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Clan: mir-28 (CL00086)


mir-28 clan

The mir-28 clan contains the RNA families mir-28 and mir-708. The following bioinformatic methods were used to confirm the relationship between these families: CMSEARCH, HMMER3 and PRC [1,2,3]. The hexamer seeds of the mature miRNA sequences from these families were manually checked for similarity using sequences obtained from miRBase [4].

This clan contains 2 families and the total number of sequence regions in the clan is 107.

Literature references

  1. Nawrocki EP, Kolbe DL, Eddy SR, Bioinformatics. 2009;25:1335-7.: Infernal 1.0: inference of RNA alignments. 19307242
  2. Eddy SR, PLoS Comput Biol. 2008;4:e1000069.: A probabilistic model of local sequence alignment that simplifies statistical significance estimation. 18516236
  3. Madera M, Bioinformatics. 2008;24:2630-2631.: Profile Comparer: a program for scoring and aligning profile hidden Markov models. 18845584
  4. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ, Nucleic Acids Res. 2008;36:D154-8.: miRBase: tools for microRNA genomics. 17991681


This clan contains the following 2 member families:

mir-28 mir-708

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.


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
mir-708 (RF00917) 35 (32.7%) View
mir-28 (RF00655) 72 (67.3%) View