Most lincRNAs are predominantly localized to the nucleus. (a) Boxplots describing the distribution of the fraction of molecules localized to the nucleus (Y axis) for each validated lncRNA-cell pair (X axis, orange: HeLa, blue: hFF, purple: hLF). Red bar: medians. Whiskers are at 1.5* the inner quartile range. (b) Scatter plot of the relationship between expression level (X axis; median number of molecules per cell) and nuclear localization (Y axis, median fraction of nuclear spots across all expressing cells). Each data point is one gene-cell pair and is colored by its classification to the localization classes I to V (Methods) of Figure 2. mRNA sets 1 to 2 (yellow) serve as a reference. Histograms on top and right are the distribution of all lncRNAs- (black) and mRNA- (yellow) cell pairs. (c) Scatter and histograms as in (b) but for lncRNA with (red) or without (black) a divergently transcribed mRNA counterpart. (d) Scatter and histograms as (b) but for lncRNA with (red) or without (black) a syntenic ortholog. (e) Representative image of mitotic cells (marked with white arrows) lacking foci that are seen in interphase cells (marked with yellow arrows). Scale bar, 5 μm.