Table 11.
Origination of Novel Exons (“Exonization”) from Mobile DNA Elements.
| Taxa | Mobile DNA Exonized |
|---|---|
| Green algae | Transposable elements (TEs) |
| Plants (coffee, rice, Arabidopsis, etc.) | Ds transposons and other transposable elements |
| Ancestral vertebrate | “…a more than 200-base-pair ultraconserved region, 100% identical in mammals, and 80% identical to the coelacanth SINE, contains a 31-amino-acid-residue alternatively spliced exon of the messenger RNA processing gene PCBP2…” |
| Mammal | “Although…not evolutionarily related, mammalian TMPO and ZNF451…both code for splice isoforms that contain LAP2alpha domains…related to the first ORF from a DIRS1-like retrotransposon…domestication happened separately and resulted in proteins that combine retrotransposon and host protein domains. The alternative splicing of the retrotransposed sequence allowed the production of both the new and the untouched original isoforms…” |
| Mammal, Primate | MIR retrotransposons |
| Mouse | L1 retrotransposons; “antisense insertions results in an increased potential for exonization” |
| Rat | L1 retrotransposon and ERV (endogenous retrovirus) in embryonically expressed Rtdpoz-T1 and -T2 locus |
| Human and mouse | “…exonization of transposed elements is biased towards the beginning of the coding sequence in both human and mouse genes…cases of primate-specific Alu elements that depend on RNA editing for their exonization…” |
| Primate | Alu exonization in BCS1L, RNA edited Alu element in human nuclear prelamin A recognition factor gene transcript |
| Primate | LINE retrotransposon in ZRANB2 locus |
| Human | Anti-sense Alu SINEs; Alu-derived segments in two Bcl-family proteins. |
| Human | “Exons derived from Alu SINEs but also the exons from the TEs of other families were preferentially established in zinc finger (ZNF) genes.” |
| Human | “Long Terminal Repeat (LTR) retrotransposons are associated with 1057 human genes (5.8%). In 256 cases LTR retrotransposons were observed in protein-coding regions, while 50 distinct protein coding exons in 45 genes were comprised exclusively of LTR RetroTransposon Sequence (LRTS)…an alternatively spliced exon of the Interleukin 22 receptor, alpha 2 gene (IL22RA2) derived from a sequence of retrotransposon of the Mammalian apparent LTR retrotransposons (MaLR) family …hypothesize that the recruitment of the part of LTR as a novel exon…a result of a single mutation in the proto-splice site…” |
| Human | “…human nuclear prelamin A recognition factor contains a primate-specific Alu-exon that exclusively depends on RNA editing for its exonization.” |
A more complete, detailed and fully referenced version of this table is available as Supplementary Table S11.