Description

This 312pb sequence, located in the upstream region of KH.L13.2, is not active in notochord. It contains 2 Myb, 2 E-box and 2 Brachyury putative binding sites. Compared to the larger active 530pb enhancer, it lacks 1 E-box, 2 Myb and 1 Brachyury putative binding sites.

Hierarchy of Regulatory Regions

Modification of Cirobu.REG.KH2012.L13:47071-47600|KH.L13.2 by deletion

Regulated gene(s)

KH2012:KH.L13.2 (CORIN; HSPG2; LRP2)

Construct(s) made to test this region

CONS00001309: p.Cirobu.REG.KH2012.L13:47289-47600>LacZ

Overview of functional TF binding sites in this region

47,28947,600

	Motif Name	Binding Factor(s)	Sequence	Position in Region	Comment
1	Helix Turn Helix / Tryptophane clusters	n/a	ccgttg	[47,301 / 47,307]	This is one of the 3 Myb#3 binding sites located in the notochord-active enhancer of KH.C13.2.
2	Helix Turn Helix / Tryptophane clusters	n/a	ccgtta	[47,371 / 47,377]	This is one of the 3 Myb#3 binding sites located in the notochord-active enhancer of KH.C13.2.
3	bHLH	n/a	caactg	[47,386 / 47,392]	This putative E-box binding site is located in the upstream 530pb enhancer of KH.L13.2.
4	T-Box	n/a	tctcac	[47,481 / 47,487]	This putative Brachyury binding site is located in the upstream 530pb enhancer of KH.L13.2. When this TFBS (3rd of 4 Brachyury binding sites) is mutated, the 530pb enhancer is still active in the notochord and its tail muscle activity is increased.
5	T-Box	n/a	gtgata	[47,551 / 47,557]	This putative Brachyury binding site is located in the upstream 530pb enhancer of KH.L13.2.
6	bHLH	n/a	caaatg	[47,591 / 47,597]	This putative E-box binding site is located in the upstream 530pb enhancer of KH.L13.2.

Sequence

Aniseed Coordinates: [47,289 / 47,600] on scaffold KhL13

Sequence of the primers used : Forward : AtctagaGGAAGTGGGTGACCGTTGAATC Reverse : not indicated Lowercase letters correspond to XbaI/NcoI restriction site.

Reference(s)

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