0  structures 290  species 586  sequences

Family: group-II-D1D4-5 (RF02004)

Description: Group II catalytic intron D1-D4-5



This family is a member of clan (CL00102), which contains the following 7 members:

group-II-D1D4-1 group-II-D1D4-2 group-II-D1D4-3 group-II-D1D4-4 group-II-D1D4-5 group-II-D1D4-6 group-II-D1D4-7

Wikipedia annotation Edit Wikipedia article

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

Motif matches

There are 1 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 RM00008 GNRA tetraloop 60 0.432 733.9 Match Image


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

Literature references

  1. Bonen L, Vogel J Trends Genet 2001;17:322-331. The ins and outs of group II introns. PUBMED:11377794

  2. Chu VT, Adamidi C, Liu Q, Perlman PS, Pyle AM EMBO J 2001;20:6866-6876. Control of branch-site choice by a group II intron. PUBMED:11726522

  3. Lehmann K, Schmidt U Crit Rev Biochem Mol Biol 2003;38:249-303. Group II introns: structure and catalytic versatility of large natural ribozymes. PUBMED:12870716

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 Weinberg Z
Structure source Predicted; Weinberg Z
Type Intron;
Author Weinberg ZORCID logo, Gardner PPORCID logo
Alignment details
Alignment Number of
full 447
seed 139

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 0 --verbose --nohmmonly -T 30.00 -Z 742849.287494 CM SEQDB
Gathering cutoff 34.5
Trusted cutoff 34.6
Noise cutoff 34.3
Covariance model Download