U4 clan

The U4 clan contains the RNA families U4 and U4atac. Homology between these families has been established in the published literature [1-5].

This clan contains 2 families and the total number of sequence regions in the clan is 33,826.

Literature references

1. Shukla GC, Cole AJ, Dietrich RC, Padgett RA, Nucleic Acids Res. 2002;30:4650-4657.: Domains of human U4atac snRNA required for U12-dependent splicing in vivo. 12409455
2. Siliciano PG, Brow DA, Roiha H, Guthrie C, Cell. 1987;50:585-92.: An essential snRNA from S. cerevisiae has properties predicted for U4, including interaction with a U6-like snRNA. 2440583
3. Tarn WY, Steitz JA, Science. 1996;273:1824-32.: Highly diverged U4 and U6 small nuclear RNAs required for splicing rare AT-AC introns. 8791582
4. Zwieb C, Nucleic Acids Res. 1996;24:76-9.: The uRNA database. 8594606
5. Zwieb C, Nucleic Acids Res 1997;25:102-103.: The uRNA database. 9016512

Members

This clan contains the following 2 member families:

U4 U4atac

External database links

External sites:

1: http://rnp.uthct.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
U4atac (RF00618)	1,648 (4.9%)	View
U4 (RF00015)	32,178 (95.1%)	View