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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 279 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	RF00003	U1 spliceosomal RNA	30	0.300	246.7
3	RF00008	Hammerhead ribozyme (type III)	2	0.024	18.2
3	RF00009	Nuclear RNase P	23	0.198	194.0
3	RF00010	Bacterial RNase P class A	147	0.321	1410.3
3	RF00011	Bacterial RNase P class B	19	0.167	163.3
3	RF00017	Metazoan signal recognition particle RNA	44	0.484	412.3
3	RF00018	CsrB/RsmB RNA family	38	1.000	4480.4
3	RF00023	transfer-messenger RNA	113	0.237	983.3
3	RF00024	Vertebrate telomerase RNA	12	0.324	115.4
3	RF00030	RNase MRP	10	0.152	73.7
3	RF00057	RyhB RNA	8	0.308	72.3
3	RF00078	MicA sRNA	5	0.294	40.4
3	RF00079	OmrA-B family	5	0.217	36.0
3	RF00084	CsrC RNA family	4	1.000	134.6
3	RF00094	Hepatitis delta virus ribozyme	13	0.394	113.4
3	RF00100	7SK RNA	24	0.533	187.5
3	RF00101	SraC/RyeA RNA	13	1.000	101.0
3	RF00102	VA RNA	19	0.345	172.8
3	RF00113	Short Intergenic Abundant RNA	4	0.235	32.2
3	RF00126	ryfA RNA	2	0.222	15.6
3	RF00155	Small nucleolar RNA SNORA66	3	0.120	27.3
3	RF00166	PrrB/RsmZ RNA family	37	1.000	1495.1
3	RF00174	Cobalamin riboswitch aptamer	61	0.141	540.6
3	RF00177	Bacterial small subunit ribosomal RNA	94	0.949	1739.0
3	RF00178	mir-24 microRNA precursor family	60	0.952	462.0
3	RF00195	RsmY RNA family	11	1.000	294.3
3	RF00222	Bag-1 internal ribosome entry site (IRES)	2	0.133	18.0
3	RF00224	FGF-2 internal ribosome entry site (IRES)	5	0.833	47.7
3	RF00322	Small nucleolar RNA SNORA31	3	0.600	30.6
3	RF00335	Small nucleolar RNA Z13/snr52	3	0.071	23.5
3	RF00353	Small nucleolar RNA snoR31/Z110/Z27	3	0.375	22.5
3	RF00373	Archaeal RNase P	19	0.271	165.2
3	RF00374	Gammaretrovirus core encapsidation signal	5	0.200	37.8
3	RF00409	Small nucleolar RNA SNORA7	3	0.097	25.0
3	RF00411	Small nucleolar RNA SNORA9	4	0.111	35.3
3	RF00425	Small nucleolar RNA SNORA18	2	0.069	14.9
3	RF00435	Repression of heat shock gene expression (ROSE) element	6	0.462	47.7
3	RF00436	UnaL2 LINE 3' element	8	0.267	56.0
3	RF00442	Guanidine-I riboswitch aptamer	11	0.110	102.8
3	RF00448	Epstein-Barr virus nuclear antigen (EBNA) IRES	2	0.333	16.4
3	RF00449	HIF-1 alpha IRES	5	0.294	41.6
3	RF00468	Hepatitis C virus stem-loop VII	13	0.228	119.8
3	RF00470	Togavirus 5' plus strand cis-regulatory element	2	0.061	17.4
3	RF00494	Small nucleolar RNA U2-19	2	0.069	16.3
3	RF00503	RNAIII	4	0.400	36.8
3	RF00517	serC leader	14	0.200	132.7
3	RF00545	Small nucleolar RNA psi18S-841/snoR66	2	0.083	18.5
3	RF00547	TrkB IRES	3	0.188	25.7
3	RF00564	Small Cajal body specific RNA 11	4	0.167	29.2
3	RF00573	Small nucleolar RNA SNORD67	7	0.467	53.1
3	RF00584	Small nucleolar RNA SNORD105	2	0.133	18.8
3	RF00593	Small nucleolar RNA U83B	3	0.143	25.7
3	RF00602	Small Cajal body specific RNA 21	2	0.083	15.8
3	RF00604	Small nucleolar RNA SNORD88	7	0.200	57.1
3	RF00608	Small nucleolar RNA SNORD99	4	0.174	38.2
3	RF00613	Small nucleolar RNA SNORD94	3	0.143	32.8
3	RF00614	Small nucleolar RNA SNORA11	8	0.229	63.3
3	RF00624	Pseudomonas sRNA P9	10	0.588	96.3
3	RF00625	Pseudomonas sRNA P11	8	0.533	65.3
3	RF00649	microRNA mir-128	2	0.035	15.1
3	RF00656	microRNA mir-205	6	0.207	47.8
3	RF00665	mir-290 microRNA precursor family	3	0.111	25.0
3	RF00673	microRNA mir-217	8	0.286	64.4
3	RF00679	microRNA mir-210	2	0.077	17.2
3	RF00758	mir-346 microRNA precursor family	4	0.800	29.2
3	RF00773	microRNA mir-298	4	0.800	40.2
3	RF00775	mir-432 microRNA precursor family	4	0.667	30.4
3	RF00853	microRNA mir-304	9	0.818	68.4
3	RF00875	microRNA mir-692	2	0.182	16.5
3	RF00886	microRNA MIR807	5	0.167	38.0
3	RF00994	mir-1255 microRNA precursor family	4	0.364	34.8
3	RF01016	mir-584 microRNA precursor family	3	0.188	29.5
3	RF01050	Saccharomyces telomerase	7	0.538	50.9
3	RF01070	SucA RNA motif	4	0.114	32.0
3	RF01071	Ornate Large Extremophilic RNA	2	0.100	17.3
3	RF01211	Small nucleolar RNA SNORD124	9	0.500	72.8
3	RF01231	Small nucleolar RNA snoR74	2	0.222	15.6
3	RF01233	Small nucleolar RNA U109	2	0.077	15.2
3	RF01234	Small nucleolar RNA SNORA47	5	0.250	44.7
3	RF01254	Small nucleolar RNA snR34	4	1.000	29.6
3	RF01263	Small nucleolar RNA snR191	2	0.182	16.5
3	RF01294	Small nucleolar RNA U89	2	0.125	18.7
3	RF01296	Small nucleolar RNA U85	4	0.190	29.6
3	RF01401	rseX Hfq binding RNA	7	0.583	75.8
3	RF01486	Listeria sRNA rli62	2	1.000	18.5
3	RF01502	Fungal signal recognition particle RNA	16	0.320	148.9
3	RF01512	A. fumigatus sRNA Afu_309	2	0.200	17.0
3	RF01532	Trypanosomatid snoRNA TB10Cs3H2	4	0.667	35.8
3	RF01673	PhrS	3	0.231	22.8
3	RF01675	Pseudomonas sRNA CrcZ	3	0.158	22.9
3	RF01684	MALAT1-associated small cytoplasmic RNA/MEN beta RNA	7	0.132	63.2
3	RF01702	Cyano-2 RNA	10	0.175	120.0
3	RF01712	Methylobacterium-1 RNA	3	0.088	27.9
3	RF01717	PhotoRC-II RNA	40	0.118	348.2
3	RF01729	Termite-flg RNA	12	0.923	118.0
3	RF01731	TwoAYGGAY RNA	193	0.919	3179.0
3	RF01732	MarS sRNA	3	0.097	45.6
3	RF01736	flg-Rhizobiales RNA	4	0.308	29.9
3	RF01740	gyrA RNA	6	0.333	72.5
3	RF01745	manA RNA	21	0.127	174.8
3	RF01755	rmf RNA	6	0.375	71.3
3	RF01756	rne-II RNA	2	0.125	14.4
3	RF01757	sbcD RNA	5	0.833	61.0
3	RF01760	traJ-II RNA	10	0.213	85.5
3	RF01762	Whalefall-1 RNA	4	0.286	39.6
3	RF01763	Guanidine-III riboswitch aptamer (yKKC-III)	10	0.244	91.8
3	RF01768	ribosomal frameshift site	2	0.286	14.4
3	RF01794	sok antitoxin (CssrC)	12	0.132	94.0
3	RF01803	Editing element of GABA-3 exon 9	6	0.115	44.8
3	RF01841	venezuelan equine encephalitis virus ribosomal frameshift element	5	0.500	39.5
3	RF01844	SmY spliceosomal RNA	7	0.115	56.4
3	RF01845	Early nodulin 40	5	0.143	46.0
3	RF01846	Fungal small nucleolar RNA U3	9	0.136	87.9
3	RF01847	Plant small nucleolar RNA U3	4	0.167	40.0
3	RF01848	ACEA small nucleolar RNA U3	3	0.107	26.6
3	RF01851	Cyanobacteria transfer-messenger RNA	17	0.630	169.7
3	RF01857	Archaeal signal recognition particle RNA	22	0.407	206.7
3	RF01867	caulobacter sRNA CC2171	2	0.154	24.8
3	RF01872	Maternally expressed 3 conserved region 2	16	1.000	261.7
3	RF01874	Myocardial infarction associated transcript exon 1	4	0.400	41.3
3	RF01875	Myocardial infarction associated transcript exon 5 conserved region 1	2	0.222	17.8
3	RF01897	microRNA mir-188	3	0.214	34.8
3	RF01909	CDKN2B antisense RNA 1 intronic convserved region	2	0.080	18.5
3	RF01946	KCNQ1 overlapping transcript 1 conserved region 1	6	0.750	57.9
3	RF01947	KCNQ1 overlapping transcript 1 conserved region 2	13	0.722	117.3
3	RF01951	SOX2 overlapping transcript exon 1	4	0.138	31.6
3	RF01953	SOX2 overlapping transcript exon 3	9	0.818	93.6
3	RF01957	Nuclear enriched abundant transcript 1 conserved region 3	13	0.722	117.2
3	RF01959	Archaeal small subunit ribosomal RNA	80	0.930	1596.2
3	RF01960	Eukaryotic small subunit ribosomal RNA	38	0.422	419.4
3	RF01963	Rhabdomyosarcoma 2 associated transcript conserved region 2	3	0.188	25.5
3	RF01966	Rhabdomyosarcoma 2 associated transcript conserved region 5	3	0.143	23.4
3	RF01969	Rhabdomyosarcoma 2 associated transcript conserved region 8	2	0.091	17.8
3	RF02032	Giant, ornate, lake- and Lactobacillales-derived (GOLLD) RNA	7	0.200	76.4
3	RF02033	HNH endonuclease-associated RNA and ORF (HEARO) RNA	29	0.209	241.7
3	RF02041	HOXA transcript at the distal tip, conserved region 2	3	0.120	27.0
3	RF02047	Sphinx conserved region 2	2	0.054	15.9
3	RF02057	Salmonella enterica sRNA STnc40	9	0.529	78.0
3	RF02071	Salmonella enterica sRNA STnc280	3	1.000	22.0
3	RF02084	Enterobacteria sRNA STnc130	3	0.231	28.1
3	RF02094	mir-1803 microRNA precursor	2	0.333	14.5
3	RF02101	Highly up-regulated in liver cancer conserved region	6	0.316	62.1
3	RF02103	Deleted in lymphocytic leukemia 1 conserved region 1	2	0.077	14.6
3	RF02104	Deleted in lymphocytic leukemia 1 conserved region 2	2	0.125	16.1
3	RF02111	IS009	7	0.636	70.2
3	RF02113	DLG2 antisense RNA 1 conserved region 2	3	0.130	24.2
3	RF02116	FAS antisense RNA 1 conserved region	2	0.105	19.0
3	RF02117	FMR1 antisense RNA 1 conserved region 1	4	0.200	32.8
3	RF02121	FTX transcript, XIST regulator conserved region 3	10	0.714	103.6
3	RF02122	FTX transcript, XIST regulator conserved region 5	3	0.214	24.3
3	RF02123	FTX transcript, XIST regulator conserved region 4	4	0.308	32.3
3	RF02124	JPX transcript, XIST activator conserved region 1	2	0.143	14.6
3	RF02127	GNAS antisense RNA 1 conserved region 1	6	0.286	44.1
3	RF02138	HOXA11 antisense RNA 1 conserved region 2	6	0.286	51.0
3	RF02143	Hydatidiform mole associated and imprinted conserved region 1	10	0.625	93.9
3	RF02144	rsmX	16	1.000	510.4
3	RF02145	Maternally expressed 8 exon 1	8	0.348	70.3
3	RF02151	MER1 repeat containing imprinted transcript 1 conserved region 1	2	0.095	22.2
3	RF02164	Pvt1 oncogene conserved region 1	4	0.235	41.8
3	RF02165	Pvt1 oncogene conserved region 2	15	0.882	142.2
3	RF02170	Pvt1 oncogene conserved region 7	5	0.625	40.0
3	RF02188	ST7 overlapping transcript 4 conserved region 2	5	0.172	45.4
3	RF02189	ST7 overlapping transcript 4 conserved region 3	5	0.250	41.7
3	RF02195	TP53 target 1 conserved region 1	2	0.125	15.2
3	RF02196	TP53 target 1 conserved region 2	7	0.583	55.2
3	RF02197	TP73 antisense RNA 1 conserved region	3	0.750	33.7
3	RF02198	TTC28 antisense RNA 1 conserved region 1	2	0.143	16.8
3	RF02201	TTC28 antisense RNA 1 conserved region 4	2	0.111	15.9
3	RF02204	WT1 antisense RNA conserved region 2	2	0.111	18.0
3	RF02205	WT1 antisense RNA conserved region 3	11	0.579	116.5
3	RF02212	ZFAT antisense RNA 1 conserved region 2	2	0.182	14.4
3	RF02213	ZFAT antisense RNA 1 conserved region 3	4	0.800	32.3
3	RF02225	Proteobacterial sRNA sX6	4	0.500	35.0
3	RF02226	Xanthomonas sRNA sX7	16	2.000	146.0
3	RF02234	Xanthomonadaceae sRNA sX15	11	0.786	107.5
3	RF02238	Xanthomonas sRNA asX4/Xoo4	8	1.000	151.3
3	RF02241	Xanthomonadaceae sRNA Xoo2	2	0.667	20.9
3	RF02243	Proteobacterial sRNA Xoo8	3	0.750	28.4
3	RF02247	Six3os1 conserved region 2	8	0.533	68.3
3	RF02250	Six3os1 conserved region 5	3	0.200	22.7
3	RF02270	Neisseria sigma-E sRNA	6	0.857	43.8
3	RF02276	Hammerhead ribozyme (type II)	2	0.083	14.3
3	RF02342	Alphaproteobacterial sRNA ar7	2	0.069	14.8
3	RF02355	Bradyrhizobiaceae sRNA BjrC174	3	0.200	21.8
3	RF02356	Alphaproteobacterial sRNA BjrC1505	7	0.280	61.6
3	RF02377	SurA sRNA	7	1.750	57.1
3	RF02405	Pseudomonas sRNA P34	9	1.800	83.5
3	RF02422	Burkholderia sRNA Bp1_Cand738_SIPHT	9	0.429	67.1
3	RF02424	Burkholderia sRNA Bp2_Cand287_SIPHT	2	0.143	16.7
3	RF02430	Streptococcus sRNA SpF19	2	0.667	17.4
3	RF02433	Streptococcus sRNA SpF36	4	1.000	29.6
3	RF02462	Ascomycota telomerase RNA	4	1.000	56.2
3	RF02463	Mycobacterium sRNA Ms_AS-1	4	0.800	36.4
3	RF02514	5' ureB small RNA	2	0.154	14.8
3	RF02540	Archaeal large subunit ribosomal RNA	83	0.912	1779.4
3	RF02541	Bacterial large subunit ribosomal RNA	90	0.882	1771.2
3	RF02542	Microsporidia small subunit ribosomal RNA	21	0.457	355.6
3	RF02543	Eukaryotic large subunit ribosomal RNA	65	0.739	940.9
3	RF02545	Trypanosomatid mitochondrial small subunit ribosomal RNA	3	0.750	22.8
3	RF02605	Streptomyces sRNA scr5239	4	0.667	33.2
3	RF02683	NiCo (Nickel/Cobalt) riboswitch aptamer	10	0.122	123.0
3	RF02687	RAGATH-8 RNA	26	0.377	217.3
3	RF02689	hilD 3'UTR	4	0.800	46.4
3	RF02757	Erse small RNA	4	0.667	43.3
3	RF02767	Yersinia sRNA 186/sR026/CsrC	4	1.000	107.1
3	RF02790	sodF sRNA	5	0.833	35.5
3	RF02794	Pab19 RNA	2	0.667	23.4
3	RF02809	RsmW RNA family	3	1.000	58.0
3	RF02824	Legionella RNA 10	3	1.000	23.0
3	RF02830	Streptomyces RNA 1601	2	0.333	14.6
3	RF02832	Streptomyces RNA 5676	4	0.800	32.4
3	RF02840	Enterococcus sRNA 68 (Lacto-3 RNA)	31	0.397	335.4
3	RF02841	Enterococcus sRNA 70	3	1.000	24.0
3	RF02856	Leptospira sRNA 30_292	3	1.000	24.3
3	RF02870	Burkholderia sRNA 35	2	0.667	18.1
3	RF02917	Burkholderiales-2 RNA	2	0.105	16.7
3	RF02919	ilvB-OMG RNA	15	0.536	133.3
3	RF02928	Actinomyces-1 RNA	26	0.110	211.9
3	RF02929	algC RNA	11	0.022	94.9
3	RF02935	che1 RNA	11	0.112	97.3
3	RF02936	Chloroflexus-1 RNA	3	0.750	26.2
3	RF02937	Clostridiales-2 RNA	10	0.227	84.5
3	RF02941	COG3943 RNA	8	0.296	70.2
3	RF02942	Clostridiales-3 RNA	12	0.076	132.2
3	RF02948	cow-rumen-4 RNA	5	0.625	46.4
3	RF02953	DUF1874 RNA	12	0.158	93.3
3	RF02957	EFASI RNA	191	0.426	2109.5
3	RF02960	DUF2800 RNA	26	0.168	223.2
3	RF02961	DUF3800-II RNA	3	0.130	32.3
3	RF02962	DUF3800-III RNA	20	0.364	209.0
3	RF02966	DUF3268 RNA	19	0.176	196.4
3	RF02968	DUF3800-IX RNA	22	0.096	225.2
3	RF02981	FTHFS RNA	4	0.148	39.3
3	RF02984	DUF3800-X RNA	20	0.227	210.5
3	RF02988	GEBRO RNA	3	0.071	22.8
3	RF02999	ivy-DE RNA	222	0.895	2176.9
3	RF03001	leuA-Halobacteria RNA	6	0.039	52.6
3	RF03006	M23 RNA	13	0.419	97.9
3	RF03007	Mahella-1 RNA	3	0.158	23.3
3	RF03009	malK-III RNA	10	0.256	91.0
3	RF03012	Mu-gpT-DE RNA	47	0.149	378.1
3	RF03016	RT-12 RNA	8	0.190	84.2
3	RF03017	RT-13 RNA	3	0.231	25.3
3	RF03026	RT-5 RNA	16	0.225	150.8
3	RF03028	RT-7 RNA	20	0.370	158.9
3	RF03041	poplar-1 RNA	3	0.136	26.8
3	RF03044	Proteo-phage-1 RNA	7	0.104	52.5
3	RF03045	proV RNA	13	0.812	172.4
3	RF03059	raiA-hairpin RNA	9	0.113	65.1
3	RF03065	IS605-orfB-I RNA	31	0.120	260.1
3	RF03066	COG3610-DE RNA	59	1.000	623.5
3	RF03069	malK-I RNA	31	0.096	284.6
3	RF03074	Rhodo-rpoB RNA	53	0.203	428.5
3	RF03077	RT-2 RNA	36	0.185	351.7
3	RF03079	MISL RNA	18	0.409	190.1
3	RF03082	dinG RNA	15	0.174	140.1
3	RF03087	ROOL RNA	44	0.152	521.3
3	RF03090	lysM-Actino RNA	48	0.857	380.6
3	RF03128	L31-Coriobacteria ribosomal protein leader	58	0.773	437.8
3	RF03135	L4-Archaeoglobi ribosomal protein leades	40	0.106	341.6
3	RF03162	TD-2 RNA	26	0.722	466.1
3	RF03311	MIR169 microRNA precursor family	2	0.250	15.6
3	RF03483	MIR319 microRNA precursor family	3	0.273	21.4
3	RF03542	Insect-Specific Flavivirus 3' UTR repeats Ra and Rb elements	2	0.167	15.0
3	RF03543	Insect-Specific Flavivirus 3' UTR repeats Rb	7	0.368	60.4
3	RF03749	MIR2617 microRNA precursor family	3	1.000	23.7
3	RF03881	mir-59 microRNA precursor family	2	0.500	22.6
3	RF04023	MIR1314 microRNA precursor family	2	1.000	16.7
3	RF04104	MIR918 microRNA precursor family	2	1.000	26.5
3	RF04134	MIR7504 microRNA precursor family	2	0.250	26.5
3	RF04191	Hairpin ribozyme 2 from viruses-like metatranscriptomes	6	0.125	46.8
3	RF04218	Hepatitis C virus stem-loop I	5	0.088	41.6
3	RF04219	J750 non-coding RNA (containing SLSL761 and SL783)	6	0.105	45.8
3	RF04220	SL588 non-coding RNA	17	0.298	166.0
3	RF04227	mir-9215 microRNA precursor family	5	1.000	45.5
3	RF04230	mir-9261 microRNA precursor family	3	1.000	21.9
3	RF04244	MIR169_6 microRNA precursor family	4	0.500	43.7
3	RF04295	mir-329 microRNA precursor family	17	0.370	136.3
3	RF04306	Hepatitis C virus stem-loop SL8001 RNA	5	0.088	38.9