Back-splicing

Back-splicing is an RNA splicing arrangement in which a downstream splice donor site joins an upstream splice acceptor site. In a common circularization event, the retained segment becomes circular RNA with a new junction joining a later part of the precursor to an earlier part. The donor is conventionally called a $5^{\prime }$ splice site and the acceptor a $3^{\prime }$ splice site; those labels describe splice-boundary roles, not the order of their coordinates along the precursor.

For a precursor with ordered exons $1\to 2\to 3\to 4$, a circle containing exons 2 and 3 has the ordinary internal junction $2\to 3$ and a circularizing junction $3\to 2$. A sequence read spanning $3\mid 2$ thus reports a different adjacency from the reference transcript order. The example specifies a possible connectivity, not a prediction that every such precursor forms this circle.

A 2013 study combined RNA sequencing with and without RNase R treatment. Reads crossing back-splice junctions were enriched among the more resistant RNA population, and complementary tests supported circular products.^[ref] A non-colinear junction read alone can also raise questions about mapping, another RNA arrangement or genomic structure. Agreement between junction evidence and a test of molecular connectivity makes the circular interpretation stronger; it does not by itself establish the circle's biological function.