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 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.

Retrogene Statistics table:

• Expression of Retrogene: The following values are possible where those that are not expressed are classed as pseudogene or mrna:
• pseudogene indicates that the parent gene has been annotated by one of NCBI's RefSeq, UCSC Genes or Mammalian Gene Collection (MGC).
• mrna indicates that the parent gene is a spliced mrna that has no annotation in NCBI's RefSeq, UCSC Genes or Mammalian Gene Collection (MGC). Therefore, the retrogene is a product of a potentially non-annotated parent gene and is a putative pseudogene of that putative parent gene.
• expressed weak indicates that there is a mRNA overlapping the retrogene, indicating possible transcription. noOrf indicates that an ORF was not identified by BESTORF.
• expressed indicates that there is a medium level of mRNAs/ESTs mapping to the retrogene locus, indicating possible transcription.
• expressed strong indicates that there is a mRNA overlapping the retrogene, and at least five spliced ESTs indicating probable transcription. noOrf indicates that an ORF was not identified by BESTORF.
• expressed shuffle indicates that the retrogene was inserted into a pre-existing annotated gene.
• Score: Based on features of the potential retrogene.
• Percent Gene Alignment Coverage (Bases Matching Parent): Shows the percentage of the parent gene aligning to this region.
• Intron Count: Number of introns is the number of gaps in the alignment between the parent mRNA and the genome where gaps are >80 bp and the ratio of the mRNA alignment gap to the genome alignment gap is less than 30% after removing repeats.
• Gap Count: Numer of gaps in the alignment of between the parent mRNA and the genome after removing repeats. Gaps are not counted if the gap on the mRNA side of the alignment is a similar size to the gap in the genome alignment.
• BESTORF Score: BESTORF (written by Victor Solovyev) predicts potential open reading frames (ORFs) in mRNAs/ESTs with very high accuracy using a Markov chain model of coding regions and a probabilistic model of translation start codon potential. The score threshold for finding an ORF is 50 (Jim Kent, personal communication).

Break in Orthology table:

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.

Credits

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

References

Baertsch R, Diekhans M, Kent WJ, Haussler D, Brosius J. Retrocopy contributions to the evolution of the human genome. BMC Genomics. 2008 Oct 8;9:466. PMID: 18842134; PMC: PMC2584115

Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784

Pei B, Sisu C, Frankish A, Howald C, Habegger L, Mu XJ, Harte R, Balasubramanian S, Tanzer A, Diekhans M et al. The GENCODE pseudogene resource. Genome Biol. 2012 Sep 26;13(9):R51. PMID: 22951037; PMC: PMC3491395

Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961

Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW, Lu Y, Denoeud F, Antonarakis SE, Snyder M et al. Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res. 2007 Jun;17(6):839-51. PMID: 17568002; PMC: PMC1891343