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Things you should know

How your contribution will be recorded

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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 52 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		42 - 49
2	1E8O		110 - 117
2	1GAX		952 - 960
2	1H3E		31 - 39
2	1J1U		532 - 540
2	1J2B		932 - 940
2	1J5E		259 - 267
2	1MJI		38 - 44
2	1MMS		1092 - 1099
2	1N78		531 - 539
2	1NBS		118 - 125
2	1QA6		142 - 149
2	1QTQ		953 - 961
2	1QU2		53 - 61
2	1S72		1196 - 1203
2	1U0B		31 - 39
2	1U9S		181 - 189
2	1VFG		53 - 61
2	1WZ2		965 - 973
2	1Y0Q		224 - 234
2	1Y69		1103 - 1110
2	2A2E		156 - 164
2	2A64		69 - 76
2	2AVY		259 - 267
2	2AW4		1092 - 1099
2	2AZX		531 - 539
2	2BH2		1949 - 1957
2	2BTE		53 - 61
2	2CT8		53 - 61
2	2D6F		953 - 961
2	2DER		31 - 39
2	2DET		31 - 39
2	2DEU		31 - 39
2	2DR2		31 - 39
2	2G9C		46 - 53
2	2HOP		65 - 74
2	2IL9		6118 - 6124
2	2IY5		31 - 39
2	2J01		1949 - 1957
2	2DU3		952 - 960
2	2FK6		53 - 61
2	2NQP		53 - 61
2	2NR0		53 - 61
2	2NRE		53 - 61
2	2R8S		166 - 174
2	387D		4 - 13
2	3B31		6184 - 6193
2	2i82	E	3 - 19
2	1ser	T	67 - 83
2	2zzn	C	48 - 64
2	1j4y	A	1 - 17
2	2zue	B	51 - 67

There are 166 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	39	0.188	400.1
3	RF00005	tRNA	567	0.594	8155.1
3	RF00007	U12 minor spliceosomal RNA	33	0.532	395.4
3	RF00009	Nuclear RNase P	15	0.129	170.9
3	RF00010	Bacterial RNase P class A	393	0.858	6917.8
3	RF00011	Bacterial RNase P class B	9	0.079	90.1
3	RF00013	6S / SsrS RNA	14	0.093	158.8
3	RF00017	Metazoan signal recognition particle RNA	11	0.121	109.1
3	RF00022	GcvB RNA	3	0.111	29.9
3	RF00023	transfer-messenger RNA	352	0.738	4368.9
3	RF00030	RNase MRP	7	0.106	73.6
3	RF00050	FMN riboswitch aptamer (RFN element)	16	0.110	173.2
3	RF00066	U7 small nuclear RNA	7	0.143	71.7
3	RF00078	MicA sRNA	2	0.118	19.3
3	RF00079	OmrA-B family	10	0.435	93.0
3	RF00082	SraG RNA	2	0.286	21.5
3	RF00096	U8 small nucleolar RNA	7	0.127	67.7
3	RF00102	VA RNA	10	0.182	113.4
3	RF00113	Short Intergenic Abundant RNA	7	0.412	69.4
3	RF00126	ryfA RNA	3	0.333	29.1
3	RF00166	PrrB/RsmZ RNA family	34	0.919	427.3
3	RF00174	Cobalamin riboswitch aptamer	95	0.219	1005.1
3	RF00177	Bacterial small subunit ribosomal RNA	61	0.616	864.8
3	RF00236	ctRNA	2	0.133	23.4
3	RF00304	Small nucleolar RNA Z279/snoR105/snoR108	3	0.150	29.8
3	RF00370	sroD RNA	4	0.800	42.9
3	RF00373	Archaeal RNase P	16	0.229	181.6
3	RF00386	Enterovirus 5' cloverleaf cis-acting replication element	24	0.150	237.8
3	RF00391	RtT RNA	7	0.123	71.3
3	RF00438	Small nucleolar RNA SNORA33	3	0.107	30.4
3	RF00513	Tryptophan operon leader	9	0.409	102.3
3	RF00547	TrkB IRES	3	0.188	31.5
3	RF00553	Small Cajal body specific RNA 1	11	0.379	110.6
3	RF00558	Ribosomal protein L20 leader	4	0.093	44.0
3	RF00604	Small nucleolar RNA SNORD88	4	0.114	39.6
3	RF00617	Flavivirus capsid hairpin cHP	15	0.254	155.3
3	RF00625	Pseudomonas sRNA P11	3	0.200	33.6
3	RF00630	Pseudomonas sRNA P26	7	0.259	70.0
3	RF00634	SAM (S-adenosyl methionine) riboswitch aptamer	17	0.425	197.1
3	RF00664	microRNA mir-223	2	0.074	20.7
3	RF00685	microRNA mir-36	8	0.174	86.9
3	RF00717	microRNA mir-315	3	0.111	37.2
3	RF00972	mir-651 microRNA precursor family	2	0.500	21.0
3	RF01050	Saccharomyces telomerase	3	0.231	27.9
3	RF01067	ATPC RNA motif	8	0.089	77.6
3	RF01071	Ornate Large Extremophilic RNA	12	0.600	135.6
3	RF01085	Pseudoknot of tRNA-like structure	2	1.000	20.9
3	RF01116	Cyanobacterial functional RNA 1	6	0.162	83.8
3	RF01267	Small nucleolar RNA snR37	4	0.444	42.3
3	RF01290	Small nucleolar RNA SNORD10	2	0.091	18.6
3	RF01317	CRISPR RNA direct repeat element	5	0.152	47.6
3	RF01322	CRISPR RNA direct repeat element	3	0.429	31.5
3	RF01394	isrK Hfq binding RNA	14	0.269	165.9
3	RF01401	rseX Hfq binding RNA	9	0.750	103.5
3	RF01510	2dG-I riboswitch aptamer (M. florum)	3	0.750	35.1
3	RF01518	NoRC associated RNA, pRNA	6	0.261	57.8
3	RF01583	small nucleolar RNA snoR01	2	0.667	21.1
3	RF01684	MALAT1-associated small cytoplasmic RNA/MEN beta RNA	36	0.679	397.3
3	RF01687	Acido-Lenti-1 RNA	20	0.230	212.6
3	RF01700	Collinsella-1 RNA	4	0.667	42.1
3	RF01721	Pseudomon-groES RNA	5	0.278	56.1
3	RF01729	Termite-flg RNA	3	0.231	35.3
3	RF01730	Termite-leu RNA	14	0.700	316.0
3	RF01731	TwoAYGGAY RNA	80	0.381	1056.1
3	RF01732	MarS sRNA	3	0.097	31.5
3	RF01754	radC RNA	23	0.155	236.9
3	RF01758	sucA-II RNA	15	0.882	210.6
3	RF01766	cspA thermoregulator	2	0.133	31.1
3	RF01770	Gammaprotebacteria rimP leader	14	0.304	134.2
3	RF01776	RNA anti-toxin A	2	0.125	21.3
3	RF01796	Fumarate/nitrate reductase regulator sRNA	5	0.312	49.4
3	RF01808	MicX Vibrio cholerae sRNA	4	0.400	39.3
3	RF01815	rpsB sRNA	2	0.500	18.9
3	RF01820	RNA Staph. aureus E (RoxS)	2	0.133	19.1
3	RF01849	Alphaproteobacteria transfer-messenger RNA	23	0.207	224.4
3	RF01850	Betaproteobacteria transfer-messenger RNA	4	0.571	39.4
3	RF01851	Cyanobacteria transfer-messenger RNA	3	0.111	31.0
3	RF01852	Selenocysteine transfer RNA	96	0.881	1312.9
3	RF01871	Metastasis associated lung adenocarcinoma transcript 1	15	0.882	138.6
3	RF01877	Myocardial infarction associated transcript exon 5 conserved region 3	9	0.562	88.5
3	RF01909	CDKN2B antisense RNA 1 intronic convserved region	3	0.120	32.7
3	RF01946	KCNQ1 overlapping transcript 1 conserved region 1	4	0.500	38.0
3	RF01959	Archaeal small subunit ribosomal RNA	77	0.895	2180.0
3	RF01960	Eukaryotic small subunit ribosomal RNA	33	0.367	414.8
3	RF01973	H19 conserved region 2	12	0.522	110.4
3	RF02003	Group II catalytic intron D1-D4-4	15	0.167	155.5
3	RF02029	sraA	17	0.850	213.1
3	RF02032	Giant, ornate, lake- and Lactobacillales-derived (GOLLD) RNA	6	0.171	76.1
3	RF02033	HNH endonuclease-associated RNA and ORF (HEARO) RNA	45	0.324	499.1
3	RF02055	Enterobacterial sRNA STnc380	3	0.600	29.4
3	RF02089	CLRN1 antisense RNA 1 conserved region	2	0.105	19.4
3	RF02090	DAOA antisense RNA 1 conserved region 1	2	0.083	18.6
3	RF02140	HOXA11 antisense RNA 1 conserved region 4	9	0.450	84.6
3	RF02151	MER1 repeat containing imprinted transcript 1 conserved region 1	4	0.190	43.2
3	RF02164	Pvt1 oncogene conserved region 1	2	0.118	20.6
3	RF02165	Pvt1 oncogene conserved region 2	2	0.118	21.1
3	RF02205	WT1 antisense RNA conserved region 3	6	0.316	58.8
3	RF02223	Proteobacterial sRNA sX4	12	2.400	138.0
3	RF02276	Hammerhead ribozyme (type II)	9	0.375	95.7
3	RF02354	Bradyrhizobiaceae sRNA BjrC80	5	0.333	48.3
3	RF02356	Alphaproteobacterial sRNA BjrC1505	8	0.320	80.4
3	RF02373	PyrD leader	23	0.852	236.7
3	RF02376	SR1 sRNA	2	0.333	22.8
3	RF02399	Nitrogen stress-induced RNA 1	3	0.176	31.9
3	RF02401	ClpQY promoter	6	0.154	65.7
3	RF02423	Burkholderia sRNA Bp1_Cand871_SIPHT	12	0.800	138.9
3	RF02428	Streptococcus sRNA SpF11	3	1.000	34.7
3	RF02431	Streptococcus sRNA SpF22	5	0.227	48.4
3	RF02435	Streptococcus sRNA SpF41	3	0.333	33.2
3	RF02464	Actinobacteria sRNA Ms_AS-4	2	0.222	22.1
3	RF02496	Rhizobiales sRNA Atu_At1	8	0.242	109.7
3	RF02502	Rhizobiales sRNA Atu_C8	2	0.074	21.3
3	RF02540	Archaeal large subunit ribosomal RNA	88	0.967	3648.2
3	RF02541	Bacterial large subunit ribosomal RNA	101	0.990	3137.1
3	RF02542	Microsporidia small subunit ribosomal RNA	22	0.478	242.8
3	RF02543	Eukaryotic large subunit ribosomal RNA	39	0.443	526.0
3	RF02553	Y RNA-like	4	0.667	42.1
3	RF02630	Hfq-regulated sRNA 12	2	1.000	19.8
3	RF02657	Sense overlapping transcript RNA 2652 (sot)	2	1.000	21.1
3	RF02681	Twister_sister_ribozyme	18	0.159	177.5
3	RF02684	Type-P5 twister ribozyme	28	0.130	312.5
3	RF02728	Haemophilus regulatory RNA responsive to iron	5	0.714	46.1
3	RF02784	Singlet oxygen resistance RNA X	5	0.625	51.2
3	RF02830	Streptomyces RNA 1601	4	0.667	63.9
3	RF02837	Burkholderia RNA 7 (anti-hemB)	9	0.346	99.8
3	RF02860	Actinobacillus sRNA 14	2	0.500	20.3
3	RF02866	Burkholderia sRNA 16 (Bc_KC_sr1)	2	0.500	29.3
3	RF02900	Aggregatibacter sRNA 82	2	0.500	19.0
3	RF02913	pemK RNA	107	0.069	1300.0
3	RF02915	DUF3800-VI RNA	10	0.115	101.6
3	RF02919	ilvB-OMG RNA	11	0.393	112.5
3	RF02957	EFASI RNA	87	0.194	966.8
3	RF02969	DUF3800-I RNA	31	0.097	361.0
3	RF02980	freshwater-2 RNA	25	0.125	275.6
3	RF02988	GEBRO RNA	4	0.095	47.4
3	RF02991	GP20-a RNA	8	0.148	91.4
3	RF02992	hya RNA	2	0.074	19.1
3	RF02993	ilvH RNA	4	0.235	37.5
3	RF03006	M23 RNA	4	0.129	39.9
3	RF03015	Transposase-2 RNA	18	0.119	194.4
3	RF03016	RT-12 RNA	3	0.071	31.6
3	RF03049	RAGATH-24 RNA	6	0.273	61.6
3	RF03058	sul1 RNA	12	0.222	120.6
3	RF03066	COG3610-DE RNA	3	0.051	30.8
3	RF03072	raiA RNA	39	0.080	405.9
3	RF03074	Rhodo-rpoB RNA	22	0.084	214.9
3	RF03079	MISL RNA	19	0.432	194.7
3	RF03083	cow-rumen-3 RNA	2	0.250	19.7
3	RF03087	ROOL RNA	37	0.128	422.7
3	RF03094	LAGLIDADG-2 RNA	10	0.400	104.9
3	RF03103	RAGATH-34 RNA	14	0.583	140.9
3	RF03110	throat-1 RNA	12	0.444	126.4
3	RF03137	S15-Methanomicrobia ribosomal protein leader	12	0.120	126.9
3	RF03150	RAGATH-15 RNA	5	0.357	49.8
3	RF03155	TD-1 RNA	2	0.071	21.6
3	RF03162	TD-2 RNA	8	0.222	98.4
3	RF03163	a1, b1 targets of C4 antisense RNA	36	0.468	394.0
3	RF03532	Cis-regulator of HTH transcription factor	4	0.070	44.4
3	RF03536	Tick-borne Flavivirus exoribonuclease-resistant RNA element	4	0.222	40.0
3	RF03544	Insect-Specific Flavivirus 3' UTR repeats Ra	7	0.233	76.2
3	RF03546	Flavivirus 5' UTR	3	0.375	30.0
3	RF04027	mir-1422 microRNA precursor family	4	0.222	39.7
3	RF04063	MIR2629 microRNA precursor family	5	0.625	52.5
3	RF04181	rteR sRNA	5	0.500	47.9
3	RF04189	icd-II ncRNA motif	7	0.467	75.4
3	RF04310	nqrA-II ncRNA motif	5	0.333	48.5