[Genome] accession number error

[Robert Kuhn]

Dear Adrienne,

We also use an automated process to generate the Known Genes
track.  The accession you describe mapped in two places.  As
described on the information page about Known Genes (click on 
the little minibutton to the left of the track in the browser
image or on the Known Genes link in the track controls):

"RefSeq alignments having a base identity level within 0.1% of the best 
and at least 96% base identity with the genomic sequence were kept. 
GenBank mRNA alignments having a base identity level within 0.2% of the 
best and at least 97% base identity with the genomic sequence were kept."

Recent pseudogenes may pass that filter and an RNA would map to two
locations.  We do have two tracks that map pseudogenes that you
could use to filter your list: Retroposed Genes and Yale Pseudo.
The first of these does annotate the chr20 alignment as a pseudogene.

We are working on new version of Known Genes, due for release in a
few months, which will have enhanced filtering of pseudogenes.
We are sorry for any difficulty the use of our data may have caused 
you.

best wishes,

			--b0b kuhn
			ucsc genome bioinformatics group


> From genome-bounces at soe.ucsc.edu  Fri Feb 23 10:21:44 2007
> To: genome at soe.ucsc.edu
> Subject: [Genome] accession number error
> 
> Dear UCSC Genome Bioinformatics
> 
> There appears to be an error in the accession number given the human gene
> BAK1 located on chromosome 6, the accession number given is NM_001188.
> This is the same accession number as the BAK1 pseudogene located on
> chromosome 20.
> 
> We use these accession numbers to retrieve sequence for automatic primer
> selection to resequence genes. It was annoying to find we have four plates
> worth of pseudogene sequence.
> 
> Other than that your database is an excellent resource.
> 
> Yours
> 
> Adrienne Hilton
> 
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