5  structures 0  species 0  sequences

Clan: IRES1 (CL00017)

Summary

IRES1 clan

The IRES1 clan contains the RNA families IRES_HCV and IRES_Pesti. The following bioinformatic methods were used to confirm the relationship between these families: CMSEARCH and PRC [1,2].

This clan contains 2 families and the total number of sequence regions in the clan is 10,039.

Literature references

  1. Nawrocki EP, Kolbe DL, Eddy SR, Bioinformatics. 2009;25:1335-7.: Infernal 1.0: inference of RNA alignments. 19307242
  2. Madera M, Bioinformatics. 2008;24:2630-2631.: Profile Comparer: a program for scoring and aligning profile hidden Markov models. 18845584

Members

This clan contains the following 2 member families:

IRES_HCV IRES_Pesti

Structures

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.

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Secondary structures

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.

Alignments

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
IRES_Pesti (RF00209) 2,122 (21.1%) View
IRES_HCV (RF00061) 7,917 (78.9%) View