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CIS-REGULATION

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  1. Transcript 'KH2012:KH.C3.51.v1.A...' > 
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  4. Region 'REG00001278'

Cis-regulatory Region

Name

Cirobu.REG.KH2012.C7:3853138-3853945|Ephrin3

Short name

Ephrin3_CRM66_CRM66_814pb

Region ID

REG00001278

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 814pb sequence, located in an intronic region of Ephrin3 (KH.C7.568), drives no reporter gene expression in notochord.

Hierarchy of Regulatory Regions

Modification of Cirobu.REG.KH2012.C7:3853138-3854780|Ephrin3 by deletion

Regulated gene(s)

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

Construct(s) made to test this region

CONS00001297: p.Cirobu.REG.KH2012.C7:3853138-3853945>LacZ

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

3,853,1383,853,945

Motif Name Binding Factor(s) Sequence Position in Region Comment

Sequence

Aniseed Coordinates: [3,853,138 / 3,853,945] on scaffold KhC7

Sequence of the primers used : Forward : TtctagaTGcACGGTTAGGTTAAAGGCC Reverse : ActcgagCAATACGACGTTTACCGTTCAATAC Lowercase letters correspond to XbaI/XhoI 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: 808

acggttaggttaaaggcccacaggaaacctctggtttggcaccggttattatcagcgcgt
ctaataacacaatggaagtggtcaagtccaatttaatggctcgtttgagcgtatactttt
gtgctcatgacacttcataataatcatgcaatgttacactggcgccacaaaaattctgtc
agcatgtttgacaaaaaggattcgttttgaactgtctaccttaacatgcataaaatctct
ttgattacaataaagctcattaaaataacagcaaatagacgatttcgcaacaaaactaca
gttgttataactaaacacgcttgggataaattaaataaaagagcattggtttaaagcggt
tcgtacggcgaaataacagtcgttataacacgctgtataataagtataatgaaaacaaaa
cagttaaaaagcttgagttacagcaaaaccacagtcgttataacgcgcttatagaataaa
acaaacgaaactgttaaaaagcgtggctgttaatcgaacacagtctattctttgtcacgc
gatcaaagactattcttacgcaatattaggtgaaatccacagtcgtcccgttactttaca
aacgccgcttataagagcctttgtcacgttagcaaacatgccgctgtaaaacatttcgtg
tcaatattttccgctgtagtttgatcgcttaagcaattattgaatatgccgtgttaaaag
cggccaattcggtatattatagcaaagataatactgttaacattacgacattgaaatcta
aatgtattgaacggtaaacgtcgtattg

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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