Discrepancy Between Splice Junction Annotations and GTEx RNA-Seq Coverage in UCSC Genome Browser

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Hi UCSC Developers,

I’ve noticed a discrepancy between the annotated splice junctions and the GTEx RNA-Seq coverage tracks in the UCSC Genome Browser. For example, on chr15:56,103,540–56,103,563 (hg38), which corresponds to a splicing donor site in the RFX7 gene, the annotated junction appears to be shifted a few bases upstream relative to the RNA-Seq coverage evidence from GTEx. The annotation of the corresponding splicing acceptor of this donor (chr15:56,102,217-56,102,283) also appears to be shifted a few bases upstream relative to the RNA-Seq coverage evidence from GTEx.

Could you please look into whether this offset reflects a known annotation issue?

Thank you for your time and support!

Best regards,

Xiao