Extended Data Fig. 1: Alternative splicing of Lphn3 (Adgrl3) transcripts (a & b) and demonstration that a subset of the sites of alternative splicing of Lphn3 exhibits a high degree of cell type-specific expression as revealed by RNAseq analyses (c–e).

a, Analysis of a long-read PacBio sequencing¹⁶ uncovers extensive combinatorial alternative splicing of Lphn3. Reads are depicted as heatmaps (green boxes = Included exons; light grey boxes = excluded exons; asterisks = alternatively spliced exon). Each row represents a splice variant combination whose abundance is shown on the right. Note ‘a’ and ‘b’ designations (such as ‘30a’ and ‘30b’) are alternative splicing donor or acceptor variants within an exon. For a similar analysis of Lphn1 and Lphn2, see Extended Data Fig. 2a–d. b, Details of alternative splicing in the cytoplasmic region of Lphn3. The diagram depicts the amino acid sequences of alternatively spliced variants (asterisk = stop codon; only the 7 TMR region and cytoplasmic sequences of Lphn3 are shown). Note Exons 28 and 29 are in-frame but Exon30 can be present as Exon30a or Exon30b, of which Exon30b shifts the reading frame of Exon31. c, Neuron type-specific alternative splicing of Lphn3 from a ribosome-associated transcriptome study¹⁸. The abundance of each exon in PSI (percent spliced in) for 8 indicated neuron types from two brain regions (HP: hippocampus, CT: cortex). Each datapoint (n = 4) represents one sample from 1 animal for excitatory neurons, and 2 animals for inhibitory neurons. d & e, Analyses of Lphn3 Exon31 and Exon32 level in single-cell datasets from primary visual cortex and anterior lateral motor cortex⁴² (d), or of medial prefrontal cortex³⁷ (e). In d, all neurons corresponding to an indicated type were combined as one datapoint. The percent spliced-in for Exon31 and Exon32 of Lphn3 is shown for each type. Two-sided t-test was used to calculate statistical significance (n = 8 biologically independent excitatory neurons and n = 5 for biologically independent inhibitory neurons). In e, the cumulative probability of splicing percentage for all neurons of each type were plotted.