In eubacteria the SECIS element appears soon after the UGA codon affects. In archaea and eukaryotes, it occurs in the 3' UTR of an mRNA, and can cause multiple UGA codons within the mRNA to code for selenocysteine.
The SECIS element appears defined by sequence characteristics, i.e. particular nucleotides tend to be at particular positions in it, and a characteristic secondary structure. The secondary structure is the result of base-pairing of complementary RNA nucleotides, and causes a hairpin-like structure. The SECIS element includes A-G base pairs, which are uncommon in nature, but are critically important to correct SECIS element function.
In bioinformatics, several computer programs have been created that search for SECIS elements within a genome sequence, based on the sequence and secondary structure characteristics of SECIS elements.