3  structures 0  species 0  sequences

Motif: Domain-V (RM00007)

Description: Splicing domain V


Wikipedia annotation Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam data in Wikipedia. This motif is described by a Wikipedia entry entitled Group II intron. More...

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


You can either download the motif alignment or view it directly in your browser window. More...

Formatting options

You can view or download motif 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:


There are 3 PDB entires which have been used to build the motif model.

The table of results below may be sorted by clicking on the column titles, or restored to the original order here.

Original order PDB ID PDB chain ID PDB Residues
2 1kxk A -
2 1r2p A -
2 1xhp A -

Family matches

There are 21 Rfam families which match this motif.

This section shows the families which have been annotated with this motif. 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 Family Accession Family Description Number of Hits Fraction of Hits Sum of Bits Image
3 RF00011 Bacterial RNase P class B 16 0.140 174.9 Match Image
3 RF00018 CsrB/RsmB RNA family 19 0.500 202.5 Match Image
3 RF00026 U6 spliceosomal RNA 172 0.915 3759.8 Match Image
3 RF00029 Group II catalytic intron 92 1.000 3204.8 Match Image
3 RF00300 Small nucleolar RNA Z221/R21b 2 0.167 22.1 Match Image
3 RF00413 Small nucleolar RNA SNORA19 2 0.059 27.6 Match Image
3 RF00449 HIF-1 alpha IRES 6 0.353 73.6 Match Image
3 RF00553 Small Cajal body specific RNA 1 4 0.138 44.2 Match Image
3 RF00724 mir-282 microRNA precursor family 2 0.133 20.2 Match Image
3 RF01071 Ornate Large Extremophilic RNA 2 0.100 27.8 Match Image
3 RF01699 Clostridiales-1 RNA 20 0.103 255.8 Match Image
3 RF01749 pan motif 8 0.108 95.6 Match Image
3 RF02356 Alphaproteobacterial sRNA BjrC1505 2 0.080 22.3 Match Image
3 RF02384 FasX small RNA 2 0.250 20.4 Match Image
3 RF02540 Archaeal large subunit ribosomal RNA 16 0.176 236.7 Match Image
3 RF02541 Bacterial large subunit ribosomal RNA 21 0.206 258.2 Match Image
3 RF02542 Microsporidia small subunit ribosomal RNA 6 0.130 64.8 Match Image
3 RF02543 Eukaryotic large subunit ribosomal RNA 23 0.261 295.7 Match Image
3 RF02837 Burkholderia RNA 7 (anti-hemB) 2 0.077 21.6 Match Image
3 RF03041 poplar-1 RNA 4 0.182 44.9 Match Image
3 RF03084 DUF2815 RNA 3 0.136 34.1 Match Image


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

Literature references

  1. Seetharaman M, Eldho NV, Padgett RA, Dayie KT RNA. 2006;12:235-47. Structure of a self-splicing group II intron catalytic effector domain 5: parallels with spliceosomal U6 RNA. PUBMED:16428604

  2. Valadkhan S RNA Biol. ;7:345-53. Role of the snRNAs in spliceosomal active site. PUBMED:20458185

External database links

Curation and motif details

This section shows the detailed information about the Rfam motif. 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 CMfinder
Structure source N/A
Type Stem Loop
Author Gardner PP
Alignment details
Alignment Number of
Average length Sequence
identity (%)
seed 62 33.26 53

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate CM
Gathering cutoff 10.0
Covariance model Download the Infernal CM for the motif here