Uup RNA motif
RNA family
The uup RNA motif is a conserved RNA structure that was discovered by bioinformatics.
uup motif RNAs are found in Bacillota and Gammaproteobacteria.
uup motif RNAs likely function as cis-regulatory elements, in view of their positions upstream of protein-coding genes. uup RNAs are consistently found upstream of genes encoding an ATPase. The precise role of these ATPases is not known, but they are usually predicted to either function as part of an ATP-binding cassette transporter or as fungal elongation factor 3. In some cases, the ATPase genes downstream of uup RNAs seem to be transcribed as part of a larger operon. In a handful of these cases, one of the operon's genes encodes the DUF2992 conserved protein domain. This gene is, in turn, regulated by the yjdF RNA motif, which might function to sense azaaromatic compounds.
uup RNAs are usually located 100 nucleotides upstream of predicted Rho-independent transcription terminators. Since these transcription terminators are located somewhat far away, it is not clear that they are functionally related.
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