I assembled a number of transcripts from a non-model organism and used TransDecoder to predict ones with complete ORFs. I see that a number of the transcripts containing complete ORFs don't have a hit in protein or RNA BLAST databases, but are identical to entries in the BLAST EST database from the same species. What are these transcripts? Are they protein-coding genes that don't have homology with known genes, or are they pseudogenes? Or both?
Thank you very much!