RNA 3D Hub //

8UQP Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_8UQP_0071/D/12:22No text annotation
homologous
HL_4LFB_001
HL_73535.1
HL_8UQP_0231/D/786:796No text annotation
homologous
HL_5J7L_017
NA
HL_8UQP_0301/D/1076:1081GNRA
homologous
HL_5J7L_023
NA
HL_8UQP_0551/a/566:575T-loop with 2 stacked bulged bases
homologous
HL_5J7L_150
NA
HL_8UQP_0611/a/779:785No text annotation
homologous
HL_5J7L_156
NA
HL_8UQP_0711/a/1324:1330Pseudoknot geometry with 3' bulge
homologous
HL_5J7L_166
NA
HL_8UQP_0831/a/1777:1787No text annotation
homologous
HL_5J7L_178
NA
HL_8UQP_0871/a/1949:1957No text annotation
homologous
HL_5J7L_182
NA
HL_8UQP_1011/a/2594:2599GNRA
homologous
HL_5J7L_196
NA

Problematic loops

#loop idProblemSequence
HL_8UQP_001No text annotation
HL_8UQP_002tRNA anticodon loop
HL_8UQP_003No text annotation
HL_8UQP_004No text annotation
HL_8UQP_005tRNA anticodon loop
HL_8UQP_006No text annotation
HL_8UQP_008No text annotation
HL_8UQP_009GNRA
HL_8UQP_010GNRA
HL_8UQP_110No text annotation
HL_8UQP_011UNCG
HL_8UQP_012GNRA related
HL_8UQP_013GNRA
HL_8UQP_014No text annotation
HL_8UQP_015UNCG
HL_8UQP_016GNRA
HL_8UQP_017UNCG
HL_8UQP_018GNRA wlth extra near cWW
HL_8UQP_019tRNA D-loop
HL_8UQP_020GNRA-like with tWH
HL_8UQP_021No text annotation
HL_8UQP_022GNRA
HL_8UQP_024No text annotation
HL_8UQP_025GNRA
HL_8UQP_026GNRA
HL_8UQP_027No text annotation
HL_8UQP_028GNRA
HL_8UQP_029No text annotation
HL_8UQP_031T-loop related
HL_8UQP_111No text annotation
HL_8UQP_032No text annotation
HL_8UQP_033GNRA
HL_8UQP_034GNRA
HL_8UQP_035T-loop with 3 stacked bulged bases
HL_8UQP_036No text annotation
HL_8UQP_037UNCG
HL_8UQP_038GNRA
HL_8UQP_039No text annotation
HL_8UQP_040No text annotation
HL_8UQP_041No text annotation
HL_8UQP_042UNCG
HL_8UQP_043No text annotation
HL_8UQP_044No text annotation
HL_8UQP_045No text annotation
HL_8UQP_046No text annotation
HL_8UQP_047T-loop with 2 stacked bulged bases
HL_8UQP_048No text annotation
HL_8UQP_049T-loop with unstacked turn
HL_8UQP_050No text annotation
HL_8UQP_051Pseudoknot geometry
HL_8UQP_052GNRA
HL_8UQP_053GNRA
HL_8UQP_054No text annotation
HL_8UQP_056No text annotation
HL_8UQP_057GNRA
HL_8UQP_058No text annotation
HL_8UQP_059GNRA wlth tandem sheared
HL_8UQP_060No text annotation
HL_8UQP_062No text annotation
HL_8UQP_112No text annotation
HL_8UQP_063No text annotation
HL_8UQP_064No text annotation
HL_8UQP_065No text annotation
HL_8UQP_066No text annotation
HL_8UQP_067GNRA wlth tandem sheared
HL_8UQP_068No text annotation
HL_8UQP_069GNRA
HL_8UQP_070T-loop with 2 stacked bulged bases
HL_8UQP_072GNRA
HL_8UQP_073No text annotation
HL_8UQP_074Mini UNCG with extended bulge
HL_8UQP_075Pseudoknot geometry with 3' bulge
HL_8UQP_076UNCG
HL_8UQP_077Mini UNCG
HL_8UQP_078No text annotation
HL_8UQP_079GNRA
HL_8UQP_080UNCG
HL_8UQP_113No text annotation
HL_8UQP_081No text annotation
HL_8UQP_082No text annotation
HL_8UQP_084GNRA related
HL_8UQP_085GNRA variation
HL_8UQP_086No text annotation
HL_8UQP_088No text annotation
HL_8UQP_089No text annotation
HL_8UQP_090No text annotation
HL_8UQP_091No text annotation
HL_8UQP_092No text annotation
HL_8UQP_093No text annotation
HL_8UQP_116No text annotation
HL_8UQP_094Pseudoknot geometry
HL_8UQP_095GNRA
HL_8UQP_096GNRA
HL_8UQP_097No text annotation
HL_8UQP_098No text annotation
HL_8UQP_099GNRA variation
HL_8UQP_100No text annotation
HL_8UQP_102GNRA
HL_8UQP_103Ribsomal LSU H95
HL_8UQP_104No text annotation
HL_8UQP_105No text annotation
HL_8UQP_114UNCG variation
HL_8UQP_106No text annotation
HL_8UQP_107GNRA
HL_8UQP_115No text annotation
HL_8UQP_108No text annotation
HL_8UQP_109Mini UNCG

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_8UQP_0011/D/30:32,
1/D/552:553		Single bulged G
homologous
IL_5J7L_001
NA
IL_8UQP_0141/D/242:247,
1/D/277:284		Kink-turn with non-sequential stacking
homologous
IL_5J7L_014
NA
IL_8UQP_0161/D/292:293,
1/D/304:308		C-loop
homologous
IL_4LFB_013
IL_06671.1
IL_8UQP_0241/D/504:511,
1/D/540:541		SSU/LSU pseudoknot
homologous
IL_5J7L_024
NA
IL_8UQP_0261/D/569:575,
1/D/880:881		No text annotation
homologous
IL_5J7L_026
NA
IL_8UQP_0381/D/887:894,
1/D/905:910		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_5J7L_038
NA
IL_8UQP_0391/D/922:923,
1/D/1393:1395		Single bulged A
homologous
IL_5J7L_039
NA
IL_8UQP_0411/D/933:935,
1/D/1380:1384		Minor groove platform
homologous
IL_5J7L_041
NA
IL_8UQP_0481/D/1052:1056,
1/D/1204:1206		Isolated cWS basepair
geometric
IL_4LFB_044
IL_82453.1
IL_8UQP_0501/D/1060:1061,
1/D/1195:1197		Single bulged A
homologous
IL_5J7L_049
NA
IL_8UQP_0511/D/1061:1063,
1/D/1193:1195		Isolated non-canonical cWW pair
geometric
IL_5J7L_050
NA
IL_8UQP_0591/D/1399:1401,
1/D/1501:1504		No text annotation
homologous
IL_5J7L_058
NA
IL_8UQP_0621/D/1412:1414,
1/D/1486:1488		Isolated non-canonical cWW pair
homologous
IL_5J7L_061
NA
IL_8UQP_0631/D/1416:1419,
1/D/1481:1484		Double sheared
homologous
IL_5J7L_062
NA
IL_8UQP_0791/a/564:566,
1/a/575:577		Isolated non-canonical cWW pair
geometric
IL_5J7L_257
NA
IL_8UQP_0821/a/674:678,
1/a/799:806		tHW-tHW cross-strand stack
geometric
IL_7RQB_018
NA
IL_8UQP_0861/a/738:740,
1/a/757:758		Major groove platform
homologous
IL_5J7L_264
NA
IL_8UQP_0871/a/775:777,
1/a/787:791		Multiple bulged bases
homologous
IL_5J7L_265
NA
IL_8UQP_1011/a/1004:1011,
1/a/1150:1151		SSU/LSU pseudoknot
homologous
IL_5J7L_278
NA
IL_8UQP_1141/a/1262:1269,
1/a/2011:2017		8x7 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_289
NA
IL_8UQP_1321/a/1651:1656,
1/a/2004:2006		No text annotation
homologous
IL_5J7L_304
NA
IL_8UQP_1331/a/1663:1665,
1/a/1995:1997		Isolated tWW turn
homologous
IL_4WF9_063
IL_10432.1
IL_8UQP_1341/a/1666:1669,
1/a/1993:1994		Major groove platform; stack outside cWW
geometric
IL_5J7L_306
NA
IL_8UQP_2061/a/1666:1674,
1/a/1990:1994		No text annotation
homologous
IL_5J7L_386
NA
IL_8UQP_1351/a/1669:1674,
1/a/1990:1993		Intercalated tWH
homologous
IL_5J7L_307
NA
IL_8UQP_1471/a/1933:1934,
1/a/1964:1967		Bulged stacked bases
geometric
IL_5J7L_318
NA
IL_8UQP_1491/a/2050:2052,
1/a/2617:2618		Major groove platform
homologous
IL_5J7L_320
NA
IL_8UQP_1501/a/2054:2056,
1/a/2612:2615		No text annotation
homologous
IL_5J7L_321
NA
IL_8UQP_1531/a/2070:2071,
1/a/2438:2441		Minor groove platform
homologous
IL_5J7L_324
NA
IL_8UQP_1701/a/2459:2461,
1/a/2489:2493		Major groove minor groove platform with extra cWW
homologous
IL_7A0S_086
IL_36931.2
IL_8UQP_1731/a/2510:2512,
1/a/2574:2578		Isolated non-canonical cWW with bulges
homologous
IL_5J7L_340
NA
IL_8UQP_1741/a/2512:2513,
1/a/2571:2574		No text annotation
geometric
IL_5J7L_341
NA
IL_8UQP_1751/a/2522:2523,
1/a/2540:2543		Major groove platform with intercalation
homologous
IL_7A0S_091
IL_94991.2
IL_8UQP_1771/a/2591:2592,
1/a/2601:2603		Single bulged A
homologous
IL_7RQB_101
NA
IL_8UQP_1801/a/2680:2684,
1/a/2725:2727		C-loop
homologous
IL_7RQB_104
NA
IL_8UQP_1811/a/2687:2691,
1/a/2718:2722		UAA/GAN related, with intercalation
homologous
IL_5J7L_348
NA

Problematic loops

#loop idProblemSequence
IL_8UQP_193No text annotation
IL_8UQP_194No text annotation
IL_8UQP_195No text annotation
IL_8UQP_196No text annotation
IL_8UQP_197No text annotation
IL_8UQP_198No text annotation
IL_8UQP_002Single bulged A
IL_8UQP_003No text annotation
IL_8UQP_004Minor groove platform
IL_8UQP_005Multiple bulged bases
IL_8UQP_006Minor groove platform with extra cWW
IL_8UQP_007Minor groove platform
IL_8UQP_199Single bulged G
IL_8UQP_008Single bulged G, near cWW
IL_8UQP_009Isolated non-canonical cWW pair
IL_8UQP_010Minor groove platform related
IL_8UQP_011Isolated cWH basepair
IL_8UQP_200No text annotation
IL_8UQP_012tWH-tWH-tHW-tHW
IL_8UQP_013No text annotation
IL_8UQP_015No text annotation
IL_8UQP_017Single bulged U
IL_8UQP_018C-loop
IL_8UQP_019Single bulged G
IL_8UQP_020No text annotation
IL_8UQP_021No text annotation
IL_8UQP_022tSH-tHW-tWW
IL_8UQP_023No text annotation
IL_8UQP_025Kink-turn related
IL_8UQP_027tSH-tHW-tHS
IL_8UQP_028Major groove platform
IL_8UQP_029Major groove minor groove platform; mini C-loop
IL_8UQP_030No text annotation
IL_8UQP_031Major groove platform; stack outside cWW
IL_8UQP_032Single stack bend
IL_8UQP_033Tandem non-canonical cWW pairs
IL_8UQP_201Triple non-canonical cWW pairs
IL_8UQP_034No text annotation
IL_8UQP_035Kink-turn
IL_8UQP_036Left turn
IL_8UQP_037tSH-tHW-tHS
IL_8UQP_040Single bulged G
IL_8UQP_042No text annotation
IL_8UQP_043Minor groove platform
IL_8UQP_208Single stack bend
IL_8UQP_044No text annotation
IL_8UQP_202No text annotation
IL_8UQP_045Tandem non-canonical cWW pairs
IL_8UQP_046Single bulged U
IL_8UQP_047No text annotation
IL_8UQP_049Minor groove platform
IL_8UQP_052No text annotation
IL_8UQP_053Minor groove platform
IL_8UQP_054No text annotation
IL_8UQP_055No text annotation
IL_8UQP_056180 degree turn
IL_8UQP_057Double sheared with non-canonical cWW
IL_8UQP_058No text annotation
IL_8UQP_060No text annotation
IL_8UQP_061Partly complementary
IL_8UQP_064Triple sheared related
IL_8UQP_065Single bulged A
IL_8UQP_066No text annotation
IL_8UQP_067Triple sheared with non-canonical cWW
IL_8UQP_068Single bulged A
IL_8UQP_069Minor groove platform
IL_8UQP_070No text annotation
IL_8UQP_071Single stack bend
IL_8UQP_0728x7 Sarcin-Ricin; G-bulge
IL_8UQP_0737x6 Sarcin-Ricin; G-bulge
IL_8UQP_074No text annotation
IL_8UQP_075No text annotation
IL_8UQP_076No text annotation
IL_8UQP_077No text annotation
IL_8UQP_078Double sheared
IL_8UQP_080AAA cross-strand stack
IL_8UQP_081No text annotation
IL_8UQP_083Single bulged A
IL_8UQP_084Single bulged G
IL_8UQP_085Triple sheared
IL_8UQP_088Single stack bend
IL_8UQP_08990 degree turn
IL_8UQP_203No text annotation
IL_8UQP_090Stack outside cWW
IL_8UQP_091Single stack bend
IL_8UQP_0927x7 Sarcin-Ricin with intercalated A; G-bulge
IL_8UQP_093Single bulged G
IL_8UQP_094C-loop with bulged stacked A's
IL_8UQP_095Isolated non-canonical cWW pair
IL_8UQP_096Double sheared with non-canonical cWW
IL_8UQP_204No text annotation
IL_8UQP_209Single bulged A
IL_8UQP_097Tandem non-canonical cWW pairs
IL_8UQP_098Single stack bend
IL_8UQP_099Single bulged C
IL_8UQP_100UAA/GAN
IL_8UQP_102Single bulged U
IL_8UQP_103Kink-turn related
IL_8UQP_104No text annotation
IL_8UQP_105Isolated non-canonical cWW pair
IL_8UQP_106Tandem non-canonical cWW pairs
IL_8UQP_210No text annotation
IL_8UQP_107No text annotation
IL_8UQP_108No text annotation
IL_8UQP_109Major groove platform
IL_8UQP_110Tandem non-canonical cWW pairs
IL_8UQP_111Isolated cWS basepair
IL_8UQP_112No text annotation
IL_8UQP_113Kink-turn
IL_8UQP_115Major groove platform; stack outside cWW
IL_8UQP_116C-loop
IL_8UQP_117UAA/GAN
IL_8UQP_118tSH-tHW-tHS
IL_8UQP_119No text annotation
IL_8UQP_120Single stack bend
IL_8UQP_121Single stack bend
IL_8UQP_205No text annotation
IL_8UQP_122No text annotation
IL_8UQP_123UAA/GAN
IL_8UQP_124Tandem non-canonical cWW pairs
IL_8UQP_125tSH-tHW
IL_8UQP_126Single bulged U
IL_8UQP_127No text annotation
IL_8UQP_128tSH-tHW-tHS
IL_8UQP_129180 degree turn
IL_8UQP_130Single bulged A
IL_8UQP_131UAA/GAN variation
IL_8UQP_136tSH-tSH-tHH-tHS
IL_8UQP_1376x5 Sarcin-Ricin; G-bulge
IL_8UQP_138Triple sheared
IL_8UQP_139Single bulged C
IL_8UQP_140Single bulged A
IL_8UQP_141Kink-turn related
IL_8UQP_142Minor groove platform, major groove intercalation
IL_8UQP_143Major groove intercalation
IL_8UQP_144Major groove minor groove platform; mini C-loop
IL_8UQP_207No text annotation
IL_8UQP_145UAA/GAN related
IL_8UQP_146Intercalated cWW
IL_8UQP_148No text annotation
IL_8UQP_151No text annotation
IL_8UQP_152Decoding loop related
IL_8UQP_154Isolated tHS basepair with bulges
IL_8UQP_155Isolated non-canonical cWW pair
IL_8UQP_156Tandem non-canonical cWW pairs
IL_8UQP_157Isolated cWH basepair
IL_8UQP_158Isolated non-canonical cWW pair
IL_8UQP_159Tandem non-canonical cWW pairs
IL_8UQP_160Isolated non-canonical cWW pair
IL_8UQP_161Isolated non-canonical cWW pair
IL_8UQP_162No text annotation
IL_8UQP_163Isolated non-canonical cWW pair
IL_8UQP_164Kink-turn
IL_8UQP_165Single bulged U
IL_8UQP_166Double sheared
IL_8UQP_167No text annotation
IL_8UQP_168No text annotation
IL_8UQP_169No text annotation
IL_8UQP_171Double sheared with non-canonical cWW
IL_8UQP_172No text annotation
IL_8UQP_176No text annotation
IL_8UQP_178tSH-tHS-tHW
IL_8UQP_179Sarcin-Ricin target in LSU H95; G-bulge
IL_8UQP_182Multiple bulged bases
IL_8UQP_183UAA/GAN with extra cWW
IL_8UQP_184No text annotation
IL_8UQP_185Major groove intercalation
IL_8UQP_186Multiple bulged bases with non-canonical cWW
IL_8UQP_187tHS double platform
IL_8UQP_188Major groove intercalation
IL_8UQP_189No text annotation
IL_8UQP_190Major groove minor groove platform; mini C-loop
IL_8UQP_191Symmetric double minor groove platform
IL_8UQP_192Bacterial 5S Loop E

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_8UQP_0071/D/1063:1068,
1/D/1107:1113,
1/D/1187:1193		No text annotation
homologous
J3_5J7L_008
NA
J3_8UQP_0101/a/683:689,
1/a/773:775,
1/a/791:794		No text annotation
homologous
J3_5J7L_038
NA
J3_8UQP_0111/a/698:700,
1/a/732:736,
1/a/760:763		No text annotation
homologous
J3_5J7L_039
NA
J3_8UQP_0141/a/1306:1309,
1/a/1605:1611,
1/a/1620:1622		No text annotation
homologous
J3_7A0S_007
J3_47341.1
J3_8UQP_0171/a/2517:2520,
1/a/2545:2547,
1/a/2561:2567		No text annotation
homologous
J3_5J7L_046
NA
J4_8UQP_0031/D/115:122,
1/D/239:240,
1/D/286:289,
1/D/311:312		No text annotation
homologous
J4_5J7L_001
NA
J4_8UQP_0051/D/575:577,
1/D/764:769,
1/D/810:821,
1/D/879:880		No text annotation
homologous
J4_5J7L_003
NA
J4_8UQP_0091/a/1270:1276,
1/a/1294:1295,
1/a/1645:1648,
1/a/2009:2010		No text annotation
homologous
J4_5J7L_021
NA
J4_8UQP_0151/a/2643:2646,
1/a/2674:2676,
1/a/2731:2735,
1/a/2769:2771		No text annotation
homologous
J4_5J7L_028
NA
J5_8UQP_0051/a/531:533,
1/a/560:564,
1/a/577:579,
1/a/1261:1262,
1/a/2017:2018		No text annotation
homologous
J5_5J7L_014
NA
J5_8UQP_0061/a/584:589,
1/a/668:671,
1/a/809:812,
1/a/1195:1196,
1/a/1250:1256		No text annotation
homologous
J5_5J7L_015
NA
J5_8UQP_0071/a/1674:1682,
1/a/1706:1707,
1/a/1751:1752,
1/a/1756:1764,
1/a/1988:1990		No text annotation
homologous
J5_5J7L_016
NA
J7_8UQP_0011/a/8:15,
1/a/525:531,
1/a/2018:2023,
1/a/2040:2043,
1/a/2625:2630,
1/a/2788:2789,
1/a/2894:2895		No text annotation

Problematic loops

#loop idProblemSequence
J3_8UQP_020No text annotation
J3_8UQP_021No text annotation
J3_8UQP_022No text annotation
J3_8UQP_023No text annotation
J3_8UQP_024No text annotation
J3_8UQP_001No text annotation
J3_8UQP_002No text annotation
J3_8UQP_003No text annotation
J3_8UQP_025No text annotation
J3_8UQP_004No text annotation
J3_8UQP_005No text annotation
J3_8UQP_026No text annotation
J3_8UQP_006No text annotation
J3_8UQP_027No text annotation
J3_8UQP_008No text annotation
J3_8UQP_028No text annotation
J3_8UQP_009No text annotation
J3_8UQP_029No text annotation
J3_8UQP_030No text annotation
J3_8UQP_031No text annotation
J3_8UQP_032No text annotation
J3_8UQP_033No text annotation
J3_8UQP_012No text annotation
J3_8UQP_013No text annotation
J3_8UQP_034No text annotation
J3_8UQP_035No text annotation
J3_8UQP_015Kink-turn 3-way junction
J3_8UQP_036No text annotation
J3_8UQP_016No text annotation
J3_8UQP_037No text annotation
J3_8UQP_018No text annotation
J3_8UQP_019No text annotation
J4_8UQP_001tRNA junction
J4_8UQP_002tRNA junction
J4_8UQP_004No text annotation
J4_8UQP_006No text annotation
J4_8UQP_007No text annotation
J4_8UQP_008No text annotation
J4_8UQP_010No text annotation
J4_8UQP_011No text annotation
J4_8UQP_012No text annotation
J4_8UQP_013No text annotation
J4_8UQP_014No text annotation
J5_8UQP_001No text annotation
J5_8UQP_002No text annotation
J5_8UQP_003No text annotation
J5_8UQP_004No text annotation
J6_8UQP_001No text annotation
J7_8UQP_002No text annotation

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