Editing SECIS element (section)

{{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 [[International_Union_of_Pure_and_Applied_Chemistry#Amino_acid_and_nucleotide_base_codes|IUPAC notation system]] for nucleotides.
| Symbol = SECIS_1
| AltSymbols = SECIS
| Rfam = RF00031
| miRBase = 
| miRBase_family = 
| RNA_type = [[Cis-regulatory element|Cis-reg]]
| Tax_domain = [[Eukaryota]]
| GO = {{GO|0001514}} 
| SO = {{SO|1001274}} 
| CAS_number = 
| EntrezGene = 
| HGNCid = 
| OMIM = 
| PDB = 
| RefSeq = 
| Chromosome = 
| Arm = 
| Band = 
| LocusSupplementaryData = 
}}

In [[biology]], the '''SECIS element''' (SECIS: '''''se'''leno'''c'''ysteine '''i'''nsertion '''s'''equence'') is an [[cis-regulatory element|RNA element]] around 60 [[nucleotides]] in length that adopts a [[stem-loop]] structure.<ref>{{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 }}</ref> This [[structural motif]] (pattern of nucleotides) directs the [[cell (biology)|cell]] to [[translation (biology)|translate]] UGA [[codon]]s as [[selenocysteine]]s (UGA is normally a [[stop codon]]). SECIS elements are thus a fundamental aspect of [[messenger RNA]]s encoding [[selenoprotein]]s, proteins that include one or more [[selenocysteine]] residues.

In [[bacteria]] the SECIS element appears soon after the UGA codon it affects. In [[archaea]] and [[eukaryote]]s, 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]].<ref>{{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 }}</ref><ref>{{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 }}</ref>

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 [[Wobble base pair|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.<ref name="MariottiLobanov2016">{{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}}</ref>

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.<ref name="pmid=12458087">{{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 }}</ref>