page_title: R2 RNA element
section_title: The 5′ R2 protein binding site
hierarchical_section_title: R2 RNA element / The 5′ R2 protein binding site
caption_attribution_description: English: 5' Psuedoknot of 5 silk moth species
context_page_description: The R2 RNA element is a non-long terminal repeat retrotransposable element that inserts at a specific site in the 28S ribosomal RNA genes of most insect genomes. In order to insert itself into the genome, retrotransposon encoded protein protein makes a specific nick in one of the DNA strands at the insertion site and uses the 3′ hydroxyl group exposed by this nick to prime the reverse transcription process termed target primed reverse transcription, where the RNA genome is transcribed into DNA.
context_section_description: The 5′ R2 protein binding site occurs in a region that spans part of the 5' UTR and the start of the R2 ORF. This region also has a conserved secondary structure, which has been deduced from binding to oligonucleotide microarrays, structure probing, and free energy minimization. To date, conservation of structure has only been described in five moth species: Bombyx mori (R2Bm), Samia cynthia (R2Sc), Coscinocera hercules (R2Ch), Callosamia promethea (R2Cpr), Saturnia pyri (R2Spy)
   
  Within this 5' protein binding site an RNA pseudoknot structure occurs. The pseudoknot is highly conserved between the 5 silk moth species. Sequence comparisons show evidence for compensatory mutations within the helical regions indicating the secondary structure of the RNA is of biological importance. In particular, this pseudoknot is proposed to have implications for initiation of translation.
caption: Structural Comparison of 5' R2 Pseudoknot RNAs
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