Hi Nicholas, The IRGM gene labeled uc011dcl.1 in the UCSC Genes track is annotated as a non-protein-coding gene (see http://en.wikipedia.org/wiki/Non-coding_RNA). I can't really tell you if this region should be regarded as a pseudogene or not, but I can at least point you to some more information about it.
The UCSC Genes track is created by an automated process, and the genes are shaded in the Genome Browser according to the available evidence for any particular annotation (see the Methods page: http://genome.ucsc.edu/cgi-bin/hgGene?hgg_do_kgMethod=1). This particular annotation is colored light blue, which indicates the lowest level of support. You can also turn on the other tracks in the Genes and Gene Predictions track group to get an idea of whether and how this region is annotated in different datasets. Click on the "mini-button" to the left of the track or an item in a track to read more about how each gene set was made. I hope this is helpful. Please send any future questions to [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 01/04/11 04:05, Nicholas Price wrote: > Hi > > I am sorry but I don't understand...I never heard of an untranslated > exon...Is it just transcribed? and what is the end product? and if so, > should the region be regarded as a pseudogene? > > > Nicholas > > On 3 January 2011 19:48, Brooke Rhead <[email protected]> wrote: > >> Hi Nicholas, >> >> The UCSC Genes track has an (untranslated) exon in the position you >> specified. When you retrieve alignments for regions that have *no* overlap >> with the UCSC Genes track, the exon is considered overlap, and you don't get >> any alignments for that region. Does that make sense? >> >> If you have further questions, please feel free to contact us again at >> [email protected]. >> >> -- >> Brooke Rhead >> UCSC Genome Bioinformatics Group >> >> >> >> On 01/03/11 13:20, Nicholas Price wrote: >> >>> Hi >>> >>> Position: chr5:150257537-150257677 is suppose to be the location of a >>> human >>> pseudogene. When I use tables group:Comparative geomics, Multiz46way >>> Intersection: no overlap with known genes ....I get no alignments back. >>> Why >>> is that? >>> >>> >>> Nicholas >>> > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
