Hello, Some of your question are a matter of data interpretation that you will need to make yourself, but I can provide some guidance regarding the annotation conventions within the assembly browser window. That said, in my opinion, for each of your three examples, there are no strongly characterized genes. But each have slightly different evidence.
(1) rs10399749 This SNP does not appear to have any known overlapping Gene/mRNA/EST data. It does have some homology to a LINE element (Long interspersed nuclear elements, Repeat Masker track) and it is in a region of genomic duplication (Segmental Dups track). (2) rs17019583 This SNP has overlap with many tracks, but appears to fall within an intron region. To interpret the UCSC Gene, Human Gene BC031255, click on the gene name to determine if you think the gene is high or low quality based on the annotation provided (this one is listed as having 9 non-coding exons). It has only human representation (no orthologs or other mRNA or other EST data). (3) rs13328714 This SNP also has overlap with several tracks, and it appears to be in an intron region for some and exon for others. The UCSC Gene, Human Gene AK125248, shares many characteristics with the #2 region above. The only putative exonic overlap seems to be pointing to the same two spliced human ESTs propagated into a few different datasets (Spliced EST, UniGene, etc.). It does have more homology with other species than the two above. These links may be helpful to you: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#FineTuning http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#GeneDisplay Also, to determine if a region is uncharacterized, it is important to not only look at UCSC Genes, but RefSeq and all of the other EST/mRNA data tracks, plus the repeat, variation, and cross-species tracks. That way when you can evaluate the quality of the evidence as a whole. Read the help sections above - I think they will aid you in understanding at least what the data you are viewing represents (display conventions for coding vs non-coding, spliced vs unspliced, from a single source or multiple-independent sources, etc.). Good luck with your research, Jennifer Jackson UCSC Genome Bioinformatics Group 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 > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
