Schema for RetroGenes V9 - Retroposed Genes V9, Including Pseudogenes
Database: hg38 Primary Table: ucscRetroAli9 Row Count: 15,491   Data last updated: 2015-01-15|
Format description: Summary info about a patSpace alignment
|field||example||SQL type ||info ||description |
|bin ||585||smallint(5) unsigned ||range ||Indexing field to speed chromosome range queries.|
|matches ||2032||int(10) unsigned ||range ||Number of bases that match that aren't repeats|
|misMatches ||25||int(10) unsigned ||range ||Number of bases that don't match|
|repMatches ||0||int(10) unsigned ||range ||Number of bases that match but are part of repeats|
|nCount ||0||int(10) unsigned ||range ||Number of 'N' bases|
|qNumInsert ||0||int(10) unsigned ||range ||Number of inserts in query|
|qBaseInsert ||0||int(10) unsigned ||range ||Number of bases inserted in query|
|tNumInsert ||0||int(10) unsigned ||range ||Number of inserts in target|
|tBaseInsert ||0||int(10) unsigned ||range ||Number of bases inserted in target|
|strand ||-||char(2) ||values ||+ or - for strand. First character query, second target (optional)|
|qName ||AK021903.1-1||varchar(255) ||values ||Query sequence name|
|qSize ||2057||int(10) unsigned ||range ||Query sequence size|
|qStart ||0||int(10) unsigned ||range ||Alignment start position in query|
|qEnd ||2057||int(10) unsigned ||range ||Alignment end position in query|
|tName ||chr1||varchar(255) ||values ||Target sequence name|
|tSize ||248956422||int(10) unsigned ||range ||Target sequence size|
|tStart ||87548||int(10) unsigned ||range ||Alignment start position in target|
|tEnd ||89605||int(10) unsigned ||range ||Alignment end position in target|
|blockCount ||1||int(10) unsigned ||range ||Number of blocks in alignment|
|blockSizes ||2057,||longblob || ||Size of each block|
|qStarts ||0,||longblob || ||Start of each block in query.|
|tStarts ||87548,||longblob || ||Start of each block in target.|
Connected Tables and Joining Fields
|73||2588||471||0||0||0||0||0||0||+||NM_015125.3-1||5473||0||5471||chr1||248956422||131067||134836||47||32,28,87,12,246,220,35,95,33,67,112,59,176,7,93,79,92,61,27,112,149,233,21,47,56,7,9,7,7,8,12,11,28,12,6,36,66,53,45,52,22,11,9, ...||0,33,70,160,188,435,655,690,788,847,914,1034,1094,1278,1286,1380,1461,1554,1617,1644,1757,4198,4432,4454,4502,4558,4565,4574,458 ...||131067,131099,131127,131214,131226,131472,131693,131733,131828,131861,131929,132041,132100,132276,132283,132376,132455,132547,13 ...|
Note: all start coordinates in our database are 0-based, not
1-based. See explanation
RetroGenes V9 (ucscRetroAli9) Track Description
Retrotransposition is a process involving the copying of DNA by a group of
enzymes that have the ability to reverse transcribe spliced mRNAs, and the
insertion of these processed mRNAs back into the genome resulting
in single-exon copies of genes and sometime chimeric genes. Retrogenes are
mostly non-functional pseudogenes but some are functional genes that have
acquired a promoter from a neighboring gene, or transcribed pseudogenes, and
some are anti-sense transcripts that may impede mRNA translation.
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, percent coverage of the
retrogene alignment to the parent, degree of synteny with mouse, coverage of repetitive
elements, number of exons that can still be aligned to the retrogene, number of putative
introns removed at the retrogene locus 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
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: Weighted sum of features (mentioned above) 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).
Retrogenes inserted into the genome since the mouse/human divergence show a break
in the human genome syntenic net alignments to the mouse genome. A break in orthology score is
calculated and weighted before contributing to the final retrogene score. The break in orthology score
ranges from 0-130 and it represents the portion of the genome that is missing in each species relative
to the reference genome (human hg38) at the retrogene locus as defined by syntenic
alignment nets. If the score is 0, there is orthologous DNA and no break in ortholog with the other species; this
could be an ancient retrogene; duplicated pseudogenes may also score low because they are often generated
via large segmental duplication events so the size of the pseudogene is small relative to the size of the
inserted duplicated sequence. Scores greater than 100 represent cases where the retrogene alignment has no
flanking alignment resulting from an ancient insertion or other complex rearrangement.
Breaks in orthology with human and dog tend to be due to genomic
insertions in the rodent lineage so sequence gaps are not treated as orthology breaks.
Relative orthology of human/mouse and dog/mouse nets are used to avoid false positives due to deletions
in the human genome. Since older retrogenes will not show a break in orthology, this feature is
weighted lower than other features when scoring putative retrogenes.
The RetroFinder program and browser track were developed by
Robert Baertsch at UCSC.
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
Genome Res. 2007 Jun;17(6):839-51.
PMID: 17568002; PMC: PMC1891343