U3 clan

The U3 clan contains the U3 RNA families specific to metazoa, fungi, plants and basal eukaryotes. The homology and divisions between these families has been established in the published literature [1].

This clan contains 4 families and the total number of sequence regions in the clan is 26,306.

Literature references

1. Marz M, Stadler PF, RNA Biol. 2010;6:503-507.: Comparative analysis of eukaryotic U3 snoRNA. 19875933

Members

This clan contains the following 4 member families:

U3 Fungi_U3 Plant_U3 ACEA_U3

External database links

External sites:

1: http://turl.ca/nobn 2: http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR17a 3: http://rnp.uthscsa.edu/index.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
ACEA_U3 (RF01848)	2,156 (8.2%)	View
Plant_U3 (RF01847)	3,759 (14.3%)	View
Fungi_U3 (RF01846)	1,319 (5.0%)	View
U3 (RF00012)	19,072 (72.5%)	View