Motif HL_89380.1 Version HL_89380.1 of this group appears in releases 3.77 to 3.79

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Pairwise interactions
Sequence variants
History

#S	Loop id	PDB	Disc	#Non-core	Annotation	Chain(s)	Standardized name		1		2		3		4		5		6		7	1-7	2-6
1	HL_6CZR_100	6CZR	0.2563	3	T-loop with 3 stacked bulged bases	1a	SSU rRNA	C	1296	U	1297	G	1298	C	1299	A	1300	A	1301	G	1305	cWW	ntWH
2	HL_4LFB_029	4LFB	0.2518	3	T-loop with 3 stacked bulged bases	A	SSU rRNA	C	1314	U	1315	G	1316	C	1317	A	1318	A	1319	G	1323	cWW	tWH
3	HL_5J7L_028	5J7L	0.2786	3	T-loop with 3 stacked bulged bases	AA	SSU rRNA	C	1314	U	1315	G	1316	C	1317	A	1318	A	1319	G	1323	cWW	tWH
4	HL_2A64_002	2A64	0.2985	1	T-loop with 2 stacked bulged bases	A	ribonuclease P RNA	C	69	U	70	G	71	A	72	G	73	A	74	G	76	cWW	tWH
5	HL_4WF9_010	4WF9	0.2421	1	T-loop with 2 stacked bulged bases	X	LSU rRNA	C	348	U	349	G	350	G	351	A	352	A	353	G	355	cWW	tWH
6	HL_7RQB_010	7RQB	0.2422	1	T-loop with 1 bulged base (H)	1A	LSU rRNA	U	305	U	306	G	307	G	308	G	309	A	310	G	312	cWW	tWH
7	HL_5T5A_001	5T5A	0.1715	2	T-loop with 2 stacked bulged bases	A	DNA/RNA (71-MER)	G	21	U	22	G	23	C	24	A	25	A	26	C	29	cWW	tWH
8	HL_7A0S_010	7A0S	0.1410	1	T-loop with 1 bulged base	X	LSU rRNA	C	316	U	317	G	318	G	319	A	320	A	321	G	323	cWW	tWH
9	HL_5J7L_142	5J7L	0.1571	1	T-loop with 2 stacked bulged bases	DA	LSU rRNA	C	305	U	306	G	307	G	308	A	309	A	310	G	312	cWW	tWH
10	HL_5DH6_002	5DH6	0.1458	1	T-loop with 2 stacked bulged bases	A	Hammerhead ribozyme (type III)	C	27	U	28	G	29	G	30	G	31	A	32	G	34	cWW	tWH
11	HL_5Y85_003	5Y85	0.1405	2	T-loop with 2 stacked bulged bases	D	DNA/RNA (50-MER)	G	11	U	12	G	13	C	14	A	15	A	16	C	19	cWW	tWH
12	HL_4FRN_005	4FRN	0.1467	2	T-loop with 2 bulged bases not stacked	B	Cobalamin riboswitch aptamer domain	G	28	U	29	G	30	U	31	A	32	A	33	C	36	cWW	tWH
13	HL_4V9F_034	4V9F	0.2014	2	T-loop with 2 stacked bulged bases	0	LSU rRNA	G	1387	U	1388	G	1389	A	1390	G	1391	A	1392	C	1395	cWW	tWH
14	HL_7A0S_032	7A0S	0.2003	2	T-loop with 2 stacked bulged bases	X	LSU rRNA	G	1294	U	1295	G	1296	A	1297	G	1298	A	1299	C	1302	cWW	tWH
15	HL_7RQB_033	7RQB	0.2110	2	T-loop with 2 stacked bulged bases (H)	1A	LSU rRNA	G	1281	U	1282	G	1283	A	1284	G	1285	A	1286	C	1289	cWW	tWH
16	HL_4WF9_032	4WF9	0.2233	2	T-loop with 2 stacked bulged bases	X	LSU rRNA	G	1318	U	1319	G	1320	A	1321	G	1322	A	1323	C	1326	cWW	tWH
17	HL_5TBW_031	5TBW	0.1988	2	T-loop with 2 stacked bulged bases	1	LSU rRNA	A	1462	U	1463	G	1464	A	1465	G	1466	A	1467	U	1470	cWW	tWH
18	HL_5J7L_165	5J7L	0.2482	2	T-loop with 2 stacked bulged bases	DA	LSU rRNA	G	1281	U	1282	G	1283	A	1284	A	1285	A	1286	C	1289	cWW	tWH
19	HL_6UFG_008	6UFG	0.2634	2	T-loop with 2 stacked bulged bases	B	tRNA	G	54	U	55	U	56	C	57	A	58	A	59	C	62	cWW	tWH
20	HL_6MJ0_009	6MJ0	0.1987	2	T-loop with 2 stacked bulged bases	B	tRNA-like 3' UTR element	G	66	U	67	G	68	C	69	A	70	A	71	C	74	cWW	tWH
21	HL_4V9F_010	4V9F	0.1453	1	T-loop with 2 stacked bulged bases	0	LSU rRNA	U	312	U	313	G	314	G	315	A	316	A	317	A	319	cWW	tWH
22	HL_5TBW_005	5TBW	0.1716	1	T-loop with 2 stacked bulged bases	1	LSU rRNA	U	194	U	195	G	196	G	197	A	198	A	199	A	201	cWW	tWH
23	HL_3F2X_004	3F2X	0.0786	2	T-loop with 2 bulged bases not stacked	X	FMN riboswitch	G	68	U	69	G	70	A	71	A	72	A	73	C	76	cWW	tWH
24	HL_6DN2_003	6DN2	0.0000	2	T-loop with 2 bulged bases not stacked	Y	RNA (56-MER)	G	68	U	69	G	70	A	71	A	72	A	73	C	76	cWW	tWH
25	HL_5C45_003	5C45	0.0708	2	T-loop with 2 bulged bases not stacked	Y	FMN Riboswitch	G	68	U	69	G	70	A	71	A	72	A	73	C	76	cWW	tWH
26	HL_4FRG_001	4FRG	0.1051	2	T-loop with 2 bulged bases not stacked	B	cobalamin riboswitch aptamer domain	G	28	U	29	G	30	A	31	A	32	A	33	C	36	cWW	tWH
27	HL_6DN2_001	6DN2	0.1178	2	T-loop with 2 bulged bases not stacked	X	RNA RIBOSWITCH	G	17	U	18	G	19	A	20	A	21	A	22	C	25	cWW	tWH
28	HL_3F2X_001	3F2X	0.1097	2	T-loop with 2 bulged bases not stacked	X	FMN riboswitch	G	17	U	18	G	19	A	20	A	21	A	22	C	25	cWW	tWH
29	HL_5C45_001	5C45	0.1118	2	T-loop with 2 bulged bases not stacked	X	FMN Riboswitch	G	17	U	18	G	19	A	20	A	21	A	22	C	25	cWW	tWH
30	HL_4WF9_018	4WF9	0.2536	3	T-loop with 2 stacked bulged bases	X	LSU rRNA	U	609	U	610	U	611	U	612	G	613	U	614	A	618	cWW
31	HL_5J7L_150	5J7L	0.2723	3	T-loop with 2 stacked bulged bases	DA	LSU rRNA	U	566	U	567	U	568	U	569	G	570	U	571	A	575	cWW
32	HL_7RQB_018	7RQB	0.2728	3	T-loop with 2 stacked bulged bases (H)	1A	LSU rRNA	U	566	A	567	U	568	U	569	G	570	A	571	A	575	cWW
33	HL_7A0S_018	7A0S	0.3229	3	T-loop with 2 stacked bulged bases	X	LSU rRNA	U	575	A	576	U	577	U	578	G	579	A	580	A	584	cWW
34	HL_5TBW_014	5TBW	0.3240	3	T-loop with 2 stacked bulged bases	1	LSU rRNA	U	640	C	641	U	642	U	643	G	644	A	645	A	649	cWW

3D structures

Complete motif including flanking bases

Sequence	Counts
GUGAAAUUC	7
CUGGAAAG	3
GUGAGAAUC	3
CUGCAACCCG	2
UAUUGAAGCA	2
CUGCAACUCG	1
CUGAGAUG	1
UUGGGAAG	1
GUGCAAGCC	1
CUGGGAUG	1
GUGCAAGUC	1
GUGUAAUUC	1
GUGAGAACC	1
AUGAGAACU	1
GUGAAAAGC	1
GUUCAAGUC	1
GUGCAACUC	1
UUGGAAUA	1
UUGGAACA	1
UUUUGUAGAA	1
UUUUGUAUAA	1
UCUUGAAACA	1

Non-Watson-Crick part of the motif

Sequence	Counts
UGAAAUU	7
UGGAAA	3
UGAGAAU	3
UGCAACCC	2
UGAGAAC	2
AUUGAAGC	2
UGCAACUC	1
UGAGAU	1
UGGGAA	1
UGCAAGC	1
UGGGAU	1
UGCAAGU	1
UGUAAUU	1
UGAAAAG	1
UUCAAGU	1
UGCAACU	1
UGGAAU	1
UGGAAC	1
UUUGUAGA	1
UUUGUAUA	1
CUUGAAAC	1

Release history

Release	3.77	3.78	3.79
Date	2023-12-06	2024-01-03	2024-01-03
Status	New id, > 2 parents	Exact match	Exact match

Parent motifs

This motif has no parent motifs.

Children motifs

This motif has no children motifs.

Annotations: T-loop with 2 stacked bulged bases (19)
T-loop with 2 bulged bases not stacked (8)
T-loop with 3 stacked bulged bases (3)
T-loop with 2 stacked bulged bases (H) (2)
T-loop with 1 bulged base (1)
T-loop with 1 bulged base (H) (1)
Basepair signature: cWW-tWH-F-F-F
Heat map statistics: Min 0.07 | Avg 0.27 | Max 0.83

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