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Old 12-30-2010, 03:36 PM   #1
doublehelix82
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Default UCSC introns

Hello, I have a newbie question: How does UCSC genome browser determine where the introns are in the genomes? I read how they build the gene annotations @ http://genome.ucsc.edu/cgi-bin/hgTra...r1&g=knownGene, but could not understand how they determine where the introns are. I am just wondering if the introns come with the gene predictions from other databases, i.e., refseq, genbank, ... or if the introns are downloaded from a whole another database? Thanks!

DH.
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Old 01-04-2011, 09:02 AM   #2
ntremblay
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The UCSC Genes track shows gene predictions based on data from RefSeq, Genbank, CCDS and UniProt. Following all the steps mention in the link you provided, they annotate all the exons to the reference genome. The introns are only the remaining, un-annotated, reference genomic sequence. Thus, they are not downloaded from another database, but only sequence that shows no significant evidence for a exonic function. ...
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