SRP clan

The SRP clan contains the RNA families for Metazoa_SRP, Bacterial_small_SRP, Bacterial_large_SRP, Fungal_SRP, Plant_SRP, Protozoa_SRP, Archaea_SRP and Dictyostelium_SRP. Homology between these families has been established in the published literature [1-8].

This clan contains 9 families and the total number of sequence regions in the clan is 399,031.

Literature references

1. Struck JC, Vogel DW, Ulbrich N, Erdmann VA, Nucleic Acids Res. 1988;16:2719.: The Bacillus subtilis scRNA is related to the 4.5S RNA from Escherichia coli. 2452405
2. Poritz MA, Strub K, Walter P, Cell. 1988;55:4-6.: Human SRP RNA and E. coli 4.5S RNA contain a highly homologous structural domain. 2458843
3. Poritz MA, Bernstein HD, Strub K, Zopf D, Wilhelm H, Walter P, Science. 1990;250:1111-7.: An E. coli ribonucleoprotein containing 4.5S RNA resembles mammalian signal recognition particle. 1701272
4. Larsen N, Zwieb C, Nucleic Acids Res. 1991;19:209-15.: SRP-RNA sequence alignment and secondary structure. 1707519
5. Larsen N, Zwieb C, Nucleic Acids Res. 1993;21:3019-20.: The signal recognition particle database (SRPDB). 7687350
6. Zwieb C, van Nues RW, Rosenblad MA, Brown JD, Samuelsson T, RNA. 2005;11:7-13.: A nomenclature for all signal recognition particle RNAs. 15611297
7. Andersen ES, Rosenblad MA, Larsen N, Westergaard JC, Burks J, Wower IK, Wower J, Gorodkin J, Samuelsson T, Zwieb C, Nucleic Acids Res. 2006;34:D163-8.: The tmRDB and SRPDB resources. 16381838
8. Rosenblad MA, Larsen N, Samuelsson T, Zwieb C, RNA Biol. 2009;6:508-516.: Kinship in the SRP RNA family. 19838050
9. Aspegren A, Hinas A, Larsson P, Larsson A, Söderbom F, Nucleic Acids Res. 2004;32:4646-4656.: Novel non-coding RNAs in Dictyostelium discoideum and their expression during development. 15333696

Members

This clan contains the following 9 member families:

Metazoa_SRP Bacteria_small_SRP Fungi_SRP Dictyostelium_SRP Bacteria_large_SRP Plant_SRP Protozoa_SRP Archaea_SRP Bacteroidales_small_SRP

External database links

External sites:

1: http://rnp.uthscsa.edu/rnp/SRPDB/SRPDB.html

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 mapping between the Rfam families in this clan, the corresponding EMBL entries, and the region of the three-dimensional structures that are available for that sequence.

This tool allows you to view the secondary structure images of two clan members side-by-side. Choose the family structures using the two drop-down menus below.

The table below shows the number of occurrences of each family throughout the sequence database. In brackets beside each number is the percentage of the total number of sequence hits for the clan that are represented by this family. The rightmost column provides a link to the alignments tab for each family.

Rfam family	Num. regions	Alignment
Bacteroidales_small_SRP (RF04183)	1,028 (0.3%)	View
Archaea_SRP (RF01857)	294 (0.1%)	View
Protozoa_SRP (RF01856)	111 (0.0%)	View
Plant_SRP (RF01855)	4,988 (1.3%)	View
Bacteria_large_SRP (RF01854)	1,447 (0.4%)	View
Dictyostelium_SRP (RF01570)	4 (0.0%)	View
Fungi_SRP (RF01502)	748 (0.2%)	View
Bacteria_small_SRP (RF00169)	6,888 (1.7%)	View
Metazoa_SRP (RF00017)	383,523 (96.1%)	View