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CIS-REGULATION

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  1. Transcript 'Harore.CG.MTP2014.S2...' > 
  2. Transcript 'KH2012:KH.C7.568.v1....' > 
  3. Molecular Tool 'Hr-FoxA mRNA (Kumano 2066)' > 
  4. Molecular Tool 'FOG::Nodal' > 
  5. Region 'REG00001282'

Cis-regulatory Region

Name

Cirobu.REG.KH2012.C7:3853970-3854157|Ephrin3

Short name

Ephrin3_CRM66_188pb

Region ID

REG00001282

Status

Curated

Origin

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

Type of Activity

no_output

Author

Diana S. José-Edwards (2018-02-27)

Annotator

Marion Gueroult-Bellone (2018-02-27)

Curator

Marion Gueroult-Bellone (2018-02-27)

View position in WashU

Description

This 188pb sequence, located in an intronic region of Ephrin3 (KH.C7.568), drives no reporter gene expression in notochord. It contains 1 Sp1/Kif, 1 Brachyury and 1 Fox putative binding sites.

Hierarchy of Regulatory Regions

Modification of Cirobu.REG.KH2012.C7:3853970-3854222|Ephrin3 by deletion

Regulated gene(s)

KH2012:KH.C7.568 (EPHA4; EPHA7; EPHB2)

Construct(s) made to test this region

CONS00001301: p.Cirobu.REG.KH2012.C7:3853970-3854157>LacZ

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

3,853,9703,854,157

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 ZnF_(C2H2) n/a ccacc [3,853,992 / 3,853,997] This Sp1/Klf binding site is located in the intronic enhancer of Ephrin3 (KH.C7.568).
2 T-Box n/a tcacac [3,854,037 / 3,854,043] This Brachyury binding site is located in the intronic enhancer of Ephrin3 (KH.C7.568).
3 Fox n/a tatttgt [3,854,049 / 3,854,056] This Fox binding site is located in the intronic enhancer of Ephrin3 (KH.C7.568).

Sequence

Aniseed Coordinates: [3,853,970 / 3,854,157] on scaffold KhC7

Sequence of the primers used : Forward : GTtctagaCTCTACAGTATACGGAGAGTCC Reverse : TTccatggCCTAGATTGACCTGACTTAATCAAC Lowercase letters correspond to XbaI/NcoI restriction site.

Show sequence

Length: 188


ctctacagtatacggagagtccccacccattaaacaaacgtaatattaattgttagatag
atatgattcacacaggatgtatttgtggtgtctggattaacccccagtaagaattctctg
ccatacaatagcagcgtgtttgaattactgcttgttttggcaagttgattaagtcaggtc
aatctagg

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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