NRG1 has many alternative isoforms [
1]. Although the original cDNA, AF009227 [
11], lacks the cytoplasmic exons 12 to 18, terminating in exon 11ext (Fig.
1; Supplementary Tables
1,
2), which defines normal β3 isoforms such as Heregulin-β3 (RefSeq NM_013958) and
NRG1 Type III-β3, we detected expression in MDA-MB-175 of all the later exons as well, in fusion transcripts (Fig.
1). We amplified complete cDNAs extending from
PPP6R3 exon 1 to the last
NRG1 exon, exon 18, which on cloning included at least three isoforms: we detected both the alpha and beta forms of
NRG1 (respectively including
NRG1 exon 10 or 11), and two transcripts included an additional, unannotated exon we designated ‘exon int15’. This exon is in reverse orientation within intron 15 of
TENM4, at hg19/chr11:78,506,385-78,506,462 (hg38 chr11:78795340-78795417), and therefore must be transcribed from an inverted fragment of chromosome 11 inserted into the main
TENM4-NRG1 junction (Fig.
1; Supplementary Table
2; Supplementary Textfile
1). RNAseq confirmed the presence of this exon (Supplementary Figure
2 panel C), but showed it was a minor variant, as only 24% (38/160) of split reads across the junction with
NRG1 exon 3 were from this exon (the others were all from
TENM4 exon 12). This exon would insert 26 amino acids and preserve the reading frame downstream.