Examples of newly annotated protein-coding and lncRNA genes. Read count profiles of RNAseq alignments to a selected set of newly annotated genes, viewed using IGV (Broad Institute, Cambridge, MA) [86,87]. Chromosomal coordinate scales vary among panels. AGAP designations are given for genes encoding mRNAs (blue boxes for exons) that are complementary to newly annotated antisense lncRNAs (green boxes for exons). Strandedness of lncRNAs is determined by Cufflinks and based on output GTF file (Additional files 4 and 8). Each panel consists of the top graph indicating read depth (Log scale maximum of 6) with a PhyloCSF track below (scale −70 to 50, red indicating values above 0 and blue indicating values below 0), followed by the gene GTF track. Colored triangles indicate the orientation of the given gene. A. Putative protein-coding gene Merged.4500.1 maps antisense to the 3’ untranslated region of protein-coding gene AGAP007209. Regions with red boxes of Merged.4500.1 indicate the protein-coding segments of the gene (107 amino acids in length). B. lncRNA Merged.6207.1 maps intronically with respect to AGAP002451. C. lncRNA Merged.11296.1 is antisense and overlapping to AGAP011074.