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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 21 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	1I6U		16 - 21
2	1J5E		1134 - 1140
2	1KUQ		8 - 13
2	1NBS		152 - 157
2	1S72		136 - 142
2	1UN6		15 - 64
2	1YKV		220 - 225
2	1YLS		220 - 225
2	1ZHO		15 - 20
2	2AVY		1449 - 1454
2	2AW4		1533 - 1538
2	2HW8		15 - 20
2	2J01		1691 - 1696
2	3kyl	E	6 - 19
2	1ekz	B	9 - 22
2	1p6v	B	22 - 35
2	3izz	A	12 - 25
2	2gip	A	8 - 21
2	1ikd	A	3 - 16
2	1f6x	A	8 - 21
2	2l3e	A	14 - 27

There are 267 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	RF00002	5.8S ribosomal RNA	7	0.115	75.5
3	RF00003	U1 spliceosomal RNA	47	0.470	501.1
3	RF00004	U2 spliceosomal RNA	32	0.154	365.3
3	RF00009	Nuclear RNase P	31	0.267	397.0
3	RF00010	Bacterial RNase P class A	155	0.338	2427.3
3	RF00011	Bacterial RNase P class B	32	0.281	419.1
3	RF00012	Small nucleolar RNA U3	32	0.368	343.7
3	RF00015	U4 spliceosomal RNA	38	0.215	533.7
3	RF00018	CsrB/RsmB RNA family	19	0.500	157.5
3	RF00020	U5 spliceosomal RNA	57	0.317	676.5
3	RF00022	GcvB RNA	10	0.370	105.7
3	RF00023	transfer-messenger RNA	57	0.119	636.7
3	RF00024	Vertebrate telomerase RNA	21	0.568	237.4
3	RF00026	U6 spliceosomal RNA	113	0.601	1320.7
3	RF00028	Group I catalytic intron	2	0.167	30.3
3	RF00030	RNase MRP	10	0.152	140.0
3	RF00032	Histone 3' UTR stem-loop	7	0.140	61.2
3	RF00033	MicF RNA	2	0.500	21.0
3	RF00034	RprA RNA	4	0.308	35.3
3	RF00045	Small nucleolar RNA SNORA73 family	8	0.121	97.3
3	RF00057	RyhB RNA	2	0.077	17.0
3	RF00061	Hepatitis C virus internal ribosome entry site	25	0.316	281.2
3	RF00066	U7 small nuclear RNA	9	0.184	96.3
3	RF00080	Manganese Mn2+ riboswitch aptamer (yybP-ykoY)	5	0.172	58.2
3	RF00090	Small nucleolar RNA SNORA74	7	0.292	61.3
3	RF00096	U8 small nucleolar RNA	13	0.236	163.1
3	RF00103	mir-1 microRNA precursor family	4	0.061	32.9
3	RF00106	RNAI	4	0.400	40.4
3	RF00114	Ribosomal S15 leader	10	0.128	105.1
3	RF00126	ryfA RNA	9	1.000	184.7
3	RF00128	Glm Y RNA activator of glmS mRNA	2	0.118	19.7
3	RF00132	Small nucleolar RNA R24	6	0.500	67.8
3	RF00149	Small nucleolar RNA Z103	3	0.250	40.6
3	RF00156	Small nucleolar RNA SNORA70	4	0.093	38.3
3	RF00171	Tombusvirus 5' UTR	2	0.222	21.8
3	RF00174	Cobalamin riboswitch aptamer	51	0.118	655.0
3	RF00175	Human immunodeficiency virus type 1 dimerisation initiation site	2	0.029	16.6
3	RF00176	Tombusvirus 3' UTR region IV	16	0.889	191.7
3	RF00177	Bacterial small subunit ribosomal RNA	88	0.889	2261.3
3	RF00190	Small nucleolar RNA SNORA16B/SNORA16A family	4	0.138	36.5
3	RF00191	Small nucleolar RNA SNORA57	7	0.269	67.3
3	RF00195	RsmY RNA family	7	0.636	136.9
3	RF00214	Retrovirus direct repeat 1 (dr1)	8	0.308	72.2
3	RF00215	Tombus virus defective interfering (DI) RNA region 3	10	0.357	92.0
3	RF00252	Alfalfa mosaic virus coat protein binding (CPB) RNA	4	0.222	35.2
3	RF00262	sar RNA	4	1.000	40.8
3	RF00263	Small nucleolar RNA SNORA68	5	0.192	42.9
3	RF00272	Small nucleolar RNA SNORA67	4	0.333	34.7
3	RF00345	Small nucleolar RNA snoR1	3	0.231	29.3
3	RF00373	Archaeal RNase P	10	0.143	116.1
3	RF00391	RtT RNA	6	0.105	49.9
3	RF00428	Small nucleolar RNA SNORA38	5	0.200	50.8
3	RF00435	Repression of heat shock gene expression (ROSE) element	4	0.308	47.2
3	RF00444	PrrF RNA	8	0.444	82.1
3	RF00449	HIF-1 alpha IRES	5	0.294	57.1
3	RF00452	mir-172 microRNA precursor family	2	0.182	17.2
3	RF00472	Small nucleolar RNA snR55/Z10	3	0.500	32.6
3	RF00480	HIV Ribosomal frameshift signal	61	0.415	615.8
3	RF00488	Yeast U1 spliceosomal RNA	2	0.400	23.1
3	RF00506	Threonine operon leader	3	0.120	28.4
3	RF00513	Tryptophan operon leader	7	0.318	63.9
3	RF00514	Histidine operon leader	3	0.091	25.6
3	RF00515	PyrR binding site	10	0.244	97.4
3	RF00519	Makes More Granules Regulator RNA (mmgR)	38	0.437	474.1
3	RF00524	R2 RNA element	3	0.200	30.4
3	RF00548	U11 spliceosomal RNA	8	0.111	96.1
3	RF00551	Bicoid 3'-UTR regulatory element	3	0.200	29.6
3	RF00557	Ribosomal protein L10 leader	23	0.237	234.8
3	RF00558	Ribosomal protein L20 leader	4	0.093	41.0
3	RF00598	Small nucleolar RNA SNORA76	5	0.227	46.2
3	RF00618	U4atac minor spliceosomal RNA	13	0.213	176.1
3	RF00619	U6atac minor spliceosomal RNA	13	0.210	185.3
3	RF00625	Pseudomonas sRNA P11	14	0.933	123.9
3	RF00627	Pseudomonas sRNA P15	3	0.136	28.0
3	RF00629	Pseudomonas sRNA P24	7	0.500	64.1
3	RF00630	Pseudomonas sRNA P26	9	0.333	82.7
3	RF00639	mir-515 microRNA precursor family	41	0.227	401.4
3	RF00648	microRNA MIR396	5	0.192	45.8
3	RF00664	microRNA mir-223	2	0.074	17.8
3	RF00668	microRNA mir-302	6	0.136	54.9
3	RF00675	microRNA mir-145	25	0.962	299.9
3	RF00717	microRNA mir-315	13	0.481	124.3
3	RF00727	bantam microRNA precursor family	3	0.273	24.6
3	RF00763	microRNA mir-339	3	0.214	24.6
3	RF00779	microRNA MIR474	4	0.364	33.8
3	RF00802	microRNA mir-207	2	0.333	18.5
3	RF00957	mir-663 microRNA precursor family	2	0.167	16.5
3	RF00959	mir-612 microRNA precursor family	3	0.500	27.7
3	RF01015	microRNA mir-885	3	1.000	28.7
3	RF01036	microRNA mir-567	3	0.333	26.4
3	RF01066	6C RNA	3	0.167	27.5
3	RF01067	ATPC RNA motif	5	0.056	67.7
3	RF01071	Ornate Large Extremophilic RNA	2	0.100	17.1
3	RF01084	Pseudoknot of tRNA-like structure	5	0.556	50.0
3	RF01116	Cyanobacterial functional RNA 1	7	0.189	84.1
3	RF01188	Small nucleolar RNA snR56	2	0.125	20.9
3	RF01219	Small nucleolar RNA snoR100	2	0.222	27.9
3	RF01227	Small nucleolar RNA snoR83	3	0.429	31.9
3	RF01233	Small nucleolar RNA U109	3	0.115	32.5
3	RF01234	Small nucleolar RNA SNORA47	6	0.300	55.6
3	RF01243	Small nucleolar RNA snR33	4	0.800	32.4
3	RF01260	Small nucleolar RNA snR11	2	0.333	16.5
3	RF01267	Small nucleolar RNA snR37	2	0.222	39.2
3	RF01268	Small Cajal body-specific RNA 2	9	0.450	113.8
3	RF01271	Small nucleolar RNA snR30	3	0.600	39.4
3	RF01318	CRISPR RNA direct repeat element	4	0.333	41.6
3	RF01322	CRISPR RNA direct repeat element	2	0.286	23.7
3	RF01386	isrB Hfq binding RNA	3	1.000	37.4
3	RF01400	istR Hfq binding RNA	7	1.000	113.9
3	RF01411	BsrF	7	0.636	74.8
3	RF01470	Listeria sRNA rli38	6	0.300	49.8
3	RF01473	Listeria sRNA rli41	5	0.833	47.9
3	RF01496	A. fumigatus sRNA Afu_182	5	0.263	78.4
3	RF01502	Fungal signal recognition particle RNA	15	0.300	288.2
3	RF01509	A. fumigatus snoRNA Afu_300	6	0.600	71.6
3	RF01512	A. fumigatus sRNA Afu_309	4	0.400	61.7
3	RF01656	Nematode sRNA ceN72-3_ceN74-2	4	0.308	40.4
3	RF01673	PhrS	11	0.846	198.7
3	RF01675	Pseudomonas sRNA CrcZ	16	0.842	310.8
3	RF01687	Acido-Lenti-1 RNA	26	0.299	229.7
3	RF01693	Bacteroidales-1 6S-Bacteroidales RNA suggested	34	0.829	395.5
3	RF01694	Bacteroides-1 RNA	7	0.175	59.2
3	RF01695	C4 antisense RNA	223	0.489	3216.5
3	RF01702	Cyano-2 RNA	7	0.123	66.1
3	RF01706	Gut-1 RNA	23	0.605	262.8
3	RF01715	Pedo-repair RNA	2	0.333	16.8
3	RF01716	PhotoRC-I RNA	56	0.862	616.9
3	RF01719	Pseudomon-1/ErsA RNA	3	0.158	43.1
3	RF01728	STAXI RNA	37	0.860	836.6
3	RF01732	MarS sRNA	15	0.484	188.0
3	RF01736	flg-Rhizobiales RNA	2	0.154	21.7
3	RF01740	gyrA RNA	2	0.111	18.7
3	RF01743	leu/phe leader RNA from Lactococcus	9	1.000	86.0
3	RF01746	mraW RNA	6	0.133	76.4
3	RF01748	nuoG RNA	2	0.065	19.0
3	RF01752	psaA RNA	21	0.677	447.4
3	RF01754	radC RNA	18	0.122	190.6
3	RF01758	sucA-II RNA	5	0.294	43.2
3	RF01762	Whalefall-1 RNA	6	0.429	78.7
3	RF01766	cspA thermoregulator	13	0.867	139.9
3	RF01769	Enterobacteria greA leader	4	0.160	33.2
3	RF01772	Pseudomonas rnk leader	8	0.533	120.3
3	RF01773	Pseudomonas rpsL leader	2	0.222	35.6
3	RF01793	ffh sRNA	12	0.135	108.5
3	RF01794	sok antitoxin (CssrC)	11	0.121	92.8
3	RF01814	rhtB sRNA	4	0.286	38.8
3	RF01819	RNA Staph. aureus D	7	0.875	67.5
3	RF01820	RNA Staph. aureus E (RoxS)	6	0.400	69.7
3	RF01830	Salmonella enterica Typhi npcRNA 44	7	0.206	93.4
3	RF01838	sobemovirus ribosomal frameshift elemental	4	0.800	60.1
3	RF01844	SmY spliceosomal RNA	7	0.115	81.6
3	RF01846	Fungal small nucleolar RNA U3	36	0.545	552.6
3	RF01847	Plant small nucleolar RNA U3	5	0.208	50.5
3	RF01848	ACEA small nucleolar RNA U3	8	0.286	99.2
3	RF01849	Alphaproteobacteria transfer-messenger RNA	39	0.351	433.5
3	RF01850	Betaproteobacteria transfer-messenger RNA	5	0.714	109.2
3	RF01851	Cyanobacteria transfer-messenger RNA	9	0.333	140.2
3	RF01857	Archaeal signal recognition particle RNA	15	0.278	136.2
3	RF01867	caulobacter sRNA CC2171	7	0.538	73.4
3	RF01872	Maternally expressed 3 conserved region 2	2	0.125	22.5
3	RF01927	microRNA MIR1222	2	0.400	19.1
3	RF01938	microRNA mir-1251	7	1.000	83.3
3	RF01952	SOX2 overlapping transcript exon 2	4	0.286	42.8
3	RF01959	Archaeal small subunit ribosomal RNA	59	0.686	1201.2
3	RF01960	Eukaryotic small subunit ribosomal RNA	57	0.633	1238.7
3	RF02025	microRNA mir-3017	9	0.250	76.6
3	RF02030	tp2	8	0.333	73.2
3	RF02032	Giant, ornate, lake- and Lactobacillales-derived (GOLLD) RNA	7	0.200	82.8
3	RF02033	HNH endonuclease-associated RNA and ORF (HEARO) RNA	14	0.101	152.7
3	RF02036	IMES-3 RNA motif	15	0.469	132.6
3	RF02051	Enterobacterial sRNA STnc450	4	0.333	36.1
3	RF02065	Enterobacterial sRNA STnc340	3	0.750	26.4
3	RF02069	Enterobacterial sRNA STnc70	4	2.000	40.2
3	RF02075	Enterobacterial sRNA STnc230	3	0.273	25.4
3	RF02076	Gammaproteobacterial sRNA STnc100	17	0.708	299.3
3	RF02079	Enterobacterial sRNA STnc180	5	0.500	78.7
3	RF02100	Translational regulator of tfoXVC	2	0.200	20.7
3	RF02143	Hydatidiform mole associated and imprinted conserved region 1	2	0.125	21.6
3	RF02144	rsmX	16	1.000	331.7
3	RF02165	Pvt1 oncogene conserved region 2	3	0.176	26.6
3	RF02168	Pvt1 oncogene conserved region 5	5	0.217	50.7
3	RF02184	ST7 overlapping transcript 3 conserved region 2	3	0.600	25.2
3	RF02189	ST7 overlapping transcript 4 conserved region 3	2	0.100	20.9
3	RF02198	TTC28 antisense RNA 1 conserved region 1	2	0.143	17.4
3	RF02221	sRNA-Xcc1	16	0.216	191.1
3	RF02225	Proteobacterial sRNA sX6	6	0.750	66.6
3	RF02240	Xanthomonadaceae sRNA Xoo1	4	0.800	53.0
3	RF02241	Xanthomonadaceae sRNA Xoo2	3	1.000	27.0
3	RF02249	Six3os1 conserved region 4	6	0.857	99.7
3	RF02276	Hammerhead ribozyme (type II)	4	0.167	60.7
3	RF02278	Betaproteobacteria toxic small RNA	8	0.157	70.3
3	RF02342	Alphaproteobacterial sRNA ar7	15	0.517	158.4
3	RF02343	Alphaproteobacterial sRNA ar9	6	0.214	71.1
3	RF02344	Alphaproteobacterial ar14	16	0.136	151.8
3	RF02345	Alphaproteobacterial ar15	10	0.164	104.8
3	RF02354	Bradyrhizobiaceae sRNA BjrC80	3	0.200	48.0
3	RF02355	Bradyrhizobiaceae sRNA BjrC174	2	0.133	18.6
3	RF02356	Alphaproteobacterial sRNA BjrC1505	4	0.160	40.6
3	RF02366	Cyanobacterial functional RNA 19	2	0.333	17.5
3	RF02371	PyrG leader	7	0.700	59.1
3	RF02399	Nitrogen stress-induced RNA 1	2	0.118	38.0
3	RF02402	A. fumigatus snoRNA Afu_263	10	0.526	119.2
3	RF02405	Pseudomonas sRNA P34	2	0.400	31.2
3	RF02423	Burkholderia sRNA Bp1_Cand871_SIPHT	15	1.000	179.2
3	RF02424	Burkholderia sRNA Bp2_Cand287_SIPHT	10	0.714	97.3
3	RF02442	Streptococcus sRNA SpF66	8	0.889	83.6
3	RF02455	Dianthovirus RNA2 cap-independent translation element	2	1.000	20.6
3	RF02462	Ascomycota telomerase RNA	4	1.000	100.3
3	RF02471	Actinobacteria sRNA Ms_IGR-5	3	0.143	31.2
3	RF02501	Rhizobiales sRNA Atu_C7	3	1.000	25.0
3	RF02502	Rhizobiales sRNA Atu_C8	8	0.296	85.1
3	RF02509	Pyrrolysine insertion sequence mtbB	2	0.087	19.5
3	RF02540	Archaeal large subunit ribosomal RNA	81	0.890	2169.7
3	RF02541	Bacterial large subunit ribosomal RNA	89	0.873	1992.0
3	RF02543	Eukaryotic large subunit ribosomal RNA	79	0.898	2528.8
3	RF02679	Pistol ribozyme	5	0.111	88.4
3	RF02681	Twister_sister_ribozyme	19	0.168	278.7
3	RF02684	Type-P5 twister ribozyme	25	0.116	386.3
3	RF02784	Singlet oxygen resistance RNA X	3	0.375	44.2
3	RF02798	Chromosome-encoded Shigella sRNA A	4	1.000	35.8
3	RF02806	Pyrobaculum sRNA 208	2	0.500	18.4
3	RF02809	RsmW RNA family	2	0.667	16.9
3	RF02830	Streptomyces RNA 1601	3	0.500	35.0
3	RF02837	Burkholderia RNA 7 (anti-hemB)	6	0.231	61.8
3	RF02838	Enterococcus sRNA 55	3	0.750	24.8
3	RF02840	Enterococcus sRNA 68 (Lacto-3 RNA)	26	0.333	318.3
3	RF02843	Enterococcus sRNA A5	3	1.000	28.5
3	RF02865	Burkholderia sRNA 1	4	1.000	32.4
3	RF02867	Burkholderia sRNA 11	4	1.000	50.0
3	RF02894	Staphylococcus sRNA 35 (srn_0335)	3	1.000	43.6
3	RF02898	Aggregatibacter sRNA 20	2	0.333	21.8
3	RF02902	Aggregatibacter sRNA 22	3	0.429	27.2
3	RF02922	RAGATH-32 RNA	15	0.789	210.7
3	RF02954	DUF3577 RNA	30	0.349	378.3
3	RF02969	DUF3800-I RNA	68	0.212	829.7
3	RF02972	engA RNA	25	0.162	265.9
3	RF02993	ilvH RNA	3	0.176	25.8
3	RF03000	LOOT RNA	66	0.179	714.9
3	RF03006	M23 RNA	4	0.129	35.0
3	RF03009	malK-III RNA	8	0.205	89.5
3	RF03019	RT-16 RNA	13	0.125	141.5
3	RF03022	RT-10 RNA	68	0.602	788.1
3	RF03061	uxuA RNA	17	0.515	199.3
3	RF03062	xerDC RNA	12	0.167	116.8
3	RF03074	Rhodo-rpoB RNA	56	0.215	538.2
3	RF03078	chrB-a RNA	22	0.135	212.9
3	RF03079	MISL RNA	27	0.614	626.5
3	RF03080	RT-9 RNA	16	0.333	196.0
3	RF03089	cold-seep-1 RNA	5	0.333	55.1
3	RF03105	RAGATH-7-assoc RNA	8	0.308	73.6
3	RF03106	RT-11 RNA	2	0.667	17.6
3	RF03109	Thermales-rpoB RNA	12	0.857	108.0
3	RF03112	Staphylococcus-1 RNA	2	0.095	18.1
3	RF03116	Alphacoronavirus 5'UTR	7	0.412	78.3
3	RF03121	Alphacoronavirus 3'UTR	2	0.118	18.4
3	RF03131	L25-Gammaproteobacteria ribosomal protein leader	3	0.008	27.2
3	RF03142	L2-Alphaproteobacteria ribosomal protein leader	306	0.677	3694.8
3	RF03148	RAGATH-11 RNA	7	0.700	69.8
3	RF03155	TD-1 RNA	21	0.750	243.9
3	RF03162	TD-2 RNA	3	0.083	27.4
3	RF03544	Insect-Specific Flavivirus 3' UTR repeats Ra	3	0.100	25.3
3	RF03941	mir-3158 microRNA precursor family	2	1.000	27.8
3	RF04114	MIR4374 microRNA precursor family	2	0.667	17.6
3	RF04179	Bacteroides sRNA BTnc049	5	0.556	43.9
3	RF04180	Bacteroides sRNA BTnc231	7	1.000	62.6
3	RF04190	Hairpin ribozyme 1 from viruses-like metatranscriptomes	11	0.131	110.6
3	RF04219	J750 non-coding RNA (containing SLSL761 and SL783)	13	0.228	122.2