In molecular biology ctRNA (counter-transcribed RNA) is a plasmid encoded noncoding RNA that binds to the mRNA of repB and causes translational inhibition.

[1] ctRNA is encoded by plasmids and functions in rolling circle replication to maintain a low copy number.

In Corynebacterium glutamicum, it achieves this by antisense pairing with the mRNA of RepB, a replication initiation protein.

[1] In Enterococcus faecium the plasmid pJB01 contains three open reading frames, copA, repB, and repC.

The pJB01 ctRNA is coded on the opposite strand from the {{chem name|copA}/repB intergenic region and partially overlaps an atypical ribosome binding site for repB.