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. 2006 Oct 1;15(5):657–686. doi: 10.1111/j.1365-2583.2006.00689.x

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© 2006 The Authors Journal compilation © 2006 The Royal Entomological Society

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Characteristics of the honey bee R2 element ORF, 3′-UTR and potential imprecise insertion site. Bold amino acid residues are conserved across 80% or more arthropod R2 elements (Burke et al., 1999). Boxed aligned regions depict highly conserved sequence across parasitic Hymenoptera. Single-boxed residues depict codons with IUPAC ambiguity codes with the alternative nucleotide causing a stop codon. (A) Non-conserved 5′ sequence of the ORF with the putative initiation codon Met. (B) Comparison of jewel wasp B sequence (Nasonia sp., Pteromalidae) (GenBank accession no. AF090145) to honey bee in the conserved amino-terminal domains. Shaded regions depict conserved motifs of DNA-binding proteins, with dashed boxes showing the three residues believed to interact with the α-helical region of DNA. CCHH, Cys-His motifs; c-myb, proto-oncogene protein. (C) Non-conserved sequence flanked by the conserved amino-terminal motifs and the 5′-end of the RT domain. Note: the jewel wasp B sequence contains 255 amino acid residues compared to the 178 of the honey bee. The shaded glycine residue was recovered in only one unassembled read. (D) Comparison of jewel wasp sp. B and honey bee in the highly conserved reverse transcriptase (RT) domain, including the fingers/palm and thumb motifs. The 11 shaded regions depict motifs conserved in the RTs of all retroelements (Xiong & Eickbush, 1990; Burke et al., 1999). (E) Comparison of jewel wasp B and honey bee in the conserved carboxyl-terminal domains. The DNA-binding motif CCHC and the KPDI sequence (ENDO) are shaded and within dashed boxes, representing the endonculease domain. Other shaded motifs depict conserved residues in arthropods (Burke et al., 1999). (F) Predicted 3′-UTR. The shaded sequence is the 3′-junction with the 28S rDNA (see Fig. 5), with the space depicting the potential imprecise insertion site of R2 element type 3. (G) Consensus sequence of R2 element type 3, which seemingly inserts 12 nucleotides downstream from the typical R2 insertion site. No ORF has been predicted for this element (see text).

Characteristics of the honey bee R2 element ORF, 3′-UTR and potential imprecise insertion site. Bold amino acid residues are conserved across 80% or more arthropod R2 elements (Burke et al., 1999). Boxed aligned regions depict highly conserved sequence across parasitic Hymenoptera. Single-boxed residues depict codons with IUPAC ambiguity codes with the alternative nucleotide causing a stop codon. (A) Non-conserved 5′ sequence of the ORF with the putative initiation codon Met. (B) Comparison of jewel wasp B sequence (Nasonia sp., Pteromalidae) (GenBank accession no. AF090145) to honey bee in the conserved amino-terminal domains. Shaded regions depict conserved motifs of DNA-binding proteins, with dashed boxes showing the three residues believed to interact with the α-helical region of DNA. CCHH, Cys-His motifs; c-myb, proto-oncogene protein. (C) Non-conserved sequence flanked by the conserved amino-terminal motifs and the 5′-end of the RT domain. Note: the jewel wasp B sequence contains 255 amino acid residues compared to the 178 of the honey bee. The shaded glycine residue was recovered in only one unassembled read. (D) Comparison of jewel wasp sp. B and honey bee in the highly conserved reverse transcriptase (RT) domain, including the fingers/palm and thumb motifs. The 11 shaded regions depict motifs conserved in the RTs of all retroelements (Xiong & Eickbush, 1990; Burke et al., 1999). (E) Comparison of jewel wasp B and honey bee in the conserved carboxyl-terminal domains. The DNA-binding motif CCHC and the KPDI sequence (ENDO) are shaded and within dashed boxes, representing the endonculease domain. Other shaded motifs depict conserved residues in arthropods (Burke et al., 1999). (F) Predicted 3′-UTR. The shaded sequence is the 3′-junction with the 28S rDNA (see Fig. 5), with the space depicting the potential imprecise insertion site of R2 element type 3. (G) Consensus sequence of R2 element type 3, which seemingly inserts 12 nucleotides downstream from the typical R2 insertion site. No ORF has been predicted for this element (see text).