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Transposable elements (TEs), such as short interspersed elements (SINEs), evolve rapidly and are generally restricted to specific lineages. Here, we demonstrate that a central core of the previously described Deu-domain located within DeuSINEs (Nishihara et al. 2006) is widely distributed throughout the Metazoa. We characterize five new SINEs with this core sequence from the genomes of cnidarians, molluscs, annelids, and arthropods. Because this domain can be traced back to the cnidarian-bilaterian split >600 Ma, we propose naming it the “Nin” domain (the meaning of the Japanese character “Nin” is to endure and hide). Given that conserved noncoding DNA, such as that derived from the activity of SINEs, can be functionally relevant for the host genome (Sasaki et al. 2008), our findings highlight the need to understand these functions and the roles they may have played in supporting the evolution of multicellular genomes.