Human transposable elements in Repbase: genomic footprints from fish to humans.

Repbase is a comprehensive database of eukaryotic transposable elements (TEs) and repeat sequences, containing over 1300 human repeat sequences. Recent analyses of these repeat sequences have accumulated evidences for their contribution to human evolution through becoming functional elements, such as protein-coding regions or binding sites of transcriptional regulators. However, resolving the origins of repeat sequences is a challenge, due to their age, divergence, and degradation. Ancient repeats have been continuously classified as TEs by finding similar TEs from other organisms. Here, the most comprehensive picture of human repeat sequences is presented. The human genome contains traces of 10 clades ( and ) of non-long terminal repeat (non-LTR) retrotransposons (long interspersed elements, LINEs), 3 types (, and ) of short interspersed elements (SINEs), 1 composite retrotransposon () family, 5 classes (, and ) of LTR retrotransposons, and 12 superfamilies (, , , and ) of DNA transposons. These TE footprints demonstrate an evolutionary continuum of the human genome.