Thank you both kindly. Michal
On May 2, 2012, at 5:59, Steve Lianoglou <[email protected]> wrote: > 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
