Fig S3. Alignment of the terminal exon and flanking 3' sequence of ALG11 from the bush baby, human, marmoset and squirrel monkey identifies potential points of retrogene insertion and deletion. from Lineage-independent retrotransposition of UTP14 associated with male fertility has occurred multiple times throughout mammalian evolution

The terminal exon sequence ALG11 from bush baby, human marmoset and squirrel monkey were aligned. In all four species the terminal exons share a common 5′ splice site indicating an extremely high level of cross species conservation of the ALG11 gene. This is reinforced by the high level of conservation within the ALG11 coding sequence (highlighted in yellow) present in the terminal exon and perfect alignment of the stop codon (highlighted in red) that is present in all four species. This identity is maintained for seventy four bases upstream of the stop codon at which point the bush baby sequence diverges (indicated by arrowhead and highlighted in blue). The remaining species share a high level of homology for a further ninety bases at which point the squirrel monkey sequence diverges (indicated by a second arrowhead and highlighted in blue). Marmoset and human ALG11 terminal exon sequence maintains homology throughout its remaining length and contains a substantial part of UTP14C coding sequence (highlighted in gray). This would indicate that a single retrotransposition event resulted in the creation of UTP14C within the terminal exon of ALG11 in an ancestral species shared by marmoset and modern humans. In addition, this alignment illustrates that the terminal exon of squirrel monkey ALG11 does not contain any sequence which can be aligned with that of the UTP14C retrogene present in humans and marmosets. This could either be the result of the squirrel monkey possessing a copy of ALG11 that predating the retrotransposition event which created UTP14C, or alternatively, any copy of UTP14C that may have been present has been deleted or degraded to the point it is no longer identifiable.