The PA-seq strategy. (a) Schematic diagram of the PA-seq procedure. Dual-biotin labeled DNA oligo was used for the reverse transcription. ‘U’ stands for the deoxyuracil. ‘V’ denotes any nucleotide but Thymine and ‘N’ represents any nucleotide. USER (Uracil-Specific Excision Reagent) enzyme catalyzes the excision of the uracil base in the double-stranded DNA and cleaves the abasic site to form 5′ phosphorylated (p) end. (b) Overlap between PA sites identified by PA-seq and those annotated in polyA_DB . The background is obtained by permuting the reads within the same UTRs and then assessing the overlap. (c) Distance between experimentally identified PA cleavage sites and polyA_DB annotations. For genes with multiple PA sites, the shortest distance was used. (d) A snap view of PA cleavage sites identified by PA-seq. PA sites were separated by plus (Red) and minus (Blue) strands. Known RefSeq transcripts are shown at the bottom.