0  structures 512  species 1353  sequences

Family: SNORD31 (RF00089)

Description: Small nucleolar RNA SNORD31

Summary

Clan

This family is a member of clan (CL00053), which contains the following 4 members:

snoR35 SNORD31 snoZ17 snR67

Wikipedia annotation Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam families in Wikipedia. This family is described by a Wikipedia entry Small nucleolar RNA SNORD31. 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. Tycowski KT, Shu MD, Steitz JA Nature 1996;379:464-466. A mammalian gene with introns instead of exons generating stable RNA products. PUBMED:8559254

  2. Tycowski KT, Smith CM, Shu MD, Steitz JA Proc Natl Acad Sci U S A 1996;93:14480-14485. A small nucleolar RNA requirement for site-specific ribose methylation of rRNA in Xenopus. PUBMED:8962077

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 Griffiths-Jones SR, INFERNAL
Structure source Predicted; Daub J
Type Gene; snRNA; snoRNA; CD-box;
Author Griffiths-Jones SRORCID logo
Alignment details
Alignment Number of
sequences
full 1,327
seed 26

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 25.85 -Z 2958934 CM SEQDB
Gathering cutoff 40.0
Trusted cutoff 40.0
Noise cutoff 39.9
Covariance model Download