tRNA clan

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

This clan contains 7 families and the total number of sequence regions in the clan is 5,350,003.

Literature references

1. Tyagi JS, Kinger AK, Nucleic Acids Res. 1992;20:138.: Identification of the 10Sa RNA structural gene of Mycobacterium tuberculosis. 1371186
2. Komine Y, Kitabatake M, Yokogawa T, Nishikawa K, Inokuchi H, Proc Natl Acad Sci U S A. 1994;91:9223-7.: A tRNA-like structure is present in 10Sa RNA, a small stable RNA from Escherichia coli. 7524073
3. Mao C, Bhardwaj K, Sharkady SM, Fish RI, Driscoll T, Wower J, Zwieb C, Sobral BW, Williams KP, RNA Biol. 2010;6:355-361.: Variations on the tmRNA gene. 19617710
4. 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
5. Burks J, Zwieb C, Mueller F, Wower I, Wower J, BMC Mol Biol. 2005;6:14.: Comparative 3-D modeling of tmRNA. 15958166

Members

This clan contains the following 7 member families:

tRNA tmRNA alpha_tmRNA beta_tmRNA cyano_tmRNA tRNA-Sec mt-tmRNA

External database links

External sites:

1: http://www.indiana.edu/~tmrna/ 2: http://rnp.uthscsa.edu/rnp/tmRDB/tmRDB.html 3: http://trnadb.bioinf.uni-leipzig.de 4: http://gtrnadb.ucsc.edu

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
mt-tmRNA (RF02544)	97 (0.0%)	View
tRNA-Sec (RF01852)	4,211 (0.1%)	View
cyano_tmRNA (RF01851)	25 (0.0%)	View
beta_tmRNA (RF01850)	60 (0.0%)	View
alpha_tmRNA (RF01849)	1,543 (0.0%)	View
tmRNA (RF00023)	8,092 (0.2%)	View
tRNA (RF00005)	5,335,975 (99.7%)	View