Fig. 3

Most L1 ASP transcripts are sense to cognate genes and possess protein coding potential. a L1 ASP transcripts tend to be in sense strandedness relative to the cognate gene, typically serving as an alternative TSS of the canonical gene TSS (left panel). Rarely, ESTs supporting L1 ASP transcripts overlap anti-sense to cognate gene (right panel). The bias towards sense-strandedness of L1 ASP transcripts suggested the possibility for protein coding potential. ESTs supporting L1 ASP transcripts that had multiple alignments in the database (~2.3 % of all ESTs) were excluded. b Independent analysis of long-read PacBio RNA-seq data identified transcript isoforms supporting 124/988 L1 ASP transcripts. We validated both instances where the L1 ASP transcript was sense to the cognate gene (L1-PPP1R1C, left panel). We also validated the opposite strand L1 ASP transcript (L1-ABCA9, right panel). The red indicates the positive strand and the blue indicates the negative strand for the genome browser view. c Coding potential of L1 ASP transcripts was assessed by the ability to encode an open reading frame (ORF) of at least 100 amino acids (aa) and to begin with a start codon. We identified that 27.1 % of ESTs contained the potential for coding by these criteria