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CIS-REGULATION

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  1. Region 'REG00000891' > 
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  3. Region 'REG00000703' > 
  4. Region 'REG00001495' > 
  5. Region 'REG00001277'

Cis-regulatory Region

Name

Cirobu.REG.KH2012.C7:3853138-3854780|Ephrin3

Short name

Ephrin3_CRM66_1642pb

Region ID

REG00001277

Status

Curated

Origin

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

Type of Activity

regulatory_region
(complex_region)

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 1642pb sequence, located in an intronic region of Ephrin3 (KH.C7.568), drives reporter gene expression in notochord. It contains 2 Myb #2, 1 Sp1/Kif, 1 E-box, 2 Brachyury and 3 Fox putative binding sites and one AC repeat (six repeats).

Hierarchy of Regulatory Regions

Regulated gene(s)

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

Construct(s) made to test this region

CONS00001296: p.Cirobu.REG.KH2012.C7:3853138-3854780>LacZ

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

3,853,1383,854,779

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 [3,853,959 / 3,853,966] This Fox binding site is one of the 3 putative binding sites located in the 313pb enhancer of Ephrin3 (KH.C7.568).
4 ZnF_(C2H2) n/a cacc [3,853,993 / 3,853,997] This Sp1/Klf binding site is located in the intronic enhancer of Ephrin3 (KH.C7.568).
5 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).
6 Fox n/a atttgt [3,854,049 / 3,854,056] This Fox binding site is located in the intronic enhancer of Ephrin3 (KH.C7.568).
7 T-Box n/a tcacac [3,854,157 / 3,854,163] This Brachyury binding site is located in the intronic enhancer of Ephrin3 (KH.C7.568).
8 bHLH n/a cagatg [3,854,194 / 3,854,200] This E-box binding site is located in the intronic enhancer of Ephrin3 (KH.C7.568).
9 Fox n/a ataaaca [3,854,204 / 3,854,211] This Fox binding site is located in the intronic enhancer of Ephrin3 (KH.C7.568).

Sequence

Aniseed Coordinates: [3,853,138 / 3,854,779] on scaffold KhC7

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: 1,642


acggttaggttaaaggcccacaggaaacctctggtttggcaccggttattatcagcgcgt
ctaataacacaatggaagtggtcaagtccaatttaatggctcgtttgagcgtatactttt
gtgctcatgacacttcataataatcatgcaatgttacactggcgccacaaaaattctgtc
agcatgtttgacaaaaaggattcgttttgaactgtctaccttaacatgcataaaatctct
ttgattacaataaagctcattaaaataacagcaaatagacgatttcgcaacaaaactaca
gttgttataactaaacacgcttgggataaattaaataaaagagcattggtttaaagcggt
tcgtacggcgaaataacagtcgttataacacgctgtataataagtataatgaaaacaaaa
cagttaaaaagcttgagttacagcaaaaccacagtcgttataacgcgcttatagaataaa
acaaacgaaactgttaaaaagcgtggctgttaatcgaacacagtctattctttgtcacgc
gatcaaagactattcttacgcaatattaggtgaaatccacagtcgtcccgttactttaca
aacgccgcttataagagcctttgtcacgttagcaaacatgccgctgtaaaacatttcgtg
tcaatattttccgctgtagtttgatcgcttaagcaattattgaatatgccgtgttaaaag
cggccaattcggtatattatagcaaagataatactgttaacattacgacattgaaatcta
aatgtattgaacggtaaacgtcgtattgaaaaatgaatctctatttataactctctacag
tatacggagagtccccacccattaaacaaacgtaatattaattgttagatagatatgatt
cacacaggatgtatttgtggtgtctggattaacccccagtaagaattctctgccatacaa
tagcagcgtgtttgaattactgcttgttttggaagttgattaagtcaggtcaatctaggt
cacacacacacacacactgtatgtatatacacaacacagatgtaatataaacattgtagt
attgaaatagtagtaaaccattttaaatgtacttagctctgagcacattgtatgttgtat
gccatatatagtagggtgggggaagatgggacaccttttcattctattttctcgttccag
ttggtagtaaacaaagaacgttcaaagaattattggatattgtgtgcttaaggtttccca
tctttccccatcctactatatatgcagtacagacgcttgttttatcttgattgaaaagta
atgcattatgcatgtagtaacaataatgtacattctttaaaagtccaaacataattaaat
gattttatctccacacaggctgcatggttggcaagtacaaatctacaaatggcaatacac
cttgtcaagtctgcccacagcacagcgtaacacattcaacatccgctagtcactgtactt
gtgtggctggacattatcgagccgaaaacgacccaatcagccaagcctgcactcgtaagt
agttttgtcaaatatttcacattcctttcgaaatatgatgccgatgtttcctttggtttt
taaaacaatgcctctaatattt

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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