We used CAGE-seq (5′ cap-targeted RNA isolation and sequencing) to identify 62,403 transcription start sites (TSSs) at high confidence (IDR of 0.01) in Tier 1 and 2 cell types. Of these, 27,362 (44%) are within 100 bp of the 5′ end of a GENCODE-annotated transcript or previously reported full-length mRNA. The remaining regions predominantly lie across exons and 3′ UTRs, and some exhibit cell type restricted expression; these may represent the start sites of novel, cell type-specific transcripts.
