0  structures 100  species 1398  sequences

Family: Plant_SRP (RF01855)

Description: Plant signal recognition particle RNA

Summary

Clan

This family is a member of clan (CL00003), which contains the following 8 members:

Archaea_SRP Bacteria_large_SRP Bacteria_small_SRP Dictyostelium_SRP Fungi_SRP Metazoa_SRP Plant_SRP Protozoa_SRP

Wikipedia annotation Edit Wikipedia article

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

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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:
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Download

Download a gzip-compressed, Stockholm-format file containing the seed alignment for this family. You may find RALEE useful when viewing sequence alignments.

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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...

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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.

Motif matches

There are 4 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 8 0.127 121.4 Match Image
7 RM00008 GNRA tetraloop 49 0.778 527.7 Match Image
7 RM00010 Kink turn 1, 3' bulge 12 0.190 126.3 Match Image
7 RM00020 Signal recognition particle small S-domain 63 1.000 2604.7 Match Image

References

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

Literature references

  1. Wild K, Weichenrieder O, Strub K, Sinning I, Cusack S Curr Opin Struct Biol 2002;12:72-81. Towards the structure of the mammalian signal recognition particle. PUBMED:11839493

  2. Batey RT, Rambo RP, Lucast L, Rha B, Doudna JA Science 2000;287:1232-1239. Crystal structure of the ribonucleoprotein core of the signal recognition particle. PUBMED:10678824

  3. Batey RT, Sagar MB, Doudna JA J Mol Biol 2001;307:229-246. Structural and energetic analysis of RNA recognition by a universally conserved protein from the signal recognition particle. PUBMED:11243816

  4. Rosenblad MA, Gorodkin J, Knudsen B, Zwieb C, Samuelsson T Nucleic Acids Res 2003;31:363-364. SRPDB: Signal Recognition Particle Database. PUBMED:12520023

  5. Regalia M, Rosenblad MA, Samuelsson T Nucleic Acids Res 2002;30:3368-3377. Prediction of signal recognition particle RNA genes. PUBMED:12140321

  6. Rosenblad MA, Larsen N, Samuelsson T, Zwieb C RNA Biol. 2009;6:508-516. Kinship in the SRP RNA family. PUBMED:19838050

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:19838050
Structure source Published; PMID:19838050
Type Gene;
Author Gardner PPORCID logo
Alignment details
Alignment Number of
sequences
full 1,335
seed 63

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
Gathering cutoff 105.0
Trusted cutoff 105.1
Noise cutoff 104.9
Covariance model Download