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CIS-REGULATION

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  1. Clone 'AHC0AAA262YA01' > 
  2. Clone 'AHC0AAA54YJ22' > 
  3. Clone 'citb068i02' > 
  4. Transcript 'KH2012:KH.C1.1212.v1...' > 
  5. Region 'REG00001381'

Cis-regulatory Region

Name

Cirobu.REG.KH2012.C7:3853970-3854222_LSM6|Ephrin3

Short name

n/a

Region ID

REG00001381

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. It contains 2 Brachyury, 2 Fox and 1 Sp1/Klf putative binding sites and an (AC) repeat. Compared to the WT 253pb enhancer, its ability to direct notochord gene expression conserved.

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

CONS00001401: p.Cirobu.REG.KH2012.C7:3853970-3854222_LSM6>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 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.b and TableS5 of Jose-Edwards et al. 2015. This construct is part of mutational series of the last 59bp. Mutated bases are shown in upper-case letters.

Show sequence

Length: 253


ctctacagtatacggagagtccccacccattaaacaaacgtaatattaattgttagatag
atatgattcacacaggatgtatttgtggtgtctggattaacccccagtaagaattctctg
ccatacaatagcagcgtgtttgaattactgcttgttttggcaagttgattaagtcaggtc
aatctaggtcacacacacacacacactgtatgtatatacacaacacagaGTGCCGataaa
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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