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CIS-REGULATION

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  1. Transcript 'KH2012:KH.L152.2.v1....' > 
  2. Transcript 'Boschl.CG.Botznik201...' > 
  3. Molecular Tool 'Hr-FoxDa mRNA (Kumano 2006)' > 
  4. Region 'REG00000639' > 
  5. Region 'REG00001281'

Cis-regulatory Region

Name

Cirobu.REG.KH2012.C7:3853970-3854222|Ephrin3

Short name

Ephrin3_CRM66_253pb

Region ID

REG00001281

Status

Curated

Origin

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

Type of Activity

regulatory_region
(enhancer)

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 253pb sequence, located in an intronic region of Ephrin3 (KH.C7.568), drives reporter gene expression in notochord. It contains 1 E-box, 1 Sp1/Kif, 2 Brachyury and 2 Fox putative binding sites and one AC repeat (six repeats).

Hierarchy of Regulatory Regions

Modification of Cirobu.REG.KH2012.C7:3853910-3854222|Ephrin3 by deletion

Regulated gene(s)

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

Construct(s) made to test this region

CONS00001300: p.Cirobu.REG.KH2012.C7:3853970-3854222>LacZ

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

3,853,9703,854,222

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).
4 T-Box n/a tcacac [3,854,158 / 3,854,164] This Brachyury binding site is located in the intronic enhancer of Ephrin3 (KH.C7.568).
5 bHLH n/a cagatg [3,854,195 / 3,854,201] This E-box binding site is located in the intronic enhancer of Ephrin3 (KH.C7.568).
6 Fox n/a ataaaca [3,854,205 / 3,854,212] This Fox binding site is located in the intronic enhancer of Ephrin3 (KH.C7.568).

Sequence

Aniseed Coordinates: [3,853,970 / 3,854,222] on scaffold KhC7

Sequence of the primers used : Forward : GtctagaGAAATCTAAATGTATTGAACGGTAAACG Reverse : TTCGtctagaGTAAGCGAGCACGAGGTGTGTG Lowercase letters correspond to XbaI/NcoI restriction site. This sequence was retrieved using ANISEED Blast tool, thanks to the information provided in FigS3.a and TableS5 of Jose-Edwards et al. 2015.

Show sequence

Length: 253


ctctacagtatacggagagtccccacccattaaacaaacgtaatattaattgttagatag
atatgattcacacaggatgtatttgtggtgtctggattaacccccagtaagaattctctg
ccatacaatagcagcgtgtttgaattactgcttgttttggcaagttgattaagtcaggtc
aatctaggtcacacacacacacacactgtatgtatatacacaacacagatgtaatataaa
cattgtagtattg

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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