RetroFinder

Description

The retroGene track shows processed mRNAs that have been inserted back into the genome since the mouse/human split. 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. These features are combined heuristic weighting based on analysis of known processed pseudogenes. RetroGenes in the final set have a score threshold greater than 425 based on a ROC plot against the Vega annotated pseudogenes. The "type" field has four possible values:

singleExon indicates that the parent gene is a single exon gene.
mrna indicates that the parent gene is a spliced mrna that has no annotation in NCBI refSeq, UCSC knownGene or Mammalian Gene Collection (MGC).
annotated indicates that the parent gene has been annotated by one of refSeq, knownGene or MGC.
expressed indicates that there is a mrna overlapping the retrogene, indicating probable transcription.

These features can be downloaded from the table pseudoGeneLink in many formats using the Table Browser option on the blue bar.

References

Kent WJ, Baertsch R, Hinrichs A, Miller W, and Haussler D (2003). Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci USA 100(20):11484-11489 Sep 30 2003.

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

Credits

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