Description

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.

Methods

All mRNAs of a species from GenBank were aligned to the genome using blastz. 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 retrotranspostion events. These features include 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 are classified using a threshold score function that is a linear combination of this set of features. RetroGenes in the final set have a score threshold based on a ROC plot against the Vega annotated pseudogenes.

The "type" field has the following possible values:

• pseudogene indicates that the parent gene has been annotated by one of refSeq, knownGene or MGC.
• mrna indicates that the parent gene is a spliced mrna that has no annotation in NCBI refSeq, UCSC knownGene or Mammalian Gene Collection (MGC).
• expressed weak indicates that there is a mrna overlapping the retrogene, indicating possible transcription.
• expressed strong indicates that there is a mrna overlapping the retrogene, and at least five spliced Ests indicating probable transcription.
• expressed strong shuffle indicates that the retro was inserted into a pre-existing annotated gene.

Credits

The RetroFinder program and browser track were developed by Robert Baertsch at UCSC.

References

Baertsch R, Diekhans M, Kent J, Haussler D, Brosius J. Retrocopy contributions to the evolution of the human genome. BMC Genomics 2008 Oct 8;9:466.

Deyou Zheng, Adam Frankish, Robert Baertsch, Philipp Kapranov, Alexandre Reymond , Siew Woh Choo , Yontao Lu , France Denoeud , Stylianos E Antonarakis , Michael Snyder , Yijun Ruan, Chia-Lin Wei , Thomas R. Gingeras , Roderic Guigo , Jennifer Harrow , and Mark B. Gerstein Pseudogenes in the ENCODE Regions: Consensus Annotation, Analysis of Transcription and Evolution. Genome Res. 2007 Jun;17(6):839-51.

Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).

Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R., Haussler, D., and Miller, W. Human-Mouse Alignments with BLASTZ. Genome Res. 13(1), 103-7 (2003).