0  structures 68  species 135  sequences

Family: VA (RF00102)

Description: VA RNA

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 VA 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.

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.

Motif matches

There are 5 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 RM00003 C-loop motif 3 0.056 31.9 Match Image
7 RM00005 CsrA/RsmA binding motif 19 0.352 172.8 Match Image
7 RM00008 GNRA tetraloop 12 0.222 95.3 Match Image
7 RM00024 T-loop 9 0.167 100.4 Match Image
7 RM00028 UMAC tetraloop 21 0.389 296.5 Match Image

References

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

Literature references

  1. Kidd AH, Garwicz D, Oberg M Virology 1995;207:32-45. Human and simian adenoviruses: phylogenetic inferences from analysis of VA RNA genes. PUBMED:95176559

  2. Thimmappaya B, Weinberger C, Schneider RJ, Shenk T Cell 1982;31:543-551. Adenovirus VAI RNA is required for efficient translation of viral mRNAs at late times after infection. PUBMED:6297772

  3. Svensson C, Akusjarvi G Mol Cell Biol 1984;4:736-742. Adenovirus VA RNAI: a positive regulator of mRNA translation. PUBMED:6201722

  4. Strijker R, Fritz DT, Levinson AD EMBO J 1989;8:2669-2675. Adenovirus VAI-RNA regulates gene expression by controlling stability of ribosome-bound RNAs. PUBMED:2583126

  5. Mathews MB Curr Top Microbiol Immunol 1995;199:173-187. Structure, function, and evolution of adenovirus virus-associated RNAs. PUBMED:7555067

  6. Ma Y, Mathews MB RNA 1996;2:937-951. Secondary and tertiary structure in the central domain of adenovirus type 2 VA RNA I. PUBMED:8809020

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 Bateman A, Moxon SJ
Structure source Published; PMID:8809020, Moxon SJ
Type Gene;
Author Bateman AORCID logo, Moxon SJORCID logo
Alignment details
Alignment Number of
sequences
full 81
seed 54

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 28 -Z 549862.597050 CM SEQDB
Gathering cutoff 37.0
Trusted cutoff 37.0
Noise cutoff 36.9
Covariance model Download