Hello Researchers

Teacher gave work to do transcritpome annotation with only transcriptome annotation GTF file which was obtained after cufflinks of 2 expression data control and test, the GTF file only contains exon.

How to find all annotation from these after cufflinks GTF file

promoter/cds?

Work I tried already : from reference genome GTF file I separated all annotated regions and extracted sequences than did blastn with transcriptome sequences and took top most hit, but teacher told focus on only transcriptome sequences for annotation, I am confused, please help me.

Thank you