607  structures 2616  species 107553  sequences

Family: LSU_rRNA_eukarya (RF02543)

Description: Eukaryotic large subunit ribosomal RNA

Summary

Clan

This family is a member of clan (CL00112), which contains the following 5 members:

5_8S_rRNA LSU_rRNA_archaea LSU_rRNA_bacteria LSU_rRNA_eukarya LSU_trypano_mito

Wikipedia annotation Edit Wikipedia article

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

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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...

Tree controls

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

Structures

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 LSU_rRNA_eukarya family has been found.

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Motif matches

There are 18 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 26 0.295 335.2 Match Image
7 RM00004 CRC binding motif 25 0.284 401.9 Match Image
7 RM00005 CsrA/RsmA binding motif 65 0.739 940.9 Match Image
7 RM00007 Splicing domain V 23 0.261 295.7 Match Image
7 RM00008 GNRA tetraloop 87 0.989 5123.0 Match Image
7 RM00009 HuR binding site 27 0.307 520.5 Match Image
7 RM00010 Kink turn 1, 3' bulge 46 0.523 914.8 Match Image
7 RM00011 Kink turn 2, 5' bulge 30 0.341 682.0 Match Image
7 RM00018 Sarcin-ricin motif 1 84 0.955 3479.0 Match Image
7 RM00019 Sarcin-ricin motif 2 72 0.818 1507.2 Match Image
7 RM00021 Tandem GA/AG loop 46 0.523 695.9 Match Image
7 RM00022 Rho independent terminator 1 24 0.273 531.2 Match Image
7 RM00023 Rho independent terminator 2 37 0.420 871.6 Match Image
7 RM00024 T-loop 39 0.443 526.0 Match Image
7 RM00027 UAA/GAN Internal Loop Motif 39 0.443 885.3 Match Image
7 RM00028 UMAC tetraloop 11 0.125 219.5 Match Image
7 RM00029 UNCG tetraloop 79 0.898 2528.8 Match Image
7 RM00030 U-turn motif 80 0.909 2165.6 Match Image

References

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

Literature references

  1. Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JH, Noller HF Science 2001;292:883-896. Crystal structure of the ribosome at 5.5 A resolution. PUBMED:11283358

  2. Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng B, Lin N, Madabusi LV, Muller KM, Pande N, Shang Z, Yu N, Gutell RR BMC Bioinformatics. 2002;3:2. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. PUBMED:11869452

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 Published; PMID:11869452
Structure source Published; PMID:11869452
Type Gene; rRNA;
Author Gutell RRORCID logo, Nawrocki EORCID logo
Alignment details
Alignment Number of
sequences
full 107,465
seed 88

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 17.38 -Z 2958934 CM SEQDB
Gathering cutoff 50.0
Trusted cutoff 50.0
Noise cutoff 49.9
Covariance model Download