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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]