Origination of Novel Exons from Mobile DNA Elements (Volff 2006; Bowen and Jordan 2007; Piriyapongsa, Rutledge et al. 2007; Sorek 2007; Sorek 2009; Schmitz and Brosius 2011; Zhang, Edwards et al. 2013; Park, Kim et al. 2015) (Ponicsan, Kugel et al. 2010)

Taxa

Mobile DNA Exonized

Reference(s)

Green algae

Transposable elements

(Philippsen, Avaca-Crusca et al. 2016)

Plants (coffee, rice, Arabidopsis, etc.)

Transposable elements

(Lopes, Carazzolle et al. 2008; Hoen and Bureau 2015)

Plants

Ds transposons

(Liu and Charng 2012)

Rice

Ds transposons

(Chien, Liu et al. 2013)

Non-mammalian vertebrates and invertebrates

“…transcriptomes of vertebrates exhibit significant levels of exonization of TEs, only anecdotal cases were found in invertebrates. In vertebrates, as in mammals, the exonized TEs are mostly alternatively spliced…”

(Sela, Kim et al. 2010)

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…”

(Bejerano, Lowe et al. 2006)

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...”

(Abascal, Tress et al. 2015)

Mammal

MIR retrotransposons

(Annibalini, Bielli et al. 2016) (Krull, Petrusma et al. 2007)

Mouse

L1 retrotransposons; “antisense insertions results in an increased potential for exonization”

(Zemojtel, Penzkofer et al. 2007)

Rat

Exonization of L1 and ERV (endogenous retrovirus) in embryonically expressed Rtdpoz-T1 and -T2 locus

(Huang, Lin et al. 2009)

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…”

(Sela, Mersch et al. 2010; Mandal, Pandey et al. 2013; Zarnack, Konig et al. 2013) (Moller-Krull, Zemann et al. 2008)

Primate

Alu exonization in BCS1L, other loci

(Park, Kim et al. 2015) (Krull, Brosius et al. 2005)

Primate

RNA edited Alu element in human nuclear prelamin A recognition factor gene transcript

(Moller-Krull, Zemann et al. 2008)

Primate

MIR retrotransposon

(Lin, Jiang et al. 2009)

Primate

LINE retrotransposon in ZRANB2 locus

(Park, Huh et al. 2012)

Human

SINE retrotransposons

(Vorechovsky 2010)

Human

Anti-sense Alu elements; Alu-derived segments in two Bcl-family proteins.

(Huda and Bushel 2013) (Wu, Li et al. 2007; Corvelo and Eyras 2008) (Schwartz, Gal-Mark et al. 2009)

Human

Exons derived from Alu elements but also the exons from the TEs of other families were preferentially established in zinc finger (ZNF) genes.”

(Zhang, Edwards et al. 2013)

Human

“Long Terminal Repeat (LTR) retrotransposons are associated with 1,057 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…”

(Piriyapongsa, Polavarapu et al. 2007)

Human

“…human nuclear prelamin A recognition factor contains a primate-specific Alu-exon that exclusively depends on RNA editing for its exonization.”

(Lev-Maor, Sorek et al. 2007)