The gene examples are not a valid GFF3 files
ctg123 example mRNA 1050 9000 . + . ID=EDEN.1;Parent=EDEN;Name=EDEN.1;Index=1
ctg123 example five_prime_UTR 1050 1200 . + . Parent=EDEN.1
ctg123 example CDS 1201 1500 . + 0 Parent=EDEN.1
...
ctg123 example three_prime_UTR 7609 9000 . + . Parent=EDEN.1
“Index” is not a application defined attribute, the GFF3 specification states:
“All attributes that begin with an uppercase letter are reserved for later use. Attributes that begin with a lowercase letter can be used freely by applications.”
As far a I can tell, the type values are case-sensitive, and UTR should have the types
five_prime_utr SO:0000204
three_prime_utr SO:0000205