RNA 3D Hub //

5A9Z Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_5A9Z_0031/AA/123:128No text annotation
homologous
HL_4WF9_003
HL_75660.7
HL_5A9Z_0101/AA/305:312No text annotation
homologous
HL_7RQB_010
NA
HL_5A9Z_0181/AA/564:577No text annotation
HL_5A9Z_0231/AA/744:753No text annotation
homologous
HL_7A0S_022
HL_50204.1
HL_5A9Z_0251/AA/826:831No text annotation
homologous
HL_7A0S_024
HL_27530.1
HL_5A9Z_1041/AA/872:905No text annotation
HL_5A9Z_0261/AA/873:904No text annotation
HL_5A9Z_0281/AA/978:985No text annotation
homologous
HL_7RQB_028
NA
HL_5A9Z_0311/AA/1221:1228Externally structured
geometric
HL_8C3A_022
NA
HL_5A9Z_0351/AA/1389:1398No text annotation
homologous
HL_5J7L_168
NA
HL_5A9Z_0391/AA/1612:1619No text annotation
homologous
HL_4WF9_038
HL_28592.2
HL_5A9Z_0411/AA/1691:1696UNCG
homologous
HL_5J7L_175
NA
HL_5A9Z_0441/AA/1779:1785No text annotation
geometric
HL_2Y8W_001
HL_40612.1
HL_5A9Z_0481/AA/1950:1956Mini UNCG
geometric
HL_5T16_002
HL_12626.2
HL_5A9Z_0491/AA/2027:2036No text annotation
homologous
HL_7A0S_049
HL_78372.1
HL_5A9Z_0521/AA/2249:2255No text annotation
HL_5A9Z_0611/AA/2551:2557No text annotation
homologous
HL_4WF9_058
HL_48677.1
HL_5A9Z_0621/AA/2594:2599GNRA
homologous
HL_5J7L_196
NA
HL_5A9Z_0651/AA/2746:2758No text annotation
HL_5A9Z_0881/BA/862:867GNRA
homologous
HL_4LFB_019
HL_34789.4
HL_5A9Z_0891/BA/897:902GNRA
homologous
HL_4LFB_020
HL_34789.4

Problematic loops

#loop idProblemSequence
HL_5A9Z_001No text annotation
HL_5A9Z_002No text annotation
HL_5A9Z_004No text annotation
HL_5A9Z_005No text annotation
HL_5A9Z_006No text annotation
HL_5A9Z_007No text annotation
HL_5A9Z_008tRNA D-loop
HL_5A9Z_113No text annotation
HL_5A9Z_009No text annotation
HL_5A9Z_102No text annotation
HL_5A9Z_011No text annotation
HL_5A9Z_012T-loop with unstacked turn
HL_5A9Z_013No text annotation
HL_5A9Z_014No text annotation
HL_5A9Z_015GNRA
HL_5A9Z_016GNRA
HL_5A9Z_103No text annotation
HL_5A9Z_017No text annotation
HL_5A9Z_019No text annotation
HL_5A9Z_020GNRA
HL_5A9Z_021No text annotation
HL_5A9Z_022No text annotation
HL_5A9Z_024UNCG variation
HL_5A9Z_027GNRA
HL_5A9Z_105No text annotation
HL_5A9Z_029No text annotation
HL_5A9Z_030No text annotation
HL_5A9Z_032No text annotation
HL_5A9Z_033Pseudoknot geometry with 3' bulge
HL_5A9Z_034No text annotation
HL_5A9Z_114GNRA
HL_5A9Z_036No text annotation
HL_5A9Z_037No text annotation
HL_5A9Z_038UNCG
HL_5A9Z_115Pseudoknot geometry with 3' bulge
HL_5A9Z_040No text annotation
HL_5A9Z_042No text annotation
HL_5A9Z_043No text annotation
HL_5A9Z_045No text annotation
HL_5A9Z_046GNRA
HL_5A9Z_047No text annotation
HL_5A9Z_050No text annotation
HL_5A9Z_051No text annotation
HL_5A9Z_053No text annotation
HL_5A9Z_054No text annotation
HL_5A9Z_055Pseudoknot geometry
HL_5A9Z_056GNRA with extra cWW
HL_5A9Z_057GNRA
HL_5A9Z_058No text annotation
HL_5A9Z_059No text annotation
HL_5A9Z_060No text annotation
HL_5A9Z_106tRNA anticodon loop
HL_5A9Z_063No text annotation
HL_5A9Z_064No text annotation
HL_5A9Z_066No text annotation
HL_5A9Z_067GNRA
HL_5A9Z_107No text annotation
HL_5A9Z_068No text annotation
HL_5A9Z_069GNRA
HL_5A9Z_070No text annotation
HL_5A9Z_116No text annotation
HL_5A9Z_108No text annotation
HL_5A9Z_071No text annotation
HL_5A9Z_072GNRA
HL_5A9Z_073No text annotation
HL_5A9Z_109No text annotation
HL_5A9Z_074Mini UNCG
HL_5A9Z_075GNRA related
HL_5A9Z_076GNRA
HL_5A9Z_077No text annotation
HL_5A9Z_078UNCG
HL_5A9Z_079GNRA
HL_5A9Z_080UNCG
HL_5A9Z_081GNRA
HL_5A9Z_082No text annotation
HL_5A9Z_083No text annotation
HL_5A9Z_110No text annotation
HL_5A9Z_084No text annotation
HL_5A9Z_085GNRA
HL_5A9Z_086No text annotation
HL_5A9Z_087Mini UNCG
HL_5A9Z_090No text annotation
HL_5A9Z_091GNRA
HL_5A9Z_092No text annotation
HL_5A9Z_093GNRA
HL_5A9Z_094T-loop related
HL_5A9Z_095No text annotation
HL_5A9Z_111No text annotation
HL_5A9Z_096GNRA
HL_5A9Z_097No text annotation
HL_5A9Z_112No text annotation
HL_5A9Z_098T-loop with 3 stacked bulged bases
HL_5A9Z_099No text annotation
HL_5A9Z_100UNCG
HL_5A9Z_101GNRA

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_5A9Z_0061/AA/188:194,
1/AA/201:208		8x7 Sarcin-Ricin; G-bulge
homologous
IL_7RQB_006
NA
IL_5A9Z_0151/AA/672:674,
1/AA/806:808		Isolated non-canonical cWW pair
geometric
IL_8C3A_029
NA
IL_5A9Z_1671/AA/672:678,
1/AA/799:808		No text annotation
IL_5A9Z_0181/AA/703:707,
1/AA/724:729		Triple sheared
homologous
IL_7RQB_021
NA
IL_5A9Z_0401/AA/1208:1215,
1/AA/1234:1238		Kink-turn
homologous
IL_7RQB_047
NA
IL_5A9Z_1701/AA/1423:1429,
1/AA/1564:1575		No text annotation
IL_5A9Z_0571/AA/1686:1691,
1/AA/1696:1702		tSH-tSH-tHH-tHS
homologous
IL_4WF9_066
IL_20700.1
IL_5A9Z_0611/AA/1798:1804,
1/AA/1813:1821		Kink-turn related
homologous
IL_4WF9_069
IL_17069.6
IL_5A9Z_0621/AA/1836:1840,
1/AA/1902:1904		No text annotation
IL_5A9Z_0631/AA/1841:1842,
1/AA/1898:1901		Major groove intercalation
homologous
IL_4WF9_071
IL_71421.2
IL_5A9Z_0671/AA/1934:1945,
1/AA/1961:1964		No text annotation
homologous
IL_7A0S_072
IL_04332.3
IL_5A9Z_0691/AA/2054:2056,
1/AA/2612:2615		No text annotation
homologous
IL_4WF9_079
IL_80025.1
IL_5A9Z_0711/AA/2070:2071,
1/AA/2438:2441		Minor groove platform
homologous
IL_5J7L_324
NA
IL_5A9Z_0841/AA/2507:2508,
1/AA/2580:2582		Major groove platform
homologous
IL_7RQB_096
NA
IL_5A9Z_0861/AA/2512:2513,
1/AA/2571:2574		No text annotation
geometric
IL_5J7L_341
NA
IL_5A9Z_0881/AA/2591:2592,
1/AA/2601:2603		Single bulged A
homologous
IL_7RQB_101
NA
IL_5A9Z_0891/AA/2637:2640,
1/AA/2774:2781		No text annotation
IL_5A9Z_0931/AA/2695:2696,
1/AA/2711:2714		Multiple bulged bases
homologous
IL_7A0S_097
IL_44609.2
IL_5A9Z_1051/BA/30:32,
1/BA/552:553		Single bulged G
homologous
IL_5J7L_001
NA
IL_5A9Z_1451/BA/1057:1058,
1/BA/1199:1203		Minor groove platform
homologous
IL_6CZR_155
NA
IL_5A9Z_1571/BA/1405:1410,
1/BA/1490:1496		No text annotation
IL_5A9Z_1611/BA/1435:1437,
1/BA/1464:1466		Isolated non-canonical cWW pair
homologous
IL_6CZR_171
NA
IL_5A9Z_1781/BA/1437:1449,
1/BA/1454:1464		No text annotation

Problematic loops

#loop idProblemSequence
IL_5A9Z_001No text annotation
IL_5A9Z_002Single bulged A
IL_5A9Z_003Minor groove platform
IL_5A9Z_004Kink-turn
IL_5A9Z_005No text annotation
IL_5A9Z_0077x6 Sarcin-Ricin; G-bulge
IL_5A9Z_008Multiple bulged bases
IL_5A9Z_164No text annotation
IL_5A9Z_009No text annotation
IL_5A9Z_010Isolated non-canonical cWW pair
IL_5A9Z_179No text annotation
IL_5A9Z_165No text annotation
IL_5A9Z_011Isolated non-canonical cWW pair
IL_5A9Z_166No text annotation
IL_5A9Z_012No text annotation
IL_5A9Z_013No text annotation
IL_5A9Z_014Isolated non-canonical cWW pair
IL_5A9Z_016tHW-tHW cross-strand stack
IL_5A9Z_017Single bulged A
IL_5A9Z_019Major groove platform with extra cWW
IL_5A9Z_020Single stack bend
IL_5A9Z_021Intercalated cWW
IL_5A9Z_022No text annotation
IL_5A9Z_023No text annotation
IL_5A9Z_024No text annotation
IL_5A9Z_025Minor groove platform related
IL_5A9Z_026C-loop
IL_5A9Z_027Isolated cWS basepair
IL_5A9Z_028No text annotation
IL_5A9Z_029Single bulged C
IL_5A9Z_030UAA/GAN
IL_5A9Z_031SSU/LSU pseudoknot
IL_5A9Z_032Single bulged U
IL_5A9Z_033No text annotation
IL_5A9Z_034Isolated non-canonical cWW pair
IL_5A9Z_168No text annotation
IL_5A9Z_035No text annotation
IL_5A9Z_169No text annotation
IL_5A9Z_036No text annotation
IL_5A9Z_037No text annotation
IL_5A9Z_038Single bulged G
IL_5A9Z_180No text annotation
IL_5A9Z_039No text annotation
IL_5A9Z_041Intercalated cWW
IL_5A9Z_181C-loop
IL_5A9Z_042C-loop with extra cWW pair
IL_5A9Z_043UAA/GAN
IL_5A9Z_044tSH-tHW-tHS
IL_5A9Z_045No text annotation
IL_5A9Z_046Isolated non-canonical cWW pair
IL_5A9Z_047No text annotation
IL_5A9Z_048tSH-tHW
IL_5A9Z_049Single stack bend
IL_5A9Z_050No text annotation
IL_5A9Z_051No text annotation
IL_5A9Z_052No text annotation
IL_5A9Z_182Single bulged A
IL_5A9Z_053No text annotation
IL_5A9Z_054Isolated non-canonical cWW pair
IL_5A9Z_055No text annotation
IL_5A9Z_056No text annotation
IL_5A9Z_058No text annotation
IL_5A9Z_059Single bulged A
IL_5A9Z_060No text annotation
IL_5A9Z_064Major groove minor groove platform; mini C-loop
IL_5A9Z_065UAA/GAN with extra stack
IL_5A9Z_066Triple sheared
IL_5A9Z_068Major groove platform
IL_5A9Z_070Single bulged U
IL_5A9Z_072Isolated tHS basepair with bulges
IL_5A9Z_073No text annotation
IL_5A9Z_074Isolated non-canonical cWW pair
IL_5A9Z_075No text annotation
IL_5A9Z_076No text annotation
IL_5A9Z_077No text annotation
IL_5A9Z_078Isolated tHS basepair with bulges
IL_5A9Z_079Double sheared
IL_5A9Z_080Major groove platform
IL_5A9Z_081Major groove platform
IL_5A9Z_171No text annotation
IL_5A9Z_082No text annotation
IL_5A9Z_083Double sheared with non-canonical cWW
IL_5A9Z_085Isolated non-canonical cWW with bulges
IL_5A9Z_087No text annotation
IL_5A9Z_090Isolated non-canonical cWW pair
IL_5A9Z_091C-loop
IL_5A9Z_092No text annotation
IL_5A9Z_094Isolated non-canonical cWW pair
IL_5A9Z_095UAA/GAN with extra cWW
IL_5A9Z_096Single bulged C
IL_5A9Z_097No text annotation
IL_5A9Z_098No text annotation
IL_5A9Z_183tHS double platform
IL_5A9Z_099Isolated non-canonical cWW pair
IL_5A9Z_100Major groove intercalation
IL_5A9Z_101No text annotation
IL_5A9Z_184No text annotation
IL_5A9Z_102No text annotation
IL_5A9Z_103No text annotation
IL_5A9Z_104Bacterial 5S Loop E
IL_5A9Z_106Intercalated cWW
IL_5A9Z_107No text annotation
IL_5A9Z_108Minor groove platform
IL_5A9Z_109Multiple bulged bases
IL_5A9Z_110Isolated non-canonical cWW pair
IL_5A9Z_111Multiple bulged bases
IL_5A9Z_112No text annotation
IL_5A9Z_113tWH-tWH-tHW-tHW
IL_5A9Z_114No text annotation
IL_5A9Z_172Isolated non-canonical cWW pair
IL_5A9Z_115Kink-turn with non-sequential stacking
IL_5A9Z_116No text annotation
IL_5A9Z_117C-loop
IL_5A9Z_118Single bulged U
IL_5A9Z_173No text annotation
IL_5A9Z_119C-loop
IL_5A9Z_120Single bulged G
IL_5A9Z_121No text annotation
IL_5A9Z_1226x5 Sarcin-Ricin; G-bulge
IL_5A9Z_123No text annotation
IL_5A9Z_124SSU/LSU pseudoknot
IL_5A9Z_125Kink-turn related
IL_5A9Z_126tSH-tHW-tHS-cWW
IL_5A9Z_174tSH-tHW-tHS
IL_5A9Z_127Major groove platform
IL_5A9Z_128Major groove minor groove platform; mini C-loop
IL_5A9Z_129No text annotation
IL_5A9Z_130Major groove platform; stack outside cWW
IL_5A9Z_131Major groove platform
IL_5A9Z_132Tandem non-canonical cWW pairs
IL_5A9Z_133Triple non-canonical cWW pairs
IL_5A9Z_134Kink-turn
IL_5A9Z_135Left turn
IL_5A9Z_136tSH-tHW-tHS
IL_5A9Z_1378x6 Sarcin-Ricin with inserted Y; G-bulge
IL_5A9Z_138Single bulged A
IL_5A9Z_139Single bulged G
IL_5A9Z_140Minor groove platform
IL_5A9Z_141Minor groove platform
IL_5A9Z_142No text annotation
IL_5A9Z_143No text annotation
IL_5A9Z_144Isolated cWS basepair
IL_5A9Z_146Single bulged U
IL_5A9Z_147Isolated non-canonical cWW pair
IL_5A9Z_148No text annotation
IL_5A9Z_175No text annotation
IL_5A9Z_149No text annotation
IL_5A9Z_150No text annotation
IL_5A9Z_151No text annotation
IL_5A9Z_152180 degree turn
IL_5A9Z_153Double sheared with non-canonical cWW
IL_5A9Z_185No text annotation
IL_5A9Z_154No text annotation
IL_5A9Z_155No text annotation
IL_5A9Z_156No text annotation
IL_5A9Z_176No text annotation
IL_5A9Z_158Isolated non-canonical cWW pair
IL_5A9Z_159No text annotation
IL_5A9Z_177No text annotation
IL_5A9Z_160Triple sheared related
IL_5A9Z_186UAA/GAN variation
IL_5A9Z_162No text annotation
IL_5A9Z_163Isolated non-canonical cWW contact

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_5A9Z_0341/AA/32:35,
1/AA/445:461,
1/AA/468:473		No text annotation
homologous
J3_9DFE_003
J3_07616.1
J3_5A9Z_0211/AA/601:605,
1/AA/623:628,
1/AA/635:656		No text annotation
J3_5A9Z_0041/AA/1306:1309,
1/AA/1605:1611,
1/AA/1620:1622		No text annotation
homologous
J3_7RQB_008
NA
J3_5A9Z_0231/AA/2282:2284,
1/AA/2384:2395,
1/AA/2421:2427		No text annotation
homologous
J3_7A0S_020
J3_04772.1
J3_5A9Z_0071/AA/2295:2297,
1/AA/2321:2323,
1/AA/2332:2337		No text annotation
homologous
J3_7RQB_011
NA
J3_5A9Z_0081/AA/2517:2520,
1/AA/2545:2547,
1/AA/2561:2567		No text annotation
homologous
J3_7RQB_012
NA
J4_5A9Z_0011/AA/47:54,
1/AA/116:121,
1/AA/130:131,
1/AA/148:178		No text annotation
J4_5A9Z_0031/AA/1270:1276,
1/AA/1294:1295,
1/AA/1645:1648,
1/AA/2009:2010		No text annotation
homologous
J4_9DFE_003
J4_64571.6
J4_5A9Z_0041/AA/1309:1313,
1/AA/1339:1343,
1/AA/1404:1405,
1/AA/1597:1605		No text annotation
J4_5A9Z_0061/AA/1772:1775,
1/AA/1789:1792,
1/AA/1827:1830,
1/AA/1975:1979		No text annotation
J4_5A9Z_0071/AA/1833:1835,
1/AA/1905:1909,
1/AA/1922:1945,
1/AA/1961:1972		No text annotation
J4_5A9Z_0141/BA/569:577,
1/BA/764:769,
1/BA/810:821,
1/BA/879:881		No text annotation
J5_5A9Z_0021/AA/584:589,
1/AA/668:671,
1/AA/809:812,
1/AA/1195:1198,
1/AA/1247:1256		No text annotation
J5_5A9Z_0091/AA/1667:1683,
1/AA/1705:1707,
1/AA/1751:1752,
1/AA/1756:1764,
1/AA/1988:1993		No text annotation
J5_5A9Z_0041/AA/2057:2064,
1/AA/2446:2455,
1/AA/2496:2507,
1/AA/2582:2588,
1/AA/2606:2611		No text annotation
J5_5A9Z_0051/AA/2074:2077,
1/AA/2243:2246,
1/AA/2258:2259,
1/AA/2281:2282,
1/AA/2427:2435		No text annotation
homologous
J5_7A0S_007
J5_39529.2
J6_5A9Z_0021/AA/2074:2077,
1/AA/2243:2246,
1/AA/2258:2259,
1/AA/2281:2284,
1/AA/2384:2395,
1/AA/2421:2435		No text annotation
J7_5A9Z_0011/AA/817:822,
1/AA/835:837,
1/AA/942:946,
1/AA/971:976,
1/AA/987:991,
1/AA/1163:1164,
1/AA/1185:1190		No text annotation
J10_5A9Z_0011/AA/4:15,
1/AA/525:533,
1/AA/560:564,
1/AA/577:579,
1/AA/1261:1269,
1/AA/2011:2023,
1/AA/2040:2043,
1/AA/2625:2630,
1/AA/2788:2811,
1/AA/2889:2899		No text annotation

Problematic loops

#loop idProblemSequence
J3_5A9Z_018No text annotation
J3_5A9Z_019No text annotation
J3_5A9Z_020No text annotation
J3_5A9Z_001No text annotation
J3_5A9Z_002No text annotation
J3_5A9Z_003No text annotation
J3_5A9Z_005No text annotation
J3_5A9Z_022No text annotation
J3_5A9Z_006No text annotation
J3_5A9Z_024No text annotation
J3_5A9Z_025No text annotation
J3_5A9Z_035No text annotation
J3_5A9Z_009No text annotation
J3_5A9Z_026No text annotation
J3_5A9Z_027No text annotation
J3_5A9Z_028No text annotation
J3_5A9Z_029No text annotation
J3_5A9Z_030No text annotation
J3_5A9Z_010No text annotation
J3_5A9Z_011No text annotation
J3_5A9Z_012No text annotation
J3_5A9Z_013No text annotation
J3_5A9Z_014No text annotation
J3_5A9Z_031No text annotation
J3_5A9Z_015No text annotation
J3_5A9Z_036No text annotation
J3_5A9Z_032No text annotation
J3_5A9Z_033No text annotation
J3_5A9Z_037No text annotation
J3_5A9Z_016No text annotation
J3_5A9Z_017No text annotation
J4_5A9Z_002No text annotation
J4_5A9Z_013No text annotation
J4_5A9Z_005No text annotation
J4_5A9Z_008No text annotation
J4_5A9Z_009No text annotation
J4_5A9Z_010No text annotation
J4_5A9Z_011No text annotation
J4_5A9Z_012No text annotation
J5_5A9Z_001No text annotation
J5_5A9Z_008No text annotation
J5_5A9Z_003No text annotation
J5_5A9Z_006No text annotation
J5_5A9Z_007No text annotation
J6_5A9Z_003No text annotation
J6_5A9Z_001No text annotation

Coloring options:
Copyright 2025 BGSU RNA group. Page generated in 0.0957 s