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CIS-REGULATION

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  1. Clone 'cien76417' > 
  2. Region 'REG00001363' > 
  3. Region 'REG00001316' > 
  4. Region 'REG00001341' > 
  5. Region 'REG00001323'

Cis-regulatory Region

Name

Cirobu.REG.KH2012.C9:35651-35739_Bra2mut|Fkbp9

Short name

n/a

Region ID

REG00001323

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 89bp sequence, located in the upstream region of KH.C9.778, drives reporter gene expression in mesenchyme and tail muscles, but not in notochord. It contains 1 Sp1/Klf, 3 E-box and 2 Brachyury putative binding sites. Compared to the active WT enhancer, it lacks the second 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

CONS00001343: p.Cirobu.REG.KH2012.C9:35651-35739_Bra2mut>LacZ

Show in situ data
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 gtgcaa [35,668 / 35,674] This is the third of the 3 Brachyury binding sites located in the notochord enhancer of KH.C9.778. Its mutation does not affect enhancer activity in the notochord. Deletion of the region containing 2nd and 3rd Brachyury binding sites 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 bHLH n/a caattg [35,725 / 35,731] This is one of the 3 E-box binding sites located in the notochord enhancer of KH.C9.778. Its mutation does not affect ehnacer activity.
6 ZnF_(C2H2) n/a ggtgg [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 second Brachyury binding site is mutated. TTTCAC replaced by TTTTCT. This sequence was retrieved using ANISEED Blast tool, thanks to the information provided in FigS1ab and TableS5 of Jose-Edwards et al. 2015.

Show sequence

Length: 89


cagcatgtctagcttttgtgcaataaggcAGAaaaagtaacacgtgacttcaacatttgc
tcaatgctggaaagcaattggtggataag

Reference(s)

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

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