SECIS element

{{short description|RNA sequence directing the translation of UGA codons as selenocysteines}}

{{Infobox rfam

| Name = Selenocysteine insertion sequence 1

| image = RF00031.jpg

| width =

| caption = Predicted secondary structure and sequence conservation of SECIS_1. Letters correspond to the IUPAC notation system for nucleotides.

| Symbol = SECIS_1

| AltSymbols = SECIS

| Rfam = RF00031

| miRBase =

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| RNA_type = Cis-reg

| Tax_domain = Eukaryota

| GO = {{GO|0001514}}

| SO = {{SO|1001274}}

| CAS_number =

| EntrezGene =

| HGNCid =

| OMIM =

| PDB =

| RefSeq =

| Chromosome =

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| LocusSupplementaryData =

}}

In biology, the SECIS element (SECIS: selenocysteine insertion sequence) is an RNA element around 60 nucleotides in length that adopts a stem-loop structure.{{cite journal | vauthors = Walczak R, Westhof E, Carbon P, Krol A | title = A novel RNA structural motif in the selenocysteine insertion element of eukaryotic selenoprotein mRNAs | journal = RNA | volume = 2 | issue = 4 | pages = 367–379 | date = April 1996 | pmid = 8634917 | pmc = 1369379 }} This structural motif (pattern of nucleotides) directs the cell to translate UGA codons as selenocysteines (UGA is normally a stop codon). SECIS elements are thus a fundamental aspect of messenger RNAs encoding selenoproteins, proteins that include one or more selenocysteine residues.

In bacteria the SECIS element appears soon after the UGA codon it 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.{{cite journal | vauthors = Wilting R, Schorling S, Persson BC, Böck A | title = Selenoprotein synthesis in archaea: identification of an mRNA element of Methanococcus jannaschii probably directing selenocysteine insertion | journal = Journal of Molecular Biology | volume = 266 | issue = 4 | pages = 637–641 | date = March 1997 | pmid = 9102456 | doi = 10.1006/jmbi.1996.0812 }}{{cite journal | vauthors = Rother M, Resch A, Wilting R, Böck A | title = Selenoprotein synthesis in archaea | journal = BioFactors | volume = 14 | issue = 1–4 | pages = 75–83 | date = 2001 | pmid = 11568443 | doi = 10.1002/biof.5520140111 }}

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 for correct SECIS element function. Although the eukaryotic, archaeal and bacterial SECIS elements each share a general hairpin structure, they are not alignable, e.g. an alignment-based scheme to recognize eukaryotic SECIS elements will not be able to recognize archaeal SECIS elements. However, in Lokiarcheota, SECIS elements are more similar to eukaryotic elements.{{cite journal|last1=Mariotti|first1=Marco|last2=Lobanov|first2=Alexei V.|last3=Manta|first3=Bruno|last4=Santesmasses|first4=Didac|last5=Bofill|first5=Andreu|last6=Guigó|first6=Roderic|last7=Gabaldón|first7=Toni|last8=Gladyshev|first8=Vadim N.|title=LokiarchaeotaMarks the Transition between the Archaeal and Eukaryotic Selenocysteine Encoding Systems|journal=Molecular Biology and Evolution|volume=33|issue=9|year=2016|pages=2441–2453|issn=0737-4038|doi=10.1093/molbev/msw122|pmid=27413050|pmc=4989117|doi-access=free}}

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.{{cite journal | vauthors = Lambert A, Lescure A, Gautheret D | title = A survey of metazoan selenocysteine insertion sequences | journal = Biochimie | volume = 84 | issue = 9 | pages = 953–959 | date = September 2002 | pmid = 12458087 | doi = 10.1016/S0300-9084(02)01441-4 }}