0  structures 36  species 76  sequences

Family: SCARNA17 (RF00492)

Description: small Cajal body-specific RNA 17

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 Small Cajal body specific RNA 17. 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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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, Aab A, Steitz JA; Curr Biol. 2004;14:1985-1995. Guide RNAs with 5' caps and novel box C/D snoRNA-like domains for modification of snRNAs in metazoa. PUBMED:15556860

  2. Darzacq X, Jady BE, Verheggen C, Kiss AM, Bertrand E, Kiss T; EMBO J. 2002;21:2746-2756. Cajal body-specific small nuclear RNAs: a novel class of 2'-O-methylation and pseudouridylation guide RNAs. PUBMED:12032087

  3. 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
Structure source Published;PMID:15556860
Type Gene; snRNA; snoRNA; scaRNA;
Author Moxon SJORCID logo, Daub JORCID logo
Alignment details
Alignment Number of
sequences
full 70
seed 6

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
Gathering cutoff 75.0
Trusted cutoff 76.3
Noise cutoff 74.7
Covariance model Download