Hello, These three regions are highly similar on mm9 and mm10. Unfortunately, we did not assemble these genomes here, and we do not provide scientific direction on external data. If you have further questions you might contact NCBI (where the genomes were assembled). A good starting point might be the Mouse Genome Assembly Information site at NCBI:
http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/mouse/data/index.shtml Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 5/16/12 9:49 AM, Osama Youssef wrote: > Hi, > > I performed RIP-Seq analysis on Mouse Embryonic Fibroblast cells. I > aligned my reads against the mouse genome (mm9). Three of the highly > upregulated regions in my data each matches a certain chromosome and ChrM. > > ChrI 24,618,377 - 24,623,019 and ChrM 6398 - 11039 are 100% identical > Chr2 22,442,815 - 22,445,697 and ChrM 4798 - 7692 are 98% identical > Chr13 852,661,71 - 852,669,91 and ChrM 12576 - 13395 are 95.4% identical > > Is this right or there is a kind of mistake in the mouse genome assembly. > Can you please let me know what do you think about these particular regions > as my project's direction depends on your answer. > > thanks, > Osama Youssef > Postdoctoral Fellow > Bass' Lab > Biochemistry Department > School of Medicine > University of Utah > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
