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. Author manuscript; available in PMC: 2024 Jan 1.
Published in final edited form as: Nat Cell Biol. 2023 Jan;25(1):1–5. doi: 10.1038/s41556-022-01066-9

Figure 1. Suggested naming scheme to clarify the complexity of circular RNA expression patterns.

Figure 1.

a. (Top) Pre-RNAs can be spliced to generate mature linear RNAs that are capped and polyadenylated as well as intron lariats that are debranched and degraded (denoted by dashed lines). However, some lariats fail to be debranched leading to the accumulation of stable ciRNAs. (Bottom) In addition to generating linear RNAs, a gene can generate circRNAs when a 5’ splice site (ss) is joined to an upstream 3’ ss via a process known as back-splicing. Of note, the efficiency of back-splicing (thin arrow) is often low compared with that of canonical splicing (heavy arrow) at the same gene locus.

b. Naming of human circRNAs produced from the gene FAM120A (ENST00000277165.11) that have different BSJ sites.

c. Naming of circRNAs produced from the gene COX5A (ENST00000322347.11) that have different BSJ sites.

d. Naming of two alternative circRNAs produced from the gene TIMMDC1 (ENST00000494664.6) that differ in their inclusion of a cassette exon.

e. Naming of circRNAs produced from the gene CAMSAP1 (ENST00000389532.9) that differ in their inclusion of a retained intron.

f. Naming of circRNAs produced from the gene MCU (ENST00000603649.5) that differ in their use of an alternative 3’ ss. A longer exon 3 (L3) with additional sequence at the 5’-end of the annotated exon 3 can be alternatively spliced within the circRNA produced from the MCU gene locus.

g. Naming of circRNAs produced from the gene SNX25 (ENST00000618785.4) that differ in their use of an alternative 5’ ss.

h. Naming of circRNAs produced from the gene ZNF292 (ENST00000369578.6) that differ in their BSJ and presence of a novel exon.

i. Naming of circRNAs produced from the gene XPO1 (ENST00000401558.7) that differ in their inclusion of a novel cassette exon.

j. Naming of fusion circRNAs produced from the KMT2A::MLLT3 (also known as MLL::AF9) translocation in leukemic cell lines.

Gene assembly: bars, exons; black lines, introns. Canonical splice junctions (SJs, polylines) and back-splice junctions (BSJs, arc lines) are shown in sequencing data. Short-read (purple) and long-read (orange) examples are shown.