Description

This 89bp sequence, located in the downstream region of KH.C5.399, drives reporter gene expression in notochord, mesenchyme and tail muscles. It contains 5 Myb#1, 2 E-box, 2 Fox, 3 Myb#2 and 1 Myb#3 putative binding sites. Compared to the active WT enhancer, it lacks the Brachyury binding site.

Hierarchy of Regulatory Regions

Modification of Cirobu.REG.KH2012.C5:4471851-4472163|Rfx1/2/3 by substitution

Regulated gene(s)

KH2012:KH.C5.399 (RFX1; RFX2; RFX3)

Construct(s) made to test this region

CONS00001367: p.Cirobu.REG.KH2012.C5:4471851:-4472163_BraMut>LacZ

Overview of functional TF binding sites in this region

4,471,8514,472,163

	Motif Name	Binding Factor(s)	Sequence	Position in Region	Comment
1	Helix Turn Helix / Tryptophane clusters	n/a	gtta	[4,471,870 / 4,471,874]	This is one of the 5 Myb#1 binding sites located in the notochord-active enhancer of KH.C5.399.
2	Helix Turn Helix / Tryptophane clusters	n/a	gtta	[4,471,875 / 4,471,879]	This is one of the 5 Myb#1 binding sites located in the notochord-active enhancer of KH.C5.399.
3	Helix Turn Helix / Tryptophane clusters	n/a	taac	[4,471,912 / 4,471,916]	This is one of the 5 Myb#1 binding sites located in the notochord-active enhancer of KH.C5.399.
4	bHLH	n/a	catttg	[4,471,920 / 4,471,926]	This is one of the 2 E-box binding sites located in the notochord-active enhancer of KH.C5.399.
5	Fox	n/a	tgtttac	[4,471,981 / 4,471,988]	This is one of the 2 Fox binding sites located in the notochord-active enhancer of KH.C5.399.
6	Helix Turn Helix / Tryptophane clusters	n/a	attgaa	[4,472,025 / 4,472,031]	This is one of the 3 Myb#2 binding sites located in the notochord-active enhancer of KH.C5.399. Mutation of this Myb#2 binding site does not affect the enhancer activity in the notochord.
7	Helix Turn Helix / Tryptophane clusters	n/a	taac	[4,472,039 / 4,472,043]	This is one of the 5 Myb#1 binding sites located in the notochord-active enhancer of KH.C5.399. Mutation of this Myb#1 binding site does not affect the enhancer activity in the notochord.
8	Helix Turn Helix / Tryptophane clusters	n/a	taac	[4,472,044 / 4,472,048]	This is one of the 5 Myb#1 binding sites located in the notochord-active enhancer of KH.C5.399. Mutation of this Myb#1 binding site alone does not affect the enhancer activity in the notochord. Mutation of both this binding site and the neighbouring Myb#2 binding site inhibits enhancer activity in the notochord.
9	Helix Turn Helix / Tryptophane clusters	n/a	attgaa	[4,472,052 / 4,472,058]	This is one of the 3 Myb#2 binding sites located in the notochord-active enhancer of KH.C5.399. Mutation of this Myb#2 binding site alone does not affect the enhancer activity in the notochord. Mutation of both this binding site and the neighbouring Myb#1 binding site inhibits enhancer activity in the notochord.
10	bHLH	n/a	caaatg	[4,472,076 / 4,472,082]	This is one of the 2 E-box binding sites located in the notochord-active enhancer of KH.C5.399.
11	Fox	n/a	tgtttgt	[4,472,101 / 4,472,108]	This is one of the 2 Fox binding sites located in the notochord-active enhancer of KH.C5.399.
12	Helix Turn Helix / Tryptophane clusters	n/a	ttcaat	[4,472,129 / 4,472,135]	This is one of the 3 Myb#2 binding sites located in the notochord-active enhancer of KH.C5.399.
13	Helix Turn Helix / Tryptophane clusters	n/a	ccgttg	[4,472,145 / 4,472,151]	This Myb#3 binding site is located in the notochord-active enhancer of KH.C5.399. Its mutation does not affect the enhancer activity in the notochord.

Sequence

Aniseed Coordinates: [4,471,851 / 4,472,163] on scaffold KhC5

The Brachyury binding site is mutated. TAACAC replaced by TAATAT. This sequence was retrieved using ANISEED Blast tool, thanks to the information provided in FigS1.d and TableS5 of Jose-Edwards et al. 2015.

Reference(s)

José-Edwards et al. (2015). Brachyury, Foxa2 and the cis-Regulatory Origins of the Notochord. PLoS Genet. 11(12):e1005730