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Table 2 SP1 putative binding sites in the ANRIL promoter region by JASPAR

From: Long non-coding RNA ANRIL is upregulated in hepatocellular carcinoma and regulates cell proliferation by epigenetic silencing of KLF2

13 putative sites were predicted with these settings (90 %) in sequence named gi 568815589: 21992791–21994791
Model ID Model name Score Relative score Start End Strand Predicted site sequence
MA0079.3 SP1 11.960 0.931611173530848 1241 1251 1 TCTCCTCCTCC
MA0079.3 SP1 11.933 0.931271482620182 1244 1254 1 CCTCCTCCTCC
MA0079.3 SP1 11.615 0.927270678561222 1647 1657 1 GCACCGCCCCC
MA0079.3 SP1 11.673 0.928000384961913 1664 1674 1 TCTCCGCCCCG
MA0079.3 SP1 12.920 0.943689072576764 1702 1712 1 CGCCCGCCCCC
MA0079.3 SP1 10.466 0.912814943140641 1709 1719 1 CCCCCACCTTC
MA0079.3 SP1 14.400 0.962309166939219 1721 1731 1 CCCCCACCCCC
MA0079.3 SP1 11.514 0.925999982932433 1727 1737 1 CCCCCACCCCA
MA0079.3 SP1 13.360 0.949224776306143 1732 1742 1 ACCCCACCCCC
MA0079.3 SP1 10.179 0.909204154571706 1864 1874 1 CTCCCGCCTAC
MA0079.3 SP1 9.496 0.90061123264633 1882 1892 1 TTCCCGCCCTG
MA0079.3 SP1 14.400 0.962309166939219 1899 1909 1 CCCCCACCCCC
MA0079.3 SP1 10.467 0.912827524285481 1919 1929 1 TTCCCACCCTC
  1. This type of analysis has a high sensitivity but abysmal selectivity. In other words, while true function will be detected in most cases, most predictions will correspond to sites bound in vitro but with no function in vivo. A number of additional constraints of the analysis can improve the prediction; phylogenetic footprinting is the most common. We recommend using the ConSite service, which uses the JASPAR datasets. The review Nat Rev Genet. 2004 Apr;5(4):276–87 gives a comprehensive overview of transcription binding site prediction [33]