In the recent database issue of NAR, there are two reports of transposable element (TE) databases. I already discussed one in an earlier post. That one is a database that includes Gypsy elements (non-LTR retroposons) and retroviruses and aims to be a database “devoted to the non-redundantanalysis and evolutionary-based classification of mobile geneticelements.” Hopefully to develop into a database of all TE’s. The other paper, by Levy et al. (“TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates“)1, I’ll discus briefly here introduces a somewhat different database of transposable elements.
As the paper discusses, TE’s have been implicated in a large number of effects on the vertebrate genome: affecting expression and “contributing to genetic diversity, genomic expansion,genomic content and genomic rearrangements.” Whether these immense changes are the raison d’être for transposable elements or the byproduct of a parasitic DNA element, I’ll leave for discussion (though I would side with the latter), but they are unarguably major factors in genome evolution and don’t fit the definition of “junk DNA.” :D.
A commenter, McBlawg‘s Graham Steel, left a comment about Silobreaker as a possible search engine. Indeed, it is a pretty nice tool. It’s more general news than genomics :), but I did a quick search on “transposon” and found this hilarious, and informative, video clip explaining how transpose rearranges parts of the genome. The video is done in the 50′s “Learning about Sex” style. For your viewing pleasure .
I started my Ph.D. studies into the evolution of non-LTR retrotransposable elements in 1990 and found the world of mobile genetic elements or transposons (aka a long time ago… jumping genes) to be varied, complicated and fascinating. In 1993 I discovered the web. I’ve hoped for and searched for a database of these “Mobile geneticelements [that] are self-contained genomic units capable of proliferatingwithin their host genomes”1 to little satisfaction. Such databases exist such as the Mouse Transposon Insertion Database and the dbRIP (human retrotransposon polymorphisms in humans) and several others. But these almost entirely organism-specific databases. This helps the study of the organism (mobile elements have an effect on the genome), but little in the study of transposons as a class.