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Things you should know

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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 254 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	RF00018	CsrB/RsmB RNA family	31	0.816	440.7
3	RF00021	Spot 42 RNA	14	0.737	178.9
3	RF00022	GcvB RNA	16	0.593	216.2
3	RF00028	Group I catalytic intron	2	0.167	49.7
3	RF00034	RprA RNA	2	0.154	25.0
3	RF00079	OmrA-B family	22	0.957	289.3
3	RF00082	SraG RNA	3	0.429	41.7
3	RF00083	GlmZ RNA activator of glmS mRNA	15	0.714	209.4
3	RF00084	CsrC RNA family	4	1.000	137.7
3	RF00106	RNAI	10	1.000	164.9
3	RF00112	CyaR/Rye RNA	3	0.176	34.4
3	RF00121	MicC RNA	8	1.000	210.0
3	RF00124	IS102 RNA	4	0.800	74.6
3	RF00125	IS128 RNA	5	1.000	82.3
3	RF00126	ryfA RNA	3	0.333	38.4
3	RF00130	mir-192/215 microRNA precursor	7	0.146	85.8
3	RF00195	RsmY RNA family	7	0.636	95.5
3	RF00210	Aphthovirus internal ribosome entry site (IRES)	29	0.315	324.9
3	RF00236	ctRNA	8	0.533	126.0
3	RF00238	ctRNA	36	0.750	479.5
3	RF00242	ctRNA	10	0.625	145.2
3	RF00369	sroC RNA	4	0.667	44.6
3	RF00372	sroH RNA	2	1.000	30.5
3	RF00378	Qrr RNA	26	0.867	385.2
3	RF00397	Small nucleolar RNA SNORA14	4	0.222	48.0
3	RF00414	Small nucleolar RNA SNORA22	3	0.097	34.2
3	RF00444	PrrF RNA	2	0.111	23.7
3	RF00460	U1A polyadenylation inhibition element (PIE)	3	0.077	32.9
3	RF00489	ctRNA	5	0.500	66.8
3	RF00503	RNAIII	5	0.500	52.1
3	RF00506	Threonine operon leader	25	1.000	667.3
3	RF00512	Leucine operon leader	5	0.833	113.8
3	RF00513	Tryptophan operon leader	13	0.591	184.1
3	RF00514	Histidine operon leader	29	0.879	547.0
3	RF00515	PyrR binding site	20	0.488	274.6
3	RF00516	ylbH leader	3	1.000	50.3
3	RF00519	Makes More Granules Regulator RNA (mmgR)	72	0.828	1153.1
3	RF00534	SgrS RNA	3	0.375	35.4
3	RF00557	Ribosomal protein L10 leader	61	0.629	1067.5
3	RF00558	Ribosomal protein L20 leader	31	0.721	504.7
3	RF00563	Small nucleolar RNA SNORA53	4	0.143	57.8
3	RF00598	Small nucleolar RNA SNORA76	6	0.273	76.6
3	RF00624	Pseudomonas sRNA P9	8	0.471	105.9
3	RF00628	RgsA sRNA	8	0.296	86.7
3	RF00630	Pseudomonas sRNA P26	3	0.111	33.0
3	RF00639	mir-515 microRNA precursor family	46	0.254	585.4
3	RF00714	MIR535 microRNA precursor family	7	0.350	102.0
3	RF00722	microRNA mir-451	8	0.364	102.1
3	RF00746	microRNA mir-454	2	0.100	25.0
3	RF00768	MIR405 microRNA precursor family	3	1.000	34.4
3	RF00779	microRNA MIR474	3	0.273	38.4
3	RF00834	microRNA mir-268	2	0.667	24.7
3	RF00840	microRNA mir-374	8	0.615	121.5
3	RF00885	microRNA MIR821	3	0.375	43.6
3	RF00887	mir-802 microRNA precursor family	9	0.692	114.2
3	RF00906	microRNA MIR1122	5	0.417	83.2
3	RF00969	microRNA mir-556	2	1.000	32.4
3	RF01045	microRNA mir-544	7	0.438	86.3
3	RF01050	Saccharomyces telomerase	7	0.538	148.0
3	RF01061	microRNA mir-548	2	0.182	22.1
3	RF01066	6C RNA	3	0.167	33.5
3	RF01071	Ornate Large Extremophilic RNA	3	0.150	36.5
3	RF01227	Small nucleolar RNA snoR83	2	0.286	23.7
3	RF01241	Small nucleolar RNA SNORA81	8	0.286	91.1
3	RF01253	Small nucleolar RNA snR46	3	0.500	33.2
3	RF01264	Small nucleolar RNA snR83	5	1.000	86.9
3	RF01270	Small nucleolar RNA snR84	3	0.500	35.9
3	RF01291	Small nucleolar RNA SNORD97	7	0.350	91.5
3	RF01400	istR Hfq binding RNA	3	0.429	43.7
3	RF01405	STnc490 Hfq binding RNA	63	0.829	667.8
3	RF01407	STnc560 Hfq binding RNA	12	1.000	179.9
3	RF01411	BsrF	4	0.364	50.4
3	RF01412	BsrG	3	0.500	38.3
3	RF01419	Antisense RNA which regulates isiA expression	35	0.114	421.9
3	RF01459	Listeria sRNA rliE	4	1.000	119.0
3	RF01470	Listeria sRNA rli38	12	0.600	198.9
3	RF01472	Listeria sRNA rli40	4	1.000	74.7
3	RF01473	Listeria sRNA rli41	6	1.000	145.5
3	RF01491	Listeria sRNA rli54	7	1.400	73.2
3	RF01521	caulobacter sRNA CC1840	2	0.667	21.7
3	RF01577	Plasmodium RNase_P	4	2.000	62.2
3	RF01602	small nucleolar RNA snoR27	3	0.750	37.1
3	RF01606	small nucleolar RNA snoR31	2	0.667	27.9
3	RF01670	Pseudomonas sRNA P17	3	1.000	38.8
3	RF01673	PhrS	2	0.154	21.0
3	RF01675	Pseudomonas sRNA CrcZ	6	0.316	81.8
3	RF01702	Cyano-2 RNA	11	0.193	156.0
3	RF01705	Flavo-1 RNA	19	0.095	273.6
3	RF01719	Pseudomon-1/ErsA RNA	19	1.000	308.1
3	RF01723	Rhizobiales-2 RNA	8	0.533	85.3
3	RF01730	Termite-leu RNA	14	0.700	268.3
3	RF01732	MarS sRNA	3	0.097	52.0
3	RF01743	leu/phe leader RNA from Lactococcus	6	0.667	93.5
3	RF01766	cspA thermoregulator	10	0.667	166.2
3	RF01770	Gammaprotebacteria rimP leader	46	1.000	1150.8
3	RF01771	Enterobacteria rnk leader	13	1.000	218.3
3	RF01772	Pseudomonas rnk leader	15	1.000	317.0
3	RF01773	Pseudomonas rpsL leader	2	0.222	29.5
3	RF01774	Rickettsia rpsL leader	7	1.000	92.5
3	RF01796	Fumarate/nitrate reductase regulator sRNA	4	0.250	49.5
3	RF01808	MicX Vibrio cholerae sRNA	10	1.000	256.9
3	RF01816	RNA Staph. aureus A	2	0.286	24.2
3	RF01819	RNA Staph. aureus D	8	1.000	99.8
3	RF01820	RNA Staph. aureus E (RoxS)	10	0.667	161.4
3	RF01859	Phenylalanine leader peptide	63	0.887	1242.3
3	RF01867	caulobacter sRNA CC2171	5	0.385	60.3
3	RF01882	Taurine upregulated gene 1 conserved region 1	17	0.810	215.7
3	RF01946	KCNQ1 overlapping transcript 1 conserved region 1	6	0.750	95.1
3	RF01959	Archaeal small subunit ribosomal RNA	16	0.186	196.1
3	RF01960	Eukaryotic small subunit ribosomal RNA	13	0.144	228.4
3	RF01987	ZEB2 antisense RNA 1 conserved region 4	2	0.154	21.5
3	RF02029	sraA	14	0.700	233.2
3	RF02031	tpke11	4	0.143	45.3
3	RF02045	CDKN2B antisense RNA 1 convserved region 3	2	0.111	21.3
3	RF02051	Enterobacterial sRNA STnc450	2	0.167	23.5
3	RF02053	Enterobacterial sRNA STnc430	6	0.857	170.4
3	RF02055	Enterobacterial sRNA STnc380	4	0.800	86.1
3	RF02057	Salmonella enterica sRNA STnc40	17	1.000	335.8
3	RF02058	Gammaproteobacterial sRNA STnc400	2	1.000	31.2
3	RF02063	Salmonella enterica sRNA STnc350	2	1.000	24.2
3	RF02064	Enterobacterial sRNA STnc370	10	1.000	174.6
3	RF02065	Enterobacterial sRNA STnc340	3	0.750	73.5
3	RF02067	Salmonella enterica sRNA STnc310	4	0.500	84.4
3	RF02074	Enterobacterial sRNA STnc240	13	0.867	186.0
3	RF02075	Enterobacterial sRNA STnc230	8	0.727	120.8
3	RF02076	Gammaproteobacterial sRNA STnc100	10	0.417	155.5
3	RF02079	Enterobacterial sRNA STnc180	4	0.400	81.8
3	RF02082	Enterobacterial sRNA STnc540	3	1.000	89.2
3	RF02083	OrzO-P RNA antitoxin family	6	0.857	63.0
3	RF02084	Enterobacteria sRNA STnc130	10	0.769	142.2
3	RF02101	Highly up-regulated in liver cancer conserved region	2	0.105	23.9
3	RF02105	Deleted in lymphocytic leukemia 2 conserved region 1	7	0.259	77.6
3	RF02110	Deleted in lymphocytic leukemia 2 conserved region 6	3	0.094	31.2
3	RF02144	rsmX	12	0.750	185.1
3	RF02190	ST7 overlapping transcript 4 conserved region 4	2	0.077	29.2
3	RF02225	Proteobacterial sRNA sX6	8	1.000	117.9
3	RF02230	Proteobacterial sRNA sX11	5	0.500	70.0
3	RF02278	Betaproteobacteria toxic small RNA	40	0.784	604.1
3	RF02342	Alphaproteobacterial sRNA ar7	28	0.966	372.9
3	RF02343	Alphaproteobacterial sRNA ar9	13	0.464	218.2
3	RF02344	Alphaproteobacterial ar14	83	0.703	1267.2
3	RF02345	Alphaproteobacterial ar15	12	0.197	216.6
3	RF02346	Alphaproteobacterial sRNA ar35	9	0.692	119.0
3	RF02351	Proteobacteria sRNA psRNA14	2	0.667	47.5
3	RF02353	Bradyrhizobiaceae sRNA BjrC68	4	0.333	49.0
3	RF02356	Alphaproteobacterial sRNA BjrC1505	23	0.920	335.8
3	RF02362	Cyanobacterial functional RNA 10	5	0.833	87.3
3	RF02366	Cyanobacterial functional RNA 19	6	1.000	132.5
3	RF02368	Cyanobacterial functional RNA 21	2	1.000	24.6
3	RF02370	Bacillus tryptophan operon leader	5	0.556	52.4
3	RF02371	PyrG leader	9	0.900	114.3
3	RF02375	Aar sRNA	13	1.000	203.7
3	RF02376	SR1 sRNA	6	1.000	121.0
3	RF02378	SurC sRNA	4	1.000	49.4
3	RF02379	Cia-dependent small RNA csRNA1	28	0.583	394.5
3	RF02384	FasX small RNA	7	0.875	85.5
3	RF02385	Staphylococcus sRNA sau-13	3	0.500	40.8
3	RF02386	Staphylococcus sRNA sau-19	4	1.000	66.3
3	RF02399	Nitrogen stress-induced RNA 1	2	0.118	24.2
3	RF02405	Pseudomonas sRNA P34	5	1.000	88.2
3	RF02409	Small nucleolar RNA snoR125	4	0.800	51.0
3	RF02411	Small nucleolar RNA snoR138	3	0.429	34.4
3	RF02420	Burkholderia sRNA Bp1_Cand612_SIPHT	4	0.364	51.0
3	RF02423	Burkholderia sRNA Bp1_Cand871_SIPHT	7	0.467	80.4
3	RF02424	Burkholderia sRNA Bp2_Cand287_SIPHT	8	0.571	93.0
3	RF02425	Streptococcus sRNA SpF01	8	0.615	129.8
3	RF02430	Streptococcus sRNA SpF19	3	1.000	49.9
3	RF02432	Streptococcus sRNA SpF25	18	0.900	340.7
3	RF02433	Streptococcus sRNA SpF36	4	1.000	112.4
3	RF02434	Streptococcus sRNA SpF39	8	0.615	107.0
3	RF02435	Streptococcus sRNA SpF41	2	0.222	28.8
3	RF02442	Streptococcus sRNA SpF66	9	1.000	175.2
3	RF02445	Streptococcus sRNA SpR14	3	0.600	33.6
3	RF02449	Bacillus sRNA ncr1015	16	1.000	300.6
3	RF02450	Bacillus sRNA ncr1175	4	1.000	66.5
3	RF02452	Bacillus sRNA ncr1575	7	0.241	96.4
3	RF02470	Mycobacterium sRNA Ms_IGR-8	2	0.667	22.5
3	RF02495	Oppression of Hydrophobic ORF by sRNA	19	0.559	208.1
3	RF02502	Rhizobiales sRNA Atu_C8	27	1.000	451.2
3	RF02503	Rhizobiales sRNA Atu_C9	9	1.000	136.0
3	RF02524	Streptococcus sRNA sagA	5	0.833	58.8
3	RF02526	Streptococcus sRNA SSRC34	8	0.500	94.8
3	RF02528	Streptococcus sRNA SSRC41	2	0.250	23.9
3	RF02543	Eukaryotic large subunit ribosomal RNA	24	0.273	531.2
3	RF02545	Trypanosomatid mitochondrial small subunit ribosomal RNA	3	0.750	37.7
3	RF02551	ABC transporter regulator	4	0.667	58.9
3	RF02552	RcsR1 sRNA	10	1.000	141.6
3	RF02569	IhtA sRNA	2	0.400	23.1
3	RF02631	Hfq-regulated sRNA 13	2	1.000	24.8
3	RF02657	Sense overlapping transcript RNA 2652 (sot)	2	1.000	27.6
3	RF02713	Mycoplasma sRNA MCS4	5	1.000	114.3
3	RF02728	Haemophilus regulatory RNA responsive to iron	6	0.857	113.7
3	RF02732	Aggregatibacter sRNA JA04	5	0.833	81.1
3	RF02737	Soft rot Enterobacteriaceae Rev 13 asRNA	3	1.000	51.5
3	RF02742	Soft rot Enterobacteriaceae Rev 72 asRNA	3	1.000	42.6
3	RF02744	Soft rot Enterobacteriaceae Rev 39 5'UTR	4	1.000	97.8
3	RF02767	Yersinia sRNA 186/sR026/CsrC	4	1.000	85.0
3	RF02790	sodF sRNA	5	0.833	76.1
3	RF02837	Burkholderia RNA 7 (anti-hemB)	11	0.423	153.1
3	RF02842	Enterococcus sRNA A1	4	1.000	94.1
3	RF02844	Enterococcus sRNA A9	2	0.500	31.2
3	RF02846	Enterococcus sRNA 84	2	0.400	21.8
3	RF02859	Actinobacillus sRNA 11	2	1.000	43.7
3	RF02860	Actinobacillus sRNA 14	4	1.000	56.9
3	RF02863	Enterococcus sRNA 2410	2	0.667	35.5
3	RF02865	Burkholderia sRNA 1	4	1.000	70.4
3	RF02867	Burkholderia sRNA 11	4	1.000	80.4
3	RF02880	Mesorhizobail RNA 15	2	1.000	30.1
3	RF02883	Burkholderia sRNA 2	2	0.400	24.0
3	RF02884	Burkholderia sRNA 7	5	1.000	69.8
3	RF02891	ArsR-gov region gene B	4	1.000	71.1
3	RF02898	Aggregatibacter sRNA 20	4	0.667	52.4
3	RF02900	Aggregatibacter sRNA 82	4	1.000	47.1
3	RF02901	Aggregatibacter sRNA 41	2	1.000	42.5
3	RF02909	Listeria sRNA rli117	2	0.667	37.6
3	RF02969	DUF3800-I RNA	166	0.517	3006.8
3	RF02986	FuFi-1 RNA	47	0.276	669.8
3	RF02988	GEBRO RNA	4	0.095	45.6
3	RF02998	IS605-orfB-II RNA	9	0.161	126.8
3	RF03119	Deltacoronavirus 5'UTR	2	0.286	22.1
3	RF03155	TD-1 RNA	2	0.071	22.1
3	RF03162	TD-2 RNA	6	0.167	68.4
3	RF03530	cis-regulatory element of the bglG/LicT operon	8	1.000	119.0
3	RF03532	Cis-regulator of HTH transcription factor	15	0.263	270.3
3	RF03533	Clostridioides difficile sRNA SQ1002	6	1.000	169.0
3	RF03534	Staphylococcus sRNA71 small RNA	2	0.154	28.0
3	RF03560	mir-3926 microRNA precursor family	2	1.000	44.9
3	RF03589	mir-5583 microRNA precursor family	2	1.000	30.8
3	RF03637	mir-5879 microRNA precursor family	2	1.000	37.1
3	RF03751	mir-7445 microRNA precursor family	2	1.000	42.0
3	RF03796	mir-5984 microRNA precursor family	2	1.000	29.3
3	RF03799	mir-3202 microRNA precursor family	2	1.000	27.4
3	RF03800	mir-4477 microRNA precursor family	2	1.000	30.5
3	RF03843	MIR2600 microRNA precursor family	2	0.400	22.4
3	RF03896	MIR2275 microRNA precursor family	2	0.154	27.4
3	RF03940	MIR9563 microRNA precursor family	2	1.000	29.2
3	RF03941	mir-3158 microRNA precursor family	2	1.000	20.7
3	RF04068	mir-3927 microRNA precursor family	3	1.000	39.2
3	RF04088	MIR812 microRNA precursor family	6	0.273	75.0
3	RF04120	MIR5998 microRNA precursor family	2	1.000	26.6
3	RF04128	MIR8562 microRNA precursor family	2	0.667	37.8
3	RF04134	MIR7504 microRNA precursor family	3	0.375	34.2
3	RF04161	mir-3688 microRNA precursor family	2	1.000	28.4
3	RF04171	MIR1509 microRNA precursor family	2	0.250	22.6
3	RF04178	Bacteroides sRNA BTnc005	2	0.667	39.4
3	RF04180	Bacteroides sRNA BTnc231	7	1.000	120.0
3	RF04182	GibS sRNA	10	0.769	179.9
3	RF04184	Bacteroides sRNA BTnc060	6	1.000	149.0
3	RF04198	MIR8670 microRNA precursor family	2	1.000	22.1
3	RF04239	mir-4679 microRNA precursor family	2	1.000	24.2
3	RF04248	MIR7486 microRNA precursor family	2	0.222	28.6
3	RF04252	mir-8186 microRNA precursor family	2	1.000	28.8
3	RF04262	MIR1319 microRNA precursor family	2	1.000	37.4
3	RF04282	mir-507 microRNA precursor family	5	0.200	73.4