Primary/first/upstream ORF

We defined three different types of putative open reading frames (ORFs) on a lncRNA (Fig. 1). A primary ORF (pORF) is the longest ORF starting with ATG. A first ORF (fORF) starts with ATG and is closest to the 5 ^′ end of the lncRNA. An upstream ORF (uORF) starts with a near-cognate initiation site (i.e. CTG, GTG, or TTG [9]). Here, the uORF is considered only when an existing pORF located in the lncRNA; the beginning and end of uORF should be upstream of the pORF. These three types of ORFs above are all terminated with a TAG, TGA, or TAA. In addition, the upstream ORF overlapping with the primary ORF was not analyzed in this study.

Example of feature extraction. a Representation of primary ORF (pORF, gray), first ORF (fORF, blue), and upstream ORF (uORF, red) in a lncRNA. Horizontal line indicates a mature lncRNA, boxes represent putative open reading frames (ORFs) defined on this lncRNA. b Relationship (distance) between m⁶A/G4 and transcript initiation site (TIS), transcript termination site (TTS), and starts or ends of u/f/pORF were used as features. Direct distance (bases in log scale) and relative distance (percentage of the length of lncRNA) were considered to express the relationship