16  structures 0  species 0  sequences

Motif: U-turn (RM00030)

Description: U-turn motif

Summary

Wikipedia annotation Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam data in Wikipedia. This motif is described by a Wikipedia entry entitled Stem-loop but we are unable to retrieve the article content at this time. More...

Alignments

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:
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Structures

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

Family matches

There are 108 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 Match Image
3 RF00007 U12 minor spliceosomal RNA 31 0.500 372.3 Match Image
3 RF00009 Nuclear RNase P 30 0.259 386.0 Match Image
3 RF00010 Bacterial RNase P class A 376 0.821 5926.2 Match Image
3 RF00018 CsrB/RsmB RNA family 8 0.211 80.8 Match Image
3 RF00023 transfer-messenger RNA 73 0.153 949.3 Match Image
3 RF00024 Vertebrate telomerase RNA 4 0.108 47.5 Match Image
3 RF00029 Group II catalytic intron 13 0.141 139.3 Match Image
3 RF00043 R1162-like plasmid antisense RNA 4 0.500 47.1 Match Image
3 RF00050 FMN riboswitch (RFN element) 14 0.097 154.6 Match Image
3 RF00078 MicA sRNA 2 0.118 24.3 Match Image
3 RF00082 SraG RNA 5 0.714 73.3 Match Image
3 RF00096 U8 small nucleolar RNA 11 0.200 123.8 Match Image
3 RF00107 FinP 5 0.833 65.8 Match Image
3 RF00126 ryfA RNA 3 0.333 45.3 Match Image
3 RF00156 Small nucleolar RNA SNORA70 9 0.209 96.8 Match Image
3 RF00166 PrrB/RsmZ RNA family 35 0.946 493.9 Match Image
3 RF00168 Lysine riboswitch 8 0.170 113.2 Match Image
3 RF00177 Bacterial small subunit ribosomal RNA 99 1.000 2802.4 Match Image
3 RF00209 Pestivirus internal ribosome entry site (IRES) 2 0.080 20.4 Match Image
3 RF00224 FGF-2 internal ribosome entry site (IRES) 4 0.667 41.9 Match Image
3 RF00263 Small nucleolar RNA SNORA68 5 0.192 59.3 Match Image
3 RF00291 Small nucleolar RNA snoR639/H1 5 0.556 55.8 Match Image
3 RF00357 Small nucleolar RNA R44/J54/Z268 family 2 0.069 20.0 Match Image
3 RF00369 sroC RNA 6 1.000 68.1 Match Image
3 RF00373 Archaeal RNase P 9 0.129 147.4 Match Image
3 RF00386 Enterovirus 5' cloverleaf cis-acting replication element 68 0.425 724.3 Match Image
3 RF00391 RtT RNA 6 0.105 85.1 Match Image
3 RF00403 Small nucleolar RNA SNORA41 2 0.065 23.7 Match Image
3 RF00495 Heat shock protein 70 (Hsp70) internal ribosome entry site (IRES) 7 0.500 74.9 Match Image
3 RF00513 Tryptophan operon leader 3 0.136 36.0 Match Image
3 RF00514 Histidine operon leader 9 0.273 96.5 Match Image
3 RF00515 PyrR binding site 5 0.122 83.6 Match Image
3 RF00534 SgrS RNA 2 0.250 22.4 Match Image
3 RF00547 TrkB IRES 2 0.125 23.1 Match Image
3 RF00548 U11 spliceosomal RNA 7 0.097 77.0 Match Image
3 RF00558 Ribosomal protein L20 leader 11 0.256 135.9 Match Image
3 RF00602 Small Cajal body specific RNA 21 6 0.250 99.9 Match Image
3 RF00603 Small nucleolar RNA SNORD23 2 0.133 21.5 Match Image
3 RF00604 Small nucleolar RNA SNORD88 2 0.057 23.1 Match Image
3 RF00617 flavivirus capsid hairpin cHP 11 0.186 123.1 Match Image
3 RF00629 Pseudomonas sRNA P24 7 0.500 101.1 Match Image
3 RF00630 Pseudomonas sRNA P26 10 0.370 108.3 Match Image
3 RF00634 S-adenosyl methionine (SAM) riboswitch, 3 0.075 34.9 Match Image
3 RF00683 microRNA mir-143 11 0.611 111.1 Match Image
3 RF00723 microRNA mir-448 5 0.263 65.4 Match Image
3 RF00788 microRNA mir-287 7 0.778 74.8 Match Image
3 RF01071 Ornate Large Extremophilic RNA 5 0.250 58.5 Match Image
3 RF01089 Pseudoknot of the regulatory region of the repBA gene 2 0.286 20.2 Match Image
3 RF01268 Small Cajal body-specific RNA 2 3 0.150 31.2 Match Image
3 RF01330 CRISPR RNA direct repeat element 6 1.000 78.3 Match Image
3 RF01390 isrG Hfq binding RNA 5 1.000 51.7 Match Image
3 RF01401 rseX Hfq binding RNA 7 0.583 79.8 Match Image
3 RF01529 Cauldobacter sRNA CC3552 2 1.000 24.7 Match Image
3 RF01673 PhrS 2 0.154 21.0 Match Image
3 RF01675 Pseudomonas sRNA CrcZ 17 0.895 191.9 Match Image
3 RF01687 Acido-Lenti-1 RNA 7 0.080 107.8 Match Image
3 RF01702 Cyano-2 RNA 4 0.070 44.4 Match Image
3 RF01703 Dictyoglomi-1 RNA 2 0.500 27.3 Match Image
3 RF01706 Gut-1 RNA 3 0.079 35.7 Match Image
3 RF01708 L17 ribosomal protein downstream element 6 0.115 71.2 Match Image
3 RF01721 Pseudomon-groES RNA 3 0.167 32.6 Match Image
3 RF01730 Termite-leu RNA 15 0.750 476.4 Match Image
3 RF01752 psaA RNA 2 0.065 21.6 Match Image
3 RF01756 rne-II RNA 5 0.312 60.9 Match Image
3 RF01796 Fumarate/nitrate reductase regulator sRNA 3 0.188 34.0 Match Image
3 RF01808 MicX Vibrio cholerae sRNA 5 0.500 61.9 Match Image
3 RF01849 Alphaproteobacteria transfer-messenger RNA 11 0.099 140.2 Match Image
3 RF01850 Betaproteobacteria transfer-messenger RNA 2 0.286 22.8 Match Image
3 RF01852 Selenocysteine transfer RNA 9 0.083 106.3 Match Image
3 RF01942 microRNA mir-1937 32 0.187 361.0 Match Image
3 RF01959 Archaeal small subunit ribosomal RNA 86 1.000 4568.1 Match Image
3 RF01960 Eukaryotic small subunit ribosomal RNA 36 0.396 526.2 Match Image
3 RF02029 sraA 18 0.900 271.4 Match Image
3 RF02031 tpke11 4 0.143 45.0 Match Image
3 RF02033 HNH endonuclease-associated RNA and ORF (HEARO) RNA 12 0.109 145.4 Match Image
3 RF02053 Enterobacterial sRNA STnc430 5 0.714 55.8 Match Image
3 RF02055 Enterobacterial sRNA STnc380 4 0.800 50.8 Match Image
3 RF02057 Salmonella enterica sRNA STnc40 2 0.118 23.8 Match Image
3 RF02065 Enterobacterial sRNA STnc340 3 0.750 34.8 Match Image
3 RF02074 Enterobacterial sRNA STnc240 8 0.533 89.3 Match Image
3 RF02103 Deleted in lymphocytic leukemia 1 conserved region 1 3 0.115 35.4 Match Image
3 RF02118 FMR1 antisense RNA 1 conserved region 2 9 0.360 112.2 Match Image
3 RF02189 ST7 overlapping transcript 4 conserved region 3 2 0.100 22.8 Match Image
3 RF02219 ZNRD1 antisense RNA 1 conserved region 2 2 0.059 22.0 Match Image
3 RF02230 Proteobacterial sRNA sX11 2 0.200 20.2 Match Image
3 RF02249 Six3os1 conserved region 4 2 0.286 20.4 Match Image
3 RF02276 Hammerhead ribozyme (type II) 3 0.125 34.3 Match Image
3 RF02278 Betaproteobacteria toxic small RNA 7 0.137 87.0 Match Image
3 RF02342 Alphaproteobacterial sRNA ar7 6 0.207 68.7 Match Image
3 RF02343 Alphaproteobacterial sRNA ar9 16 0.571 166.8 Match Image
3 RF02351 Proteobacteria sRNA psRNA14 2 0.667 23.7 Match Image
3 RF02354 Bradyrhizobiaceae sRNA BjrC80 7 0.467 83.6 Match Image
3 RF02356 Alphaproteobacterial sRNA BjrC1505 3 0.120 35.7 Match Image
3 RF02357 RNaseP truncated form 7 0.778 92.6 Match Image
3 RF02375 Aar sRNA 2 0.154 21.9 Match Image
3 RF02376 SR1 sRNA 2 0.333 26.3 Match Image
3 RF02379 Cia-dependent small RNA csRNA1 8 0.167 97.7 Match Image
3 RF02423 Burkholderia sRNA Bp1_Cand871_SIPHT 14 0.933 170.8 Match Image
3 RF02471 Actinobacteria sRNA Ms_IGR-5 6 0.286 66.5 Match Image
3 RF02502 Rhizobiales sRNA Atu_C8 3 0.111 31.2 Match Image
3 RF02524 Streptococcus sRNA sagA 3 0.500 37.0 Match Image
3 RF02540 Archaeal large subunit ribosomal RNA 83 0.912 3404.2 Match Image
3 RF02541 Bacterial large subunit ribosomal RNA 102 1.000 3700.8 Match Image
3 RF02542 Microsporidia small subunit ribosomal RNA 43 0.935 832.7 Match Image
3 RF02543 Eukaryotic large subunit ribosomal RNA 80 0.909 2165.6 Match Image
3 RF02630 Hfq-regulated sRNA 12 2 1.000 28.6 Match Image
3 RF02684 Type-P5 twister ribozyme 4 0.267 47.2 Match Image

References

This section shows the database cross-references that we have for this Rfam motif.

Literature references

  1. Sarver M, Zirbel CL, Stombaugh J, Mokdad A, Leontis NB J Math Biol. 2008;56:215-52. FR3D: finding local and composite recurrent structural motifs in RNA 3D structures. PUBMED:17694311

  2. Zirbel CL, Sponer JE, Sponer J, Stombaugh J, Leontis NB Nucleic Acids Res. 2009;37:4898-918. Classification and energetics of the base-phosphate interactions in RNA. PUBMED:19528080

  3. Gutell RR, Cannone JJ, Konings D, Gautheret D J Mol Biol. 2000;300:791-803. Predicting U-turns in ribosomal RNA with comparative sequence analysis. PUBMED:10891269

  4. Quigley GJ, Rich A Science. 1976;194:796-806. Structural domains of transfer RNA molecules. PUBMED:790568

External database links

Curation and motif details

This section shows the detailed information about the Rfam motif. We're happy to receive updated or improved alignments for new or existing families. Submit your new alignment and we'll take a look.

Curation

Seed source Published; PMID:19528080
Structure source N/A
Type Stem Loop
Author Gardner PP
Alignment details
Alignment Number of
sequences
Average length Sequence
identity (%)
seed 19 21.95 45

Model information

Build commands
cmbuild -F U-CM U-SEED
cmcalibrate --mpi --seed 1 U-CM
Gathering cutoff 10.0
Covariance model Download the Infernal CM for the motif here