Flow chart of lncRNA and potential coding gene identification and expression/exonic structure of defined gene classes. A. Flow chart of lncRNA and novel protein-coding gene identification. RNAseq data sets were merged and used to produce a transcriptome that was supported by both Cufflinks and Scripture. Length, PhyloCSF score, maximum peptide length, protein domain and total coding-sequence length were used to set inclusion and exclusion criteria for the sets of lncRNAs and putative protein-coding RNAs, among the previously unannotated transcripts. B. Density plot of exons per-gene for lncRNAs (blue) and novel protein-coding RNAs (red). C. Expression values [Log10 (FPKM + 1)] calculated by Cufflinks for previously annotated genes in VectorBase (red), lncRNAs (green), and newly identified putative protein-coding RNAs (blue) for all genes that had an FPKM greater than zero for the merged RNAseq data set.