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Figure 1 | Mobile DNA

Figure 1

From: PGBD5: a neural-specific intron-containing piggyBac transposase domesticated over 500 million years ago and conserved from cephalochordates to humans

Figure 1

Clustal alignment of representative PGBD5 orthologs including Petromyzon marinus (sea lamprey) and Branchiostoma floridae (lancelet or amphioxus). For simplicity, many complete or partial vertebrate PGBD5s have been omitted from the alignment. The N-terminal motifs encoded by exon 1 are moderately conserved in all species including zebra finch, suggesting that chicken exon 1 lies within an unsequenced 770 bp gap located 29 kb upstream of exon 2 and immediately downstream of the sole substantial CpG island in the vicinity of the gene. Although human PGBD5 lacks 3 of the 4 catalytically active aspartates that are often conserved among diverse piggyBac elements, the positions of these four aspartates in a ClustalW alignment of piggyBac proteins most closely related to the active cabbage looper moth (Trichoplusia ni) transposase including human PGBD1, 2, 3, 4, and 5 [21] are highlighted in yellow. The Pfam homology with eubacterial and archeal IS4 transposases of the RNase H clan spans almost all of human PGBD5 exons 2–7 (residues 121–487). Figure key: black carets, vertebrate introns; blue caret, lamprey intron apparently orthologous to lancelet although shifted by 3 residues; red carets, lancelet introns; red underline, lancelet protein sequence derived from genomic tandem repeats (Additional file 1); red dashes, 13 residue deletion resulting from exclusion of predicted lancelet exon 5 which is embedded within the 108 bp genomic tandem repeats and would, if included, result in the 57 residue insertion; magenta underline, predicted nuclear localization signal not conserved in active Trichoplusia ni transposase; yellow highlight, position of four conserved, catalytic aspartates in active piggyBac transposases and homologs including human PGBD1, 2, 3, 4, and 5; gray XXX, regions of known length but undetermined sequence arbitrarily positioned in the clustal alignment; zfish, zfinch, xenopu, coelac, lampre, lancel are zebrafish, zebra finch, Xenopus tropicalis, coelacanth, lamprey, and lancelet respectively. Amino acid residues are colored according to the EBI Clustal convention for side chains (red, AVFPMILW; blue, DE; magenta, RK; green, STYHCNGQ; others, grey). To avoid prejudicial judgments regarding the relationship between highly divergent sequences, we refrained from assigning a similarity or homology score to each residue.

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