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Things you should know

How your contribution will be recorded

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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.

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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.

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You can either download the motif alignment or view it directly in your browser window. More...

Formatting options

You can view or download motif 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".

Alignment format:	Stockholm Pfam FASTA (gapped) FASTA (UNgapped)
Download/view:	Download View

There are 16 PDB entires which have been used to build the motif model.

The table of results below may be sorted by clicking on the column titles, or restored to the original order here.

Original order	PDB ID	PDB chain ID	PDB Residues
2	1c04	E	37 - 52
2	1j5e	A	243 - 273
2	1mms	C	37 - 52
2	1qa6	C	37 - 52
2	1s72	0	1189 - 1208
2	2avy	A	247 - 277
2	1u9s	A	102 - 120
2	1y69	0	2323 - 2350
2	2aw4	B	1086 - 1103
2	2j01	A	718 - 741
2	2a2e	A	150 - 170
2	2i82	E	1 - 21
2	1ffk	0	1698 - 1718
2	1giy	A	1133 - 1152
2	1mt4	A	2 - 23
2	3hhn	C	102 - 121

There are 145 Rfam families which match this motif.

This section shows the families which have been annotated with this motif. 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	Family Accession	Family Description	Number of Hits	Fraction of Hits	Sum of Bits	Image
3	RF00004	U2 spliceosomal RNA	30	0.144	392.1
3	RF00007	U12 minor spliceosomal RNA	31	0.500	372.3
3	RF00009	Nuclear RNase P	30	0.259	386.0
3	RF00010	Bacterial RNase P class A	376	0.821	5926.2
3	RF00018	CsrB/RsmB RNA family	8	0.211	80.8
3	RF00023	transfer-messenger RNA	73	0.153	949.3
3	RF00024	Vertebrate telomerase RNA	4	0.108	47.5
3	RF00029	Group II catalytic intron	13	0.141	139.3
3	RF00043	R1162-like plasmid antisense RNA	4	0.500	47.1
3	RF00050	FMN riboswitch aptamer (RFN element)	14	0.096	154.6
3	RF00078	MicA sRNA	2	0.118	24.3
3	RF00082	SraG RNA	5	0.714	73.3
3	RF00096	U8 small nucleolar RNA	11	0.200	123.8
3	RF00107	FinP	5	0.833	65.8
3	RF00126	ryfA RNA	3	0.333	45.3
3	RF00156	Small nucleolar RNA SNORA70	9	0.209	96.8
3	RF00166	PrrB/RsmZ RNA family	35	0.946	493.9
3	RF00168	Lysine riboswitch aptamer	8	0.170	113.2
3	RF00177	Bacterial small subunit ribosomal RNA	99	1.000	2802.4
3	RF00209	Pestivirus internal ribosome entry site (IRES)	2	0.080	20.4
3	RF00224	FGF-2 internal ribosome entry site (IRES)	4	0.667	41.9
3	RF00260	Hepatitis C virus (HCV) cis-acting replication element (CRE)	4	0.071	43.4
3	RF00263	Small nucleolar RNA SNORA68	5	0.192	59.3
3	RF00291	Small nucleolar RNA snoR639/H1	5	0.556	55.8
3	RF00357	Small nucleolar RNA R44/J54/Z268 family	2	0.069	20.0
3	RF00369	sroC RNA	6	1.000	68.1
3	RF00373	Archaeal RNase P	9	0.129	147.4
3	RF00374	Gammaretrovirus core encapsidation signal	11	0.440	137.1
3	RF00386	Enterovirus 5' cloverleaf cis-acting replication element	68	0.425	724.3
3	RF00391	RtT RNA	6	0.105	85.1
3	RF00403	Small nucleolar RNA SNORA41	2	0.065	23.7
3	RF00442	Guanidine-I riboswitch aptamer	10	0.100	143.8
3	RF00495	Heat shock protein 70 (Hsp70) internal ribosome entry site (IRES)	7	0.500	74.9
3	RF00513	Tryptophan operon leader	3	0.136	36.0
3	RF00514	Histidine operon leader	9	0.273	96.5
3	RF00515	PyrR binding site	5	0.122	83.6
3	RF00534	SgrS RNA	2	0.250	22.4
3	RF00547	TrkB IRES	2	0.125	23.1
3	RF00548	U11 spliceosomal RNA	7	0.097	77.0
3	RF00558	Ribosomal protein L20 leader	11	0.256	135.9
3	RF00602	Small Cajal body specific RNA 21	6	0.250	99.9
3	RF00603	Small nucleolar RNA SNORD23	2	0.133	21.5
3	RF00604	Small nucleolar RNA SNORD88	2	0.057	23.1
3	RF00617	Flavivirus capsid hairpin cHP	11	0.186	123.1
3	RF00629	Pseudomonas sRNA P24	7	0.500	101.1
3	RF00630	Pseudomonas sRNA P26	10	0.370	108.3
3	RF00634	SAM (S-adenosyl methionine) riboswitch aptamer	3	0.075	34.9
3	RF00683	microRNA mir-143	11	0.611	111.1
3	RF00711	mir-449 microRNA precursor family	8	0.195	85.6
3	RF00723	mir-448 microRNA precursor family	5	0.263	65.4
3	RF00788	microRNA mir-287	10	0.833	106.9
3	RF01071	Ornate Large Extremophilic RNA	5	0.250	58.5
3	RF01089	Pseudoknot of the regulatory region of the repBA gene	2	0.286	20.2
3	RF01268	Small Cajal body-specific RNA 2	3	0.150	31.2
3	RF01330	CRISPR RNA direct repeat element	6	1.000	78.3
3	RF01390	isrG Hfq binding RNA	5	1.000	51.7
3	RF01401	rseX Hfq binding RNA	7	0.583	79.8
3	RF01529	Cauldobacter sRNA CC3552	2	1.000	24.7
3	RF01673	PhrS	2	0.154	21.0
3	RF01675	Pseudomonas sRNA CrcZ	17	0.895	191.9
3	RF01687	Acido-Lenti-1 RNA	7	0.080	107.8
3	RF01702	Cyano-2 RNA	4	0.070	44.4
3	RF01703	Dictyoglomi-1 RNA	2	0.500	27.3
3	RF01706	Gut-1 RNA	3	0.079	35.7
3	RF01708	L17 ribosomal protein downstream element	6	0.115	71.2
3	RF01721	Pseudomon-groES RNA	3	0.167	32.6
3	RF01730	Termite-leu RNA	15	0.750	476.4
3	RF01752	psaA RNA	2	0.065	21.6
3	RF01756	rne-II RNA	5	0.312	60.9
3	RF01757	sbcD RNA	3	0.500	32.9
3	RF01796	Fumarate/nitrate reductase regulator sRNA	3	0.188	34.0
3	RF01808	MicX Vibrio cholerae sRNA	5	0.500	61.9
3	RF01848	ACEA small nucleolar RNA U3	3	0.107	31.5
3	RF01849	Alphaproteobacteria transfer-messenger RNA	11	0.099	140.2
3	RF01850	Betaproteobacteria transfer-messenger RNA	2	0.286	22.8
3	RF01852	Selenocysteine transfer RNA	9	0.083	106.3
3	RF01856	Protozoan signal recognition particle RNA	2	0.111	22.0
3	RF01879	Non-coding RNA LOC285194	20	0.800	263.7
3	RF01959	Archaeal small subunit ribosomal RNA	86	1.000	4568.1
3	RF01960	Eukaryotic small subunit ribosomal RNA	35	0.389	509.8
3	RF01990	Selenocysteine insertion sequence 4	10	0.417	101.6
3	RF02029	sraA	18	0.900	271.4
3	RF02031	tpke11	4	0.143	45.0
3	RF02033	HNH endonuclease-associated RNA and ORF (HEARO) RNA	24	0.173	281.9
3	RF02053	Enterobacterial sRNA STnc430	5	0.714	55.8
3	RF02055	Enterobacterial sRNA STnc380	4	0.800	50.8
3	RF02057	Salmonella enterica sRNA STnc40	2	0.118	23.8
3	RF02065	Enterobacterial sRNA STnc340	3	0.750	34.8
3	RF02074	Enterobacterial sRNA STnc240	8	0.533	89.3
3	RF02103	Deleted in lymphocytic leukemia 1 conserved region 1	3	0.115	35.4
3	RF02118	FMR1 antisense RNA 1 conserved region 2	9	0.360	112.2
3	RF02189	ST7 overlapping transcript 4 conserved region 3	2	0.100	22.8
3	RF02219	ZNRD1 antisense RNA 1 conserved region 2	2	0.059	22.0
3	RF02230	Proteobacterial sRNA sX11	2	0.200	20.2
3	RF02247	Six3os1 conserved region 2	2	0.133	22.6
3	RF02249	Six3os1 conserved region 4	2	0.286	20.4
3	RF02276	Hammerhead ribozyme (type II)	3	0.125	34.3
3	RF02278	Betaproteobacteria toxic small RNA	7	0.137	87.0
3	RF02342	Alphaproteobacterial sRNA ar7	6	0.207	68.7
3	RF02343	Alphaproteobacterial sRNA ar9	16	0.571	166.8
3	RF02351	Proteobacteria sRNA psRNA14	2	0.667	23.7
3	RF02353	Bradyrhizobiaceae sRNA BjrC68	2	0.167	22.2
3	RF02354	Bradyrhizobiaceae sRNA BjrC80	7	0.467	83.6
3	RF02356	Alphaproteobacterial sRNA BjrC1505	3	0.120	35.7
3	RF02357	RNaseP truncated form	7	0.778	92.6
3	RF02375	Aar sRNA	2	0.154	21.9
3	RF02376	SR1 sRNA	2	0.333	26.3
3	RF02379	Cia-dependent small RNA csRNA1	8	0.167	97.7
3	RF02423	Burkholderia sRNA Bp1_Cand871_SIPHT	14	0.933	170.8
3	RF02471	Actinobacteria sRNA Ms_IGR-5	6	0.286	66.5
3	RF02502	Rhizobiales sRNA Atu_C8	3	0.111	31.2
3	RF02524	Streptococcus sRNA sagA	3	0.500	37.0
3	RF02540	Archaeal large subunit ribosomal RNA	83	0.912	3404.2
3	RF02541	Bacterial large subunit ribosomal RNA	102	1.000	3700.8
3	RF02542	Microsporidia small subunit ribosomal RNA	43	0.935	832.7
3	RF02543	Eukaryotic large subunit ribosomal RNA	80	0.909	2165.6
3	RF02630	Hfq-regulated sRNA 12	2	1.000	28.6
3	RF02681	Twister_sister_ribozyme	5	0.044	64.7
3	RF02684	Type-P5 twister ribozyme	36	0.167	434.7
3	RF02809	RsmW RNA family	3	1.000	42.2
3	RF02814	Sulfolobus sRNA133	2	0.667	24.4
3	RF02829	Streptomyces RNA 4115	5	0.833	57.1
3	RF02832	Streptomyces RNA 5676	4	0.800	51.7
3	RF02837	Burkholderia RNA 7 (anti-hemB)	2	0.077	21.6
3	RF02866	Burkholderia sRNA 16 (Bc_KC_sr1)	4	1.000	51.9
3	RF02877	Neisseria metabolic switch regulator b (RcoF1/NgncR163)	2	0.333	24.8
3	RF02880	Mesorhizobail RNA 15	2	1.000	22.4
3	RF02900	Aggregatibacter sRNA 82	4	1.000	48.8
3	RF02937	Clostridiales-2 RNA	11	0.250	140.0
3	RF03012	Mu-gpT-DE RNA	30	0.095	341.1
3	RF03016	RT-12 RNA	4	0.095	61.3
3	RF03017	RT-13 RNA	3	0.231	32.6
3	RF03018	RT-15 RNA	6	0.094	67.3
3	RF03079	MISL RNA	15	0.341	191.0
3	RF03083	cow-rumen-3 RNA	4	0.500	47.3
3	RF03087	ROOL RNA	58	0.200	665.7
3	RF03162	TD-2 RNA	4	0.111	48.1
3	RF03169	c-di-GMP-II-GAG riboswitch aptamer	66	0.140	768.2
3	RF03170	c-di-GMP-II-GCG riboswitch aptamer	3	0.091	34.4
3	RF03532	Cis-regulator of HTH transcription factor	3	0.053	39.9
3	RF03533	Clostridioides difficile sRNA SQ1002	6	1.000	69.9
3	RF03546	Flavivirus 5' UTR	2	0.250	21.8
3	RF03860	MIR1520 microRNA precursor family	2	0.111	21.3
3	RF03883	mir-9256 microRNA precursor family	8	1.000	81.5
3	RF04189	icd-II ncRNA motif	10	0.667	148.6