Fig. 3: Antigen presentation of CDC73 gene.

a UCSC genome browser (hg19) visualization of hsa_circ_0111569, hosted by CDC73 gene, which is predicted to have rolling circle translation. b Location of the nine peptides derived from gene CDC73 that were detected by MS in T1185B cell line. hsa_circ_0111569 derived peptide [TT]ENIPVVRR (green box) spans the BSJ corresponding to the exon 10 – exon 3 of CDC73 gene. The remaining peptides (blue boxes) were annotated as canonical CDC73-derived peptides. Four of these peptides can be potentially derived from both CDC73 protein and the putative infinite circRNA ORF. In red, representation of the amino acid encoded upstream of the BSJ. In blue, selection of the peptides that underwent PRM validation. c PRM visualization with Skyline of the co-elution and similar MS/MS fragmentation patterns of light (above) and heavy-labelled (below) peptides after PRM. Validation was performed for the circRNA-derived peptide [TT]ENIPVVRR and the canonical (AT)ENIPVVRR and SV(TE)GASAR peptides. Square brackets indicate the BSJ and brackets the linear junction spanning amino acids. d Divergent RT-PCR validation. Agarose gel electrophoresis showed the expected amplicon (size) in CDC73 circRNA. Arrow indicates the amplicon that was selected for direct Sanger sequencing. The image was adjusted to improve legibility. This experiment was performed once. e Sanger sequencing showed the specific sequence upstream and downstream the BSJ for the hsa_circ_0111569. Source data are provided as a Source Data file.