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Table 1 Properties of various human genome annotations.

From: Assessing the impact of human genome annotation choice on RNA-seq expression estimates

  Genome Annotations
  AceView Genes H-InvDB Genes Ensembl Genes VegaGenes UCSCKnown Genes RefSeqGenes
Version 2010 8.0 67 48 - -
Database Downloaded Date Nov. 12, 2011 Apr. 20, 2012 May 1, 2012 June 26, 2012 Dec. 21, 2011 July 23, 2012
# of Genes 72,376 43,893 48,817 44,880 28,423 23,731
# of Isoforms 259,426 236,861 177,858 158,835 75,725 41,099
# of Exons 678,503 542,099 534,400 493,509 273,711 227,710
Average # of Isoforms per Gene 3.58 5.40 3.64 3.54 2.66 1.73
Maximum # of Isoforms per Gene
(with HGNC Gene Name)
119
(TRAV37)
885
(EEF1A1)
82
(GPR56)
77
(NDRG2)
129
(UTY)
77
(UTY)
Annotated Percentage (%) Gene 52.93 45.09 49.61 48.29 44.28 40.17
Exon 5.70 3.72 3.63 3.53 2.70 2.27
Coding Sequence 1.71 1.43 1.14 1.05 1.13 1.07
  1. The annotated percentage is the total length of all genomic elements (gene, exon, or coding sequence) over the entire length of the human genome