RNA motifs consist of a pattern of features within the primary sequence and secondary structure of related RNAs.
RNA motifs can be described in two main forms: a multiple sequence alignment or an explicit search pattern.
[1] The Rfam database is a collection of multiple sequence alignments that define a large subset of reliably known RNA motifs and associated information.
[3] Many methods to discover novel RNAs use a comparative approach, in which different sequences are analyzed together in order to detect characteristic signals of a conserved RNA.
An early example is the RNA motif based around the T-box, which in 1993 was determined to be associated with aminoacyl-tRNA synthetase genes.