Group II catalytic intron D1-D4 clan

The group II catalytic intron D1-D4 clan contains the diverse RNA families from the 5` region of group II catalytic intron. Homology between these families has been established in the published literature [1-6].

This clan contains 7 families and the total number of sequence regions in the clan is 12,486.

Literature references

1. Michel F, Umesono K, Ozeki H, Gene. 1989;82:5-30.: Comparative and functional anatomy of group II catalytic introns--a review. 2684776
2. Michel F, Ferat JL, Annu Rev Biochem. 1995;64:435-461.: Structure and activities of group II introns. 7574489
3. Zimmerly S, Guo H, Eskes R, Yang J, Perlman PS, Lambowitz AM, Cell. 1995;83:529-538.: A group II intron RNA is a catalytic component of a DNA endonuclease involved in intron mobility. 7585955
4. Bonen L, Vogel J, Trends Genet 2001;17:322-331.: The ins and outs of group II introns. 11377794
5. Chu VT, Adamidi C, Liu Q, Perlman PS, Pyle AM, EMBO J 2001;20:6866-6876.: Control of branch-site choice by a group II intron. 11726522
6. Lehmann K, Schmidt U, Crit Rev Biochem Mol Biol 2003;38:249-303.: Group II introns: structure and catalytic versatility of large natural ribozymes. 12870716

Members

This clan contains the following 7 member families:

group-II-D1D4-1 group-II-D1D4-2 group-II-D1D4-3 group-II-D1D4-4 group-II-D1D4-5 group-II-D1D4-6 group-II-D1D4-7

External database links

External sites:

1: http://en.wikipedia.org/wiki/Group_II_intron

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
group-II-D1D4-7 (RF02012)	1,296 (10.4%)	View
group-II-D1D4-6 (RF02005)	1,617 (13.0%)	View
group-II-D1D4-5 (RF02004)	720 (5.8%)	View
group-II-D1D4-4 (RF02003)	840 (6.7%)	View
group-II-D1D4-3 (RF02001)	4,274 (34.2%)	View
group-II-D1D4-2 (RF01999)	1,231 (9.9%)	View
group-II-D1D4-1 (RF01998)	2,508 (20.1%)	View