Hi Frauke, It looks like the SNP you mention is an insertion, and therefore there is no DNA to color with the extended case/color options. See this previously-answered question for more info:
https://lists.soe.ucsc.edu/pipermail/genome/2006-August/011546.html I hope this helps. -- Brooke Rhead UCSC Genome Bioinformatics Group Jennifer Jackson wrote on 8/4/09 10:32 PM: > Hello, > This SNP falls into the intron (non-coding region) of all of the protein tracks (mRNA & EST from Genank, too). Therefore, there was nothing to color code. If we have misunderstood you question, please clarify. > Thanks, jen > > > ------------------------------------------------ > Jennifer Jackson > UCSC Genome Bioinformatics Group > > ----- "Frauke Coppieters" <[email protected]> wrote: > >> From: "Frauke Coppieters" <[email protected]> >> To: [email protected] >> Cc: "Elke Mersy" <[email protected]> >> Sent: Sunday, July 12, 2009 4:08:49 AM GMT -08:00 US/Canada Pacific >> Subject: [Genome] visualisation of rs58340380 in DNA sequence >> >> Dear, >> >> I have a question regarding the visualisation of a SNP in UCSC. I >> wanted >> to visualize the SNP rs58340380 in the DNA sequence of the OPA1 gene. >> >> With this purpose, I went in the "genome browser" to this gene and >> selected the tracks SNP(128) and SNP(129). At this point, the SNP was >> >> visible in the genome browser. >> Subsequently, I went to "DNA", selected "extended case/color options", >> >> and gave both SNPs (128) and SNPs (129) a red color. The result was >> the >> correct DNA sequence which however lacked coloring of the rs58340380 >> SNP. Would it be possible to explain this? Thank you in advance! >> >> Best regards, >> >> Frauke Coppieters >> Center for Medical Genetics Ghent, Belgium >> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
