Aniseed - Cis-regulation

Cis-regulatory Region

Name

Cirobu.REG.KH2012.S610:12703-12901_Bra1Mut2|Kelch-related protein

Short name

n/a

Region ID

REG00001316

Status

Curated

Origin

engineered region from C. robusta formely Ciona int. type A

Type of Activity

regulatory_region
(enhancer)

Author

Diana S. José-Edwards (2018-05-08)

Annotator

Marion Gueroult-Bellone (2018-05-08)

Curator

Marion Gueroult-Bellone (2018-05-08)

View position in WashU

Description

This 198bp sequence, located in the downtream region of KH.S610.5, drives reporter gene expression in mesenchyme and tail muscles but not in notochord. It contains 1 Sp1/Klf and 2 Brachyury putative binding sites. Compared to the active WT enhancer, it lacks the first Brachyury binding site.

Hierarchy of Regulatory Regions

Modification of Cirobu.REG.KH2012.S610:12703-12901|Kelch-related protein by substitution

Cirobu.REG.KH2012.S610:12703-12901|Kelch-related protein REG00001314 [ regulatory_region (enhancer) ]

Regulated gene(s)

KH2012:KH.S610.5 (KBTBD8; KLHL17; KLHL41)

Construct(s) made to test this region

CONS00001336: p.Cirobu.REG.KH2012.S610:12703-12901_Bra1Mut2>LacZ

Show in situ data

Overview of functional TF binding sites in this region

12,70312,901

	Motif Name	Binding Factor(s)	Sequence	Position in Region	Comment
1	ZnF_(C2H2)	n/a	ggtgg	[12,835 / 12,840]	This Sp1/Klf binding site is located in the notochord enhancer of KH.S610.5.
2	T-Box	n/a	taacac	[12,860 / 12,866]	This is the second of the 3 Brachyury binding sites located in the notochord enhancer of KH.S610.5.
3	T-Box	n/a	gtgcca	[12,883 / 12,889]	This is the 3rd of the 3 Brachyury binding sites located in the notochord enhancer of KH.S610.5.

Sequence

Aniseed Coordinates: [12,703 / 12,901] on scaffold KhS610

The first Brachyury binding site is mutated : TTGCAC replaced by TTGAGA. This sequence was retrieved using ANISEED Blast tool, thanks to the information provided in FigS3.b and TableS5 of Jose-Edwards et al. 2015.

Show sequence

Length: 199

acaaacatcttgagactaagtgctgaagaactcccctctttgtcaatttcaagacctgaa
aacattttcgtcatttatagaaagtaaaaagctacaacatgagagtgaataaatgaaact
tacttatcctcgggtggcgagaaaaccctagtcgttataacacgggtgttcatacatctc
gtgccaggttataattacg

Reference(s)

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