Hello Rachael,
To see what is happening, try opening up 2 tabs in your browser: one on hg18 and the other on hg19. If you hide all tracks but Gap in hg18 and look at chr19 as a whole, you see a centromere gap (3Mbp) flanked by two large heterochromatin gaps of 2.5Mbp each. In hg19, the centromere gap is the same size, but the two adjacent heterochromatin gaps are now only 50kbp each, making for a 5Mbp (-100kb) difference in hg19 coords on the q arm. I hope this helps to explain what you are seeing. Please write back if you have further questions. Kayla Smith UCSC Bioinformatics Group ----- "Rachael Natrajan" <[email protected]> wrote: > Dear UCSC, > > I was wondering in the new assembly for Feb 2009 why some regions have > > altered significantly in terms of their genomic DNA mapping positions > > from March 2006? For instance looking at the CCNE1 gene on chromosome > > 19q, it originally mapped to 35Mb, and now in the Feb 09 build it maps > > to 30Mb. When I look up the mapping information from Ensembl for > instance it still maps to 35Mb. > > many thanks, > > Rachael Natrajan > > The Institute of Cancer Research: Royal Cancer Hospital, a charitable > Company Limited by Guarantee, Registered in England under Company No. > 534147 with its Registered Office at 123 Old Brompton Road, London SW7 > 3RP. > > This e-mail message is confidential and for use by the addressee only. > If the message is received by anyone other than the addressee, please > return the message to the sender by replying to it and then delete the > message from your computer and network. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
