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Table 3 Genomic features significantly different in islands compared with whole genomic DNA.

From: Genome-wide sequence and functional analysis of early replicating DNA in normal human fibroblasts

    Islands that overlap with replication timing markers1
Feature Genome All Islands Islands with a ≥ 1.65-timing ratio1 Islands with a ≥ 1.75-timing ratio1 Islands with a ≥ 1.85-timing ratio1
100-kb windows 28358 1749 228 144 78
Genes 30078 2815 606 428 252
Genes/100 kb 1.06 1.60 2.66 2.97 3.23
Promoters 2 10415 948 223 170 111
Promoters/100 kb 0.37 0.55 0.98 1.18 1.42
Transcribed 37.61% 43.73% 56.37% 55.88% 54.79%
Translated 1.11% 1.81% 3.08% 3.42% 3.35%
CpG_Islands 1.94% 4.05% 5.20% 5.83% 6.58%
CpG_Content 1.96% 2.76% 3.39% 3.63% 3.86%
GC_Content 40.88% 45.51% 48.71% 49.82% 50.52%
Conserved 4.83% 5.78% 7.18% 7.50% 7.86%
All_Repeats 48.52% 45.68% 44.23% 44.78% 46.21%
SINE 13.67% 17.18% 23.28% 25.05% 27.71%
   Alu 10.75% 13.54% 18.99% 20.66% 23.59%
   MIR 2.92% 3.64% 4.29% 4.39% 4.11%
LINE 21.10% 15.94% 11.55% 10.73% 10.06%
   L1 17.48% 12.27% 7.83% 6.97% 6.53%
LTR 8.71% 7.45% 5.28% 4.98% 4.65%
   MaLR 3.79% 3.30% 2.37% 2.34% 2.18%
   ERV1 3.00% 2.58% 1.76% 1.66% 1.51%
   ERVL 1.61% 1.32% 0.85% 0.75% 0.71%
DNA transposons 3.02% 2.71% 2.35% 2.23% 2.02%
   MER2_type 1.06% 0.79% 0.63% 0.55% 0.54%
   Mariner 0.10% 0.07% 0.04% 0.04% 0.03%
Low_complexity 0.58% 0.54% 0.51% 0.50% 0.49%
Tandem_Repeats 1.82% 2.64% 2.1% 2.24% 2.44%
  1. 1- Replication timing ratio determined by Woodfine et al. [19].
  2. 2- Active promoters in IMR90 fibroblasts as determined by Kim et al. [44].