UCSC Genome Browser (Kent et al. 2002) snapshot. (A) Example of a GENCODE lncRNA, whose matching HQ gene shows protein-coding capability. From top to the bottom: the GENCODE (M4) annotations, lncRNA and splice junction CaptureSeq probes, the predicted ORF, all the assembled transcripts, GenBank mRNAs, phyloP conservation, and RepeatMasker (Smit et al. 2013–2015) tracks. The “ORF Track” reports the longest ORF predicted with Pinstripe (Gascoigne et al. 2012). “All assembled transcripts” highlights in gold the HQ transcript (TCONS_00004285) that adds new exons to the known lncRNA. (B) Dot plot alignment of the human DNAH14 gene (x-axis) with a combination of mouse TCONS_00004285 and Dnah14.
