Figure 3.

Divergence of nucleotide sequence during transposon exaptation. Multiple sequence alignment of MT2B LTR-derived alternative first exons, and flanking genomic sequences, of mouse zinc finger, BED type containing 3 (Zbed3) and ribosomal protein L41 (Rpl41) genes [2], and the full MT2B consensus sequence from RepBase [9]. Note the rapid diversification of upstream regulatory sequences, and conservation of putative TATA box. Surprisingly, despite dissimilarities in the first exons, transcription start sites and splice site boundaries are conserved between these genes. In mouse egg-to-embryo transition, these two genes have differential expression patterns, with Zbed3 transcribed in oocytes, while Rpl41 transcribed from 2-cell stage to blastocyst stage [2]. MSA was performed using MUSCLE (http://www.ebi.ac.uk/Tools/msa/muscle/). First exons are highlighted with tan background; TATA box is boxed; conserved nucleotides are highlighted in yellow; transcription start sites are in green.