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CIS-REGULATION

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  1. Region 'REG00000883' > 
  2. Region 'REG00000897' > 
  3. Molecular Tool 'Hr-FoxDb MO (Kumano 2006)' > 
  4. Transcript 'Boleac.CG.SB_v3.S244...' > 
  5. Region 'REG00001383'

Cis-regulatory Region

Name

Cirobu.REG.KH2012.C7:3853970-3854222_(AC)2mut|Ephrin3

Short name

n/a

Region ID

REG00001383

Status

Curated

Origin

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

Type of Activity

regulatory_region
(enhancer)

Author

Diana S. José-Edwards (2018-05-21)

Annotator

Marion Gueroult-Bellone (2018-05-21)

Curator

Marion Gueroult-Bellone (2018-05-21)

View position in WashU

Description

This 253bp sequence, located in an intronic region of C7.568, drives reporter gene expression in notochord and mesenchyme. It contains 2 Brachyury, 2 Fox, 1 E-box and 1 Sp1/Klf putative binding sites and an (AC)4 repeat. Compared to the WT enhancer, its ability to drive gene expression in the notochord is decreased.

Hierarchy of Regulatory Regions

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

Regulated gene(s)

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

Construct(s) made to test this region

CONS00001403: p.Cirobu.REG.KH2012.C7:3853970-3854222_(AC)2mut>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 on the notochord-active intronic enhancer of KH.C7.568.
2 T-Box n/a tcacac [3,854,037 / 3,854,043] This is the first of the 2 Brachyury binding sites located on the notochord-active intronic enhancer of KH.C7.568.
3 Fox n/a tatttgt [3,854,049 / 3,854,056] This is the 1st of the 2 Fox binding sites located on the 253bp notochord-active intronic enhancer of KH.C7.568.
4 T-Box n/a tcacac [3,854,158 / 3,854,164] This is the 2nd of the 2 Brachyury binding sites located on the 253bp notochord-active intronic enhancer of KH.C7.568. Its mutation does not inhibit enhancer activity in the notochord.
5 bHLH n/a cagatg [3,854,195 / 3,854,201] This E-box binding site is located on the 253bp notochord-active intronic enhancer of KH.C7.568.
6 Fox n/a ataaaca [3,854,205 / 3,854,212] This is the 2nd of the 2 Fox binding sites located on the 253bp notochord-active intronic enhancer of KH.C7.568.

Sequence

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

This sequence was retrieved using ANISEED Blast tool, thanks to the information provided in Fig3.c and TableS5 of Jose-Edwards et al. 2015. In this construct the 2 first (AC) of the (AC) repeat are mutated. Mutated bases are shown in upper-case letters.

Show sequence

Length: 253


ctctacagtatacggagagtccccacccattaaacaaacgtaatattaattgttagatag
atatgattcacacaggatgtatttgtggtgtctggattaacccccagtaagaattctctg
ccatacaatagcagcgtgtttgaattactgcttgttttggcaagttgattaagtcaggtc
aatctaggtcacacTTTTacacacactgtatgtatatacacaacacagatgtaatataaa
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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