Retrotransposition is a process involving the copying of DNA by a group of enzymes that have the ability to reverse transcribe spliced mRNAs, resulting in single-exon copies of genes and sometime chimeric genes. RetroGenes can be either functional genes that have acquired a promoter from a neighboring gene, non-functional pseudogenes, or transcribed pseudogenes.
All mRNAs of a species from GenBank were aligned to the genome using lastz (Miller lab, Pennsylvania State University). mRNAs that aligned twice in the genome (once with introns and once without introns) were initially screened. Next, a series of features were scored to determine candidates for retrotransposition events. These features included position and length of the polyA tail, degree of synteny with mouse, coverage of repetitive elements, number of exons that can still be aligned to the retrogene and degree of divergence from the parent gene. Retrogenes were classified using a threshold score function that is a linear combination of this set of features. Retrogenes in the final set were selected using a score threshold based on a ROC plot against the Vega annotated pseudogenes.
Retrogenes inserted into the genome since the human/mouse divergence show a break in the mouse genome syntenic net alignments to the human genome. The percentage break represents the portion of the genome that is missing in each species relative to the reference genome (human hg19) at the retrogene locus as defined by syntenic alignment nets. Breaks in orthology with mouse and dog tend to be due to genomic insertions in the primate lineage. Relative orthology of dog/human and rhesus macque/human nets are used to avoid false positives due to deletions in the mouse genome. Older retrogenes will not show a break in orthology, so this feature is weighted lower than other features when scoring putative retrogenes.
These features can be downloaded from the table retroMrnaInfo in many formats using the Table Browser option from the Tools menu in the top blue navigation bar.
The RetroFinder program and browser track were developed by Robert Baertsch at UCSC.
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