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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