Extended Data Figure 2: In-PDGFRα transcript and protein structure.

a, DNA sequencing of 3′ RACE products illustrated in Fig. 1b confirms polyadenylation sites of highly expressed variants. b, Top, the fully-spliced FL-PDGFRα transcript contains 23 exons that encode the corresponding protein domains (bottom). CT, C-terminal region; JMR, juxtramembrane region; KD1, kinase domain 1; KD2, kinase domain 2; KI, interkinase domain; TM, transmembrane region. c, The fully spliced In-PDGFRα transcript contains 16 exons (top) that encode the protein domains (bottom). Red, portions of the transcript and protein that are unique to In-PDGFRα. d, Enlarged view of the genomic sequence that codes for the unique region of the In-PDGFRα protein. In FL-PDGFRα, this region is spliced out of the transcript. e, Map of the locations of amplicons used to assess levels of In-PDGFRα and FL-PDGFRα. Primers amplifying regions of exons 7–8, 11–12, and 15–16 are common to In-PDGFRα and FL-PDGFRα. Primers designated with 16i target the region canonically referred to as intron 16. In FL-PDGFRα, this region is spliced out. In In-PDGFRα, this region becomes the 3′ UTR. Therefore 16–16i and 16i–16i are specific for In-PDGFRα. Primers amplifying regions of exons 18–19, 21–22, exon 23 (23–23) and the 3′ UTR (UTR–UTR) are specific to FL-PDGFRα. f, Levels of In-PDGFRα transcript relative to FL-PDGFRα transcript increase during regeneration. FAPs were collected from uninjured muscles (day 0) or at 3 days after injury and RNA levels were assessed via qPCR. Expression level is plotted as a ratio of In-PDGFRα to FL-PDGFRα normalized to day 0. For In-PDGFRα primers 16–16i and 16i–16i were averaged, whereas for FL-PDGFRα, primers 23–23 and UTR–UTR were averaged. For each time point, n = 3 biological replicates of pooled FAPs. Significance was calculated using an unpaired Student’s t-test, error bars represent s.e.m. g, Western blot using the C-terminal PDGFRα antibody shows knockdown of FL-PDGFRα in response to the 5′ss-AMO.

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