Yes, this is a known content issue with GTF datasets extracted from the UCSC Table Browser.
Update: It looks like they are now generating GTFs in the downloads area automatically. Capture the link and paste it into the Upload tool. danRer11 has few choices, and one of them is a match for what you used already: danRer11.ncbiRefSeq.gtf.gz
https://hgdownload.soe.ucsc.edu/goldenPath/danRer11/bigZips/genes/
How to find these:
- UCSC Genome Browser Downloads
- navigate to the genome build
- click into
Genome sequence files and select annotations (2bit, GTF, GC-content, etc), then into the folder namedgenes
This is a better way to get the GTF for all use cases. UCSC does not recommend extracting GTF data from the Table Browser for a few reasons: the gene_id = transcript_id attribute content AND the limit of about 100k lines of output (can result in a truncated output).
For you, if the original GTF was not truncated, it is probably OK to just swap the annotation at this point. But do double check – inspect/compare a few lines plus count up the total number of lines – all should match. If it doesn’t, you might need to reprocess the upstream steps using the corrected annotation.