src/hg/makeDb/trackDb/ucscRetroAli.html 1.2
1.2 2010/04/27 23:42:58 baertsch
updated description for retro track
Index: src/hg/makeDb/trackDb/ucscRetroAli.html
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<H2>Description</H2>
<P>
-The retroGene track shows processed mRNAs that have been inserted back
-into the genome since the mouse/human split. RetroGenes can be either
+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.</P>
<H2>Methods</H2>
<P>
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.
<P>
The "type" field has the following possible values:
<UL>
<LI><EM>pseudogene</EM> indicates that the parent gene has been annotated
by one of refSeq, knownGene or MGC.</LI>
<LI><EM>mrna</EM> indicates that the parent gene is a spliced mrna that
has no annotation in NCBI refSeq, UCSC knownGene or Mammalian Gene Collection
(MGC).</LI>
<LI><EM>expressed weak</EM> indicates that there is a mrna overlapping
the retrogene, indicating possible transcription.</LI>
<LI><EM>expressed strong</EM> indicates that there is a mrna overlapping
the retrogene, and at least five spliced Ests indicating probable transcription.</LI>
<LI><EM>expressed strong shuffle</EM> indicates that the retro was inserted into a pre-existing annotated gene.
</LI></UL>
These features can be downloaded from the table retroMrnaInfo in many
formats using the Table Browser option on the blue bar. </P>
<H2>Credits</H2>
<P>
The RetroFinder program and browser track were developed by
<A HREF="mailto:baertsch@soe.
ucsc.edu">Robert Baertsch</A> at UCSC.</P>
<!-- above address is baertsch at soe.ucsc.edu -->
<H2>References</H2>
<P>
Baertsch R, Diekhans M, Kent J, Haussler D, Brosius J.
<a href="http://www.biomedcentral.com/1471-2164/9/466">Retrocopy contributions to the evolution of the human genome.</a>
<I>BMC Genomics</I> 2008 Oct 8;9:466.
<P>
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
<a href="http://genome.cshlp.org/cgi/content/full/17/6/839">Pseudogenes in the ENCODE Regions: Consensus Annotation, Analysis of Transcription and Evolution.</a>
<I>Genome Res.</i> 2007 Jun;17(6):839-51.
<P>
Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.
<A HREF="http://www.pnas.org/cgi/content/abstract/1932072100v1"
TARGET=_blank>Evolution's cauldron:
Duplication, deletion, and rearrangement in the mouse and human genomes</A>.
<I>Proc Natl Acad Sci USA</I> <B>100</B>(20), 11484-11489 (2003).
<P>
Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.,
Haussler, D., and Miller, W.
<A HREF="http://www.genome.org/cgi/content/abstract/13/1/103" TARGET=_blank>Human-Mouse
Alignments with BLASTZ</A>. <em>Genome Res.</em> <B>13</B>(1), 103-7 (2003).
</P>