BGSU RNA Site //

4V9F Internal, Hairpin and 3-way Junction Loop Motifs

Download loops

Valid loops

#loop idlocationannotationmotif
1➜1/0/55:64NAHL_55136.1
2➜1/0/83:91NAHL_44769.1
3➜1/0/118:122NAHL_94352.4
4➜1/0/125:129NAHL_70970.1
5➜1/0/136:142NAHL_79299.11
6➜1/0/164:171NAHL_23481.5
7➜1/0/195:201NAHL_12053.1
8➜1/0/217:223NAHL_67216.5
9➜1/0/252:257GNRAHL_43074.18
10➜1/0/312:319T-loop with 1 bulged baseHL_68493.6
11➜1/0/326:330NAHL_98557.5
12➜1/0/334:342NAHL_08002.6
13➜1/0/390:399NAHL_10536.1
14➜1/0/416:424NAHL_46142.8
15➜1/0/468:473GNRAHL_43074.18
16➜1/0/493:499GNRA with one bulged baseHL_02361.6
17➜1/0/576:581GNRAHL_43074.18
18➜1/0/623:632NANA
19➜1/0/670:676NAHL_37407.2
20➜1/0/690:695GNRAHL_43074.18
21➜1/0/712:716NAHL_61984.1
22➜1/0/733:738Other HLHL_43074.18
23➜1/0/804:809GNRAHL_43074.18
24➜1/0/837:846NAHL_39334.5
25➜1/0/872:878NAHL_16898.3
26➜1/0/919:924NAHL_15942.5
27➜1/0/1054:1060GNRAHL_43074.18
28➜1/0/1076:1083NAHL_72451.5
29➜1/0/1274:1282NAHL_82851.1
30➜1/0/1326:1331GNRAHL_43074.18
31➜1/0/1387:1395T-loop with 2 stacked bulged basesHL_33239.17
32➜1/0/1430:1436NAHL_86880.5
33➜1/0/1468:1474GNRAHL_43074.18
34➜1/0/1498:1507NAHL_78457.4
35➜1/0/1557:1564NAHL_53760.4
36➜1/0/1594:1600Other HLHL_68493.6
37➜1/0/1628:1633GNRAHL_43074.18
38➜1/0/1651:1655NAHL_69353.7
39➜1/0/1687:1694NAHL_66171.3
40➜1/0/1705:1713NAHL_21000.1
41➜1/0/1769:1774UNCGHL_79299.11
42➜1/0/1793:1799GNRAHL_43074.18
43➜1/0/1808:1812NAHL_79272.3
44➜1/0/1833:1843NAHL_43613.4
45➜1/0/1862:1867GNRAHL_43074.18
46➜1/0/1916:1923NAHL_53760.4
47➜1/0/1990:1998NAHL_53760.4
48➜1/0/2068:2077NAHL_90642.5
49➜1/0/2248:2253GNRAHL_43074.18
50➜1/0/2281:2289NAHL_46891.3
51➜1/0/2298:2310NAHL_19870.5
52➜1/0/2338:2346NAHL_76406.3
53➜1/0/2358:2365NAHL_46142.8
54➜1/0/2389:2399NAHL_72419.1
55➜1/0/2411:2416GNRAHL_43074.18
56➜1/0/2442:2450NAHL_46142.8
57➜1/0/2506:2514NAHL_36421.5
58➜1/0/2563:2570NAHL_92681.5
59➜1/0/2585:2593NANA
60➜1/0/2629:2634GNRAHL_43074.18
61➜1/0/2695:2700GNRAHL_43074.18
62➜1/0/2737:2742Ribsomal LSU H95HL_67719.1
63➜1/0/2780:2794NAHL_56677.5
64➜1/0/2836:2844NAHL_05018.6
65➜1/0/2876:2881GNRAHL_43074.18
66➜1/9/37:43NAHL_02733.5
67➜1/9/89:94GNRAHL_43074.18

Problematic loops

#loop idProblemSequence
1➜NA
2➜NA
3➜NA
4➜NA
5➜NA

Valid loops

#loop idlocationannotationmotif
1➜1/0/21:27,1/0/516:522Triple sheared with non-canonical cWWIL_66414.5
2➜1/0/33:34,1/0/448:450Single bulged AIL_80007.16
3➜1/0/39:41,1/0/440:443Major groove platform with extra cWWIL_95485.6
4➜1/0/77:81,1/0/93:100Kink-turnIL_29549.9
5➜1/0/153:154,1/0/182:184NAIL_04038.4
6➜1/0/158:164,1/0/171:1788x7 Sarcin-Ricin; G-bulgeIL_04346.5
7➜1/0/210:216,1/0/224:2297x6 Sarcin-Ricin; G-bulgeIL_35110.5
8➜1/0/245:248,1/0/265:266Major groove platform; stack outside cWWIL_70995.6
9➜1/0/248:249,1/0/260:265NAIL_19724.1
10➜1/0/274:275,1/0/374:376Single bulged GIL_59137.10
11➜1/0/280:287,1/0/365:369NAIL_77870.1
12➜1/0/290:296,1/0/355:3628x7 Sarcin-Ricin with CC bifurcated pair; G-bulgeIL_59724.1
13➜1/0/307:309,1/0/322:323Single bulged UIL_83039.11
14➜1/0/487:491,1/0/501:515NAIL_31504.1
15➜1/0/548:553,1/0/606:608NAIL_02413.1
16➜1/0/554:555,1/0/602:605NAIL_55658.1
17➜1/0/558:560,1/0/597:599NAIL_01312.13
18➜1/0/562:567,1/0/591:595Triple sheared relatedIL_64879.1
19➜1/0/567:572,1/0/585:5917x6 Sarcin-Ricin; G-bulgeIL_35110.5
20➜1/0/663:667,1/0/679:683AAA cross-strand stackIL_56467.6
21➜1/0/699:702,1/0/726:727Multiple bulged basesIL_13730.12
22➜1/0/705:709,1/0/719:723tSH-tHW-tHSIL_39521.5
23➜1/0/763:765,1/0/899:901NAIL_01312.13
24➜1/0/765:769,1/0/892:899tHW-tHW cross-strand stackIL_17470.5
25➜1/0/788:789,1/0/856:858Single bulged AIL_80007.16
26➜1/0/793:794,1/0/819:821Single bulged GIL_59137.10
27➜1/0/794:798,1/0/815:819Triple shearedIL_56467.6
28➜1/0/830:833,1/0/849:851Major groove platform with extra cWWIL_95485.6
29➜1/0/834:836,1/0/847:848Single bulged UIL_83039.11
30➜1/0/868:870,1/0/880:884Multiple bulged basesIL_90991.5
31➜1/0/936:940,1/0/1026:1034Kink-turnIL_29549.9
32➜1/0/942:944,1/0/1023:1024Minor groove platformIL_06437.11
33➜1/0/952:956,1/0/1011:10155x5 Sarcin-Ricin with intercalated A; G-bulgeIL_83354.1
34➜1/0/956:957,1/0/1009:1011Minor groove platformIL_06437.11
35➜1/0/958:964,1/0/1004:1008NAIL_21121.1
36➜1/0/965:968,1/0/1000:1003NAIL_21570.1
37➜1/0/1095:1099,1/0/1257:1261UAA/GANIL_53523.5
38➜1/0/1101:1108,1/0/1254:1255SSU/LSU pseudoknotIL_15861.6
39➜1/0/1108:1110,1/0/1253:1254Single bulged UIL_83039.11
40➜1/0/1115:1121,1/0/1243:1248NAIL_57188.3
41➜1/0/1136:1138,1/0/1225:1226Single bulged GIL_85053.1
42➜1/0/1147:1155,1/0/1212:1216Kink-turnIL_90538.3
43➜1/0/1163:1167,1/0/1179:1183NAIL_30542.1
44➜1/0/1191:1194,1/0/1205:1206Major groove platformIL_80663.10
45➜1/0/1269:1270,1/0/1286:1289NAIL_12418.1
46➜1/0/1301:1303,1/0/1351:1354Isolated cWS basepairIL_67621.5
47➜1/0/1303:1305,1/0/1349:1351NAIL_01312.13
48➜1/0/1312:1319,1/0/1338:1342Kink-turnIL_29549.9
49➜1/0/1367:1373,1/0/2052:20577x6 Sarcin-Ricin; G-bulgeIL_35110.5
50➜1/0/1416:1419,1/0/1678:1679Major groove platform; stack outside cWWIL_70995.6
51➜1/0/1425:1429,1/0/1437:1439C-loopIL_63596.4
52➜1/0/1456:1460,1/0/1483:1489UAA/GANIL_53523.5
53➜1/0/1465:1467,1/0/1475:1478NAIL_87332.1
54➜1/0/1521:1529,1/0/1662:1665NAIL_69457.1
55➜1/0/1542:1546,1/0/1639:1643tSH-tHW-tHSIL_39521.5
56➜1/0/1570:1574,1/0/1622:1627tSH-tHH-tHSIL_62654.1
57➜1/0/1578:1583,1/0/1612:1618NAIL_66497.1
58➜1/0/1587:1592,1/0/1602:1608Kink-turnIL_16456.1
59➜1/0/1728:1734,1/0/2045:2047NAIL_12566.2
60➜1/0/1741:1743,1/0/2036:2038Isolated tWW turnIL_54997.5
61➜1/0/1744:1747,1/0/2034:2035Major groove platform; stack outside cWWIL_70995.6
62➜1/0/1747:1752,1/0/2031:2034Intercalated tWHIL_01312.13
63➜1/0/1764:1769,1/0/1774:1780tSH-tSH-tHH-tHSIL_66584.5
64➜1/0/1826:1827,1/0/2021:2023Single bulged AIL_80007.16
65➜1/0/1854:1860,1/0/1869:1877NAIL_17069.3
66➜1/0/1893:1896,1/0/1943:1944NAIL_31836.1
67➜1/0/1897:1898,1/0/1939:1942Multiple bulged basesIL_13730.12
68➜1/0/1902:1905,1/0/1934:1935Major groove minor groove platform; mini C-loopIL_09061.4
69➜1/0/1907:1913,1/0/1926:1932NAIL_36973.5
70➜1/0/1974:1975,1/0/2005:2008NAIL_69632.1
71➜1/0/1975:1986,1/0/2002:2005NAIL_70285.1
72➜1/0/2090:2093,1/0/2652:2654NAIL_23663.4
73➜1/0/2095:2097,1/0/2647:2650NAIL_54678.3
74➜1/0/2108:2110,1/0/2477:2478Single bulged UIL_83039.11
75➜1/0/2111:2112,1/0/2473:2476Minor groove platformIL_06437.11
76➜1/0/2122:2124,1/0/2269:2272Isolated tHS basepairIL_38958.6
77➜1/0/2136:2138,1/0/2237:22393x3 AA cWWIL_01312.13
78➜1/0/2279:2280,1/0/2290:2292Single bulged AIL_80007.16
79➜1/0/2331:2333,1/0/2351:2355Isolated tHS basepairIL_38958.6
80➜1/0/2436:2438,1/0/2454:2455NAIL_04038.4
81➜1/0/2489:2490,1/0/2531:2533Major groove platformIL_80663.10
82➜1/0/2492:2494,1/0/2528:2529Major groove platformIL_95601.1
83➜1/0/2494:2496,1/0/2524:2528Major groove minor groove platform with extra cWWIL_96042.4
84➜1/0/2501:2505,1/0/2515:2519Triple shearedIL_56467.6
85➜1/0/2542:2543,1/0/2615:2617Major groove platformIL_02060.4
86➜1/0/2545:2547,1/0/2609:2613Isolated non-canonical cWW with bulgesIL_55456.1
87➜1/0/2547:2548,1/0/2606:2609Multiple bulged basesIL_13730.12
88➜1/0/2557:2558,1/0/2575:2578Minor groove platform with intercalationIL_95601.1
89➜1/0/2626:2627,1/0/2636:2638Single bulged AIL_80007.16
90➜1/0/2672:2676,1/0/2809:2817NAIL_53318.1
91➜1/0/2689:2695,1/0/2700:2705Sarcin-Ricin target in LSU H95; G-bulgeIL_35110.5
92➜1/0/2717:2721,1/0/2761:2763C-loopIL_63596.4
93➜1/0/2724:2728,1/0/2754:2758UAA/GANIL_53523.5
94➜1/0/2732:2733,1/0/2746:2750NAIL_75330.1
95➜1/0/2772:2777,1/0/2797:2802UAA/GAN with extra cWWIL_49767.4
96➜1/0/2855:2857,1/0/2900:2903NAIL_01312.13
97➜1/0/2860:2861,1/0/2895:2897Single bulged AIL_80007.16
98➜1/0/2864:2869,1/0/2888:2892NAIL_83162.3
99➜1/0/2873:2876,1/0/2881:2884Double shearedIL_09705.7
100➜1/9/15:16,1/9/64:66Major groove intercalationIL_40508.4
101➜1/9/21:28,1/9/54:59NAIL_58390.1
102➜1/9/29:30,1/9/50:53Major groove minor groove platform; mini C-loopIL_09061.4
103➜1/9/33:37,1/9/43:47Symmetric double minor groove platformIL_58103.5
104➜1/9/72:74,1/9/107:109NAIL_01312.13
105➜1/9/75:81,1/9/101:1067x6 Sarcin-Ricin; G-bulgeIL_35110.5
106➜1/9/86:88,1/9/95:96Single bulged UIL_83039.11

Problematic loops

#loop idProblemSequence
1➜NA

Valid loops

#loop idlocationannotationmotif
1➜1/0/240:244,1/0/267:273,1/0/377:379NANA
2➜1/0/774:780,1/0/866:868,1/0/884:887NANA
3➜1/0/789:791,1/0/823:828,1/0/853:856NANA
4➜1/0/1159:1161,1/0/1185:1191,1/0/1206:1208NANA
5➜1/0/1404:1409,1/0/1700:1703,1/0/1715:1718NANA
6➜1/0/1412:1415,1/0/1680:1686,1/0/1695:1697NANA
7➜1/0/2131:2134,1/0/2241:2245,1/0/2256:2262NANA
8➜1/0/2329:2331,1/0/2355:2357,1/0/2366:2371NANA
9➜1/0/2552:2555,1/0/2580:2583,1/0/2595:2602NANA
10➜1/9/9:14,1/9/67:71,1/9/110:114NANA

Problematic loops

No problematic loops


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