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