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Family: StyR-3 (RF02652)

Description: Salmonella enterica Typhi npcRNA 3

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 Salmonella enterica. More...

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

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.

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.

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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. Nithya R, Ahmed SA, Hoe CH, Gopinath SC, Citartan M, Chinni SV, Lee LP, Rozhdestvensky TS, Tang TH PLoS One. 2015;10:e0118668. Non-protein coding RNA genes as the novel diagnostic markers for the discrimination of Salmonella species using PCR. PUBMED:25774907

  2. Chinni SV, Raabe CA, Zakaria R, Randau G, Hoe CH, Zemann A, Brosius J, Tang TH, Rozhdestvensky TS Nucleic Acids Res. 2010;38:5893-5908. Experimental identification and characterization of 97 novel npcRNA candidates in Salmonella enterica serovar Typhi. PUBMED:20460466

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 5
seed 5

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize 128 CM SEQDB
Gathering cutoff 59.0
Trusted cutoff 59.2
Noise cutoff 35.1
Covariance model Download