0  structures 123  species 8625  sequences

Family: Y_RNA (RF00019)

Description: Y RNA


Wikipedia annotation Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam families in Wikipedia. This family is described by a Wikipedia entry Y RNA. More...

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.



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.


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 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


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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


The tree shows the occurrence of this RNA across different species. More...


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.


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.


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

Literature references

  1. Teunissen SW, Kruithof MJ, Farris AD, Harley JB, Venrooij WJ, Pruijn GJ Nucleic Acids Res 2000;28:610-619. Conserved features of Y RNAs: a comparison of experimentally derived secondary structures. PUBMED:10606662

  2. Van Horn DJ, Eisenberg D, O'Brien CA, Wolin SL RNA 1995;1:293-303. Caenorhabditis elegans embryos contain only one major species of Ro RNP. PUBMED:7489501

  3. Chen X, Quinn AM, Wolin SL Genes Dev 2000;14:777-782. Ro ribonucleoproteins contribute to the resistance of Deinococcus radiodurans to ultraviolet irradiation. PUBMED:10766734

  4. Mosig A, Guofeng M, Stadler BM, Stadler PF Theory Biosci. 2007;126:9-14. Evolution of the vertebrate Y RNA cluster. PUBMED:18087752

  5. Dhahbi JM, Spindler SR, Atamna H, Boffelli D, Mote P, Martin DI Physiol Genomics. 2013;45:990-998. 5'-YRNA fragments derived by processing of transcripts from specific YRNA genes and pseudogenes are abundant in human serum and plasma. PUBMED:24022222

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.


Seed source Griffiths-Jones SR, Published; PMID:18087752, Gardner PP
Structure source Published; PMID:10606662
Type Gene;
Author Griffiths-Jones SRORCID logo, Gardner PPORCID logo
Alignment details
Alignment Number of
full 8,521
seed 104

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 19.00 -Z 549862.597050 CM SEQDB
Gathering cutoff 38.0
Trusted cutoff 38.0
Noise cutoff 37.9
Covariance model Download