Hello again, One more suggestion to try is using the track called "Short Match".
Enter either "CG" or "CGCG" as the match string. In both dense and squish views, a small concentration of matches around the expected promoter region can be seen, although probably not enough to really be an island. The density is not sufficient according to the calculations used for the CpG Islands track (see the details page, Methods ). Thanks, Jennifer Jackson UCSC Genome Bioinformatics Group Jennifer Jackson wrote: > Hello, > It is possible that the CpG islands that you are expecting to find are > not included in the track "CpG Islands". According to the track's > detail page, it was last updated 2005-12-14. > > If you have CpG Island information from another source, you can create > a custom track of the data and compare to rest of the annotation in > the genome browser. > > When I open up the primary BRCA1 gene region and the CpG Islands track > in the graphical display, I see one (short) candidate near the start > site. To view this, set the browser position to > chr17:38,368,685-38,612,149, turn off all tracks except for UCSC Genes > and CpG Islands. > > BRCA1 is at position: chr17:38,449,840-38,530,994 (minus strand) > A CpG track annotation is at position: chr17:38,531,661-38,531,986 > > Help for custom tracks & sessions: > http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks > http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Sessions > > Jennifer Jackson > UCSC Genome Bioinformatics Group > > oranit zadok wrote: >> HI Jennifer, >> >> thank you for your quick replay. >> I tried to follow your instructions and looked for CpG regions in the >> BRCA1 gene. I run into some difficulties. I know for sure that this >> gene has at least two CpG islands in its promoter. yet, I didnt find >> any when I was searching this gene in your browser... >> >> can you try to find the BRCA1 promoter and CpG islands and see what >> im talking about? >> >> thank you , Oranit >> >> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
