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  • #1

    Difference between isoform info in UCSC

    When I look up a location in the UCSC Genome Browser (chr6:161519351-161519390), I see 2 "isoforms" of the gene MAP3K4. One reports a coding region and the other reports an intron. I had originally used the table browser to grab the knownGenes track in BED format, and bedtools to intersect with my list of regions. This is resulted in conflicting annotation for several regions such as with the MAP3K4 isoforms.

    Is there a truthful way to decide on a single annotation for this region?
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