Motif IL_82444.4 Version IL_82444.4 of this group appears in releases 1.17 to 1.17

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Pairwise interactions
Sequence variants
History

#S	Loop id	PDB	Disc	#Non-core	Annotation	Chain(s)	Standardized name		1		2		3	break		4		5		6	1-6	2-5	3-4
1	IL_1VX6_147	1VX6	0.9272	1		C	5.8S ribosomal RNA	U	96	C	97	G	99	*	C	68	A	69	A	70	cWW	ncSW	cWW
2	IL_4CUV_157	4CUV	0.9526	1		4	5.8S RRNA	U	93	C	94	A	96	*	U	64	A	65	A	66	ncWW	ntSH	cWW
3	IL_3U5H_151	3U5H	0.9026	1		8	5.8S rRNA	U	93	C	94	A	96	*	U	64	A	65	A	66	cWW	ncSW	cWW
4	IL_3U5H_072	3U5H	0.8702	2		5	25S rRNA	U	1818	U	1819	C	1822	*	G	1623	G	1624	A	1625	cWW	ncWW	cWW
5	IL_4IOA_029	4IOA	0.6888	0	Isolated near basepair (H)	X	LSU rRNA	A	883	C	884	A	885	*	U	917	A	918	U	919	cWW		cWW
6	IL_3NJ7_001	3NJ7	0.6688	0		B+A	RNA (10-mer)	C	6	A	7	G	8	*	C	3	A	4	G	5	cWW		cWW
7	IL_3U5F_023	3U5F	0.6661	0		6	18S rRNA	C	411	A	412	U	413	*	A	420	A	421	G	422	cWW		cWW
8	IL_406D_002	406D	0.3467	0	Isolated cWH basepair	A+E	RNA (17-mer)	U	8\|\|A	G	9\|\|A	G	10\|\|A	*	U	25\|\|A	G	26\|\|A	G	27\|\|A	cWW	ncWH	cWW
9	IL_3R1D_002	3R1D	0.1863	0	Isolated cWH basepair	B+A	RNA (11-mer)	C	5	G	6	G	7	*	C	5	G	6	G	7	cWW	cWH	cWW
10	IL_4E5C_001	4E5C	0.1595	0	Isolated cWH basepair	A+B	RNA (19-mer)	C	9	G	10	G	11	*	C	9	G	10	G	11	cWW	cWH	cWW
11	IL_4KQ0_005	4KQ0	0.1514	0	Isolated cWH basepair	B+E	RNA (19-mer)	C	15	G	16	G	17	*	C	3	G	4	G	5	cWW	cWH	cWW
12	IL_4KQ0_001	4KQ0	0.1521	0	Isolated cWH basepair	E+B	RNA (19-mer)	C	15	G	16	G	17	*	C	3	G	4	G	5	cWW	cWH	cWW
13	IL_4KQ0_003	4KQ0	0.1410	0	Isolated cWH basepair	E+B	RNA (19-mer)	C	9	G	10	G	11	*	C	9	G	10	G	11	cWW	cWH	cWW
14	IL_3SJ2_001	3SJ2	0.1130	0	Isolated cWH basepair	B+A	RNA (17-mer)	C	13	G	14	G	15	*	C	7	G	8	G	9	cWW	cWH	cWW
15	IL_3SJ2_002	3SJ2	0.1145	0	Isolated cWH basepair	B+A	RNA (17-mer)	C	10	G	11	G	12	*	C	10	G	11	G	12	cWW	cWH	cWW
16	IL_3SJ2_003	3SJ2	0.1040	0	Isolated cWH basepair	A+B	RNA (19-mer) + RNA (17-mer)	C	13	G	14	G	15	*	C	7	G	8	G	9	cWW	cWH	cWW
17	IL_2R22_001	2R22	0.0685	0		A+B	RNA (13-mer)	U	6	G	7	A	8	*	U	19	G	20	A	21	cWW	cWH	cWW
18	IL_3CZW_001	3CZW	0.0000	0	Isolated cWH basepair	X	RNA (16-mer)	U	10\|\|\|\|2_555	G	11\|\|\|\|2_555	A	12\|\|\|\|2_555	*	U	7	G	8	A	9	cWW	cWH	cWW
19	IL_3CZW_002	3CZW	0.0000	0	Isolated cWH basepair	X	RNA (16-mer)	U	10	G	11	A	12	*	U	7\|\|\|\|2_555	G	8\|\|\|\|2_555	A	9\|\|\|\|2_555	cWW	cWH	cWW
20	IL_4BPP_012	4BPP	0.1015	0		A	18S RRNA	C	144	G	145	A	146	*	U	156	G	157	G	158	cWW	cWH	cWW
21	IL_4KQ0_002	4KQ0	0.1292	0	Isolated cWH basepair	E+B	RNA (19-mer)	C	12	G	13	G	14	*	C	6	G	7	G	8	cWW	cWH	cWW
22	IL_4KQ0_004	4KQ0	0.1294	0	Isolated cWH basepair	B+E	RNA (19-mer)	C	12	G	13	G	14	*	C	6	G	7	G	8	cWW	cWH	cWW
23	IL_3U5F_044	3U5F	0.2602	0		6	18S rRNA	C	848	C	849	A	850	*	U	822	G	823	G	824	cWW	ncWH	cWW
24	IL_3U5F_070	3U5F	0.2419	0		6	18S rRNA	C	1323	G	1324	A	1325	*	U	1290	G	1291	G	1292	cWW	cWH	cWW
25	IL_2AW7_011	2AW7	0.2217	0		A	16S ribosomal RNA	G	144	G	145	G	146	*	C	176	G	177	C	178	cWW	cWH	cWW
26	IL_1VX6_145	1VX6	0.2605	1		B	5S ribosomal RNA	G	82	G	83	G	85	*	C	92	G	93	C	94	cWW	cWH	cWW
27	IL_1X8W_005	1X8W	0.4672	5		A	Tetrahymena ribozyme RNA	G	134	U	135	A	136	*	U	182	A	187	C	189	cWW	cWH	cWW
28	IL_1GID_013	1GID	0.4653	5		B	P4-P6 RNA RIBOZYME DOMAIN	G	134	U	135	A	136	*	U	182	A	187	C	189	cWW	cWH	cWW
29	IL_1GID_006	1GID	0.4931	5		A	P4-P6 RNA RIBOZYME DOMAIN	G	134	U	135	A	136	*	U	182	A	187	C	189	cWW	cWH	cWW
30	IL_4KTG_005	4KTG	0.2479	0		B+E	RNA (19-mer)	G	215	G	216	C	217	*	G	203	G	204	C	205	cWW	cWH	cWW
31	IL_4KTG_001	4KTG	0.2487	0		E+B	RNA (19-mer)	G	215	G	216	C	217	*	G	203	G	204	C	205	cWW	cWH	cWW
32	IL_4KTG_002	4KTG	0.3534	0		B+E	RNA (19-mer)	G	206	G	207	C	208	*	G	212	G	213	C	214	cWW	cWH	cWW
33	IL_4KTG_004	4KTG	0.3512	0		E+B	RNA (19-mer)	G	206	G	207	C	208	*	G	212	G	213	C	214	cWW	cWH	cWW
34	IL_3W3S_003	3W3S	0.2680	0	Isolated cWH basepair	B	Selenocysteine transfer RNA	A	47\|\|\|N	G	47\|\|\|O	C	47\|\|\|P	*	G	47\|\|\|A	G	47\|\|\|B	U	47\|\|\|C	cWW	cWH	cWW
35	IL_4KTG_003	4KTG	0.3009	0		B+E	RNA (19-mer)	G	209	G	210	C	211	*	G	209	G	210	C	211	cWW	cWH	cWW
36	IL_420D_002	420D	0.3063	0		A+B	RNA (16-mer)	A	10	A	11	U	12	*	A	21	G	22	U	23	cWW	cWH	cWW
37	IL_420D_001	420D	0.2917	0		B+A	RNA (16-mer)	A	26	A	27	U	28	*	A	5	G	6	U	7	cWW	cWH	cWW
38	IL_3U5F_022	3U5F	0.3331	0		6	18S rRNA	U	406	A	407	C	408	*	G	389	G	390	A	391	cWW	cWH	cWW
39	IL_4BPP_020	4BPP	0.2997	0		A	18S RRNA	U	397	A	398	C	399	*	G	380	G	381	A	382	cWW	cWH	cWW
40	IL_3J7A_019	3J7A	0.3250	0	Isolated cWH basepair (H)	A	SSU rRNA	U	412	A	413	C	414	*	G	395	G	396	A	397	cWW	cWH	cWW
41	IL_2XXA_011	2XXA	0.4105	1		G	SSRP RNA	A	19	G	20	C	21	*	G	78	G	79	U	81	cWW	cWH	cWW
42	IL_4QCN_025	4QCN	0.7835	1		A	23S Ribosomal RNA	C	891	G	892	C	893	*	G	976	A	978	G	979	cWW		cWW

3D structures

Complete motif including flanking bases

Sequence	Counts
CGG*CGG	10
GGC*GGC	5
UGA*UGA	3
GUA*UAAUAAGC	3
UAC*GGA	3
UCGA*UAA	2
CGA*UGG	2
AAU*AGU	2
UCAG*CAA	1
UUUUC*GGA	1
ACA*UAU	1
CAG*CAG	1
CAU*AAG	1
UGG*UGG	1
CCA*UGG	1
GGG*CGC	1
GGUG*CGC	1
AGC*GGU	1
AGC*GGGU	1
CGC*GGAG	1

Non-Watson-Crick part of the motif

Sequence	Counts
G*G	23
A*G	5
U*AAUAAG	3
CG*A	2
A*A	2
CA*A	1
UUU*G	1
C*A	1
C*G	1
GU*G	1
G*GG	1
G*GA	1

Release history

Release	1.17
Date	2014-09-04
Status	Updated, 2 parents

Parent motifs

Parent motif	Common motif instances	Only in IL_82444.4	Only in the parent motif
IL_82444.3 Compare	IL_4KQ0_001, IL_4KQ0_002, IL_4KQ0_003, IL_4KQ0_004, IL_4KQ0_005, IL_420D_001, IL_4BPP_020, IL_4KTG_004, IL_4KTG_005, IL_2AW7_011, IL_4KTG_001, IL_4KTG_002, IL_4KTG_003, IL_420D_002, IL_406D_002, IL_3U5F_044, IL_3R1D_002, IL_1GID_013, IL_3W3S_003, IL_3U5F_022, IL_3U5F_070, IL_3NJ7_001, IL_4E5C_001, IL_1X8W_005, IL_4BPP_012, IL_4IOA_029, IL_3U5H_072, IL_1GID_006, IL_4CUV_157, IL_3SJ2_002, IL_3SJ2_003, IL_3SJ2_001, IL_3U5H_151, IL_3CZW_002, IL_3CZW_001, IL_2R22_001, IL_2XXA_011	IL_3U5F_023, IL_1VX6_147, IL_1VX6_145, IL_4QCN_025, IL_3J7A_019	IL_4NVV_027
IL_83000.1 Compare	IL_3U5F_023	IL_4KQ0_001, IL_4KQ0_002, IL_4KQ0_003, IL_4KQ0_004, IL_4KQ0_005, IL_420D_001, IL_4BPP_020, IL_4KTG_004, IL_4KTG_005, IL_2AW7_011, IL_4KTG_001, IL_4KTG_002, IL_4KTG_003, IL_420D_002, IL_406D_002, IL_3U5F_044, IL_3R1D_002, IL_1GID_013, IL_3W3S_003, IL_3U5F_022, IL_1VX6_147, IL_3U5F_070, IL_1VX6_145, IL_4QCN_025, IL_3NJ7_001, IL_4E5C_001, IL_1X8W_005, IL_4BPP_012, IL_4IOA_029, IL_3U5H_072, IL_1GID_006, IL_4CUV_157, IL_3SJ2_002, IL_3SJ2_003, IL_3SJ2_001, IL_3U5H_151, IL_3J7A_019, IL_3CZW_002, IL_3CZW_001, IL_2R22_001, IL_2XXA_011	IL_4CUV_026, IL_4CUV_020, IL_3TD0_002, IL_3KTW_002, IL_1FJG_010, IL_2AW7_052, IL_4IOA_010, IL_1NLC_002, IL_1T0E_002, IL_1NLC_001, IL_4FNJ_001, IL_4A1B_115, IL_3U5F_041, IL_4A1B_052, IL_1O9M_004, IL_2O3V_001, IL_4IOA_078, IL_4J5V_003, IL_4J5V_002, IL_4J5V_001, IL_4CUX_069, IL_2QBG_020, IL_4J5V_006, IL_4J5V_005, IL_3SZX_001, IL_4KNQ_001, IL_4KNQ_002, IL_4KNQ_004, IL_4KNQ_005, IL_157D_002, IL_157D_001, IL_4CUV_139, IL_1ZH5_001, IL_4CUV_133, IL_2FQN_001, IL_1YZ9_002, IL_2FQN_004, IL_4CUX_083, IL_4BPP_015, IL_4BPP_068, IL_4E59_001, IL_4CUX_089, IL_4CUV_156, IL_4A1B_048, IL_2QBG_018, IL_1VW3_079, IL_4JK0_001, IL_2O3X_004, IL_4A1B_041, IL_1Z7F_002, IL_1FJG_056, IL_3U5F_050, IL_1Z7F_001, IL_4A1B_112, IL_3GLP_001, IL_4BPP_056, IL_3BNL_004, IL_4CUX_015, IL_3U5F_015, IL_3BNL_001, IL_3TD1_006, IL_4E48_005, IL_4E48_004, IL_4E48_006, IL_4E48_001, IL_3U5H_017, IL_4E48_003, IL_4E48_002, IL_3CUN_002, IL_3FO4_001, IL_4BPP_002, IL_1XJR_003, IL_4BPP_001, IL_2QBG_083, IL_4IOA_054, IL_3U5F_082, IL_4BPP_038, IL_1VW3_009, IL_3U5H_008, IL_2QEK_002, IL_2QEK_001, IL_1S72_062, IL_4A1B_071, IL_3U5F_043, IL_1VW3_001, IL_4CUV_032, IL_1ZEV_004, IL_1ZEV_005, IL_1ZEV_006, IL_1ZEV_001, IL_1ZEV_002, IL_1ZEV_003, IL_4JK0_002, IL_2O3V_004, IL_4NVV_067, IL_4JK0_005, IL_4CUX_003, IL_3U5H_087, IL_4K31_003, IL_1S72_047, IL_4BPP_073, IL_4BPP_070, IL_3NJ7_002, IL_4K31_002, IL_4K31_001, IL_2Q1R_002, IL_4BPP_079, IL_4CUV_074, IL_4IOA_104, IL_4A1B_061, IL_4J5V_007, IL_1VW3_016, IL_4K31_004, IL_4IOA_109, IL_4IOA_025, IL_4NVV_043, IL_4KYY_001, IL_4KYY_003, IL_4NGF_002, IL_4NVV_055, IL_4CUX_034, IL_4BPP_082, IL_4BPP_083, IL_1KFO_003, IL_1KFO_002, IL_3U5F_034, IL_4JK0_004, IL_3U5F_036, IL_3U5H_028, IL_4CUV_008, IL_3UMY_001, IL_5MSF_001, IL_1ZX7_002, IL_4A1C_009, IL_1VW3_068, IL_1FJG_062, IL_3U5F_084, IL_3U5F_087, IL_3U5H_149, IL_4A1B_013, IL_3TD1_001, IL_1VW3_015, IL_4IOA_030, IL_3BNQ_001, IL_3U5F_089, IL_1MFQ_003, IL_3BNQ_006, IL_1MFQ_002, IL_4CUX_022, IL_4CUX_023, IL_3BNP_001, IL_3D0U_006, IL_3BNP_004, IL_3U5F_002, IL_3BNT_006, IL_3BNT_001, IL_4BPP_034, IL_3IVK_004, IL_405D_002, IL_4CUV_086, IL_1MWL_004, IL_405D_001, IL_1MWL_001, IL_1T0D_002, IL_4CUV_118, IL_1MZP_001, IL_1UN6_005, IL_3U5H_036, IL_4AOB_005, IL_2AW7_064, IL_2AW7_063, IL_1S72_095, IL_1VW3_031, IL_3RW6_004, IL_3U5H_133, IL_3DIR_006, IL_4CUV_122, IL_2ZKO_001, IL_3SYW_002, IL_3SYW_003, IL_3SYW_001, IL_2QBG_030, IL_1FJG_006, IL_3U5H_022, IL_3U5H_076, IL_3MEI_002, IL_4NVV_036, IL_1RPU_001, IL_4A1B_015, IL_1YZ9_001, IL_4CUV_047, IL_4CUV_049, IL_4A1B_034, IL_4NVV_093, IL_4IOA_013, IL_3RG5_001, IL_3U5H_128, IL_2OE5_001, IL_4IOA_019, IL_3U5H_121, IL_1U6B_005, IL_4M6D_011, IL_1VW3_043, IL_1S72_024, IL_4CUV_052, IL_3U5F_063, IL_3U5F_061, IL_3U5H_044, IL_1FJG_044, IL_1VW3_049, IL_2QBG_096, IL_4CUX_040, IL_4BPP_058, IL_3SZX_002, IL_3SZX_003, IL_4CUX_044, IL_2QBG_065, IL_3GLP_002, IL_3NJ6_002, IL_3NJ6_001, IL_4BPP_088, IL_4FNJ_002, IL_4A1B_083, IL_3TD0_005, IL_4NVV_083, IL_3TD0_006, IL_3TD0_001, IL_1VW3_092, IL_1ZX7_008, IL_1U6B_001, IL_4A1B_027, IL_4A1B_024, IL_4M4O_001, IL_4BPP_037, IL_4CUV_039, IL_4IOA_044, IL_4NVV_016, IL_3U5H_114, IL_4CUV_030, IL_3U5H_116, IL_3U5H_118, IL_4CUX_091, IL_3U5F_074, IL_3U5H_051, IL_2QBG_034, IL_4A1B_028, IL_3U5F_072, IL_4KYY_002, IL_2Q1R_001, IL_4A1B_104, IL_1FJG_058, IL_4M4O_002, IL_4CUX_073, IL_1U9S_007, IL_4CUV_120, IL_4IOA_091, IL_4NVV_019, IL_3U5H_049, IL_2AW7_062

Children motifs

Child motif	Common motif instances	Only in IL_82444.4	Only in the child motif
IL_85638.1 Compare	IL_4KQ0_001, IL_4KQ0_002, IL_4KQ0_003, IL_420D_002, IL_4KQ0_005, IL_420D_001, IL_4BPP_020, IL_4KTG_004, IL_4KTG_005, IL_2AW7_011, IL_4KTG_001, IL_4KTG_002, IL_4KTG_003, IL_4KQ0_004, IL_406D_002, IL_3U5F_044, IL_3R1D_002, IL_3W3S_003, IL_3U5F_023, IL_3U5F_022, IL_1VX6_147, IL_1VX6_145, IL_3NJ7_001, IL_4E5C_001, IL_4CUV_157, IL_4IOA_029, IL_3U5H_072, IL_3U5H_151, IL_4BPP_012, IL_3SJ2_002, IL_3SJ2_003, IL_3SJ2_001, IL_3U5F_070, IL_3J7A_019, IL_2R22_001, IL_3CZW_001, IL_3CZW_002	IL_1GID_006, IL_2XXA_011, IL_4QCN_025, IL_1X8W_005, IL_1GID_013	IL_4KYY_002, IL_1VW3_049, IL_2QBG_065, IL_4QCN_063, IL_2QEK_002, IL_1S72_062
IL_04238.1 Compare	IL_1GID_006, IL_1GID_013, IL_4QCN_025, IL_2XXA_011	IL_4KQ0_001, IL_4KQ0_002, IL_4KQ0_003, IL_420D_002, IL_4KQ0_005, IL_420D_001, IL_4BPP_020, IL_4KTG_004, IL_4KTG_005, IL_2AW7_011, IL_4KTG_001, IL_4KTG_002, IL_4KTG_003, IL_4KQ0_004, IL_406D_002, IL_3U5F_044, IL_3R1D_002, IL_3W3S_003, IL_3U5F_023, IL_3U5F_022, IL_1VX6_147, IL_1VX6_145, IL_3NJ7_001, IL_4E5C_001, IL_1X8W_005, IL_4CUV_157, IL_4IOA_029, IL_3U5H_072, IL_3U5H_151, IL_4BPP_012, IL_3SJ2_002, IL_3SJ2_003, IL_3SJ2_001, IL_3U5F_070, IL_3J7A_019, IL_2R22_001, IL_3CZW_001, IL_3CZW_002	IL_2ZI0_001
IL_58203.1 Compare	IL_1X8W_005	IL_4KQ0_001, IL_4KQ0_002, IL_4KQ0_003, IL_420D_002, IL_4KQ0_005, IL_420D_001, IL_4BPP_020, IL_4KTG_004, IL_4KTG_005, IL_2AW7_011, IL_4KTG_001, IL_4KTG_002, IL_4KTG_003, IL_4KQ0_004, IL_406D_002, IL_3U5F_044, IL_3R1D_002, IL_1GID_013, IL_3W3S_003, IL_3U5F_023, IL_3U5F_022, IL_1VX6_147, IL_1VX6_145, IL_4QCN_025, IL_3NJ7_001, IL_4E5C_001, IL_4CUV_157, IL_4IOA_029, IL_3U5H_072, IL_1GID_006, IL_4BPP_012, IL_3SJ2_002, IL_3SJ2_003, IL_3SJ2_001, IL_3U5H_151, IL_3U5F_070, IL_3J7A_019, IL_2R22_001, IL_3CZW_001, IL_3CZW_002, IL_2XXA_011

Annotations: (26)
Isolated cWH basepair (14)
Isolated cWH basepair (H) (1)
Isolated near basepair (H) (1)
Basepair signature: cWW-cWH-cWW
Heat map statistics: Min 0.00 | Avg 0.48 | Max 1.11

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java.vendor: Java2Script (HTML5)

java.version: 2016-04-21 14:47:41 (JSmol/j2s)

os.name: Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)

Access: ALL

memory: 0.0/0.0

processors available: 1

useCommandThread: false

appletId:jmolApplet0 (signed)

loadScript https://rna.bgsu.edu/rna3dhub//js/jsmol/j2s//core/corescript.z.js

Jmol getValue emulate null

defaults = "Jmol"

Jmol getValue boxbgcolor null

Jmol getValue bgcolor white

backgroundColor = "white"

Jmol getValue ANIMFRAMECallback null

Jmol getValue APPLETREADYCallback Jmol._readyCallback

APPLETREADYCallback = "Jmol._readyCallback"

callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY

Jmol getValue ATOMMOVEDCallback null

Jmol getValue CLICKCallback null

Jmol getValue DRAGDROPCallback null

Jmol getValue ECHOCallback null

Jmol getValue ERRORCallback null

Jmol getValue EVALCallback null

Jmol getValue HOVERCallback null

Jmol getValue IMAGECallback null

Jmol getValue LOADSTRUCTCallback null

Jmol getValue MEASURECallback null

Jmol getValue MESSAGECallback null

Jmol getValue MINIMIZATIONCallback null

Jmol getValue SERVICECallback null

Jmol getValue PICKCallback null

Jmol getValue RESIZECallback null

Jmol getValue SCRIPTCallback null

Jmol getValue SYNCCallback null

Jmol getValue STRUCTUREMODIFIEDCallback null

Jmol getValue doTranslate null

language=en_US

Jmol getValue popupMenu null

Jmol getValue script null

Jmol getValue loadInline null

Jmol getValue load null

Jmol applet jmolApplet0__36880240213278__ ready

script 1 started

loadScript https://rna.bgsu.edu/rna3dhub//js/jsmol/j2s//core/coretext.z.js

Script completed

Jmol script terminated

script 2 started

Script completed

Jmol script terminated

script 3 started

Script completed

Jmol script terminated

script 4 started

Script completed

Jmol script terminated

Coloring options: Nucleotide numbers

Motif IL_82444.4 Version IL_82444.4 of this group appears in releases 1.17 to 1.17 Download Csv Json

3D structures

Complete motif including flanking bases

Non-Watson-Crick part of the motif

Release history

Parent motifs

Children motifs

Motif IL_82444.4 Version IL_82444.4 of this group appears in releases 1.17 to 1.17

Download

Csv

Json