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. Author manuscript; available in PMC: 2013 Mar 1.
Published in final edited form as: Hum Genet. 2011 Aug 30;131(3):407–413. doi: 10.1007/s00439-011-1083-9

Fig. 3.

Fig. 3

Alu retrotransposon insertion in the ALMS1 locus. Panel a shows the region in exon 16 where the insertion was discovered. The site targeted by the Alu insertion is highlighted in yellow. Open reading frame (ORF) is shown in bold. The target site (underlined) exactly matches the proposed consensus 5'-TT^AAAA-3' of a primary nicking site for Alu insertions (Jurka, 1997). Panel b shows the nucleotide sequence of the 333 base pair Alu insertion mutation introducing a premature stop codon, denoted with an asterisk. The Alu element is highlighted in red, and target site duplication in yellow. The alternative C-terminus of the ORF is in blue font. Panel c shows the sequence alignments of the Alu discovered in this study (Alu ALMS1), the Alu element at the CLCN5 locus (Alu CLCN5) confirmed as a recent de novo germline transposition, and the Alu Ya5 sequence from Repbase (RepBase ID: AluYa5). Truncation of 34 nucleotides at the 5' end of the Alu ALMS1 element, which contains the A-box of the Alu bipartite promoter, is likely due to incomplete reverse-transcription of original RNA copy. Identical bases are highlighted in red. Interestingly, C-->A transversion (highlighted in green) is a unique SNP in publicly available human genomic databases and likely reflects a rare polymorphism among active Alu elements.