RNA 3D Hub //

9MDS Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_9MDS_0011/A/35:43Anticodon loop related
geometric
HL_4R4V_001
HL_81376.3
HL_9MDS_0021/A/68:74No text annotation
geometric
HL_9M86_002
HL_46665.2
HL_9MDS_0031/A/100:105GNRA
geometric
HL_8CRE_211
HL_34789.4
HL_9MDS_0051/A/184:189No text annotation
geometric
HL_8P9A_177
HL_12125.2
HL_9MDS_0061/A/270:276GNRA
geometric
HL_5J7L_167
NA
HL_9MDS_0071/A/303:313No text annotation
geometric
HL_4UYK_001
HL_14063.2
HL_9MDS_0081/A/363:368GNRA
geometric
HL_6CU1_002
HL_34789.4
HL_9MDS_0091/A/388:412No text annotation
HL_9MDS_0111/A/500:513No text annotation
HL_9MDS_0151/B/35:43Anticodon loop related
geometric
HL_4R4V_001
HL_81376.3
HL_9MDS_0161/B/68:74No text annotation
geometric
HL_9M86_002
HL_46665.2
HL_9MDS_0171/B/100:105GNRA
geometric
HL_8CRE_211
HL_34789.4
HL_9MDS_0191/B/184:189No text annotation
geometric
HL_8P9A_177
HL_12125.2
HL_9MDS_0201/B/270:276GNRA
geometric
HL_5J7L_167
NA
HL_9MDS_0211/B/303:313No text annotation
geometric
HL_4UYK_001
HL_14063.2
HL_9MDS_0221/B/363:368GNRA
geometric
HL_6CU1_002
HL_34789.4
HL_9MDS_0231/B/388:412No text annotation
HL_9MDS_0251/B/500:513No text annotation
HL_9MDS_0291/C/35:43Anticodon loop related
geometric
HL_4R4V_001
HL_81376.3
HL_9MDS_0301/C/68:74No text annotation
geometric
HL_9M86_002
HL_46665.2
HL_9MDS_0311/C/100:105GNRA
geometric
HL_8CRE_211
HL_34789.4
HL_9MDS_0331/C/184:189No text annotation
geometric
HL_8P9A_177
HL_12125.2
HL_9MDS_0341/C/270:276GNRA
geometric
HL_5J7L_167
NA
HL_9MDS_0351/C/303:313No text annotation
geometric
HL_4UYK_001
HL_14063.2
HL_9MDS_0361/C/363:368GNRA
geometric
HL_6CU1_002
HL_34789.4
HL_9MDS_0371/C/388:412No text annotation
HL_9MDS_0391/C/500:513No text annotation
HL_9MDS_0431/D/35:43Anticodon loop related
geometric
HL_4R4V_001
HL_81376.3
HL_9MDS_0441/D/68:74No text annotation
geometric
HL_9M86_002
HL_46665.2
HL_9MDS_0451/D/100:105GNRA
geometric
HL_8CRE_211
HL_34789.4
HL_9MDS_0471/D/184:189No text annotation
geometric
HL_8P9A_177
HL_12125.2
HL_9MDS_0481/D/270:276GNRA
geometric
HL_5J7L_167
NA
HL_9MDS_0491/D/303:313No text annotation
geometric
HL_4UYK_001
HL_14063.2
HL_9MDS_0501/D/363:368GNRA
geometric
HL_6CU1_002
HL_34789.4
HL_9MDS_0511/D/388:412No text annotation
HL_9MDS_0531/D/500:513No text annotation
HL_9MDS_0571/E/35:43Anticodon loop related
geometric
HL_4R4V_001
HL_81376.3
HL_9MDS_0581/E/68:74No text annotation
geometric
HL_9M86_002
HL_46665.2
HL_9MDS_0591/E/100:105GNRA
geometric
HL_8CRE_211
HL_34789.4
HL_9MDS_0611/E/184:189No text annotation
geometric
HL_8P9A_177
HL_12125.2
HL_9MDS_0621/E/270:276GNRA
geometric
HL_5J7L_167
NA
HL_9MDS_0631/E/303:313No text annotation
geometric
HL_4UYK_001
HL_14063.2
HL_9MDS_0641/E/363:368GNRA
geometric
HL_6CU1_002
HL_34789.4
HL_9MDS_0651/E/388:412No text annotation
HL_9MDS_0671/E/500:513No text annotation
HL_9MDS_0711/F/35:43Anticodon loop related
geometric
HL_4R4V_001
HL_81376.3
HL_9MDS_0721/F/68:74No text annotation
geometric
HL_9M86_002
HL_46665.2
HL_9MDS_0731/F/100:105GNRA
geometric
HL_8CRE_211
HL_34789.4
HL_9MDS_0751/F/184:189No text annotation
geometric
HL_8P9A_177
HL_12125.2
HL_9MDS_0761/F/270:276GNRA
geometric
HL_5J7L_167
NA
HL_9MDS_0771/F/303:313No text annotation
geometric
HL_4UYK_001
HL_14063.2
HL_9MDS_0781/F/363:368GNRA
geometric
HL_6CU1_002
HL_34789.4
HL_9MDS_0791/F/388:412No text annotation
HL_9MDS_0811/F/500:513No text annotation
HL_9MDS_0851/G/35:43Anticodon loop related
geometric
HL_4R4V_001
HL_81376.3
HL_9MDS_0861/G/68:74No text annotation
geometric
HL_9M86_002
HL_46665.2
HL_9MDS_0871/G/100:105GNRA
geometric
HL_8CRE_211
HL_34789.4
HL_9MDS_0891/G/184:189No text annotation
geometric
HL_8P9A_177
HL_12125.2
HL_9MDS_0901/G/270:276GNRA
geometric
HL_5J7L_167
NA
HL_9MDS_0911/G/303:313No text annotation
geometric
HL_4UYK_001
HL_14063.2
HL_9MDS_0921/G/363:368GNRA
geometric
HL_6CU1_002
HL_34789.4
HL_9MDS_0931/G/388:412No text annotation
HL_9MDS_0951/G/500:513No text annotation
HL_9MDS_0991/H/35:43Anticodon loop related
geometric
HL_4R4V_001
HL_81376.3
HL_9MDS_1001/H/68:74No text annotation
geometric
HL_9M86_002
HL_46665.2
HL_9MDS_1011/H/100:105GNRA
geometric
HL_8CRE_211
HL_34789.4
HL_9MDS_1031/H/184:189No text annotation
geometric
HL_8P9A_177
HL_12125.2
HL_9MDS_1041/H/270:276GNRA
geometric
HL_5J7L_167
NA
HL_9MDS_1051/H/303:313No text annotation
geometric
HL_4UYK_001
HL_14063.2
HL_9MDS_1061/H/363:368GNRA
geometric
HL_6CU1_002
HL_34789.4
HL_9MDS_1071/H/388:412No text annotation
HL_9MDS_1091/H/500:513No text annotation

Problematic loops

#loop idProblemSequence
HL_9MDS_004No text annotation
HL_9MDS_010No text annotation
HL_9MDS_012No text annotation
HL_9MDS_013No text annotation
HL_9MDS_014No text annotation
HL_9MDS_018No text annotation
HL_9MDS_024No text annotation
HL_9MDS_026No text annotation
HL_9MDS_027No text annotation
HL_9MDS_028No text annotation
HL_9MDS_032No text annotation
HL_9MDS_038No text annotation
HL_9MDS_040No text annotation
HL_9MDS_041No text annotation
HL_9MDS_042No text annotation
HL_9MDS_046No text annotation
HL_9MDS_052No text annotation
HL_9MDS_054No text annotation
HL_9MDS_055No text annotation
HL_9MDS_056No text annotation
HL_9MDS_060No text annotation
HL_9MDS_066No text annotation
HL_9MDS_068No text annotation
HL_9MDS_069No text annotation
HL_9MDS_070No text annotation
HL_9MDS_074No text annotation
HL_9MDS_080No text annotation
HL_9MDS_082No text annotation
HL_9MDS_083No text annotation
HL_9MDS_084No text annotation
HL_9MDS_088No text annotation
HL_9MDS_094No text annotation
HL_9MDS_096No text annotation
HL_9MDS_097No text annotation
HL_9MDS_098No text annotation
HL_9MDS_102No text annotation
HL_9MDS_108No text annotation
HL_9MDS_110No text annotation
HL_9MDS_111No text annotation
HL_9MDS_112No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_9MDS_0011/A/14:15,
1/A/644:646		Single bulged A
geometric
IL_8P9A_388
IL_14190.2
IL_9MDS_0021/A/24:32,
1/A/46:49		No text annotation
IL_9MDS_0031/A/54:55,
1/A/209:211		No text annotation
IL_9MDS_0041/A/125:132,
1/A/168:175		No text annotation
IL_9MDS_0051/A/135:144,
1/A/154:165		No text annotation
IL_9MDS_0061/A/215:216,
1/A/619:621		Single bulged G
geometric
IL_8TSV_002
IL_28408.2
IL_9MDS_0071/A/226:229,
1/A/607:609		Isolated non-canonical cWW pair
geometric
IL_3TD0_005
NA
IL_9MDS_0081/A/231:233,
1/A/600:605		No text annotation
IL_9MDS_0091/A/292:297,
1/A/319:324		No text annotation
IL_9MDS_0121/B/14:15,
1/B/644:646		Single bulged A
geometric
IL_8P9A_388
IL_14190.2
IL_9MDS_0131/B/24:32,
1/B/46:49		No text annotation
IL_9MDS_0141/B/54:55,
1/B/209:211		No text annotation
IL_9MDS_0151/B/125:132,
1/B/168:175		No text annotation
IL_9MDS_0161/B/135:144,
1/B/154:165		No text annotation
IL_9MDS_0171/B/215:216,
1/B/619:621		Single bulged G
geometric
IL_8TSV_002
IL_28408.2
IL_9MDS_0181/B/226:229,
1/B/607:609		Isolated non-canonical cWW pair
geometric
IL_5T3K_001
IL_01003.4
IL_9MDS_0191/B/231:233,
1/B/600:605		No text annotation
IL_9MDS_0201/B/292:297,
1/B/319:324		No text annotation
IL_9MDS_0231/C/14:15,
1/C/644:646		Single bulged A
geometric
IL_8P9A_388
IL_14190.2
IL_9MDS_0241/C/24:32,
1/C/46:49		No text annotation
IL_9MDS_0251/C/54:55,
1/C/209:211		No text annotation
IL_9MDS_0261/C/125:132,
1/C/168:175		No text annotation
IL_9MDS_0271/C/135:144,
1/C/154:165		No text annotation
IL_9MDS_0281/C/215:216,
1/C/619:621		Single bulged G
geometric
IL_8TSV_002
IL_28408.2
IL_9MDS_0291/C/226:229,
1/C/607:609		Isolated non-canonical cWW pair
geometric
IL_5T3K_001
IL_01003.4
IL_9MDS_0301/C/231:233,
1/C/600:605		No text annotation
IL_9MDS_0311/C/292:297,
1/C/319:324		No text annotation
IL_9MDS_0341/D/14:15,
1/D/644:646		Single bulged A
geometric
IL_8P9A_388
IL_14190.2
IL_9MDS_0351/D/24:32,
1/D/46:49		No text annotation
IL_9MDS_0361/D/54:55,
1/D/209:211		No text annotation
IL_9MDS_0371/D/125:132,
1/D/168:175		No text annotation
IL_9MDS_0381/D/135:144,
1/D/154:165		No text annotation
IL_9MDS_0391/D/215:216,
1/D/619:621		Single bulged G
geometric
IL_8TSV_002
IL_28408.2
IL_9MDS_0401/D/226:229,
1/D/607:609		Isolated non-canonical cWW pair
geometric
IL_5T3K_001
IL_01003.4
IL_9MDS_0411/D/231:233,
1/D/600:605		No text annotation
IL_9MDS_0421/D/292:297,
1/D/319:324		No text annotation
IL_9MDS_0451/E/14:15,
1/E/644:646		Single bulged A
geometric
IL_8P9A_388
IL_14190.2
IL_9MDS_0461/E/24:32,
1/E/46:49		No text annotation
IL_9MDS_0471/E/54:55,
1/E/209:211		No text annotation
IL_9MDS_0481/E/125:132,
1/E/168:175		No text annotation
IL_9MDS_0491/E/135:144,
1/E/154:165		No text annotation
IL_9MDS_0501/E/215:216,
1/E/619:621		Single bulged G
geometric
IL_8TSV_002
IL_28408.2
IL_9MDS_0511/E/226:229,
1/E/607:609		Isolated non-canonical cWW pair
geometric
IL_5T3K_001
IL_01003.4
IL_9MDS_0521/E/231:233,
1/E/600:605		No text annotation
IL_9MDS_0531/E/292:297,
1/E/319:324		No text annotation
IL_9MDS_0561/F/14:15,
1/F/644:646		Single bulged A
geometric
IL_8P9A_388
IL_14190.2
IL_9MDS_0571/F/24:32,
1/F/46:49		No text annotation
IL_9MDS_0581/F/54:55,
1/F/209:211		No text annotation
IL_9MDS_0591/F/125:132,
1/F/168:175		No text annotation
IL_9MDS_0601/F/135:144,
1/F/154:165		No text annotation
IL_9MDS_0611/F/215:216,
1/F/619:621		Single bulged G
geometric
IL_8TSV_002
IL_28408.2
IL_9MDS_0621/F/226:229,
1/F/607:609		Isolated non-canonical cWW pair
geometric
IL_5T3K_001
IL_01003.4
IL_9MDS_0631/F/231:233,
1/F/600:605		No text annotation
IL_9MDS_0641/F/292:297,
1/F/319:324		No text annotation
IL_9MDS_0671/G/14:15,
1/G/644:646		Single bulged A
geometric
IL_8P9A_388
IL_14190.2
IL_9MDS_0681/G/24:32,
1/G/46:49		No text annotation
IL_9MDS_0691/G/54:55,
1/G/209:211		No text annotation
IL_9MDS_0701/G/125:132,
1/G/168:175		No text annotation
IL_9MDS_0711/G/135:144,
1/G/154:165		No text annotation
IL_9MDS_0721/G/215:216,
1/G/619:621		Single bulged G
geometric
IL_8TSV_002
IL_28408.2
IL_9MDS_0731/G/226:229,
1/G/607:609		Isolated non-canonical cWW pair
geometric
IL_5T3K_001
IL_01003.4
IL_9MDS_0741/G/231:233,
1/G/600:605		No text annotation
IL_9MDS_0751/G/292:297,
1/G/319:324		No text annotation
IL_9MDS_0781/H/14:15,
1/H/644:646		Single bulged A
geometric
IL_8P9A_388
IL_14190.2
IL_9MDS_0791/H/24:32,
1/H/46:49		No text annotation
IL_9MDS_0801/H/54:55,
1/H/209:211		No text annotation
IL_9MDS_0811/H/125:132,
1/H/168:175		No text annotation
IL_9MDS_0821/H/135:144,
1/H/154:165		No text annotation
IL_9MDS_0831/H/215:216,
1/H/619:621		Single bulged G
geometric
IL_8TSV_002
IL_28408.2
IL_9MDS_0841/H/226:229,
1/H/607:609		Isolated non-canonical cWW pair
geometric
IL_5T3K_001
IL_01003.4
IL_9MDS_0851/H/231:233,
1/H/600:605		No text annotation
IL_9MDS_0861/H/292:297,
1/H/319:324		No text annotation

Problematic loops

#loop idProblemSequence
IL_9MDS_010No text annotation
IL_9MDS_011No text annotation
IL_9MDS_021No text annotation
IL_9MDS_022No text annotation
IL_9MDS_032No text annotation
IL_9MDS_033No text annotation
IL_9MDS_043No text annotation
IL_9MDS_044No text annotation
IL_9MDS_054No text annotation
IL_9MDS_055No text annotation
IL_9MDS_065No text annotation
IL_9MDS_066No text annotation
IL_9MDS_076No text annotation
IL_9MDS_077No text annotation
IL_9MDS_087No text annotation
IL_9MDS_088No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_9MDS_0011/A/62:64,
1/A/78:81,
1/A/198:202		No text annotation
J3_9MDS_0021/A/248:249,
1/A/347:358,
1/A/373:379		No text annotation
J3_9MDS_0031/A/254:265,
1/A/281:287,
1/A/329:342		No text annotation
J3_9MDS_0041/A/522:529,
1/A/541:545,
1/A/589:590		No text annotation
J3_9MDS_0051/B/62:64,
1/B/78:81,
1/B/198:202		No text annotation
J3_9MDS_0061/B/248:249,
1/B/347:358,
1/B/373:379		No text annotation
J3_9MDS_0071/B/254:265,
1/B/281:287,
1/B/329:342		No text annotation
J3_9MDS_0081/B/522:529,
1/B/541:545,
1/B/589:590		No text annotation
J3_9MDS_0091/C/62:64,
1/C/78:81,
1/C/198:202		No text annotation
J3_9MDS_0101/C/248:249,
1/C/347:358,
1/C/373:379		No text annotation
J3_9MDS_0111/C/254:265,
1/C/281:287,
1/C/329:342		No text annotation
J3_9MDS_0121/C/522:529,
1/C/541:545,
1/C/589:590		No text annotation
J3_9MDS_0131/D/62:64,
1/D/78:81,
1/D/198:202		No text annotation
J3_9MDS_0141/D/248:249,
1/D/347:358,
1/D/373:379		No text annotation
J3_9MDS_0151/D/254:265,
1/D/281:287,
1/D/329:342		No text annotation
J3_9MDS_0161/D/522:529,
1/D/541:545,
1/D/589:590		No text annotation
J3_9MDS_0171/E/62:64,
1/E/78:81,
1/E/198:202		No text annotation
J3_9MDS_0181/E/248:249,
1/E/347:358,
1/E/373:379		No text annotation
J3_9MDS_0191/E/254:265,
1/E/281:287,
1/E/329:342		No text annotation
J3_9MDS_0201/E/522:529,
1/E/541:545,
1/E/589:590		No text annotation
J3_9MDS_0211/F/62:64,
1/F/78:81,
1/F/198:202		No text annotation
J3_9MDS_0221/F/248:249,
1/F/347:358,
1/F/373:379		No text annotation
J3_9MDS_0231/F/254:265,
1/F/281:287,
1/F/329:342		No text annotation
J3_9MDS_0241/F/522:529,
1/F/541:545,
1/F/589:590		No text annotation
J3_9MDS_0251/G/62:64,
1/G/78:81,
1/G/198:202		No text annotation
J3_9MDS_0261/G/248:249,
1/G/347:358,
1/G/373:379		No text annotation
J3_9MDS_0271/G/254:265,
1/G/281:287,
1/G/329:342		No text annotation
J3_9MDS_0281/G/522:529,
1/G/541:545,
1/G/589:590		No text annotation
J3_9MDS_0291/H/62:64,
1/H/78:81,
1/H/198:202		No text annotation
J3_9MDS_0301/H/248:249,
1/H/347:358,
1/H/373:379		No text annotation
J3_9MDS_0311/H/254:265,
1/H/281:287,
1/H/329:342		No text annotation
J3_9MDS_0321/H/522:529,
1/H/541:545,
1/H/589:590		No text annotation
J4_9MDS_0011/A/83:92,
1/A/113:123,
1/A/177:178,
1/A/195:196		No text annotation
J4_9MDS_0021/B/83:92,
1/B/113:123,
1/B/177:178,
1/B/195:196		No text annotation
J4_9MDS_0031/C/83:92,
1/C/113:123,
1/C/177:178,
1/C/195:196		No text annotation
J4_9MDS_0041/D/83:92,
1/D/113:123,
1/D/177:178,
1/D/195:196		No text annotation
J4_9MDS_0051/E/83:92,
1/E/113:123,
1/E/177:178,
1/E/195:196		No text annotation
J4_9MDS_0061/F/83:92,
1/F/113:123,
1/F/177:178,
1/F/195:196		No text annotation
J4_9MDS_0071/G/83:92,
1/G/113:123,
1/G/177:178,
1/G/195:196		No text annotation
J4_9MDS_0081/H/83:92,
1/H/113:123,
1/H/177:178,
1/H/195:196		No text annotation
J5_9MDS_0011/A/17:20,
1/A/53:54,
1/A/211:212,
1/A/624:627,
1/A/640:642		No text annotation
J5_9MDS_0021/B/17:20,
1/B/53:54,
1/B/211:212,
1/B/624:627,
1/B/640:642		No text annotation
J5_9MDS_0031/C/17:20,
1/C/53:54,
1/C/211:212,
1/C/624:627,
1/C/640:642		No text annotation
J5_9MDS_0041/D/17:20,
1/D/53:54,
1/D/211:212,
1/D/624:627,
1/D/640:642		No text annotation
J5_9MDS_0051/E/17:20,
1/E/53:54,
1/E/211:212,
1/E/624:627,
1/E/640:642		No text annotation
J5_9MDS_0061/F/17:20,
1/F/53:54,
1/F/211:212,
1/F/624:627,
1/F/640:642		No text annotation
J5_9MDS_0071/G/17:20,
1/G/53:54,
1/G/211:212,
1/G/624:627,
1/G/640:642		No text annotation
J5_9MDS_0081/H/17:20,
1/H/53:54,
1/H/211:212,
1/H/624:627,
1/H/640:642		No text annotation

Problematic loops

No problematic loops


Coloring options:
Copyright 2026 BGSU RNA group. Page generated in 0.0951 s