The retroFinder pipeline for annotating retrocopies. Alignments of all human mRNAs that aligned more than once to the genome were scored for a set of features (see Methods). Number of strict ESTs, mRNAs, and size of ORF were applied to determine evidence of expression. Retrocopies that partially overlapped the protein coding region of annotated multi exon Refseq genes were classified as exon acquisition events. Numbers in parenthesis were reported previously  (Additional files 4, 5, 6, 7).