14 months ago by
The transcript you gave as an example is located on an assembly exception (see 'location' in the link below):
The FTP directory contains a number of GTF files which each contain sets of features depending on their location:
Here is a quick description of the contents of the different GTF files:
This is the default file, it should contain the full annotation for all species except human and mouse. For human and mouse, it will contain all annotation on the primary assembly, ie excluding patch and haplotype regions. All species have one.
Contains only annotation on chromosomes, so toplevel scaffolds are excluded (patch and haplotypes are not included).
Contains all annotation on all toplevel sequences, including patch and haplotype regions.
It should only exist for human and mouse