Hello, next time, please send new questions to the browser mailing list. I am sending it there now. Jennifer
Pattle Pun wrote: > ** High Priority ** > > Dear Jennifer, > > I have several more questions about your genome browser display: > > I used the following panels: (Clicking the + and turn it to -) > 1) Mapping and Sequencing: Base: dense > 2) Genes and Gene Prediction: UCSC genes: dense > 3) Comparative Genomics: 28 Way Most Conserved: dense (So > evolutionarily similar organisms, e.g. those in Mammals and Vertebrates > shall appear) > 4) Variation and Repeats: SNPs(129): pack, HapMap SNPs: dense, > Microsatellite: dense, Simple Repeat: dense, Interrupted Repeats: dense > 5) *Pilot ENCODE Regions and Genes: dense in all excepting show > Gencode Genes. Hide EGASP and Vienna RNAz > 6) *Pilot ENCODE Comparative Genomics and Variation: NHGRI DIPs: > dense > * Ignore ENCODE if there are no data available on a specific chromosome. > Encode region is not an "AND" condition but "OR" one as it's not > complete., > > I am looking for non-coding elements in the human genome: to identify > SNP� that fulfill the following criteria: > 1) In regions not listed as genes by BOTH UCSC gene codes and > ENCODE In regions shown on the most conserved areas of both Mammals and > Vertebrates > 2) Found in each of the SNP� of CEU/YRI/CHB/JPT HapMap: > > The following SNPs are examples: > > For the following SNP's, there are no horizontal lines in the UCSC gene > level displayed in your browser: > (1) rs10399749 > http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr1:44912-45412&hgsid=122530649&snp129=pack&hgFind.matches=rs10399749, > > For the following SNP's, there are horizontal lines in the UCSC gene > level displayed in your browser > > (2) rs17019583 > http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:82229473-82229973&hgsid=122530649&snp129=pack&hgFind.matches=rs17019583, > > My questions are: > > 1. Does the lack of any clickable lines in (1) suggest that they are no > data collected in this region? > > 2. Does the appearance of the clickable lines in (2) suggest that even > though there are no know UCSC genes in this region but there are clones > that have been transcribed with no known gene functions? > > For the following SNP, there are large blocks in the spliced EST's > display: > (3) rs13328714 > http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr1:81218-81718&hgsid=122525214&snp129=pack&hgFind.matches=rs13328714, > > 3. Does this mean that even there is no known UCSC gene in this region > but it has known spliced EST's? > > Thanks again for your prompt response. > > Pattle.P.T.Pun, Ph.D. > Professor of Biology, > Wheaton College, > Wheaton, IL 60187 > phone: 630-752-5303 > fax: 630-752-5996 > email: [email protected] > http://www.wheaton.edu/Biology/faculty/ppp/index.html > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
