Fig. 3: Classification of 3’ termini according to gene and transcript annotations.

In all panels, blue rectangles represent the protein coding sequence (CDS) of a gene, pink rectangles represent non-coding RNA (ncRNA) genes, and black arrows represent the transcription orientation. Genes that reside in the same transcription unit are surrounded by yellow shading. 3’ termini are divided into three groups and subgroups: (1) Primary – 3’ termini located downstream the stop codon of protein coding genes or at the end of ncRNA genes. This group includes: (i) Primary 3’ termini, positioned up to 100 nucleotides downstream the stop codon of a protein coding gene or at the end of a ncRNA gene. (ii) Distant Primary (DP) termini, positioned up to 200 nucleotides downstream the stop codon of a protein coding gene, when there is no 3’ terminus in the first 100 nucleotides. (iii) Alternative Primary (AP) termini, same as distant primary termini but there is a 3’ terminus in the first 100 nucleotides. (iv) Alternative Primary termini in Transcription Unit (AP in TU), assigned to genes that are not last in their operon (either CDS or ncRNA gene). In this case the region downstream is extended up to 250 nucleotides. (2) Premature – 3’ termini located within the 5’ UTR of genes or in their CDS or in a ncRNA gene. (3) Orphan – 3’ termini located antisense to genes (AS) or in intergenic regions distant from genes (IGR).