a C9orf72 genomic structure is illustrated; boxes represent exons. Exon 1a and 1b (navy), which do not encode protein, are alternative first exons, and exon 2 contains the translational start site (ATG, black triangle). The G4C2-repeat expansion (aqua) is in intron 1, upstream of exon 1b. Approximate position of primers used to detect various transcripts in Taqman assays are illustrated with arrows, including primers that span the exon 2–exon 3 junction (black) that detects all transcripts, primers that span the exon 1a–exon 2 junction (coral) that are specific to V3, and primers complementary to intron 1 (aqua) that detect all intron 1-containing and expansion-containing variants. b pre-mRNAs corresponding to V1–V3 are illustrated. The coral star indicates SS1b. c Mature mRNAs for all variants and the proteins they encode are shown. Primers for all variants detect all three mature mRNAs, whereas the V3 primers are specific to V3. Intron 1 primers do not detect any mature mRNAs. d Pathogenic RNA by-products resulting from the G4C2-repeat expansion in intron 1 are shown. The location of the G4C2-repeat expansion (aqua) is shown in sense and antisense RNAs. Intron 1 primers detect all pathological RNAs, and the all variants primers will detect any mis-spliced V1/V3 transcripts that include exon 2. SS1b Splice site 1b, V variant.