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CIS-REGULATION

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  1. Transcript 'KH2012:KH.L116.85.v2...' > 
  2. Region 'REG00001391' > 
  3. Transcript 'KH2012:KH.L116.85.v1...' > 
  4. Transcript 'KH2012:KH.C7.455.v1....' > 
  5. Region 'REG00001372'

Cis-regulatory Region

Name

Cirobu.REG.KH2012.L128:214719-215033|Furin,Nec1/2

Short name

n/a

Region ID

REG00001372

Status

Curated

Origin

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

Type of Activity

no_output

Author

Diana S. José-Edwards (2018-05-16)

Annotator

Marion Gueroult-Bellone (2018-05-16)

Curator

Marion Gueroult-Bellone (2018-05-16)

View position in WashU

Description

This 228bp sequence, located in an intronic region of KH.L128.2, drives reporter no gene expression in notochord. It contains 1 Myb#2, 3 Brachyury and 2 Fox putative binding sites. Compared to the longer notochord-active enhancer, it lacks 3 Brachyury, 3 E-box, 1 Myb#2 and 1 Sp1/Klf binding sites.

Hierarchy of Regulatory Regions

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

Regulated gene(s)

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

Construct(s) made to test this region

CONS00001392: p.Cirobu.REG.KH2012.L128:214719-215033>LacZ

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

214,719215,033

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 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.
2 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.
3 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.
4 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.
5 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.
6 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: [214,719 / 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. Sequence of the primers used : Forward : AAgcatgcAGCTTTTTTGGTAAGCTATTTGCTTGTG Reverse : ActcgagACATGCATACATCAAAACACATTGTATAAAG Lowercase letters correspond to XhoI/SphI restriction site. In the article, they obtain a 228bp fragment using these enhancers, but the fragment is longer (315bp) based on Genomic sequence.

Show sequence

Length: 315


agcttttttggtaagctatttgcttgtgaagctgtagcaatgtagcaggacaaactacta
aatgtggaaagtataaaacttagtgaaacgagtattttgtatatattaatctggcattta
aaaatcagcgtttatgttagtttgtataaacagaactggctcgaattcaacatcaaagct
attattgttattggtattattgaaggggatgaaaaaaacgccagtgtttggtggatatac
tgatgtgtgccatgtacgctgccgtattttatatgtattcgttactttatacaatgtgtt
ttgatgtatgcatgt

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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