation
J3_3JBO_030No text annotation
J3_3JBO_031No text annotation
J3_3JBO_032No text annotation
J3_3JBO_033No text annotation
J3_3JBO_034No text annotation
J3_3JBO_046No text annotation
J4_3JBO_001tRNA junction
J4_3JBO_002No text annotation
J4_3JBO_003No text annotation
J4_3JBO_004No text annotation
J4_3JBO_005No text annotation
J4_3JBO_006No text annotation
J4_3JBO_007No text annotation
J4_3JBO_008No text annotation
J4_3JBO_009No text annotation
J4_3JBO_010No text annotation
J4_3JBO_011No text annotation
J4_3JBO_012No text annotation
J5_3JBO_001No text annotation
J5_3JBO_014No text annotation
J5_3JBO_002No text annotation
J5_3JBO_003No text annotation
J5_3JBO_004No text annotation
J5_3JBO_005No text annotation
J5_3JBO_006No text annotation
J5_3JBO_007No text annotation
J5_3JBO_008No text annotation
J5_3JBO_010No text annotation
J5_3JBO_011No text annotation
J5_3JBO_013No text annotation
J6_3JBO_002No text annotation
J7_3JBO_001No text annotation

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