Hello, I've come across your UCSC Genome Bioinformatics Gene Table and I'm in the process of figuring out how to use it, and I was wondering if you can give me a hand.
I'm looking to see whether there are Eboxes (any) in some of my genes of interest 2000 bp upstream of the coding sequence in mice. I have found the Eboxes in the upstream region by using the sequences from UCSC Genome Bioinformatics. Recently, I've been recommended to use the PEDB Database to see if any of the Eboxes in the mouse sequence are conserved in human. When I looked through the UCSC Genome Bioinformatics, from where I got the 2000 upstream bp I noticed that, Bnip3, for examples was on the Chromosome 7 in the range 146082519-146102189. When I began looking for a conserved region between human and mice in PEDB, the gene position of Bnip3 is listed Chr 7 / 126528650 - 126547320. Could you please help me determine why the region on the chromosome is different? PEDB Database (http://promoter.cdb.riken.jp/) Promoter sequence of Bnip3 (TSS1) Species Mouse Gene position Chr 7 / 126528650 - 126547320 / reverse RefSeq Genes Genomic Sequence http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=246457341&hgSeq.promoter=on&boolshad.hgSeq.promoter=0&hgSeq.promoterSize=1000&hgSeq.utrExon5=on&boolshad.hgSeq.utrExon5=0&hgSeq.cdsExon=on&boolshad.hgSeq.cdsExon=0&hgSeq.utrExon3=on&boolshad.hgSeq.utrExon3=0&hgSeq.intron=on&boolshad.hgSeq.intron=0&boolshad.hgSeq.downstream=0&hgSeq.downstreamSize=1000&hgSeq.granularity=gene&hgSeq.padding5=0&hgSeq.padding3=0&boolshad.hgSeq.splitCDSUTR=0&hgSeq.casing=cds&boolshad.hgSeq.maskRepeats=0&hgSeq.repMasking=lower&hgta_doGenomicDna=get+sequence Bnip3 refGene_NM_009760 range=chr7:146082519-146102189 Thank you very much for your help in advance, Elena Elena Tsimakouridze, HBSc PhD Candidate Cardiovascular Research Group Biomedical Sciences, OVC University of Guelph Guelph, Ontario, Canada N1G 2W1 519-591-9763 E-mail: [email protected] http://www.uoguelph.ca/CardiovascularResearch/elena.html _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
