0  structures 127  species 433  sequences

Family: SNORD53_SNORD92 (RF00325)

Description: Small nucleolar RNA SNORD53/SNORD92

Summary

Clan

This family is a member of clan (CL00063), which contains the following 4 members:

SNORD52 SNORD53_SNORD92 snoZ157 snR78

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 SNORD53. 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:
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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...

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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.

Motif matches

There are 1 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 RM00021 Tandem GA/AG loop 6 0.162 67.7 Match Image

References

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

Literature references

  1. Kiss T; Cell 2002;109:145-148. Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse cellular functions. PUBMED:12007400

  2. Kiss-Laszlo Z, Henry Y, Bachellerie JP, Caizergues-Ferrer M, Kiss T; Cell 1996;85:1077-1088. Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. PUBMED:8674114

  3. Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H, Bachellerie JP, Brosius J; EMBO J 2001;20:2943-2953. RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse. PUBMED:11387227

  4. Lestrade L, Weber MJ; Nucleic Acids Res. 2006;34:D158-D162. snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. PUBMED:16381836

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 Moxon SJ, INFERNAL
Structure source Predicted; Moxon SJ
Type Gene; snRNA; snoRNA; CD-box;
Author Moxon SJORCID logo, Daub JORCID logo
Alignment details
Alignment Number of
sequences
full 396
seed 37

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 25.47 -Z 549862.597050 CM SEQDB
Gathering cutoff 46.0
Trusted cutoff 46.5
Noise cutoff 45.8
Covariance model Download