RTFAdb
Retrotransposons (also called class I elements) are a class of transposable element that retain the ability to mobilize and insert themselves into novel regions of the host genome through RNA intermediate (Wicker et al., 2007). In recent years, retrotransposons have been gaining increasing attention due to their regulatory roles in gene expression (Elbarbary et al., 2016). They can harbor cis-regulatory sequences, and therefore act as enhancers. In this way, retrotransposons influence transcriptional activity of nearby genes by providing binding sites for transcription factors (TFs). RTFAdb is a living database that functions as an exploration tool for computationally predicted associations of retrotransposons and TFs in the human and mouse genomes. Complementing the current transposable element databases, RTFAdb allows, by using publicly available TF ChIP-seq binding profiles, to investigate (i) retrotransposon species which are overrepresented in the binding sites of a given TF, (ii) TFs significantly associated with the retrotransposon of interest and (iii) all putative retrotransposon – transcription factor associations within the available tissue or cell types.