0  structures 375  species 2583  sequences

Family: U6atac (RF00619)

Description: U6atac minor spliceosomal RNA

Summary

Clan

This family is a member of clan (CL00009), which contains the following 2 members:

U6 U6atac

Wikipedia annotation Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam families in Wikipedia. This family is described by a Wikipedia entry U6atac minor spliceosomal RNA. 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.

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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 RM00029 UNCG tetraloop 13 0.210 185.3 Match Image

References

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

Literature references

  1. Lorkovic ZJ, Lehner R, Forstner C, Barta A RNA. 2005;11:1095-1107. Evolutionary conservation of minor U12-type spliceosome between plants and humans. PUBMED:15987817

  2. Padgett RA, Shukla GC RNA. 2002;8:125-128. A revised model for U4atac/U6atac snRNA base pairing. PUBMED:11911359

  3. Shukla GC, Padgett RA RNA 1999;5:525-538. Conservation of functional features of U6atac and U12 snRNAs between vertebrates and higher plants. PUBMED:10199569

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:10199569; Daub J, INFERNAL; PMID:18390578
Structure source Published; PMID:11911359
Type Gene; snRNA; splicing;
Author Daub JORCID logo, Gardner PPORCID logo
Alignment details
Alignment Number of
sequences
full 2,521
seed 62

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 33.0
Trusted cutoff 33.0
Noise cutoff 32.9
Covariance model Download