0  structures 7  species 42  sequences

Family: GEBRO (RF02988)

Description: GEBRO RNA

Summary

Wikipedia annotation Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam families in Wikipedia. This family is described by a Wikipedia entry GEBRO RNA motif. More...

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

Sequences

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Table view (42 sequence regions)

Original order Download FASTA Accession Bit score Type Start End Description Species View context
0
URS0000D6C378_857114 N/A seed 1 344 Streptococcus mutans NLML1 GEBRO RNA Streptococcus mutans NLML1  
1
URS0000D684CE_1309 N/A seed 1 344 Streptococcus mutans GEBRO RNA Streptococcus mutans  
2
URS0000D66DA2_1309 N/A seed 1 344 Streptococcus mutans GEBRO RNA Streptococcus mutans  
3
URS0000D6782D_1309 N/A seed 1 345 Streptococcus mutans GEBRO RNA Streptococcus mutans  
4
URS0000D6782D_857123 N/A seed 1 345 Streptococcus mutans NV1996 GEBRO RNA Streptococcus mutans NV1996  
5
URS0000D65C37_12908 N/A seed 1 330 unclassified sequences GEBRO RNA unclassified sequences  
6
URS0000D6A13B_12908 N/A seed 1 346 unclassified sequences GEBRO RNA unclassified sequences  
7
URS0000D69ED9_12908 N/A seed 1 346 unclassified sequences GEBRO RNA unclassified sequences  
8
URS0000D6734E_12908 N/A seed 1 346 unclassified sequences GEBRO RNA unclassified sequences  
9
URS0000D666C6_12908 N/A seed 1 344 unclassified sequences GEBRO RNA unclassified sequences  
10
URS0000D6BF47_12908 N/A seed 1 342 unclassified sequences GEBRO RNA unclassified sequences  
11
URS0000D68B0C_12908 N/A seed 1 346 unclassified sequences GEBRO RNA unclassified sequences  
12
URS0000D67F1F_12908 N/A seed 1 347 unclassified sequences GEBRO RNA unclassified sequences  
13
URS0000D6CB47_663954 N/A seed 1 339 Streptococcus dysgalactiae subsp. equisimilis ATCC 12394 GEBRO RNA Streptococcus dysgalactiae subsp. equisimilis ATCC 12394  
14
URS0000D6C611_759913 N/A seed 1 339 Streptococcus dysgalactiae subsp. equisimilis AC-2713 GEBRO RNA Streptococcus dysgalactiae subsp. equisimilis AC-2713  
15
URS0000D69392_1247189 N/A seed 1 338 Streptococcus dysgalactiae subsp. equisimilis 167 GEBRO RNA Streptococcus dysgalactiae subsp. equisimilis 167  
16
URS0000D65B66_12908 N/A seed 1 351 unclassified sequences GEBRO RNA unclassified sequences  
17
URS0000D689BF_12908 N/A seed 1 349 unclassified sequences GEBRO RNA unclassified sequences  
18
URS0000D6D199_12908 N/A seed 1 349 unclassified sequences GEBRO RNA unclassified sequences  
19
URS0000D6B290_12908 N/A seed 1 348 unclassified sequences GEBRO RNA unclassified sequences  
20
URS0000D6A33D_12908 N/A seed 1 347 unclassified sequences GEBRO RNA unclassified sequences  
21
URS0000D67E70_12908 N/A seed 1 345 unclassified sequences GEBRO RNA unclassified sequences  
22
URS0000D662C0_12908 N/A seed 1 351 unclassified sequences GEBRO RNA unclassified sequences  
23
URS0000D6D2AE_12908 N/A seed 1 350 unclassified sequences GEBRO RNA unclassified sequences  
24
URS0000D68169_12908 N/A seed 1 350 unclassified sequences GEBRO RNA unclassified sequences  
25
URS0000D69D75_12908 N/A seed 1 350 unclassified sequences GEBRO RNA unclassified sequences  
26
URS0000D69EFC_12908 N/A seed 1 348 unclassified sequences GEBRO RNA unclassified sequences  
27
URS0000D65882_12908 N/A seed 1 349 unclassified sequences GEBRO RNA unclassified sequences  
28
URS0000D6D2DF_12908 N/A seed 1 351 unclassified sequences GEBRO RNA unclassified sequences  
29
URS0000D6587E_12908 N/A seed 1 351 unclassified sequences GEBRO RNA unclassified sequences  
30
URS0000D69869_12908 N/A seed 1 355 unclassified sequences GEBRO RNA unclassified sequences  
31
URS0000D65C2C_12908 N/A seed 1 356 unclassified sequences GEBRO RNA unclassified sequences  
32
URS0000D665BA_12908 N/A seed 1 356 unclassified sequences GEBRO RNA unclassified sequences  
33
URS0000D6A7E8_12908 N/A seed 1 356 unclassified sequences GEBRO RNA unclassified sequences  
34
URS0000D69E6E_12908 N/A seed 1 356 unclassified sequences GEBRO RNA unclassified sequences  
35
URS0000D6A5A6_12908 N/A seed 1 356 unclassified sequences GEBRO RNA unclassified sequences  
36
URS0000D674FF_12908 N/A seed 1 356 unclassified sequences GEBRO RNA unclassified sequences  
37
URS0000D6A742_12908 N/A seed 1 356 unclassified sequences GEBRO RNA unclassified sequences  
38
URS0000D6CD9C_12908 N/A seed 1 356 unclassified sequences GEBRO RNA unclassified sequences  
39
URS0000D669AB_12908 N/A seed 1 356 unclassified sequences GEBRO RNA unclassified sequences  
40
URS0000D66D57_12908 N/A seed 1 356 unclassified sequences GEBRO RNA unclassified sequences  
41
URS0000D6D0F0_12908 N/A seed 1 356 unclassified sequences GEBRO RNA unclassified sequences  

Alignment

There are various ways to view or download the seed alignments that we store. You can use a sequence viewer to look at them, or you can look at a plain text version of the sequence in a variety of different formats. More...

View options

You can view Rfam seed alignments in your browser in various ways. Choose the viewer that you want to use and click the "View" button to show the alignment in a pop-up window.

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Formatting options

You can view or download Rfam seed 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:

Download

Download a gzip-compressed, Stockholm-format file containing the seed alignment for this family. You may find RALEE useful when viewing sequence alignments.

Submit a new alignment

We're happy receive updated seed alignments for new or existing families. Submit your new alignment and we'll take a look.

Secondary structure

This section shows a variety of different secondary structure representations for this family. More...

You can view the secondary structure of the family using the VARNA applet. You can see more information about VARNA iself here.

Current Rfam structure

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R-scape optimised structure

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  • Colours
  •  Statistically significant basepair with covariation
  •  97% conserved nucleotide
  •  90% conserved nucleotide
  •  75% conserved nucleotide
  •  50% conserved nucleotide
  • Nucleotides
  • R: A or G
  • Y: C or U

Tip: The diagrams are interactive:
you can pan and zoom to see more details
or hover over nucleotides and basepairs.

R-scape is a method for testing whether covariation analysis supports the presence of a conserved RNA secondary structure. This page shows R-scape analysis of the secondary structure from the Rfam seed alignment and a new structure with covariation support that is compatible with the same alignment.

To find out more about the method, see the R-scape paper by Rivas et al., 2016. The structures are visualised using R2R.

Species distribution

The species sunburst cannot be displayed. This can happen when all seed sequences come from the environmental samples)

Tree controls

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The tree shows the occurrence of this RNA across different species. More...

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Trees

This page displays the predicted phylogenetic tree for the alignment. More...

This tree was built using the fasttree method.

Label the trees using or

Note: You can also download the data file for the seed tree.

Motif matches

There are 5 motifs which match this family.

This section shows the Rfam motifs that match sequences within the seed alignment of this family. 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 Motif Accession Motif Description Number of Hits Fraction of Hits Sum of Bits Image
7 RM00004 CRC binding motif 7 0.167 61.7 Match Image
7 RM00005 CsrA/RsmA binding motif 3 0.071 22.8 Match Image
7 RM00008 GNRA tetraloop 34 0.810 462.2 Match Image
7 RM00022 Rho independent terminator 1 4 0.095 45.6 Match Image
7 RM00024 T-loop 4 0.095 47.4 Match Image

References

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

Literature references

  1. Weinberg Z, Lunse CE, Corbino KA, Ames TD, Nelson JW, Roth A, Perkins KR, Sherlock ME, Breaker RR Nucleic Acids Res. 2017;45:10811-10823. Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions. PUBMED:28977401

External database links

Curation and family details

This section shows the detailed information about the Rfam family. 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 Weinberg Z
Structure source Published; PMID:28977401;
Type Gene; sRNA;
Author Weinberg ZORCID logo
Alignment details
Alignment Number of
sequences
full 0
seed 42

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 18.02 -Z 2958934 CM SEQDB
Gathering cutoff 284.7
Trusted cutoff 286.1
Noise cutoff 284.6
Covariance model Download
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