Table 1. 3′ splice site organization of U2AF-regulated tandem homologous exon.

Gene	Exon (isoform)	U2AF-mediated	Reference	BP SVM score	PPT lengtha	AGEZ
FYNb,e	7a (FYNB)	Repression	Figure S20A,C	0.66	43	61
	7b (FYNT)	Activation	Figure S20A,C	1.01	11	35
TPM1e	6a	Activation	(12)	1.21	6	104
	6b	Repression	(12)	1.21	67	88
TPM2e	6a	Activation	(12)	2.34	16	34
	6b	Repression	(12)	1.75	106	131
U2AF1e	Ab (U2AF35b)	Repression (or less efficient activation)	Figure 1C–E	Not predicted	25	31
	3 (U2AF35a)	Activation	Figure 1C–E	Not predicted	9	21
CALUc,e	3a	Repression	E-MTAB-2682d	1.39	27	48
	3b	Activation	E-MTAB-2682	1.29	12	35
ACOX1	3a	Activation	E-MTAB-2682	0.98	19	24
	3b	Repression	E-MTAB-2682	1.31	10	59
MAPK14e	9a	Repression	E-MTAB-2682	0.16	32	61
	9b	Activation	E-MTAB-2682	−0.47	8	56
P4HA1e	10a	Activation	E-MTAB-2682	0.96	7	44
	10b	Repression	E-MTAB-2682	1.03	22	26

^aPPT length (nt) is for predicted BPs unless determined experimentally, as shown in Supplementary Figures S8 and S12.

^cFYN exon 7a is a younger copy of exon 7b (118). These exons encode functionally distinct FYNT and FYNB proteins regulated by U2AF (summarized in Supplementary Figure S20B).

^cActivation of alternatively spliced CALU exon 3b (also known as exon 4) was associated with a promotion of distal transcription initiation site in HEK293 cells depleted of U2AF35 (Supplementary Figure S21).

^dAccession number of RNA-Seq data for U2AF35 knockdowns.

^eTranscripts containing Evofold-detected hairpins.