Transcription of long hypothetical orfs in Trypanosoma cruzi: The epimastigote stage uses trans-splicing sites that generate short 5′ UTRs

► 5′ UTR in long hypothetical ORF from T. cruzi epimastigote has short length. ► 5′ UTR in long genes is mostly determined by the distance to neighbor gene. ► The maximum length of 5′ UTR in long genes is approximately 3% of the ORF. ► T. cruzi may use differentially the trans-splicing signal and mini-exon addition site.