Fig. 2: Novel predicted-coding genes identified in TRAILS.

A The number of predicted-coding read-through transcripts and transcripts which have no overlap with a gene locus in GENCODE. B Example of a read-through isoform (top) transcribed from the TOMM40 and APOE locus. The arrow indicates the direction of transcription in the genome. The collapsed gene structure registered in GENCODE is shown at the bottom. C Protein 3D structures of TOMM40 (left), APOE (center), and the read-though isoform (right) predicted using AlphaFold2. pLDDT is a per-residue estimate of its confidence on a scale from 0 to 100. Regions with pLDDT > 90, between 70 and 90, between 50 and 70, and <50 are expected to be high accuracy, well (a generally good backbone prediction), low confidence, and a reasonably strong predictor of disorder, respectively. D Conservation score of predicted-coding transcripts registered as lncRNAs in GENCODE (top) and predicted-coding transcripts which have no overlap with a genomic locus in GENCODE (bottom) according to their region. Shading indicates mean ±1.96 standard error. E Example of an isoform from a novel gene locus. Peaks of ATAC-seq derived from relevant non-stimulated immune cell subsets around this locus are shown. The arrow indicates the direction of transcription in the genome. F The expression of the novel isoform in each cell subset is shown. The expression value was normalized by reads per million (RPM).