BGSU RNA Site //

4WF9 Internal, Hairpin and 3-way Junction Loop Motifs

Download loops

Valid loops

#loop idlocationannotationmotif
1➜1/X/67:74NAHL_86769.2
2➜1/X/87:95NAHL_17926.5
3➜1/X/122:127NAHL_62869.3
4➜1/X/136:143NAHL_93727.5
5➜1/X/197:204NAHL_23481.5
6➜1/X/228:233NAHL_96776.3
7➜1/X/249:255NAHL_67216.5
8➜1/X/283:288NAHL_68478.1
9➜1/X/348:355T-loop with 1 bulged baseHL_68493.6
10➜1/X/362:366NAHL_98557.5
11➜1/X/370:378NAHL_08002.6
12➜1/X/427:439NAHL_42671.1
13➜1/X/456:463NAHL_32512.8
14➜1/X/508:513GNRAHL_43074.18
15➜1/X/533:538GNRAHL_43074.18
16➜1/X/587:594NAHL_23219.1
17➜1/X/609:618T-loop with 2 stacked bulged basesHL_33239.17
18➜1/X/654:662NAHL_00923.1
19➜1/X/674:679GNRAHL_43074.18
20➜1/X/686:692GNRA with one bulged baseHL_02361.6
21➜1/X/789:798NAHL_39334.5
22➜1/X/824:830NAHL_73016.1
23➜1/X/871:876NAHL_15942.5
24➜1/X/999:1006GNRAHL_43074.18
25➜1/X/1022:1029NAHL_72451.5
26➜1/X/1260:1265NAHL_68304.6
27➜1/X/1318:1326T-loop with 2 stacked bulged basesHL_33239.17
28➜1/X/1361:1367NAHL_86880.5
29➜1/X/1400:1405Other HLHL_43074.18
30➜1/X/1426:1435NAHL_78457.4
31➜1/X/1612:1615NAHL_69353.7
32➜1/X/1656:1663NAHL_66171.3
33➜1/X/1673:1681NAHL_42733.4
34➜1/X/1735:1740UNCGHL_79299.11
35➜1/X/1761:1768NAHL_93727.5
36➜1/X/1779:1783NAHL_79272.3
37➜1/X/1804:1814NAHL_43613.4
38➜1/X/1976:1984NAHL_53760.4
39➜1/X/2054:2063NAHL_90642.5
40➜1/X/2236:2242NAHL_16845.5
41➜1/X/2275:2283NAHL_46891.3
42➜1/X/2291:2303NAHL_19870.5
43➜1/X/2351:2358NAHL_46142.8
44➜1/X/2382:2389NAHL_93727.5
45➜1/X/2401:2406GNRAHL_43074.18
46➜1/X/2431:2440NAHL_48376.4
47➜1/X/2498:2506NAHL_36421.5
48➜1/X/2555:2562NAHL_92681.5
49➜1/X/2578:2584NAHL_26055.6
50➜1/X/2621:2626GNRAHL_43074.18
51➜1/X/2685:2690GNRAHL_43074.18
52➜1/X/2728:2733Ribsomal LSU H95HL_67719.1
53➜1/X/2772:2786NAHL_56677.5
54➜1/X/2839:2847NAHL_05018.6
55➜1/X/2876:2881Other HLHL_43074.18
56➜1/Y/36:42NAHL_02733.5

Problematic loops

#loop idProblemSequence
1➜NA
2➜NA
3➜NA
4➜NA
5➜NA
6➜NA
7➜NA
8➜NA
9➜NA
10➜NA

Valid loops

#loop idlocationannotationmotif
1➜1/X/24:30,1/X/555:561Triple sheared with non-canonical cWWIL_66414.5
2➜1/X/36:37,1/X/488:490Single bulged AIL_80007.16
3➜1/X/42:44,1/X/480:483Minor groove platform with extra cWWIL_87332.1
4➜1/X/81:85,1/X/97:104Kink-turnIL_29549.9
5➜1/X/152:153,1/X/175:177Single bulged AIL_80007.16
6➜1/X/186:187,1/X/215:217NAIL_04038.4
7➜1/X/190:197,1/X/204:2129x8 Sarcin-Ricin; G-bulgeIL_61812.1
8➜1/X/241:248,1/X/256:2628x7 Sarcin-Ricin; G-bulgeIL_04346.5
9➜1/X/304:306,1/X/409:413Major groove minor groove platform with extra cWWIL_96042.4
10➜1/X/336:338,1/X/386:390NAIL_69440.1
11➜1/X/527:530,1/X/541:554NAIL_60992.5
12➜1/X/581:584,1/X/597:600Double shearedIL_09705.7
13➜1/X/607:609,1/X/618:620NAIL_01312.13
14➜1/X/638:640,1/X/705:707NAIL_01312.13
15➜1/X/649:653,1/X/663:667AAA cross-strand stackIL_56467.6
16➜1/X/717:719,1/X/851:853NAIL_01312.13
17➜1/X/719:723,1/X/844:851tHW-tHW cross-strand stackIL_17470.5
18➜1/X/742:743,1/X/808:810Single bulged AIL_80007.16
19➜1/X/747:748,1/X/773:775Single bulged GIL_59137.10
20➜1/X/748:752,1/X/769:773Triple shearedIL_56467.6
21➜1/X/783:785,1/X/802:803Major groove platformIL_80663.10
22➜1/X/820:822,1/X/832:836Multiple bulged basesIL_90991.5
23➜1/X/882:883,1/X/984:986NAIL_04038.4
24➜1/X/889:893,1/X/975:978NAIL_06300.1
25➜1/X/897:898,1/X/969:971Single bulged UIL_83039.11
26➜1/X/901:907,1/X/960:9667x7 Sarcin-Ricin with intercalated A; G-bulgeIL_93830.2
27➜1/X/907:908,1/X/958:960Minor groove platformIL_06437.11
28➜1/X/909:913,1/X/954:957C-loopIL_63596.4
29➜1/X/915:917,1/X/950:952Isolated cWS basepairIL_67621.5
30➜1/X/1038:1040,1/X/1203:1204Single bulged CIL_61258.10
31➜1/X/1042:1046,1/X/1197:1201UAA/GANIL_53523.5
32➜1/X/1048:1055,1/X/1194:1195SSU/LSU pseudoknotIL_15861.6
33➜1/X/1055:1057,1/X/1193:1194Single bulged UIL_83039.11
34➜1/X/1062:1068,1/X/1184:1188NAIL_57188.3
35➜1/X/1068:1074,1/X/1168:1184NAIL_22615.1
36➜1/X/1075:1078,1/X/1165:1167Other ILIL_42589.6
37➜1/X/1081:1083,1/X/1160:1162NAIL_01312.13
38➜1/X/1235:1237,1/X/1285:1288Isolated cWS basepairIL_67621.5
39➜1/X/1243:1245,1/X/1277:1279Isolated cWH basepairIL_42589.6
40➜1/X/1246:1253,1/X/1272:1276Kink-turnIL_29549.9
41➜1/X/1257:1259,1/X/1266:1268NAIL_04038.4
42➜1/X/1300:1307,1/X/2038:20448x7 Sarcin-Ricin; G-bulgeIL_04346.5
43➜1/X/1347:1350,1/X/1647:1648Major groove platform; stack outside cWWIL_70995.6
44➜1/X/1356:1360,1/X/1368:1370Major groove minor groove platform with tHHIL_28060.3
45➜1/X/1388:1392,1/X/1413:1417UAA/GANIL_34907.2
46➜1/X/1394:1398,1/X/1407:1411tSH-tHW-tHSIL_39521.5
47➜1/X/1461:1465,1/X/1624:1627Other ILIL_09705.7
48➜1/X/1465:1467,1/X/1622:1624NAIL_01312.13
49➜1/X/1475:1480,1/X/1604:1609NAIL_86428.1
50➜1/X/1511:1516,1/X/1564:1570NAIL_94518.4
51➜1/X/1695:1700,1/X/2031:2033NAIL_12566.2
52➜1/X/1707:1709,1/X/2022:2024Isolated tWW turnIL_54997.5
53➜1/X/1710:1713,1/X/2020:2021Major groove platform; stack outside cWWIL_70995.6
54➜1/X/1713:1718,1/X/2017:2020Intercalated tWHIL_01312.13
55➜1/X/1730:1735,1/X/1740:1746NAIL_54670.1
56➜1/X/1756:1761,1/X/1768:1773NAIL_69979.1
57➜1/X/1797:1798,1/X/2007:2009Single bulged AIL_80007.16
58➜1/X/1825:1831,1/X/1840:1848NAIL_17069.3
59➜1/X/1868:1869,1/X/1925:1928Multiple bulged basesIL_13730.12
60➜1/X/1878:1882,1/X/1914:1918UAA/GAN with extra pairIL_34907.2
61➜1/X/1883:1887,1/X/1909:1913Triple shearedIL_56467.6
62➜1/X/1891:1894,1/X/1901:1905UAA/GANIL_53523.5
63➜1/X/1960:1961,1/X/1991:1994NAIL_69632.1
64➜1/X/1961:1972,1/X/1988:1991NAIL_70285.1
65➜1/X/2077:2079,1/X/2644:2645Major groove platformIL_80663.10
66➜1/X/2081:2083,1/X/2639:2642NAIL_54678.3
67➜1/X/2094:2096,1/X/2469:2470Single bulged UIL_83039.11
68➜1/X/2097:2098,1/X/2465:2468Minor groove platformIL_06437.11
69➜1/X/2108:2110,1/X/2263:2266Isolated tHS basepairIL_38958.6
70➜1/X/2111:2113,1/X/2260:2262NAIL_01312.13
71➜1/X/2122:2126,1/X/2217:2221Other ILIL_56467.6
72➜1/X/2229:2233,1/X/2245:2248Tandem non-canonical cWW pairsIL_85877.10
73➜1/X/2324:2326,1/X/2344:2348Isolated tHS basepairIL_38958.6
74➜1/X/2377:2380,1/X/2391:2394Double shearedIL_09705.7
75➜1/X/2428:2430,1/X/2441:2442Single bulged UIL_21340.1
76➜1/X/2480:2481,1/X/2525:2527NAIL_04038.4
77➜1/X/2481:2482,1/X/2523:2525Major groove platformIL_80663.10
78➜1/X/2484:2486,1/X/2520:2521Major groove platformIL_80663.10
79➜1/X/2486:2488,1/X/2516:2520Major groove minor groove platform with extra cWWIL_96042.4
80➜1/X/2493:2497,1/X/2507:2511Triple shearedIL_56467.6
81➜1/X/2534:2535,1/X/2607:2609Major groove platformIL_02060.4
82➜1/X/2537:2539,1/X/2601:2605NAIL_01312.13
83➜1/X/2539:2540,1/X/2598:2601NAIL_69632.1
84➜1/X/2549:2550,1/X/2567:2570Minor groove platform with intercalationIL_95601.1
85➜1/X/2618:2619,1/X/2628:2630Single bulged AIL_71960.4
86➜1/X/2663:2667,1/X/2801:2809tSH-tHS-tHWIL_34907.2
87➜1/X/2679:2685,1/X/2690:2695Sarcin-Ricin target in LSU H95; G-bulgeIL_35110.5
88➜1/X/2707:2711,1/X/2752:2754C-loopIL_63596.4
89➜1/X/2714:2718,1/X/2745:2749NAIL_08296.3
90➜1/X/2722:2723,1/X/2738:2741Multiple bulged basesIL_13730.12
91➜1/X/2764:2769,1/X/2789:2794UAA/GAN with extra cWWIL_49767.4
92➜1/X/2858:2859,1/X/2898:2900Major groove platform with intercalationIL_02060.4
93➜1/X/2863:2865,1/X/2891:2894NAIL_02284.3
94➜1/X/2867:2872,1/X/2885:2889NAIL_83162.3
95➜1/Y/2:5,1/Y/110:113Tandem non-canonical cWW pairsIL_85877.10
96➜1/Y/5:8,1/Y/107:110Tandem non-canonical cWW pairsIL_85877.10
97➜1/Y/8:14,1/Y/66:107NANA
98➜1/Y/15:16,1/Y/63:65Major groove intercalationIL_40508.4
99➜1/Y/20:27,1/Y/53:59NAIL_19048.1
100➜1/Y/28:30,1/Y/48:52NAIL_45289.1
101➜1/Y/32:36,1/Y/42:46Symmetric double minor groove platformIL_58103.5

Problematic loops

#loop idProblemSequence
1➜NA
2➜NA
3➜NA
4➜NA
5➜NA
6➜NA
7➜NA
8➜NA
9➜NA
10➜NA
11➜NA
12➜NA
13➜NA
14➜NA

Valid loops

#loop idlocationannotationmotif
1➜1/X/56:67,1/X/74:76,1/X/109:113NANA
2➜1/X/728:734,1/X/818:820,1/X/836:839NANA
3➜1/X/743:745,1/X/777:781,1/X/805:808NANA
4➜1/X/1335:1340,1/X/1669:1671,1/X/1683:1686NANA
5➜1/X/1342:1346,1/X/1649:1655,1/X/1664:1667NANA
6➜1/X/1860:1863,1/X/1931:1960,1/X/1994:1999NANA
7➜1/X/2118:2120,1/X/2223:2228,1/X/2249:2255NANA
8➜1/X/2322:2324,1/X/2348:2350,1/X/2359:2364NANA
9➜1/X/2544:2547,1/X/2572:2574,1/X/2588:2594NANA

Problematic loops

No problematic loops


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