Aniseed - Cis-regulation

Cis-regulatory Region

Name

Cirobu.REG.KH2012.C12:712425-712552|CbpD,CbpE,CbpN

Short name

n/a

Region ID

REG00001356

Status

Curated

Origin

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

Type of Activity

regulatory_region
(enhancer)

Author

Diana S. José-Edwards (2018-05-09)

Annotator

Marion Gueroult-Bellone (2018-05-09)

Curator

Marion Gueroult-Bellone (2018-05-09)

View position in WashU

Description

This 128bp sequence, located in the downstream region of KH.C12.16, drives reporter gene expression in notochord, central nervous system and tail muscles. It contains 3 Fox and 1 Myb#3 putative binding sites.

Hierarchy of Regulatory Regions

Modification of Cirobu.REG.KH2012.C12:712425-712628|CbpD,CbpE,CbpN by deletion

Cirobu.REG.KH2012.C12:711845-714190|CbpD,CbpE,CbpN REG00001352 [ regulatory_region (complex_region) ]
- Cirobu.REG.KH2012.C12:712425-714190|CbpD,CbpE,CbpN REG00001353 [ regulatory_region (complex_region) ]
  - Cirobu.REG.KH2012.C12:712628-713987|CbpD,CbpE,CbpN REG00001354 [ no_output ]
  - Cirobu.REG.KH2012.C12:712425-712628|CbpD,CbpE,CbpN REG00001355 [ regulatory_region (enhancer) ]
    - Cirobu.REG.KH2012.C12:712425-712552|CbpD,CbpE,CbpN REG00001356 [ regulatory_region (enhancer) ]
      - Cirobu.REG.KH2012.C12:712425-712552_Myb3Mut|CbpD,CbpE,CbpN REG00001357 [ regulatory_region (enhancer) ]
      - Cirobu.REG.KH2012.C12:712425-712503|CbpD,CbpE,CbpN REG00001358 [ no_output ]

Regulated gene(s)

KH2012:KH.C12.16 (CPD; CPE; CPN1)

Construct(s) made to test this region

CONS00001376: p.Cirobu.REG.KH2012.C12:712425-712552>LacZ

Show in situ data

Overview of functional TF binding sites in this region

712,425712,552

	Motif Name	Binding Factor(s)	Sequence	Position in Region	Comment
1	Fox	n/a	acaaaca	[712,452 / 712,459]	This is one of the 3 Fox binding sites located in the notochord-active enhancer of KH.C12.16.
2	Fox	n/a	acaaata	[712,465 / 712,472]	This is one of the 3 Fox binding sites located in the notochord-active enhancer of KH.C12.16.
3	Fox	n/a	acaata	[712,480 / 712,486]	tcacatatatgcgttgtgacgtcatatacaaacaacaagaacaaatagtgacgtaacaatacaaatatcgagtaaattcgacgtcacggttgaaccTGCgtgtggataagttaaccatgacgtcaccg
4	Helix Turn Helix / Tryptophane clusters	n/a	ccgttg	[712,519 / 712,525]	This Myb#3 binding site is located in the notochord-active enhancer of KH.C12.16. Mutation or deletion of this binding site inhibits enhancer activity in the notochord.

Sequence

Aniseed Coordinates: [712,425 / 712,552] on scaffold KhC12

This sequence was retrieved using ANISEED Blast tool, thanks to the information provided in FigS1.e and TableS5 of Jose-Edwards et al. 2015.

Show sequence

Length: 128

tcacatatatgcgttgtgacgtcatatacaaacaacaagaacaaatagtgacgtaacaat
acaaatatcgagtaaattcgacgtcacggttgaaccgttgtgtggataagttaaccatga
cgtcaccg

Reference(s)

José-Edwards et al. (2015). Brachyury, Foxa2 and the cis-Regulatory Origins of the Notochord. PLoS Genet. 11(12):e1005730