Reporter genes are nucleic acid sequences encoding easily assayed proteins, and cistrons are segments of DNA involved in producing a polypeptide chain; these include regions preceding and following the coding DNA as well as introns between the exons. When an IRES segment is located between two reporter genes in eukaryotic mRNA molecules (bi-cistronic mRNA), the site enables translation of the downstream protein coding region independently of the 5'-cap structure. This enables the cell to produce both the 5'-cap and downstream IRES proteins. The first reporter protein (first cistron) is synthesized by the cap-dependent initiation method. Translation initiation of the second protein is directed by the IRES segment located in the intercistronic spacer region (between the two reporter protein coding regions).
Internal ribosomal entry sites are distinguished from the ribosomal shunt initiation pathway, which is an alternate viral mechanism of translation initiation in which ribosomes bind to the mRNA in a normal cap-dependent mode, then jump upstream (5'–––→3') of the initiator AUG codon.
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