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CIS-REGULATION

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  1. Transcript 'KH2012:KH.C8.163.v3....' > 
  2. Region 'REG00001123' > 
  3. Region 'REG00001114' > 
  4. Region 'REG00001252'

Cis-regulatory Region

Name

Cirobu.REG.KH2012.C9:5648367-5648505_Fox1-3/Bra4mut|DDR1; DDR2; MUSK

Short name

DDR1/2_CRM24_139pb_Fox1-3/Bra4mut

Region ID

REG00001252

Status

Curated

Origin

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

Type of Activity

regulatory_region
(enhancer)

Author

Diana S. José-Edwards (2017-09-09)

Annotator

Marion Gueroult-Bellone (2017-09-09)

Curator

Marion Gueroult-Bellone (2018-05-09)

View position in WashU

Description

Notochord activity of DDR1/2 139pb enhancer is abolished by the mutation of the fourth Brachyury and three Fox binding sites. But activity remains in the mesenchyme and tail muscles.

Hierarchy of Regulatory Regions

Modification of Cirobu.REG.KH2012.C9:5648367-5648505|DDR1; DDR2; MUSK by substitution

Regulated gene(s)

KH2012:KH.C9.371 (DDR1; DDR2)

Construct(s) made to test this region

CONS00001255: p.Cirobu.REG.KH2012.C9:5648367-5648505_Fox1-3/Bra4mut>LacZ

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

5,648,3675,648,505

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 T-Box n/a tctcac [5,648,369 / 5,648,375] First Brachyury binding site of the Brachyury/Fox sites cluster contained in DDR1/2 139pb enhancer. Mutation of all four Brachyury sites strongly reduces enhancer activity in the notochord.
2 T-Box n/a gtgaca [5,648,387 / 5,648,393] Second Brachyury binding site of the Brachyury/Fox sites cluster contained in DDR1/2 139pb enhancer. Mutation of all four Brachyury sites strongly reduces enhancer activity in the notochord.
3 T-Box n/a gtgtga [5,648,400 / 5,648,406] Third Brachyury binding site of the Brachyury/Fox sites cluster contained in DDR1/2 139pb enhancer. Mutation of all four Brachyury sites strongly reduces enhancer activity in the notochord.
4 Fox n/a ccaaata [5,648,449 / 5,648,456] Fourth Fox binding site of the Brachyury/Fox sites cluster contained in DDR1/2 139pb enhancer. Mutation of the three other three Fox sites and of the fourth Brachyury site abolishes enhancer activity in the notochord.
5 Helix Turn Helix / Tryptophane clusters n/a attgaa [5,648,477 / 5,648,483] This Myb#2 binding site is located in the notochord-active enhancer of KH.C9.371.
6 ZnF_(C2H2) n/a ccacc [5,648,492 / 5,648,497] Sp1/Klf binding site located next to the Brachyury/Fox sites cluster contained in DDR1/2 139pb enhancer.

Sequence

Aniseed Coordinates: [5,648,367 / 5,648,505] on scaffold KhC9

The fourth Brachyury site and three Fox sites are mutated : Fox1 : tatttac is replaced by tgggcag Fox2 : gtaaata is replaced by tgcccgc Fox3 : ataaaca is replaced by cgcccca Bra4 : GTGTAA is replaced by TAATAA

Show sequence

Length: 139


aatctcacttacttgcgaaggtgacatcacccggtgtgacggatctcaaaccaggtttgg
gcagttcctcgttatgcccgccccaaatacagatcgcaaggctttgtcatattgaactct
gaaagccaccgctgttgcg

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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