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
