1. Figure S1. Statistics of the distances from IPACs to nearby genes
Figure S1. Statistics of the distances from IPACs to nearby genes. 5sd, distance to 5’ sense gene; 3sd, distance to 3’ sense gene; 3ad, distance to 3’ antisense gene; 5ad, distance to 5’ antisense gene. Median distances (nt) are: 5sd, 122; 3sd, 2237; 5ad, 3380; 3ad, 5165; intergenic length, 2616.

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Figure S2. Distributions of distances from IPACs to sense and antisense genes.
(A) distance from IPACs to 5’ sense genes; (B) distance from IPACs to 3’ sense genes; (C) distance from IPACs to 5’ sense genes normalized by the length of intergenic regions; (D) distance from IPACs to 5’ antisense genes; (E) distance from IPACs to 3’ antisense genes; (F) distance from IPACs to 5’ antisense genes normalized by the length of intergenic regions.

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Figure S3. Distributions of distances from randomly selected nucleotide positions in intergenic regions to neighboring genes.
Distances from random positions to 5’ sense genes (A) and 3’ sense genes (B). Distance from random positions to 5’ sense genes normalized by the length of intergenic region (C). Distances from random positions to 5’ antisense genes (D) and 3’ antisense genes (E). Distance from random positions to 5’ antisense genes normalized by the length of intergenic region (F).

4. Figure S4. Position-by-position base composition of A-IPACs whose antisense regions is 3’-UTR (A), 5’-UTR (B), CDS (C), and intron (D).

5. Figure S5. Poly(A) signal hexamer frequency of different types of IPACs. The NUE region (-30 to -5 nt) was used for identifying hexamers. 1nt-variants corresponds to any one of the 1 nt variants of AATAAA. Poly(A) sites from 3’-UTR (3’ UTR PAC) were used for comparison.

6. Figure S6. PASS score of IPACs
Figure S6. PASS score of IPACs. The randomly selected ’-UTR PACs (3’-UTR PAC) and background positions (Random BG) were used as controls.

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Figure S7. Characteristics of IPACs in oxt6 mutant. (A) Number of IPACs in different categories. Position-by-position base composition of IPACs in SE-IPAC (B), SO-IPAC (C), and A-IPAC (D).

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Figure S8. Conservation of IPACs. An IPAC was considered as conserved when it is located in (A) or within 50 nt of (B) the highly conserved blocks from 20 Angiosperm Plant Genomes.