Journal of Molecular Evolution

, Volume 67, Issue 6, pp 594-607

First online:

Evolution of Spliceosomal snRNA Genes in Metazoan Animals

  • Manuela MarzAffiliated withBioinformatics Group, Department of Computer Science, University of Leipzig Email author 
  • , Toralf KirstenAffiliated withInterdisziplinäres Zentrum für Bioinformatik, University of Leipzig
  • , Peter F. StadlerAffiliated withBioinformatics Group, Department of Computer Science, University of LeipzigInterdisziplinäres Zentrum für Bioinformatik, University of LeipzigRNomics Group, Fraunhofer Institute for Immunology and Cell TherapyInstitute for Theoretical Chemistry and Structural Biology, University of ViennaThe Santa Fe Institute

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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