0  structures 21  species 21  sequences

Family: ES239 (RF02756)

Description: ES239 sRNA

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 Escherichia coli sRNA. 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 (21 sequence regions)

Original order Download FASTA Accession Bit score Type Start End Description Species View context
0
U00096.2 N/A seed 4,434,589 4,434,711 Escherichia coli str. K-12 substr. MG1655, complete genome. Escherichia coli str. K-12 substr. MG1655 ENA graphic
1
CU928160.2 N/A seed 4,522,398 4,522,520 Escherichia coli IAI1 chromosome, complete genome. Escherichia coli IAI1 ENA graphic
2
AEZI01000045.1 N/A seed 83,214 83,336 Escherichia coli 1.2741 ctg1126932560021, whole genome shotgun sequence. Escherichia coli 1.2741 ENA graphic
3
AEVY01000053.1 N/A seed 52,442 52,564 Escherichia fergusonii ECD227 contig00104, whole genome shotgun sequence. Escherichia fergusonii ECD227 ENA graphic
4
CP001383.1 N/A seed 4,495,125 4,495,003 Shigella flexneri 2002017, complete genome. Shigella flexneri 2002017 ENA graphic
0
AE014075.1 157.40 full 5,053,684 5,053,806 Escherichia coli CFT073, complete genome. Escherichia coli CFT073 ENA graphic
1
BA000007.3 157.40 full 5,292,156 5,292,278 BA000007.3 Escherichia coli O157:H7 str. Sakai DNA, complete genome Escherichia coli O157:H7 ENA graphic
2
CP000038.1 157.40 full 4,663,573 4,663,695 Shigella sonnei Ss046, complete genome. Shigella sonnei Ss046 ENA graphic
3
CP000468.1 157.40 full 4,853,059 4,853,181 Escherichia coli APEC O1, complete genome. Escherichia coli APEC O1 ENA graphic
4
CP001063.1 157.40 full 4,440,701 4,440,823 Shigella boydii CDC 3083-94, complete genome. Shigella boydii CDC 3083-94 ENA graphic
5
CP001855.1 157.40 full 4,560,078 4,560,200 CP001855.1 Escherichia coli O83:H1 str. NRG 857C, complete genome Escherichia coli O83:H1 str. NRG 857C ENA graphic
6
CU928145.2 157.40 full 4,884,475 4,884,597 Escherichia coli 55989 chromosome, complete genome. Escherichia coli 55989 ENA graphic
7
FM180568.1 157.40 full 4,794,461 4,794,583 Escherichia coli 0127:H6 E2348/69 complete genome, strain E2348/69 Escherichia coli O127:H6 str. E2348/69 ENA graphic
8
U00096.3 157.40 full 4,436,566 4,436,688 Escherichia coli str. K-12 substr. MG1655, complete genome. Escherichia coli K-12 ENA graphic
9
CP000800.1 155.90 full 4,777,044 4,777,166 Escherichia coli E24377A, complete genome. Escherichia coli E24377A ENA graphic
10
CP000802.1 155.90 full 4,471,719 4,471,841 Escherichia coli HS, complete genome. Escherichia coli HS ENA graphic
11
AE005674.2 154.50 full 4,451,414 4,451,292 Shigella flexneri 2a str. 301, complete genome. Shigella flexneri 2a str. 301 ENA graphic
12
CABFKN010030341.1 154.50 full 674 552 CABFKN010030341.1 Panagrolaimus superbus genome assembly, contig: PSU_contig_51663, whole genome shotgun sequence Panagrolaimus superbus ENA graphic
13
CP000034.1 154.50 full 4,105,885 4,106,007 Shigella dysenteriae Sd197, complete genome. Shigella dysenteriae Sd197 ENA graphic
14
CP001665.1 154.50 full 3,992,548 3,992,426 CP001665.1 Escherichia coli 'BL21-Gold(DE3)pLysS AG', complete genome Escherichia coli BL21(DE3) ENA graphic
15
CU928161.2 154.50 full 4,767,719 4,767,841 Escherichia coli S88 chromosome, complete genome. Escherichia coli S88 ENA graphic

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

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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.

References

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

Literature references

  1. Rau MH, Bojanovic K, Nielsen AT, Long KS BMC Genomics. 2015;16:1051. Differential expression of small RNAs under chemical stress and fed-batch fermentation in E. coli. PUBMED:26653712

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 Argasinska J
Structure source Predicted; RNAfold
Type Gene; sRNA;
Author Argasinska JORCID logo
Alignment details
Alignment Number of
sequences
full 16
seed 5

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 2958934 CM SEQDB
Gathering cutoff 62.0
Trusted cutoff 147.0
Noise cutoff 47.4
Covariance model Download
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