9  structures 536  species 11696  sequences

Family: U1 (RF00003)

Description: U1 spliceosomal RNA



This family is a member of clan (CL00005), which contains the following 4 members:

Gl_U1 U1 U11 U1_yeast

Wikipedia annotation Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam families in Wikipedia. This family is described by a Wikipedia entry U1 spliceosomal 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.


For those sequences which have a structure in the Protein DataBank, we generate a mapping between EMBL, PDB and Rfam coordinate systems. The table below shows the structures on which the U1 family has been found.

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Motif matches

There are 2 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 RM00005 CsrA/RsmA binding motif 30 0.300 246.7 Match Image
7 RM00029 UNCG tetraloop 47 0.470 501.1 Match Image


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

Literature references

  1. Zwieb C Nucleic Acids Res 1997;25:102-103. The uRNA database. PUBMED:9016512

  2. Kretzner L, Krol A, Rosbash M Proc Natl Acad Sci U S A 1990;87:851-855. Saccharomyces cerevisiae U1 small nuclear RNA secondary structure contains both universal and yeast-specific domains. PUBMED:2405391

  3. Oubridge C, Ito N, Evans PR, Teo CH, Nagai K Nature 1994;372:432-438. Crystal structure at 1.92 A resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin. PUBMED:7984237

  4. Katsamba PS, Myszka DG, Laird-Offringa IA J Biol Chem 2001;276:21476-21481. Two functionally distinct steps mediate high affinity binding of U1A protein to U1 hairpin II RNA. PUBMED:11297556

  5. Pomeranz Krummel DA, Oubridge C, Leung AK, Li J, Nagai K Nature. 2009;458:475-480. Crystal structure of human spliceosomal U1 snRNP at 5.5 A resolution. PUBMED:19325628

  6. Charenton C, Wilkinson ME, Nagai K Science. 2019;364:362-367. Mechanism of 5' splice site transfer for human spliceosome activation. PUBMED:30975767

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 Zwieb C, The uRNA database, PMID:9016512
Structure source Published; PMID:2405391
Type Gene; snRNA; splicing;
Author Griffiths-Jones SRORCID logo, Mifsud WORCID logo, Moxon SJORCID logo, Ontiveros-Palacios NORCID logo
Alignment details
Alignment Number of
full 11,596
seed 100

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 742849.287494 CM SEQDB
Gathering cutoff 66.0
Trusted cutoff 66.0
Noise cutoff 65.9
Covariance model Download