Table 3.

The locations of poly(A) sites in the rice genome

Category	Sub-category	Number of transcripts	Percentage
Aligned to genome	–	54 786a	100
Located in	Coding sequences	244	0.45
the full-	Introns	511	0.93
length cDNA	5′-UTR	299	0.54
	3′-UTR	28 209	51.45
	Subtotal	29 263	53.41
Located nearby annotated transcript ends	Within 500 ntb downstream of 3′-end	19 397	35.40
	Within 100 nt upstream of 5′-end	34	0.06
	Subtotal	19 431	35.46
Located in the intergenic region	At least 500 ntb beyond currently annotated genes	6092	11.12

^aOnly those that were mapped to unique genomic sequences are shown.

^bFor those genes that do not have an annotated 3′-UTR, 1000 nt (instead of 500 nt) downstream from their stop codons was used.