Analysis of PolII location relative to ORFs. (a) Example of genes with high (top three examples) or low (bottom two) ratios of PolII at the ORF 5' end relative to the 3' end. For each gene, PolII abundance is shown on the y-axis, and gene annotation and any cryptic transcripts from Xu et al.  are shown underneath. (b) All genes ordered by 5'/3' PolII ratio. For each gene long enough to have a mid-CDS annotation (that is, at least one microarray probe located > 500 bp from either end of the gene), the PolII enrichment at the 5' (first 500 bp), mid-CDS, and 3' (last 500 bp) are shown in the three indicated columns. (c) Genes with high 5'/3' PolII abundance are highly expressed. Log(2) of mRNA abundance data from Yassour et al.  is shown as an 80-gene running-window average, with genes ordered as in (b). (d) Genes with high 3'/5' PolII abundance are associated with overlapping transcripts. Genes were scored for 3' overlap with cryptic unstable transcripts (CUTs), stable unannotated transcripts (SUTs), or ORFs as annotated in , and a running window average is plotted ordered as in (b). Pol2, RNA polymerase II.