Hello Erik, There are a few things going on that may contribute to the differences you notice, but overall, we double checked and think that the exon concatenation is being performed correctly. With a gene this large, a perfect alignment is not expected.
In your first query, data from the RefSeq Gene's track is being returned. The mRna sequence is returned. The mRna can differ slightly from the genomic reference sequence for many tracks. In the second query, data from the UCSC Gene's track is being returned. The genomic reference sequence is being returned - the portions covered by the mRna alignment. The UCSC Gene track includes the RefSeq sequence above (for this case, an earlier version, explained next), with some input from other data sources. In general, we would normally expect both tracks to have very similar data, however a closer inspection shows that the UCSC Gene uses an older version of the RefSeq (.2) and the RefSeq Gene track uses the brand new (Nov 2009) version of the RefSeq (.3). The genbank record describes the assembly process for this transcript and notes that portions of genomic were used - very likely NCBI Build 37 for version .3, where the previous version either did not use genomic or used an earlier NCBI Build (36 or earlier). The Genbank data record does not specific state which version of the human genome was used for either version, but this is a likely assumption based on the release dates of the versions, and one that you could follow up on with a little analysis (or better, by contacting the RefSeq project and asking) if the change is of interest to you. Thank you for so carefully examining the data and explaining the situation. If you notice anything else a bit off and would like us to look into it, please feel welcomed to send question like this along. Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Erik Miller" <[email protected]> wrote: > From: "Erik Miller" <[email protected]> > To: [email protected] > Sent: Monday, December 7, 2009 1:05:02 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] randomly changing shared browser sessions > > Hello, > > I created and shared a custom browser session with my colleagues but > configurations of the session (such as colors, orders, and scales of > custom tracks) often change randomly. No one else but myself has > access to my UCSC GB account. Why is this happening and how can I stop > it? > > > Thank you, > > Erik Miller > Ph.D. Student > Gerald Crabtree Lab > Genetics Department > Stanford University > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
