[Genome] "_dupX" names for transcript ID duplicates on same chromosomes

[Robert Kuhn]

hello, micha,

I'm not sure I understand where you are seeing the "_dup" part of
transcript_ids.  The chr1_mrna table does have two entries for the
accession you mention.  

One of these is definitely a better alignment than the other.  Type 
AK130020 into the position box of the browser and then click on one of 
them.  Then expand your position window to chr1:16513000-17200000.  
Both transcripts should be highlighted in the Human Mrna track.  I 
know that does not address your bulk processing issues, but I thought 
I'd mention it.

Please let me know where exactly you are seeing the "_dupX"
notation and I will try to track it down.  By the way, it is
not uncommon for mrnas to align in more than one location.  the
existence of segmental duplications virtually guarantees it.

best wishes,

			--b0b kuhn

> From genome-bounces at soe.ucsc.edu  Mon Jun 11 15:48:27 2007
> Cc: genome at soe.ucsc.edu, Micha Sammeth <micha at sammeth.net>
> Subject: [Genome] "_dupX" names for transcript ID duplicates on same
> 	chromosomes
> 
> Hello again,
> 
> thank you, Robert for the explanation on the ESTs, I got it clear now.
> 
> I have another little problem, hopefully the last one for this project: 
> when I download the (hg17) mRNA track, I get conveniently unique 
> transcript_id tags - at least on a chromosome level, which is enough 
> (e.g., "AK130020" and "AK130020_dup1" on chr1). From which field does 
> the table browser retrieve them? It does not seem to be all_mrna.qName, 
> nor did I find a field in gbCdnaInfo or other soundy tables that are up 
> to 1-2 joins away from all_mrna. I would need these "_dupX" identifiers 
> to map back the CDS info I get from hg17.cds to genomic coordinates.
> 
> Best thanks, micha.
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