1  structure 30  species 61  sequences

Family: s2m (RF00164)

Description: Coronavirus 3' stem-loop II-like motif (s2m)

Summary

Clan

This family is a member of clan (CL00117), which contains the following 7 members:

aCoV-3UTR bCoV-3UTR Corona_pk3 dCoV-3UTR gCoV-3UTR s2m Sarbecovirus-3UTR

Wikipedia annotation Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam families in Wikipedia. This family is described by a Wikipedia entry Coronavirus 3' stem-loop II-like motif (s2m). 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.

Viewer:

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

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

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

Selections

Click on a node to select that node and its sub-tree.

Clear selection

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

Hide

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

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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.

Structures

For those sequences which have a structure in the Protein DataBank, we generate a mapping between EMBL, PDB and Rfam coordinate systems. The table below shows the structures on which the s2m family has been found.

Loading structure mapping...

References

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

Literature references

  1. Jonassen CM, Jonassen TO, Grinde B J Gen Virol 1998;79:715-718. A common RNA motif in the 3' end of the genomes of astroviruses, avian infectious bronchitis virus and an equine rhinovirus. PUBMED:9568965

  2. Robertson MP, Igel H, Baertsch R, Haussler D, Ares M Jr, Scott WG PLoS Biol 2005;3:e5. The structure of a rigorously conserved RNA element within the SARS virus genome. PUBMED:15630477

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 PMID:9568965; Griffiths-Jones SR, Moxon SJ
Structure source Published; PMID:15630477
Type Cis-reg;
Author Griffiths-Jones SRORCID logo, Nawrocki EORCID logo
Alignment details
Alignment Number of
sequences
full 22
seed 39

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 50.0
Trusted cutoff 51.6
Noise cutoff 47.7
Covariance model Download