12  structures 0  species 0  sequences

Motif: C-loop (RM00003)

Description: C-loop 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 Internal 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:
Download/view:

Structures

There are 12 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 2gya 0 2535 - 2588
2 1yhq 0 544 - 612
2 1j5a A 873 - 928
2 1c2w B 2676 - 2731
2 1giy A 908 - 963
2 3cpw 0 543 - 611
2 1FFK 0 953 - 1011
2 1NKW 0 874 - 927
2 1J5E 362 - 389
2 1S1I 3 1418 - 1443
2 1S72 954 - 1010
2 2AW4 B 847 - 930

Family matches

There are 30 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 RF00010 Bacterial RNase P class A 49 0.107 668.9 Match Image
3 RF00024 Vertebrate telomerase RNA 8 0.216 92.5 Match Image
3 RF00073 mir-156 microRNA precursor 4 0.400 41.6 Match Image
3 RF00090 Small nucleolar RNA SNORA74 5 0.208 65.1 Match Image
3 RF00100 7SK RNA 5 0.111 60.7 Match Image
3 RF00102 VA RNA 3 0.056 31.9 Match Image
3 RF00177 Bacterial small subunit ribosomal RNA 32 0.323 422.7 Match Image
3 RF00222 Bag-1 internal ribosome entry site (IRES) 2 0.133 32.2 Match Image
3 RF00334 Small nucleolar RNA SNORA3/SNORA45 family 3 0.500 43.5 Match Image
3 RF00604 Small nucleolar RNA SNORD88 7 0.200 78.4 Match Image
3 RF01064 microRNA mir-253 2 0.500 23.0 Match Image
3 RF01268 Small Cajal body-specific RNA 2 2 0.100 21.5 Match Image
3 RF01497 ALIL pseudoknot 3 0.115 44.4 Match Image
3 RF01675 Pseudomonas sRNA CrcZ 2 0.105 21.4 Match Image
3 RF01755 rmf RNA 4 0.250 50.6 Match Image
3 RF01855 Plant signal recognition particle RNA 8 0.127 121.4 Match Image
3 RF01857 Archaeal signal recognition particle RNA 7 0.132 92.5 Match Image
3 RF01959 Archaeal small subunit ribosomal RNA 22 0.256 285.3 Match Image
3 RF01960 Eukaryotic small subunit ribosomal RNA 15 0.165 194.2 Match Image
3 RF01989 Selenocysteine insertion sequence 3 3 0.125 34.0 Match Image
3 RF02041 HOXA transcript at the distal tip, conserved region 2 3 0.120 31.4 Match Image
3 RF02353 Bradyrhizobiaceae sRNA BjrC68 4 0.333 47.2 Match Image
3 RF02502 Rhizobiales sRNA Atu_C8 3 0.111 33.7 Match Image
3 RF02514 5' ureB small RNA 2 0.154 20.5 Match Image
3 RF02531 Nrf2 internal ribosome entry site (IRES) 2 0.100 22.3 Match Image
3 RF02540 Archaeal large subunit ribosomal RNA 90 0.989 3182.1 Match Image
3 RF02541 Bacterial large subunit ribosomal RNA 99 0.971 3303.8 Match Image
3 RF02542 Microsporidia small subunit ribosomal RNA 6 0.130 71.9 Match Image
3 RF02543 Eukaryotic large subunit ribosomal RNA 26 0.295 335.2 Match Image
3 RF02746 antisense RNA of rseC mRNA 2 0.286 21.2 Match Image

References

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

Literature references

  1. Zhong C, Zhang S Nucleic Acids Res. 2012;40:1307-17. Clustering RNA structural motifs in ribosomal RNAs using secondary structural alignment. PUBMED:21976732

  2. Lescoute A, Leontis NB, Massire C, Westhof E Nucleic Acids Res. 2005;33:2395-409. Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments. PUBMED:15860776

  3. Zhong C, Tang H, Zhang S Nucleic Acids Res. 2010;38:e176. RNAMotifScan: automatic identification of RNA structural motifs using secondary structural alignment. PUBMED:20696653

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

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:21976732
Structure source N/A
Type Internal Loop
Author Gardner PP
Alignment details
Alignment Number of
sequences
Average length Sequence
identity (%)
seed 19 51.74 40

Model information

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