I'm trying to know the coding potential of my RNA-seq transcripts by phylogeny analysis. So I want to generate a FASTA file that includes ORF of my sequence and 29 other mammalian species. I used"Extract MAF blocks" and "Stitch MAF blocks" using my RNA-seq data(gtf file from cuffcompare) as intervals. But the final FASTA file doesn't include my sequence. How can I add my sequence to the final FASTA so that it includes both the 29 mammalian genome and my sequence?

Thanks in advance.

Lyni.