Summary

Wikipedia annotation Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam families in Wikipedia. This family is described by a Wikipedia entry IMES-2 RNA motif. More...

The Wikipedia text that you see displayed on our web site was retrieved from Wikipedia. This means that the information we display is a copy of the information from the Wikipedia database. The button above ("Edit wikipedia entry") takes you to the edit page for the article directly within Wikipedia.

Before you edit for the first time

Wikipedia is a free, online encyclopedia. Although anyone can edit or contribute to an article, Wikipedia has some strong editing guidelines and policies, which promote the Wikipedia standard of style and etiquette. Your edits and contributions are more likely to be accepted (and remain) if they are in accordance with this policy.

You should take a few minutes to view the following pages:

Things you should know

How your contribution will be recorded

Anyone can edit a Wikipedia entry. You can do this either as a new user or you can register with Wikipedia and log on. When you click on the "Edit Wikipedia entry" button, your browser will direct you to the edit page for this entry in Wikipedia. If you are a registered user and currently logged in, your changes will be recorded under your Wikipedia user name. However, if you are not a registered user or are not logged on, your changes will be logged under your computer’s IP address. This has two main implications. Firstly, as a registered Wikipedia user your edits are more likely seen as valuable contribution (although all edits are open to community scrutiny regardless). Secondly, if you edit under an IP address you may be sharing this IP address with other users. If your IP address has previously been blocked (due to being flagged as a source of 'vandalism') your edits will also be blocked. You can find more information on this and creating a user account at Wikipedia.

If you have problems editing a particular page, contact us at rfam-help@ebi.ac.uk and we will try to help.

Information we would like to see added

We would value contributions that are referenced directly to the primary literature. Information on structure and function will be especially valuable.

Adding references is explained by this Wikipedia how-to article.

For a good example of what is possible in wikipedia, look at the Hammerhead Ribozyme entry.

Does Rfam agree with the content of the Wikipedia entry ?

Rfam has chosen to create Wikipedia entries for all of our RNA families and to open them up to community annotation. While the original Wikipedia article that we import was (in most cases) generated from Rfam annotations, the Wikipedia article you see now may bear little resemblance to that original text. The Wikipedia community does monitor edits to try to ensure that (a) the quality of article annotation increases, and (b) vandalism is very quickly dealt with. However, we would like to emphasise that Rfam does not curate the Wikipedia entries and we cannot guarantee the accuracy of the information on the Wikipedia page.

Contact us

If you have problems editing or experience problems with these pages please contact us.

If you are interested in contributing to a wide range of articles relating to RNA, see the Wikiproject RNA page.

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

Sequences

Quick actions

Table view (330 sequence regions)

Original order	Accession	Bit score	Type	Start	End	Description	Species
0	URS00006C56F0_12908	N/A	seed	1	139	unclassified sequences IMES-2 RNA motif	unclassified sequences
1	URS00006397E1_12908	N/A	seed	1	139	unclassified sequences IMES-2 RNA motif	unclassified sequences
2	URS000072A131_12908	N/A	seed	1	138	unclassified sequences IMES-2 RNA motif	unclassified sequences
3	URS00006FFC07_12908	N/A	seed	1	138	unclassified sequences IMES-2 RNA motif	unclassified sequences
4	URS0000625B57_12908	N/A	seed	1	135	unclassified sequences IMES-2 RNA motif	unclassified sequences
5	URS0000D6A29F_12908	N/A	seed	1	107	unclassified sequences IMES-2 RNA motif	unclassified sequences
6	URS0000D6AB31_12908	N/A	seed	1	108	unclassified sequences IMES-2 RNA motif	unclassified sequences
7	URS000071CBD7_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
8	URS000065DB13_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
9	URS000066FF22_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
10	URS0000717293_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
11	URS000072A0EF_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
12	URS0000638D80_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
13	URS000065947B_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
14	URS000067A2FF_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
15	URS00006FDC93_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
16	URS0000724E50_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
17	URS0000D68E14_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
18	URS00006A1131_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
19	URS000070790C_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
20	URS0000624267_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
21	URS00006655EE_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
22	URS000071C4BA_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
23	URS0000D664B5_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
24	URS00006F2A79_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
25	URS000062EE34_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
26	URS00006D30A8_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
27	URS000072A149_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
28	URS0000650BB6_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
29	URS00006EB0D3_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
30	URS00006419EE_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
31	URS00006F0559_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
32	URS00006514A6_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
33	URS0000721D86_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
34	URS0000D67392_12908	N/A	seed	1	139	unclassified sequences IMES-2 RNA motif	unclassified sequences
35	URS00006DF9CC_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
36	URS00006823CC_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
37	URS000071752C_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
38	URS00006753EF_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
39	URS000069F8F5_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
40	URS000067B3BC_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
41	URS0000726230_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
42	URS00006A7A4B_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
43	URS00006DB1D4_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
44	URS000071A418_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
45	URS000063BC23_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
46	URS0000671991_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
47	URS000072AB78_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
48	URS0000689D4A_12908	N/A	seed	1	143	unclassified sequences IMES-2 RNA motif	unclassified sequences
49	URS000067A507_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
50	URS00006E5E52_12908	N/A	seed	1	143	unclassified sequences IMES-2 RNA motif	unclassified sequences
51	URS000068F323_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
52	URS0000695BAC_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
53	URS00006B021D_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
54	URS0000651847_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
55	URS000068196A_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
56	URS0000623A68_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
57	URS00006CB351_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
58	URS00006800CD_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
59	URS00006B79DC_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
60	URS000071B124_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
61	URS000065B8E8_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
62	URS00006A31CB_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
63	URS000068626B_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
64	URS000065F66E_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
65	URS000068FA7C_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
66	URS00006BA60A_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
67	URS000070012C_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
68	URS0000623AFD_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
69	URS0000728129_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
70	URS000067F859_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
71	URS00007129F0_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
72	URS00006FCCCA_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
73	URS00006B1003_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
74	URS000070AE2E_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
75	URS000072D31D_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
76	URS000071D456_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
77	URS00006A65F2_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
78	URS00006951ED_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
79	URS00006D7B72_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
80	URS0000722541_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
81	URS00006C4C7D_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
82	URS00006D22BB_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
83	URS000068B057_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
84	URS00006AB02C_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
85	URS00007020D0_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
86	URS000065B816_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
87	URS00006BC36C_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
88	URS000072C4E2_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
89	URS000070852C_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
90	URS00006952EF_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
91	URS000069245D_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
92	URS0000657DB6_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
93	URS00006C0D53_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
94	URS0000684D4E_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
95	URS00006DDF47_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
96	URS0000698759_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
97	URS00006BC9F8_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
98	URS000067871D_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
99	URS00006551B4_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
100	URS000067B2E5_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
101	URS000064D629_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
102	URS000069A719_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
103	URS0000691E52_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
104	URS000066A45E_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
105	URS00006D92A2_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
106	URS00006B9C8C_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
107	URS0000689C15_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
108	URS00007140F8_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
109	URS000071A25F_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
110	URS000069EC0A_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
111	URS000064DD5A_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
112	URS00006E9F66_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
113	URS000063533C_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
114	URS0000629A4A_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
115	URS000070B0BA_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
116	URS00006637D8_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
117	URS000070DD19_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
118	URS0000628522_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
119	URS000067F210_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
120	URS00006D0483_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
121	URS000066C09F_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
122	URS000062B5B0_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
123	URS00006829AF_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
124	URS00007214BA_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
125	URS0000668C1D_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
126	URS00006657A1_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
127	URS000070F9C7_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
128	URS0000653ACE_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
129	URS00006CC280_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
130	URS00006B4CA7_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
131	URS0000704ACC_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
132	URS000063FC7D_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
133	URS0000723357_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
134	URS0000669786_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
135	URS00006CA93B_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
136	URS00006F3B45_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
137	URS0000723829_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
138	URS000065CD0A_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
139	URS00006CF2E4_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
140	URS00006333CA_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
141	URS00006C8917_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
142	URS00006FFECD_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
143	URS00006F3016_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
144	URS000072D7D4_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
145	URS00006B56D4_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
146	URS0000702B7B_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
147	URS00006D7A8C_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
148	URS00006507F9_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
149	URS0000714117_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
150	URS0000623798_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
151	URS0000710873_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
152	URS00006C8A52_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
153	URS0000648D01_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
154	URS0000683725_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
155	URS000070132C_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
156	URS00007125C5_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
157	URS0000637B7A_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
158	URS000062A03F_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
159	URS000065AA15_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
160	URS0000707125_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
161	URS00006F9F22_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
162	URS0000673AF2_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
163	URS0000676541_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
164	URS00006CEE02_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
165	URS00006A5F92_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
166	URS00006F68B6_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
167	URS00006CDC13_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
168	URS00006BD0C1_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
169	URS0000657C21_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
170	URS0000702E5D_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
171	URS00006CD472_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
172	URS000063CD8B_12908	N/A	seed	1	143	unclassified sequences IMES-2 RNA motif	unclassified sequences
173	URS0000705725_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
174	URS0000711E0E_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
175	URS000063ECEB_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
176	URS0000654C48_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
177	URS0000687AF4_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
178	URS000072887B_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
179	URS0000659351_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
180	URS000068CC09_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
181	URS00006C2991_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
182	URS00007268B2_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
183	URS00006D81DC_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
184	URS000067723C_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
185	URS000062F608_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
186	URS00006CB6A0_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
187	URS00006D4AB2_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
188	URS000070666E_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
189	URS0000672D75_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
190	URS000069FFDE_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
191	URS00006ED9D5_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
192	URS000065E040_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
193	URS00007239A3_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
194	URS000066890E_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
195	URS00006BB47C_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
196	URS000070FD0E_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
197	URS000069C3A8_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
198	URS00006436CE_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
199	URS000068E254_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
200	URS00007115AB_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
201	URS00006A291D_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
202	URS00006969A4_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
203	URS00006CB4D3_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
204	URS0000663373_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
205	URS000067E8D1_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
206	URS00006AA4DD_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
207	URS0000657046_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
208	URS00006D6496_12908	N/A	seed	1	143	unclassified sequences IMES-2 RNA motif	unclassified sequences
209	URS00007269D9_12908	N/A	seed	1	143	unclassified sequences IMES-2 RNA motif	unclassified sequences
210	URS0000685122_12908	N/A	seed	1	143	unclassified sequences IMES-2 RNA motif	unclassified sequences
211	URS000072B160_12908	N/A	seed	1	144	unclassified sequences IMES-2 RNA motif	unclassified sequences
212	URS00006579F5_12908	N/A	seed	1	136	unclassified sequences IMES-2 RNA motif	unclassified sequences
213	URS000062951C_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
214	URS0000667997_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
215	URS00006D80DC_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
216	URS0000628BDF_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
217	URS00006618A9_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
218	URS000069C30E_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
219	URS00006771E3_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
220	URS00006EAC5C_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
221	URS0000640879_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
222	URS0000704E0F_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
223	URS00006CC043_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
224	URS00006AB157_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
225	URS00006D7AEF_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
226	URS00006C1390_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
227	URS000070EDF3_12908	N/A	seed	1	140	unclassified sequences IMES-2 RNA motif	unclassified sequences
228	URS0000640A91_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
229	URS000062A961_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
230	URS00006B0959_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
231	URS0000717228_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
232	URS00006E6C96_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
233	URS000064301B_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
234	URS000063571E_12908	N/A	seed	1	135	unclassified sequences IMES-2 RNA motif	unclassified sequences
235	URS00006495F1_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
236	URS00006FA445_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
237	URS00006DECC5_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
238	URS00006B3595_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
239	URS000072CF65_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
240	URS00006BEF4C_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
241	URS00006CB6C0_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
242	URS000069F84B_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
243	URS000069C50B_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
244	URS000064AFE7_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
245	URS00006A2B9C_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
246	URS00006E3AAC_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
247	URS00006EA3C2_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
248	URS00006F0F7F_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
249	URS00006A79D4_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
250	URS000063B22C_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
251	URS0000678F95_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
252	URS00006D023E_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
253	URS0000657194_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
254	URS00007108EC_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
255	URS000068F13F_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
256	URS00006B4C60_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
257	URS0000655B77_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
258	URS00006E5543_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
259	URS000070AF9C_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
260	URS00006D304F_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
261	URS00006E6130_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
262	URS000067EEB1_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
263	URS00006C95DA_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
264	URS00006A57CB_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
265	URS00006EEEC1_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
266	URS0000661585_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
267	URS0000717F09_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
268	URS00006E58F2_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
269	URS00007041B2_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
270	URS000070CCFC_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
271	URS0000703031_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
272	URS00006CEDB5_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
273	URS00006B5600_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
274	URS00006D6C70_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
275	URS00006B1E2F_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
276	URS00006EF05F_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
277	URS0000632EE7_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
278	URS000064BEEF_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
279	URS000072D0CE_12908	N/A	seed	1	141	unclassified sequences IMES-2 RNA motif	unclassified sequences
280	URS00006B44F1_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
281	URS00006A5249_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
282	URS00006A34ED_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
283	URS0000727EE9_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
284	URS000070CAE2_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
285	URS0000639599_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
286	URS00006D2D57_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
287	URS00006EF6CF_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
288	URS0000652BDE_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
289	URS00006D72DE_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
290	URS000067EF4C_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
291	URS0000627257_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
292	URS00006DE1FE_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
293	URS0000629B7B_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
294	URS000065E379_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
295	URS00006B7126_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
296	URS00007139A0_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
297	URS0000694FB1_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
298	URS0000693398_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
299	URS0000668CFE_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
300	URS00006A231B_12908	N/A	seed	1	142	unclassified sequences IMES-2 RNA motif	unclassified sequences
0	JACWDN010000016.1	162.30	full	15,382	15,522	JACWDN010000016.1 Pelagibacterales bacterium SAG-MED16 SAR11-SAG-MED16-C16, whole genome shotgun sequence	Pelagibacterales bacterium SAG-MED16
1	JPUP01000069.1	162.00	full	7,732	7,872	SAR11 cluster bacterium PRT-SC02 contig_388, whole genome shotgun sequence.	SAR11 cluster bacterium PRT-SC02
2	JACWEE010000010.1	161.80	full	16,462	16,602	JACWEE010000010.1 Pelagibacterales bacterium SAG-MED34 SAR11-SAG-MED34-C10, whole genome shotgun sequence	Pelagibacterales bacterium SAG-MED34
3	JACWDM010000003.1	153.00	full	106,590	106,450	JACWDM010000003.1 Pelagibacterales bacterium SAG-MED15 SAR11-SAG-MED15-C3, whole genome shotgun sequence	Pelagibacterales bacterium SAG-MED15
4	JACWEA010000007.1	151.80	full	24,669	24,529	JACWEA010000007.1 Pelagibacterales bacterium SAG-MED30 SAR11-SAG-MED30-C7, whole genome shotgun sequence	Pelagibacterales bacterium SAG-MED30
5	JACWEJ010000004.1	148.80	full	11,976	12,117	JACWEJ010000004.1 Pelagibacterales bacterium SAG-MED41 SAR11-SAG-MED41-C4, whole genome shotgun sequence	Pelagibacterales bacterium SAG-MED41
6	JACWDR010000004.1	148.20	full	28,048	27,908	JACWDR010000004.1 Pelagibacterales bacterium SAG-MED20 SAR11-SAG-MED20-C4, whole genome shotgun sequence	Pelagibacterales bacterium SAG-MED20
7	JACWEH010000007.1	141.20	full	39,996	40,135	JACWEH010000007.1 Pelagibacterales bacterium SAG-MED38 SAR11-SAG-MED38-C7, whole genome shotgun sequence	Pelagibacterales bacterium SAG-MED38
8	JAGFWC010000039.1	124.70	full	6,136	6,275	JAGFWC010000039.1 MAG: Pelagibacteraceae bacterium isolate IIa.A_ETNP2013_S06_SV51_100m_MAG_01 IIa.A_ENTP2013_S06_SV51_100m_MAG_01--39, whole genome shotgun sequence	Pelagibacteraceae bacterium
9	ADAC02000001.1	62.10	full	1,211,235	1,211,376	Alpha proteobacterium HIMB114 HIMB114_HIMB114, whole genome shotgun sequence.	alpha proteobacterium HIMB114

Alignment

There are various ways to view or download the seed alignments that we store. You can use a sequence viewer to look at them, or you can look at a plain text version of the sequence in a variety of different formats. More...

View options

You can view Rfam seed alignments in your browser in various ways. Choose the viewer that you want to use and click the "View" button to show the alignment in a pop-up window.

Formatting options

You can view or download Rfam seed alignments in several formats. Check either the "download" button, to save the formatted alignment, or "view", to see it in your browser window, and click "Generate".

Download

Download a gzip-compressed, Stockholm-format file containing the seed alignment for this family. You may find RALEE useful when viewing sequence alignments.

Submit a new alignment

We're happy receive updated seed alignments for new or existing families. Submit your new alignment and we'll take a look.

Secondary structure

This section shows a variety of different secondary structure representations for this family. More...

In this page you can view static images showing the secondary structure of this family using a variety of colouring schemes:

Conservation (cons): this plot colours each character by how well conserved it is. A site with 100% sequence conservation is coloured red, 0% is violet.

Covariation (cov): this plot colours each base-pair according to how much the corresponding nucleotides are co-varying. A base-pair position at which every pair of nucleotides is co-variant with respect to every other pair in the alignment gets a score of 2 and is coloured red. Conversely, a base-pair position at every pair is anti-co-variant with respect to every other pair (e.g. lots of mutations to non-canonical pairs) gets a score of -2 and is coloured violet. Further information on this metric can be found in this document.

Sequence entropy (ent): this plot colours each character by how under- or over-represented the residues at the site are. Sites where one or more nucleotides are over-represented while the other nucleotides are either non-existent or near the background frequencies, receive positive scores; sites where all the nucleotides are under-represented receive negative scores. Further information on this metric can be found in this document.

Fraction of canonical basepairs (fcbp): this plot colours each base-pair by the percentage of canonical basepairs (A:U, C:G, G:U) which are found in the corresponding position in the alignment. A pair of sites with 100% canonical pairs is coloured red, a site with 0% is violet.

Maximum parse of the covariance model (maxcm): this plot takes the covariance model for the family and generates the sequence with the maximum possible score for that model. Each character is coloured by how many bits it contributes to the total score.

Sequence: for most of the above cases, the representative sequence used for the backbone is the most informative sequence (MIS). Any residue that has a higher frequency than than the background frequency is projected into the IUPAC redundancy codes.

Normal: this plot simply colours each stem loop

R-chie (rchie): arc diagrams showing secondary structure, calculated using the R-chie package. The consensus secondary structure is visualized as arc diagrams on top of each diagram, where a basepair in an arc, connect two columns of the block of sequences below. The block of sequences below represent the multiple sequence alignment of the Rfam seed, where each sequence is a horizontal strip. Sequences in the alignments are ordered so sequences that best fit the structure are on top, and those that do not fit as well are towards the bottom. For seed alignments for over 500 sequences, 500 random sequences were chosen. Rfam entries without sturcture have a blank plot. Colour information can be found on the R-chie FAQ.

You can also view the secondary structure in the VARNA applet. The applet is shown in a separate pop-up window.

Acknowledgements

The bulk of the code for generating these graphics was kindly supplied by Andreas Gruber and Ivo Hofacker. The statistics were implemented by Rfam.

The VARNA applet is developed by Yann Ponty et al:

VARNA: Interactive drawing and editing of the RNA secondary structure: Kévin Darty, Alain Denise and Yann Ponty Bioinformatics (2009) 25:1974-1975

The R-chie arc diagrams were calculated using R-chie:

R-chie: a web server and R package for visualizing RNA secondary structures: Daniel Lai, Jeff R. Proctor, Jing Yun A. Zhu, and Irmtraud M. Meyer Nucleic Acids Research (2012) first published online March 19, 2012

You can view the secondary structure of the family using the VARNA applet. You can see more information about VARNA iself here.

Current Rfam structure

17 out of 44 basepairs are significant at E-value=0.05

R-scape optimised structure

18 out of 43 basepairs are significant at E-value=0.05

Colours
Statistically significant basepair with covariation
97% conserved nucleotide
90% conserved nucleotide
75% conserved nucleotide
50% conserved nucleotide
Nucleotides
R: A or G
Y: C or U

Tip: The diagrams are interactive:
you can pan and zoom to see more details
or hover over nucleotides and basepairs.

R-scape is a method for testing whether covariation analysis supports the presence of a conserved RNA secondary structure. This page shows R-scape analysis of the secondary structure from the Rfam seed alignment and a new structure with covariation support that is compatible with the same alignment.

To find out more about the method, see the R-scape paper by Rivas et al., 2016. The structures are visualised using R2R.

Move your mouse over the image to show details and click to show full image.

Arc colours
100% canonical basepair
50%
0%
Nucleotide colours
Valid basepairing
Two-sided covariation
One-sided covariation
Invalid
Unpaired
Gap
Ambiguous

Species distribution

Sunburst
Tree

Sunburst controls

Hide

Lineage

Move your mouse over the main tree to show the lineage of a particular node.

You can move this pane by dragging it.

Weight segments by...

number of sequences
number of species

Change the size of the sunburst

Small

Large

Colour assignments

Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Selections

Click on a node to select that node and its sub-tree.

Clear selection

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.

How the sunburst is generated

The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:

superkingdom
kingdom
phylum
class
order
family
genus
species

Colouring and labels

Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.

As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.

Anomalies in the taxonomy tree

There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.

Missing taxonomic levels

Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.

Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".

Sub-species

Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.

Too many species/sequences

For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.

Tree controls

Hide

The tree shows the occurrence of this RNA across different species. More...

Species trees

For the majority of our families we provide an interactive tree representation, which allows you to select specific nodes in the tree and view the selected sequences as an alignment.

Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.

Interactive tree

For all of the sequence regions (RNA annotations) in a full alignment, we count the total number that are found in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each RNA is found, which is shown in green. Note that an RNA annotation may appear multiple times on the same sequence, leading to the difference between these two numbers (think of repeats like tRNA where the same RNA is found in tandem along a single sequence).

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the RNA is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree. In these few cases if you do really need to see a representation of the tree for this entry, please contact us and we will be happy to discuss ways to generate it for you.

You can use the tree controls to manipulate how the interactive tree is displayed:

show/hide the summary boxes
highlight species that are represented in the seed alignment
expand/collapse the tree or expand it to a given depth
select a sub-tree or a set of species within the tree and view them graphically or as an alignment
save a plain text representation of the tree

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Trees

This page displays the predicted phylogenetic tree for the alignment. More...

Note: You can also download the data file for the seed tree.

Motif matches

There are 2 motifs which match this family.

This section shows the Rfam motifs that match sequences within the seed alignment of this family. Users should be aware that the motifs are structural constructs and do not necessarily conform to taxonomic boundaries in the way that Rfam families do. More...

Original order	Motif Accession	Motif Description	Number of Hits	Fraction of Hits	Sum of Bits	Image
7	RM00008	GNRA tetraloop	244	0.762	2597.7
7	RM00010	Kink turn 1, 3' bulge	10	0.031	99.3

References

This section shows the database cross-references that we have for this Rfam family.

Literature references

Weinberg Z, Perreault J, Meyer MM, Breaker RR Nature. 2009;462:656-659. Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis. PUBMED:19956260

External database links

Sequence Ontology:

SO:0001263 (ncRNA_gene);

Curation and family details

This section shows the detailed information about the Rfam family. We're happy to receive updated or improved alignments for new or existing families. Submit your new alignment and we'll take a look.

Curation

Seed source

Published; PMID:12376536; Weinberg Z

Structure source

Published; PMID:12376536; Weinberg Z

Type

Gene;

Author

Weinberg Z ORCID logo

, Eberhardt R ORCID logo

Alignment details

Alignment	Number of sequences
full	10
seed	320

Model information

Build commands

cmbuild -F CM SEED

cmcalibrate --mpi CM

Search command

cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 2958934 CM SEQDB

Gathering cutoff

54.7

Trusted cutoff

62.1

Noise cutoff

54.3

Covariance model

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Family: IMES-2 (RF02035)

Description: IMES-2 RNA motif

Summary

Wikipedia annotation Edit Wikipedia article

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Sequences

Quick actions

Table view (330 sequence regions)

Alignment

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Formatting options

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Secondary structure

Acknowledgements

Current Rfam structure

R-scape optimised structure

Species distribution

Sunburst controls

Lineage

Weight segments by...

Change the size of the sunburst

Colour assignments

Selections

Currently selected:

How the sunburst is generated

Colouring and labels

Anomalies in the taxonomy tree

Missing taxonomic levels

Unmapped species names

Sub-species

Too many species/sequences

Tree controls

Annotation

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Selected sequences

Species trees

Interactive tree

Trees

Motif matches

References

Literature references

External database links

Curation and family details

Curation

Model information

Rfam is part of the ELIXIR infrastructure