Journal of Molecular Evolution

, Volume 67, Issue 6, pp 594–607 | Cite as

Evolution of Spliceosomal snRNA Genes in Metazoan Animals

  • Manuela Marz
  • Toralf Kirsten
  • Peter F. Stadler


While studies of the evolutionary histories of protein families are commonplace, little is known on noncoding RNAs beyond microRNAs and some snoRNAs. Here we investigate in detail the evolutionary history of the nine spliceosomal snRNA families (U1, U2, U4, U5, U6, U11, U12, U4atac, and U6atac) across the completely or partially sequenced genomes of metazoan animals. Representatives of the five major spliceosomal snRNAs were found in all genomes. None of the minor splicesomal snRNAs were detected in nematodes or in the shotgun traces of Oikopleura dioica, while in all other animal genomes at most one of them is missing. Although snRNAs are present in multiple copies in most genomes, distinguishable paralogue groups are not stable over long evolutionary times, although they appear independently in several clades. In general, animal snRNA secondary structures are highly conserved, albeit, in particular, U11 and U12 in insects exhibit dramatic variations. An analysis of genomic context of snRNAs reveals that they behave like mobile elements, exhibiting very little syntenic conservation.


snRNA Homology search Secondary structure Pseudogenes Promoter Syntenic conservation Phylogenetics Paralogues 



This work was supported in part by the Graduierten-Kolleg Wissensrepräsentation and by the Bioinformatics Initiative of the Deutsche Forschungs-Gemeinschaft (DFG). Special thanks go to Petra Pregel and Jens Steuck for making the work much easier.

Supplementary material

239_2008_9149_MOESM1_ESM.pdf (26 kb)
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Copyright information

© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Manuela Marz
    • 1
  • Toralf Kirsten
    • 2
  • Peter F. Stadler
    • 1
    • 2
    • 3
    • 4
    • 5
  1. 1.Bioinformatics Group, Department of Computer ScienceUniversity of LeipzigLeipzigGermany
  2. 2.Interdisziplinäres Zentrum für Bioinformatik, University of LeipzigLeipzigGermany
  3. 3.RNomics Group, Fraunhofer Institute for Immunology and Cell TherapyLeipzigGermany
  4. 4.Institute for Theoretical Chemistry and Structural BiologyUniversity of ViennaWienAustria
  5. 5.The Santa Fe InstituteSanta FeUSA

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