Hi, Another useful site to ask such questions would also be:
http://biology.stackexchange.com/ HTH, -steve On Tue, May 1, 2012 at 6:54 PM, Brooke Rhead <[email protected]> wrote: > Hi Michal, > > This mailing list is geared more toward specific questions about using > the UCSC Genome Browser and less toward general biology questions, but > maybe we can point you in the right direction for more information. > > If you haven't already consulted Wikipedia's page on the topic, it is a > good place to start: > http://en.wikipedia.org/wiki/Pseudogene > > Here is a paper by another UCSC alumnus on retroposed genes and human > evolution: > > http://www.biomedcentral.com/1471-2164/9/466 > Baertsch R, Diekhans M, Kent J, Haussler D, Brosius J. Retrocopy > contributions to the evolution of the human genome. BMC Genomics 2008 > Oct 8;9:466. > > There is a corresponding "Retroposed Genes" track on the preview hg19 > human browser that contains annotations for these genes: > http://genome-preview.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=ucscRetroAli2 > (be aware that this is our preview server; much of the data here is > untested or experimental and will not go to the regular site). I see > that the construction of that track started with identification of > "mRNAs that aligned twice in the genome (once with introns and once > without introns)." So, in terms of the bigger picture, the lack of > introns in processed psuedogenes provides a way to identify them in the > genome. > > There are more pseudogene annotations available on the regular site, > such as in the GENCODE Genes track: > http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeGencodeV11 > > I hope this is helpful. If you have questions regarding the Genome > Browser, please contact us again at [email protected]. > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > On 5/1/12 10:30 AM, Michal Bick wrote: >> Hello, >> >> I'm a UCSC alumna, currently taking pre-med classes. I'm a bit unclear >> about pseudogenes (and I'm really interested in these regulatory genes!) >> and what it means for the processed ones to lack introns. I know that >> introns don't transcribe... but again, what does this mean in terms of the >> bigger picture? If you could provide me with a more clear explanation I >> would greatly appreciate it! I figured it would be best to get an >> explanation from someone who works daily with the genome! >> >> Thank you, >> >> Michal >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
