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CIS-REGULATION

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  1. Region 'REG00001280'

Cis-regulatory Region

Name

Cirobu.REG.KH2012.C7:3853910-3854157|Ephrin3

Short name

Ephrin3_CRM66_248pb

Region ID

REG00001280

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 248pb sequence, located in an intronic region of Ephrin3 (KH.C7.568), drives reporter no gene expression in notochord. It contains 2 Myb #2, 1 E-box, 1 Sp1/Kif, 1 Brachyury and 2 Fox putative binding sites. Compared to the larger active fragment, it lacks 1 Bra, 1 E-box and 1 Fox putative binding site and an AC repeat.

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

CONS00001299: p.Cirobu.REG.KH2012.C7:3853910-3854157>LacZ

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

3,853,9103,854,157

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 Helix Turn Helix / Tryptophane clusters n/a attgaa [3,853,923 / 3,853,929] This is one of the two Myb#2 binding sites located in the notochord-active enhancer of KH.C7.568. Deletion of the region containing these two binding sites does not affect the enhancer activity in the notochord.
2 Helix Turn Helix / Tryptophane clusters n/a attgaa [3,853,942 / 3,853,948] This is one of the two Myb#2 binding sites located in the notochord-active enhancer of KH.C7.568. Deletion of the region containing these two binding sites does not affect the enhancer activity in the notochord.
3 Fox n/a tatttat [3,854,019 / 3,854,026] This Fox binding site is one of the 3 putative binding sites located in the 313pb enhancer of Ephrin3 (KH.C7.568).
4 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)
5 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).
6 ZnF_(C2H2) n/a ccacc [3,854,052 / 3,854,057] This Sp1/Klf binding site is located in the intronic enhancer of Ephrin3 (KH.C7.568).

Sequence

Aniseed Coordinates: [3,853,910 / 3,854,157] on scaffold KhC7

Sequence of the primers used : Forward : GtctagaGAAATCTAAATGTATTGAACGGTAAACG Reverse : TTccatggCCTAGATTGACCTGACTTAATCAAC Lowercase letters correspond to XhoI/XbaI 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: 248


gaaatctaaatgtattgaacggtaaacgtcgtattgaaaaatgaatctctatttataact
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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