0  structures 820  species 2369  sequences

Family: mir-34 (RF00456)

Description: mir-34 microRNA precursor family

Summary

Clan

This family is a member of clan (CL00087), which contains the following 2 members:

mir-34 mir-449

Wikipedia annotation Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam families in Wikipedia. This family is described by a Wikipedia entry mir-34 microRNA precursor family. 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.

Current Rfam structure

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R-scape optimised structure

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  • Colours
  •  Statistically significant basepair with covariation
  •  97% conserved nucleotide
  •  90% conserved nucleotide
  •  75% conserved nucleotide
  •  50% conserved nucleotide
  • Nucleotides
  • R: A or G
  • Y: C or U

Tip: The diagrams are interactive:
you can pan and zoom to see more details
or hover over nucleotides and basepairs.

R-scape is a method for testing whether covariation analysis supports the presence of a conserved RNA secondary structure. This page shows R-scape analysis of the secondary structure from the Rfam seed alignment and a new structure with covariation support that is compatible with the same alignment.

To find out more about the method, see the R-scape paper by Rivas et al., 2016. The structures are visualised using R2R.

Species distribution

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Lineage

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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

Click on a node to select that node and its sub-tree.

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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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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.

References

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

Literature references

  1. Lim LP, Glasner ME, Yekta S, Burge CB, Bartel DP Science 2003;299:1540. Vertebrate microRNA genes. PUBMED:12624257

  2. Dostie J, Mourelatos Z, Yang M, Sharma A, Dreyfuss G RNA 2003;9:180-186. Numerous microRNPs in neuronal cells containing novel microRNAs. PUBMED:12554860

  3. Houbaviy HB, Murray MF, Sharp PA; Dev Cell. 2003;5:351-358. Embryonic stem cell-specific MicroRNAs. PUBMED:12919684

  4. Kozomara A, Birgaoanu M, Griffiths-Jones S Nucleic Acids Res. 2019;47:D155. miRBase: from microRNA sequences to function. PUBMED:30423142

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
Structure source Predicted; RNAalifold
Type Gene; miRNA;
Author Griffiths-Jones SRORCID logo
Alignment details
Alignment Number of
sequences
full 2,256
seed 113

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 25.00 -Z 2958934 CM SEQDB
Gathering cutoff 53.4
Trusted cutoff 53.4
Noise cutoff 53.3
Covariance model Download
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