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CIS-REGULATION

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  1. Transcript 'KH2012:KH.L9.23.v1.A...' > 
  2. Region 'REG00001313'

Cis-regulatory Region

Name

Cirobu.REG.KH2012.L65:311070-311303_Fox2Mut|Dyrk2/3/4

Short name

n/a

Region ID

REG00001313

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 228bp sequence, located in the upstream region of KH.L65.10, drives reporter gene expression in notochord, mesenchyme, Central nervous system and head epidermis. It contains 1 Fox, 2 E-box and 3 Brachyury putative binding sites. Compared to the active WT enhancer, it lacks the second Fox binding site.

Hierarchy of Regulatory Regions

Modification of Cirobu.REG.KH2012.L65:311070-311303|Dyrk2/3/4 by substitution

Regulated gene(s)

KH2012:KH.L65.10 (DYRK2; DYRK3; DYRK4)

Construct(s) made to test this region

CONS00001333: p.Cirobu.REG.KH2012.L65:311070-311303_Fox2Mut>LacZ

Show in situ data
Overview of functional TF binding sites in this region

311,070311,303

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 bHLH n/a catctg [311,181 / 311,187] This is one of the 2 E-box binding sites located in the notochord-active enhancer of KH.L65.10.
2 T-Box n/a gtgtta [311,190 / 311,196] This is the second of the 6 Brachyury binding sites located in the notochord-active enhancer of KH.L65.10. Its mutation can affect the enhancer activity in the notochord.
3 bHLH n/a cacatg [311,206 / 311,212] This is one of the 2 E-box binding sites located in the notochord-active enhancer of KH.L65.10.
4 T-Box n/a gtgtta [311,228 / 311,234] This is one of the 6 Brachyury binding sites located in the notochord-active enhancer of KH.L65.10.
5 Fox n/a gtaaata [311,239 / 311,246] This is one of the 2 Fox binding sites located in the notochord-active enhancer of KH.L65.10. Deletion of this Fox BS does not affect enhancer activity in the notochord.

Sequence

Aniseed Coordinates: [311,070 / 311,303] on scaffold KhL65

The second Fox binding site is mutated. GTGTTA replaced by ATATTA. This sequence was retrieved using ANISEED Blast tool, thanks to the information provided in FigS3.d and TableS5 of Jose-Edwards et al. 2015.

Show sequence

Length: 234


gatatctcgtgtgtgtctggtacatctcaatttaacagcctcgacaccaacgccttacat
gcgtttgtaagttcgcttcgcaacctatttaacaaaccggtGGGACCTtaacatctgtag
gtgttatatttagagtcacatggcggcgtacacgcctggtgttattttggtaaataaaac
ttaacgtttcaagcaaaaggtaaactgtagaatatagtaggttggggtaagtcg

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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