Hi Elena, It looks like the data at http://promoter.cdb.riken.jp/Mus_musculus/ was last updated on 03-09-2004, which corresponds to a much older release of the mouse genome assembly: mm5/May 2004 on the Genome Browser. We no longer host that browser on our main site, but it is available on our archive server:
http://genome-mm5.cse.ucsc.edu (Note that we don't necessarily expect everything to work on our archive server; see: http://genome-archive.cse.ucsc.edu/.) The chr7:146082519-146102189 coordinates that you see for Bnip3 are on a newer mouse assembly: July 2007 (NCBI37/mm9). You can use our LiftOver tool to convert coordinates from on assembly to another: http://genome.ucsc.edu/cgi-bin/hgLiftOver There is no direct conversion from mm5 to mm9, but if you choose to convert from mm5 -> mm8, and paste these coordinates into the box: chr7:126528650-126547320 you should get: chr7:138729179-138747849 (on mm8) and then paste those coordinates into the box and do another lift, from mm8 -> mm9, you should get: chr7:146082519-146101189 (on mm9) I hope this explains what you are seeing. If you have further questions, please feel free to contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 3/8/12 7:30 PM, Elena Tsimakouridze wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
