In GFF3 file, there are parent features lines and sub-feature lines like:
I SGD gene 335 649 . + . ID=gene:YAL069W;biotype=protein_coding;
I SGD mRNA 335 649 . + . ID=transcript:YAL069W;Parent=gene:YAL069W;biotype=protein_coding
Usually, parent features lines (such as gene) should appear in front of sub-feature lines (such as mRNA). I'm not sure whether it is a custom or a strict rule. In the GFF3 Specifications document (https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md), there is no such rules.