Figure 3
From: Exonization of active mouse L1s: a driver of transcriptome evolution?
Multiple splice sites are present in antisense and sense L1 sequences (for annotated cDNA examples see [22], for exemplary cDNAs see below). L1Mda2 sequence M13002 was used as a coordinate reference. A. Diverse exonization patterns as supported by cDNA evidence. The names of the splice sites incorporate the following information: prefixes of "A_" and "F_" designate sites within A- and F -type (F, TF, GF) monomers, respectively; SD: splice donor, SA: splice acceptor; the numbering indicates the position of the base after which the cleavage occurs, relative to the start of L1 ORF1, or relative to the start of alignments for monomers (for the alignments see [2, 40]); prefix of "BG_" designates sites found in L1 inserted within an intron of the beige gene, prefix of "S" stands for sense splice sites. The blue boxes mark the monomers making up the internal promoter region. Exemplary cDNAs corresponding to the identified splice sites: F_SA+100: AK017011, BC025138; F_SA+142: AI194597, AK079058; F_SA+213: AK081008; F_SA+218: AK015559; A_SA+191: AK028243; SA-154: BC056642, AF487898, BQ442932, AK039191, AK043154, BG144807, AK044020, AK145348, BB614554, BY733866, AK076999, AK015267, AK035725; SA+106: AK080034, AY167972, BG144807, BY733866, AK015267, AK007310; SA+120: AK006905, SA+1930: NM_177142; SA+4117: AK034994; SA+5260: AF529222; SA+5614: AK032656; F_SD+24: AK035725; F_SD+213: AK081008; F_SD+218: AK035725; A_SD+72: AK077067, AK015711; A_SD+122: AK032374, BC017615, AK015277, AK006354; SD+29: BY733866; SD+52: AK080034, AY167972, BG144807, AK006905, AK007235, AK161293, AK132928, AK135585, BB614554, AK016072, AK015559, AK076999, AK015267, AK015548, AK015778, AK015845; SD+106: AK015524; SD+288: AK076828, AK006905, AK015267; SD+350: AK017011; SD+1881: NM_177142; SD+2036: NM_177142; SD+5094: AF529222; BG_SA+4578: insertion in beige gene (for sequence see the online annotation); S_SA+1237: AK040102; BG_SD+4903: AK031201, AK032656; BG_SD+4694: AK134759, AK038418, DV059289, AK015958, AK034994, insertion in beige gene. B. Insertion of L1 GF element in the intron of GBP-5 gene introduced a SA site (SA-154) and resulted in creation of a novel exon coding for the C-terminal and bearing a new stop codon (solid vertical line) (cDNA transcripts GBP-5a, b: gi: 24266664, 26326418).