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Figure 1 | Virology Journal

Figure 1

From: Identification of an effective siRNA target site and functional regulatory elements, within the hepatitis B virus posttranscriptional regulatory element

Figure 1

Prediction of conserved functional elements within the HBV PRE. (A) A schematic diagram of HBV PRE with annotation of previously reported elements: human La-binding site (nucleotides 1275-1291) [30, 31], a splicing regulatory element-1 (SRE-1) (nucleotides 1252-1348), the conserved stem loop, HBV SLα (nucleotides 1292-1321) [32], the conserved stem loop HBV SLβ (nucleotides 1411-1433) [32], a subsection named PREIII (nucleotide 1485-1584) that was reported to bind to two cellular proteins in vitro, PTB and GAPDH [33, 35]. The siRNA target sites investigated in this study were also indicated (siRNA anti HBV PRE 1317-1337 and siRNA anti HBV PRE 1329-1349). (B) Detection of putative functional elements within the PRE by CDS-plotcon. PRE sequences from selected human HBV genotypes A-H were input into the CDS-plotcon programme. A high peak indicates conserved elements beyond that expected by coding. Four putative functional elements within HBV PRE were detected, at 1151-1310, 1390-1450, 1515-1610 and 1540-1684. The diagram was produced by CDS-plotcon online (C) Detection of conserved secondary RNA structures within the PRE. The same set of human HBV sequences was input into Alidot. The mountain plots indicate regions that contain conserved RNA secondary structures at 1151-1410, 1410-1433, 1440-1500 and 1530-1620. The dashed boxes indicate functional conserved elements that contain RNA secondary structures. The diagrams are to the same scale.

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