In biology, the SECIS element (SECIS: selenocysteine insertion sequence) is a structural motif (pattern of nucleotides) that directs the cell to translate UGA codons as selenocysteines. (UGA is normally a stop codon.) SECIS elements are thus a fundamental aspect of selenoproteins, which are proteins that include a selenocysteine residue.

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. One archaeal SECIS element, in Methanococcus is located in the 5' UTR.

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 eukaryotic SECIS element includes non-canonical A-G base pairs, which are uncommon in nature, but are critically important to correct SECIS element function. Although the eukaryotic, archaeal and eubacterial SECIS elements each share a general hairpin structure, they are not alignable, e.g. a scheme to recognize eukaryotic SECIS elements will not be able to recognize archaeal SECIS elements.

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. These programs have been used in searches for novel selenoproteins.