Hi Ann, We suggest that you search for the DMIT loci such as D10MIT15, in the genome browser by entering it in the position/search box for the mm9 assembly, and look at the display to see where the DMIT locus is in comparison to any genes present in the UCSC Genes Track.
Here a couple links to sessions to get you started: D10MIT15: http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Vanessa&hgS_otherUserSessionName=mm9_D10MIT15_041411 D10MIT109: http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Vanessa&hgS_otherUserSessionName=mm9_D10MIT109_041411 To compare other DMIT loci to the UCSC Genes Track: 1. Click on this session link: http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Vanessa&hgS_otherUserSessionName=mm9_D10MIT15_041411 2. Enter the DMIT locus you want to compare in the "position/search" input box which is located near the top of the screen. 3. Click on "jump" to take you to that particular DMIT locus location. Hope this helps you. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Ann Eileen Miller Baker" <[email protected]> To: [email protected] Sent: Wednesday, April 13, 2011 9:33:16 PM Subject: [Genome] how can a DMIT locus (<350bp) overlap exonplus, intron, coding exon, whole gene, 3 UTR? My objective was determining which mouse DMIT loci were in various parts of the mouse genome. Examples of output from UCSC genome analyes follow: D10MIT109 exonplus D10MIT109 intron D10MIT109 coding exon D10MIT109 whole gene D10MIT109 3UTR D10MIT15 exonplus D10MIT15 intron D10MIT15 coding exon D10MIT15 whole gene D10MIT15 3UTR IF (each DMIT locus) is <<400bp IF (exonplus + intron + coding exon + whole gene + 3 UTR) is >>>>>400bp I don't know how to interpret these data which seem to imply that the above DMIT loci span such large region. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
