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0  structures 0  species 0  sequences

Motif: tandem-GA (RM00021)

Description: Tandem GA/AG loop

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 Internal loop. More...

Internal-loops (also termed interior loops) in RNA are found where the double stranded RNA separates due to no Watson-Crick base pairing between the nucleotides. Internal-loops differ from Stem-loops as they occur in middle of a stretch of double stranded RNA. The non-canonicoal residues result in the double helix becoming distorted due to unwinding, unstacking and kinking.

Internal-loops can be classified as either symmetrical or asymmetrical, with some asymmetrical internal-loops, also known as bulges. Many important structural motifs are composed of internal loops such as the C-loop,[1] the docking-elbow,[2] kink-turns (k-turn),[3][4] the right-angle,[5] the sarcin/ricin loops (also called bulged-G motifs),[6][7][8] the twist-up motif[9] and the UAA/GAN internal loop motif.[10]

References

  1. ^ Lescoute, A; Leontis, NB; Massire, C; Westhof, E (2005). "Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments". Nucleic Acids Research. 33 (8): 2395–409. doi:10.1093/nar/gki535. PMC 1087784. PMID 15860776.
  2. ^ Lehmann, J; Jossinet, F; Gautheret, D (May 1, 2013). "A universal RNA structural motif docking the elbow of tRNA in the ribosome, RNAse P and T-box leaders". Nucleic Acids Research. 41 (10): 5494–502. doi:10.1093/nar/gkt219. PMC 3664808. PMID 23580544.
  3. ^ Klein, D.J. (2001). "The kink-turn: a new RNA secondary structure motif". The EMBO Journal. 20 (15): 4214–4221. doi:10.1093/emboj/20.15.4214. ISSN 1460-2075. PMC 149158.
  4. ^ Schroeder, KT; McPhee, SA; Ouellet, J; Lilley, DM (Aug 2010). "A structural database for k-turn motifs in RNA". RNA. 16 (8): 1463–8. doi:10.1261/rna.2207910. PMC 2905746. PMID 20562215.
  5. ^ Grabow, WW; Zhuang, Z; Swank, ZN; Shea, JE; Jaeger, L (Nov 23, 2012). "The right angle (RA) motif: a prevalent ribosomal RNA structural pattern found in group I introns". Journal of Molecular Biology. 424 (1–2): 54–67. doi:10.1016/j.jmb.2012.09.012. PMC 3488136. PMID 22999957.
  6. ^ a b c Szewczak, AA; Moore, PB (Mar 17, 1995). "The sarcin/ricin loop, a modular RNA". Journal of Molecular Biology. 247 (1): 81–98. doi:10.1006/jmbi.1994.0124. PMID 7897662.
  7. ^ Leontis, NB; Westhof, E (Oct 30, 1998). "A common motif organizes the structure of multi-helix loops in 16 S and 23 S ribosomal RNAs". Journal of Molecular Biology. 283 (3): 571–83. doi:10.1006/jmbi.1998.2106. PMID 9784367.
  8. ^ Moore PB (1999). "Structural motifs in RNA". Annu. Rev. Biochem. 68: 287–300. doi:10.1146/annurev.biochem.68.1.287. PMID 10872451.
  9. ^ a b Zhong, C; Zhang, S (Feb 2012). "Clustering RNA structural motifs in ribosomal RNAs using secondary structural alignment". Nucleic Acids Research. 40 (3): 1307–17. doi:10.1093/nar/gkr804. PMC 3273805. PMID 21976732.
  10. ^ a b Lee, JC; Gutell, RR; Russell, R (Jul 28, 2006). "The UAA/GAN internal loop motif: a new RNA structural element that forms a cross-strand AAA stack and long-range tertiary interactions". Journal of Molecular Biology. 360 (5): 978–88. doi:10.1016/j.jmb.2006.05.066. PMID 16828489.

See also

This page is based on a wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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:
Download/view:

Family matches

There are 32 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 RF00049 Small nucleolar RNA SNORD36 7 0.119 80.0 Match Image
3 RF00152 Small nucleolar RNA SNORD79 4 0.143 49.2 Match Image
3 RF00198 SL1 RNA 3 0.107 35.0 Match Image
3 RF00205 Small nucleolar RNA R41 2 0.286 23.4 Match Image
3 RF00230 T-box leader 44 0.917 1653.9 Match Image
3 RF00231 Small Cajal body specific RNA 13 2 0.083 22.7 Match Image
3 RF00267 Small nucleolar RNA R64/Z200 family 13 0.929 294.1 Match Image
3 RF00289 Small nucleolar RNA SNORD104 13 0.722 240.0 Match Image
3 RF00325 Small nucleolar RNA SNORD53/SNORD92 6 0.162 67.7 Match Image
3 RF00329 Small nucleolar RNA Z162 6 0.667 77.9 Match Image
3 RF00447 Voltage-gated potassium-channel Kv1.4 IRES 6 1.000 91.9 Match Image
3 RF00488 Yeast U1 spliceosomal RNA 3 0.600 38.7 Match Image
3 RF00537 Small nucleolar RNA Me28S-Am2634 2 0.111 23.2 Match Image
3 RF00584 Small nucleolar RNA SNORD105 7 0.467 75.3 Match Image
3 RF00612 Small nucleolar RNA SNORD75 2 0.400 24.2 Match Image
3 RF00886 microRNA MIR807 4 0.133 44.4 Match Image
3 RF01069 purD RNA motif 2 0.095 21.6 Match Image
3 RF01133 Small nucleolar RNA sR3 5 0.263 53.7 Match Image
3 RF01139 Small nucleolar RNA sR2 2 0.250 21.9 Match Image
3 RF01170 Small nucleolar RNA U61 2 0.250 27.8 Match Image
3 RF01209 Small nucleolar RNA snR76 2 0.133 20.3 Match Image
3 RF01245 Small nucleolar RNA snR9 2 0.400 20.8 Match Image
3 RF01422 small nucleolar RNA snoR116 2 0.400 21.4 Match Image
3 RF01662 Caenorhabditis snoRNA ceN89 4 1.000 52.1 Match Image
3 RF01845 Early nodulin 40 4 0.114 50.6 Match Image
3 RF01959 Archaeal small subunit ribosomal RNA 9 0.105 108.4 Match Image
3 RF01960 Eukaryotic small subunit ribosomal RNA 24 0.264 346.6 Match Image
3 RF02111 IS009 2 0.182 20.2 Match Image
3 RF02540 Archaeal large subunit ribosomal RNA 22 0.242 282.7 Match Image
3 RF02541 Bacterial large subunit ribosomal RNA 75 0.735 1600.2 Match Image
3 RF02542 Microsporidia small subunit ribosomal RNA 13 0.283 184.5 Match Image
3 RF02543 Eukaryotic large subunit ribosomal RNA 46 0.523 695.9 Match Image

References

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

Literature references

  1. Gautheret D, Konings D, Gutell RR J Mol Biol. 1994;242:1-8. A major family of motifs involving G.A mismatches in ribosomal RNA. PUBMED:8078068

  2. Cruz JA, Westhof E Nat Methods. 2011;8:513-21. Sequence-based identification of 3D structural modules in RNA with RMDetect. PUBMED:21552257

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:9784367
Structure source N/A
Type Internal Loop
Author Gardner PP
Alignment details
Alignment Number of
sequences
Average length Sequence
identity (%)
seed 74 68.28 42

Model information

Build commands
cmbuild -F tandem-CM tandem-SEED
cmcalibrate --mpi --seed 1 tandem-CM
Gathering cutoff 15.0
Covariance model Download the Infernal CM for the motif here