exonexon

Exonexon is a term encountered in some informal discussions and writings to describe the concept of exon-to-exon connections within mature messenger RNA transcripts. It is not a formally defined term in major genomics references, and its meaning can vary depending on context. In many uses, exonexon refers to the junction where two exons are joined after intron removal during splicing, or to the set of exon-exon junctions that define transcript isoforms.

In RNA sequencing analysis, reads that span exon-exon boundaries indicate exon-exon junctions. Some analysts may colloquially refer to such junctions as exonexon junctions or label junctions in tool outputs with the term exonexon. Because the term is informal, its interpretation can be ambiguous; it should be accompanied by a precise definition when used in reporting or publication to avoid confusion with related concepts such as exon-exon junctions, splice junctions, or exon skipping events.

Exonexon is thus best treated as a colloquial shorthand rather than a standardized biological concept. When precise language is required, it is preferable to refer explicitly to exon-exon junctions, splice junctions, or specific transcript isoforms and to describe the analyses or observations directly in terms of exons and their junctions.

See also: Exon, Intron, Splicing, Exon-exon junction, RNA sequencing, Transcript isoform.