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CIS-REGULATION

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  1. Transcript 'KH2012:KH.C2.14.v5.A...' > 
  2. Transcript 'Phmamm.CG.MTP2014.S3...' > 
  3. Transcript 'KH2012:KH.L5.8.v6.A....' > 
  4. Region 'REG00001224' > 
  5. Region 'REG00001373'

Cis-regulatory Region

Name

Cirobu.REG.KH2012.L128:214487-215033_Bra4Mut1|Furin,Nec1/2

Short name

n/a

Region ID

REG00001373

Status

Curated

Origin

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

Type of Activity

regulatory_region
(enhancer)

Author

n/a ()

Annotator

Marion Gueroult-Bellone (2018-05-16)

Curator

Marion Gueroult-Bellone (2018-05-16)

View position in WashU

Description

This 547bp sequence, located in an intronic region of KH.L128.2, drives reporter gene expression in tail muscles and mesenchyme. It contains 1 Myb#2, 6 Brachyury, 2 Fox, 3 E-box, 1 Myb#3 and 1 Sp1/Klf putative binding sites. Compared to the notochord-active WT enhancer, it lacks the 4th Brachyury binding site.

Hierarchy of Regulatory Regions

Modification of Cirobu.REG.KH2012.L128:214487-215033|Furin,Nec1/2 by substitution

Regulated gene(s)

KH2012:KH.L128.2 (FURIN; PCSK1; PCSK2)

Construct(s) made to test this region

CONS00001393: p.Cirobu.REG.KH2012.L128:214487-215033_Bra4Mut1>lacZ

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

214,487215,033

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 Helix Turn Helix / Tryptophane clusters n/a ccgttg [214,502 / 214,508] This Myb#3 binding site is located on the notochord-active intronic enhancer of KH.L128.2.
2 T-Box n/a tagcac [214,578 / 214,584] This is the second of the 8 Brachyury binding sites located on the notochord-active intronic enhancer of KH.L128.2.
3 bHLH n/a cacatg [214,581 / 214,587] This is the second of the 4 E-box binding sites located on the notochord-active intronic enhancer of KH.L128.2.
4 bHLH n/a catttg [214,593 / 214,599] This is the third of the 4 E-box binding sites located on the notochord-active intronic enhancer of KH.L128.2.
5 ZnF_(C2H2) n/a ccacc [214,616 / 214,621] This Sp1/Klf binding site is located on the notochord-active intronic enhancer of KH.L128.2.
6 T-Box n/a tttcac [214,633 / 214,639] This is the third of the 8 Brachyury binding sites located on the notochord-active intronic enhancer of KH.L128.2.
7 bHLH n/a cagatg [214,647 / 214,653] This is the fourth of the 4 E-box binding sites located on the notochord-active intronic enhancer of KH.L128.2.
8 T-Box n/a ttacac [214,697 / 214,703] This is the fifth of the 8 Brachyury binding sites located on the notochord-active intronic enhancer of KH.L128.2.
9 Fox n/a tatttgc [214,735 / 214,742] This is the second of the 2 Fox binding sites located on the notochord-active intronic enhancer of KH.L128.2.
10 T-Box n/a gtggaa [214,782 / 214,788] This is the 6th of the 8 Brachyury binding sites located on the notochord-active intronic enhancer of KH.L128.2.
11 T-Box n/a gtgaaa [214,801 / 214,807] This is the 7th of the 8 Brachyury binding sites located on the notochord-active intronic enhancer of KH.L128.2.
12 Fox n/a ataaaca [214,864 / 214,871] This is the third of the 3 Fox binding sites located on the notochord-active intronic enhancer of KH.L128.2. Its mutation does not affect enhancer activity in the notochord, but it increases activity in the mesenchyme.
13 Helix Turn Helix / Tryptophane clusters n/a attgaa [214,917 / 214,923] This is the second of the 2 Myb#2 binding sites located on the notochord-active intronic enhancer of KH.L128.2.
14 T-Box n/a gtgcca [214,965 / 214,971] This is the 8th of the 8 Brachyury binding sites located on the notochord-active intronic enhancer of KH.L128.2. Its mutation decreases but does not inhibit enhancer activity in the notochord.

Sequence

Aniseed Coordinates: [214,487 / 215,033] on scaffold KhL128

This sequence was retrieved using ANISEED Blast tool, thanks to the information provided in FigS3.c and TableS5 of Jose-Edwards et al. 2015. The 4th Brachyrury binding site is mutated. GTGTCA replaced by GTGGAC.

Show sequence

Length: 547


ggctcgaacccacgaccgttggattaagagtccaacgctctaccgactgagctagcaggg
cggtagagatgaactgattaaggtatcctgttagcacatgcaacttcatttgtgattata
gcattagaaccaccgccgcaacagtgtttcacaacagaagcagatgaagcattttgtttt
ttcttgtcaacacGTCcacttagttgttgattacactcgcgcgtactttgcaagcttttt
tggtaagctatttgcttgtgaagctgtagcaatgtagcaggacaaactactaaatgtgga
aagtataaaacttagtgaaacgagtattttgtatatattaatctggcatttaaaaatcag
cgtttatgttagtttgtataaacagaactggctcgaattcaacatcaaagctattattgt
tattggtattattgaaggggatgaaaaaaacgccagtgtttggtggatatactgatgtgt
gccatgtacgctgccgtattttatatgtattcgttactttatacaatgtgttttgatgta
tgcatgt

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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