Fig. 1: MapUTR captures functional 3′ UTR variants in known functional motifs.

a Experimental Design of MapUTR. Subpool-F and Subpool-R represent the 15-mer primer sequences to amplify the oligo pool. REC1 and REC2 represent restriction enzyme sites. pCAG, the CMV early enhancer/chicken beta actin (CAG) promoter. EGFP, eGFP gene. Library, oligo sequences containing the mutations/motifs. RT, sequences for gene-specific reverse transcription. polyA, polyA signals. See also Supplementary Fig. 2. b Computational workflow. c Design of oligos containing rare variants from gnomAD and quantification of variant effects. C_{DNA (ref)} represents DNA counts for the reference allele, C_{RNA (ref)} represents RNA counts for the reference allele, C_{DNA (alt)} represents DNA counts for the alternative allele, C_{RNA (alt)} represents RNA counts for the alternative allele, A_ref represents the activity score of the reference allele, A_alt represents the activity score of the alternative allele, and lnFC represents the relative activity score of the alternative allele compared to the reference allele. Created with BioRender.com. d Diagram of oligos with random mutations in the motif and its flanking regions (22–23 nt). e Mismatch rate (%) per position along the length of DNA sequences harboring known motifs: SAMD4A, sterile alpha motif ___domain containing 4A motif (in gene CHRDL1), ARE, AU-rich element (in gene CXCL2), hPUM, human pumilio motif (in gene MYOD1), CDE, constitutive decay element (in gene RBBP5), and dPUM, Drosophila pumilio motif (in gene SIPA1L2). f Relative activity scores of each mutated position of known motifs in HEK293 (red) and HeLa (blue) cells. Relative activity scores are averaged across the 3 tested alternative alleles per position. The 95% confidence intervals are shown as shades. e, f Source data are provided as a Source Data file.