Fig. 1
From: De-novo emergence of SINE retroposons during the early evolution of passerine birds
Proposed RNA secondary structures of passerine SINEs with CR1-derived tails (orange) and tRNA-derived heads. The SINE heads are tRNAIle (red) in TguSINE1 (a) and tRNAAsp (green) in PittSINE (b). Shaded regions denote promoter boxes A and B in tRNAs, as well as the reverse transcriptase binding site (RTBS) and 5′-AUUCURUG-3′ microsatellite typical for CR1 elements of amniotes [31]. Circles indicate nucleotide differences between SINE consensus sequences and the respective tRNAs or CR1 they are derived from. The RTBS hairpin structure is also visible in mfold [57] predictions of SINE secondary structure (Additional file 3: Figure S1). c DNA sequence alignment of TguSINE1 and PittSINE with respective tRNA genes and the 3′ end of CR1-X1_Pass. Black boxes denote diagnostic nucleotides present in the CR1-derived tails of TguSINE1 and PittSINE