There are ENSEMBL transcripts, for example ENST00000454382, that are findable in searches of https://useast.ensembl.org/Homo_sapiens/Info/Index, but that are not present in the provided files Homo_sapiens.GRCh37.87.gff3 or Homo_sapiens.GRCh38.95.gff3 from their ftp site
ftp://ftp.ensembl.org/pub/release-95/gff3/homo_sapiens
Shouldn't the transcript be present in the big gff3 file if it is findable on the web page? Does anyone know what's up with this?
Thank you!
Yes indeed, a gene model for the transcript in question, ENST00000454382, is in the gff3 "patch" file available at the ENSEMBL ftp site: ftp://ftp.ensembl.org/pub/release-95/gff3/homo_sapiens/Homo_sapiens.GRCh38.95.chr_patch_hapl_scaff.gff3.gz.
Thank you Ben!