Description

This 89bp sequence, located in the upstream region of KH.C9.778, drives reporter gene expression in notochord and mesenchyme. It contains 1 Sp1/Klf, 2 E-box and 2 Brachyury putative binding sites. Compared to the active WT enhancer, it lacks the first E-box and the third Brachyury binding site.

Hierarchy of Regulatory Regions

Modification of Cirobu.REG.KH2012.C9:35651-35739|Fkbp9 by substitution

Regulated gene(s)

KH2012:KH.C9.778 (FKBP10; FKBP2; FKBP9)

Construct(s) made to test this region

CONS00001342: p.Cirobu.REG.KH2012.C9:35651-35739_Ebox1/Bra3mut>LacZ

Overview of functional TF binding sites in this region

35,65135,739

	Motif Name	Binding Factor(s)	Sequence	Position in Region	Comment
1	T-Box	n/a	gtgaaa	[35,680 / 35,686]	This is the second of the 3 Brachyury binding sites located in the notochord enhancer of KH.C9.778. Its mutation or deletion inhibits enhancer activity in the notochord.
2	T-Box	n/a	taacac	[35,688 / 35,694]	This is one of the 3 Brachyury binding sites located in the notochord enhancer of KH.C9.778.
3	bHLH	n/a	cacgtg	[35,691 / 35,697]	This is one of the 3 E-box binding sites located in the notochord enhancer of KH.C9.778.
4	bHLH	n/a	catttg	[35,704 / 35,710]	This is one of the 3 E-box binding sites located in the notochord enhancer of KH.C9.778.
5	ZnF_(C2H2)	n/a	Agtgg	[35,730 / 35,735]	This Sp1/Klf binding site is located in the notochord enhancer of KH.C9.778.

Sequence

Aniseed Coordinates: [35,651 / 35,739] on scaffold KhC9

The 1st E-box and the 3rd Brachyury binding sites are mutated : CAATTG replaced by AGATCA and TTGCAC replaced by TTGTCT respectively. This sequence was retrieved using ANISEED Blast tool, thanks to the information provided in FigS1ab 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