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. 2013 Aug 21;54:14. doi: 10.1186/1999-3110-54-14

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© Charng and Liu; licensee Springer. 2013

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Ds1 termini sequences and classification of exonized transcripts. a) Ds1 termini sequences providing splice donor/acceptor junction (arrows) and premature termination codons (PTCs) in exonized transcripts (bold). * indicates the nucleotide differs with Ds element, which harbors another PTC presenting as TAA. b) Classification of exonized transcripts (black line) according to location of the PTC. Normal transcript is shown as a dashed line. The corresponding DNAs of the TE-inserted target are shown in the centre. Black box indicates the unspliced intron. Exonization occurs by using the splice donor (arrow) of TE to join the upcoming exon. The existence and location of an in-frame PTC determines the type of the exonized transcripts, classified into 5 types. As an example, for type I, a PTC (UAA in bold) locates in the skipped exon/intron consensus: italics indicate exonic sequences. Brackets indicate the boundaries of PTC location for classification. Type V transcripts have no in-frame PTC until the end of the gene.