Are there tools out there to convert a GFF3 file to a format displayable as a gene model / transcript in UCSC? eg take a GFF3 containing transcripts for genes and load them somehow into UCSC as a track so they appear like transcripts from UCSC knowngenes or Ensembl track. thanks.
You might be able to upload them directly to UCSC as a custom track, since GTF/GFF are supported formats. I suggest you visit the Table Browser at UCSC and take a look at the knownGene data as GTF format. You can select GTF as the output format instead of sequence. If your file does not look like this, then maybe you can fix it some that it does.