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Table 1 Summary of RNA polymerase II locations

From: Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells

Sites   Pol IIa Pol II
Total sites   102 550
RefSeq total exons   70 289
RefSeq first exons   63 75
RefSeq terminal exons   2 91
RefSeq internal exons   5 123
RefSeq introns   4 120
  knownGene exon 0 5
  genscan exon 1 23
  geneid or sgpGene 0 3
  Active gene introns 2 57
  Inactive introns 1 32
No RefSeq overlap   28 141
  knownGene total exons 5 38
  knownGene first exon 5 13
  knownGene terminal exon 0 4
  knownGene internal exon 0 21
  No RefSeq or knownGene 23 90
  genscan exons 7 43
  geneid or sgpGene 2 6
  1. The order indicates the flowchart of filtering through the different databases. Enrichment sites were first compared to the RefSeq database. Sites that are not near exons were then divided into two categories: locations that are in RefSeq introns; and locations that are not in a RefSeq gene. The latter are then compared with knownGene and predicted gene databases. For both RNA polymerase II phosphorylation states, the large majority of sites are near an exon.