Hi Ann, Yes, it is expected some DMIT loci will span more than one functional region. This will occur when a DMIT loci happens to cross the boundary between two functional regions.
If I select "whole gene" as the output for the custom track in step 1, then I get 156 DMIT loci that intersect with it. However, I did get 80 DMIT loci when intersecting with 3' UTR. Can you please verify that you intersected the correct custom track? Yes, you can assume that DMIT loci that are not found to intersect with the 5'UTR, the coding exons, the 3' UTR or the introns are intergenic. I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 4/11/11 3:54 PM, Ann Eileen Miller Baker wrote: > 1. Thanks for helping me to use the UCSC genomics website to find the > following mouse DMIT locus functional groups (3UTR, 5UTR, coding exon, exon > plus, intron, whole gene). > > > > > 2. A few questions and some assumptions: > > > > 2a. I assumed that each mouse DMIT locus would occur within only ONE of > the functional groups (3UTR or 5 UTR or coding exon or exon plus or > intron or whole gene). > > > > > 2b. Instead, the UCSC genomics website reports that a mouse DMIT locus can > cover more than one functional group. Is this correct? > > > > > > > > 2c. Though much of the mouse genome lacks genes, I was expecting for > ca. 7500 > mouse DMIT loci to have more DMIT loci overlapping genes. > Instead, only 80 DMIT overlap > "whole genes". Is this correct? > > > > > 3. Therefore I assume that the remainder of the DMIT loci occur within > "intergenic regions". Is this correct? > > > > > > 4. Thanks for helping me to interpret the implications of the UCSC data > analyses. > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
