Fig. 7
From: Mapping intron retention events contributing to complex traits using splice quantitative trait locus
Impacts of IR on transcription factors. a Bar plot showing the number of cis-sQTL genes encoding transcription factors. b Bar plot showing the number of cis-sQTL genes belonging to different TF families. c An example of a gene (GhARF3/GH_A06G1554) with a significant cis-sQTL (A06:104984673:104984791:clu_39823) encoding an ARF transcription factor. The IGV screenshot [51] shows the total read numbers for each junction among individuals of different haplotypes, red dotted box shows the IR locus. The structural schematic (bottom) shows the impact of IR on the GhARF3 protein. For the transcript model, blue boxes indicate coding sequence, and lines indicate introns. In the bottom, protein 2 denotes the new structure produced by IR, which lacks the ARP domain present in the original protein 1. d Distribution of gene expression (left) and PSI according to haplotype (AA, AG, and GG) of sSNP A06:105487159. Data are presented as median (minimum to maximum). p-values were calculated by two-sided Student’s t-test