The traJ-II RNA motif is a conserved RNA structure discovered in bacteria by using bioinformatics.[1]traJ-II RNAs appear to be in the 5' untranslated regions of protein-coding genes called traJ, which functions in the process of bacterial conjugation. A previously identified motif known as TraJ 5' UTR is also found upstream of traJ genes functions as the target of FinP antisense RNAs, so it is possible that traJ-II RNAs play a similar role as targets of an antisense RNA. However, some sequence features within the traJ-II RNA motif suggest that the biological RNA might be transcribed from the reverse-complement strand. Thus is it unclear whether traJ-II function as cis-regulatory elements. traJ-II RNAs are found in a variety of Pseudomonadota.
It was later observed[2] that traJ-II RNAs overlap a previously established oriT (Origin of transfer) plasmid sequence,[3][4] thus suggesting that the traJ RNA motif might function as an oriT.
