Sindbis virus capsid protein associates with viral RNA in the cytoplasm of infected cells at discrete interaction sites.

<p><b>A</b>) A schematic drawing of the genomic RNA of SINV. Protein coding and noncoding regions are labeled. For reference the graphs in panels B through D are aligned with this schematic. <b>B</b>) Coverage of anti-Capsid CLIP-seq libraries derived from purified, mature infectious viral particles. Depth of coverage is represented by the y-axis, with the x-axis representing nucleotide position. <b>C</b>) Depth of coverage for anti-Capsid libraries derived from cytoplasmic fractions. Plotted on the y-axis is the depth of coverage of the anti-Capsid libraries following subtractive analysis, with the x-axis representing nucleotide position. <b>D</b>) Statistical analysis of the data presented in panel C, with the y-axis indicating the Z-score of all represented sequences. The x-axis represents the nucleotide position, with all panels above being aligned with the indicated nucleotide numbering intervals.