xerDC RNAs function as cis-regulatory elements, in view of their positions upstream of protein-coding genes.

The precise functions of the protein product of particular xerDC genes have not been established, but they are predicted to generally fit into a recombinase or integrase role.

Given this genetic arrangement, it is likely that xerDC RNAs function as cis-regulatory elements.

Therefore, it is also possible that the xerDC motif actually operates at the level of single-stranded DNA.

In terms of secondary structure, RNA and DNA are difficult to distinguish when only sequence information is available.