Hello, Suzanne,
I'm taking a look at the genes you mention, on the hg18 assembly. The two BLAT hits you are concerned about are on either side of a "gap" in the genome. Other things to look at are the repeat tracks, and segmental duplication tracks. I've turned these on for you and saved the view as a session: http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Kayla&hgS_otherUserSessionName=hg18%2Dkayla%2Dfor_Suzanne I hope these resources help to elucidate the data you are concerned about. Please don't hesitate to contact us again if you require further assistance. Kayla Smith UCSC Genome Bioinformatics Group Hart, Suzanne (NIH/NHGRI) [E] wrote: > I am concerned that there has been a duplication of chromosome 4 > material in the current annotation (as well as in the last annotation). > Our lab works on genes involved in tooth development, such as ENAM and > AMBN. In aligning ENAM sequences to the current UCSC annotation, I got > a perfect match to ENAM, but also a perfect match to a region between > AMBN and ENAM. I hadn't noticed this before. I BLATed chunks of the > ENAM genomic sequence (1900, 2500, even over 7000 bp) and got an EXACT > match to the region in between AMBN and ENAM. This seems peculiar to > me. Could you please check this for me? Thanks. > > > > Suzanne Hart > > NHGRI > > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
