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CIS-REGULATION

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  1. Transcript 'KH2012:KH.C2.821.v1....' > 
  2. Region 'REG00001236' > 
  3. Region 'REG00001308'

Cis-regulatory Region

Name

Cirobu.REG.KH2012.L65:311070-311303|Dyrk2/3/4

Short name

n/a

Region ID

REG00001308

Status

Curated

Origin

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

Type of Activity

regulatory_region
(enhancer)

Author

Diana S. José-Edwards (2018-05-08)

Annotator

Marion Gueroult-Bellone (2018-05-08)

Curator

Marion Gueroult-Bellone (2018-05-08)

View position in WashU

Description

This 228pb sequence, located in the upstream region of KH.L65.10, drives reporter gene expression in notochord. It contains 2 Fox, 2 E-box and 3 Brachyury putative binding sites. Compared to the larger active enhancer (458pb), it lacks the 3 Brachyury binding sites.

Hierarchy of Regulatory Regions

Modification of Cirobu.REG.KH2012.L65:310840-311303|Dyrk2/3/4 by deletion

Regulated gene(s)

KH2012:KH.L65.10 (DYRK2; DYRK3; DYRK4)

Construct(s) made to test this region

CONS00001328: p.Cirobu.REG.KH2012.L65:311070-311303>LacZ

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

311,070311,303

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 T-Box n/a gtgtaa [311,169 / 311,175] This is one of the 6 Brachyrury binding sites located in the notochord-active enhancer of KH.L65.10.
2 Fox n/a gtaaata [311,171 / 311,178] This is one of the 2 Fox binding sites located in the notochord-active enhancer of KH.L65.10. Its mutation does not affect the enhancer activity in the notochord.
3 bHLH n/a catctg [311,181 / 311,187] This is one of the 2 E-box binding sites located in the notochord-active enhancer of KH.L65.10.
4 T-Box n/a gtgtta [311,190 / 311,196] This is the second of the 6 Brachyury binding sites located in the notochord-active enhancer of KH.L65.10. Its mutation can affect the enhancer activity in the notochord.
5 bHLH n/a cacatg [311,206 / 311,212] This is one of the 2 E-box binding sites located in the notochord-active enhancer of KH.L65.10.
6 T-Box n/a gtgtta [311,228 / 311,234] This is one of the 6 Brachyury binding sites located in the notochord-active enhancer of KH.L65.10.
7 Fox n/a gtaaata [311,239 / 311,246] This is one of the 2 Fox binding sites located in the notochord-active enhancer of KH.L65.10. Deletion of this Fox BS does not affect enhancer activity in the notochord.

Sequence

Aniseed Coordinates: [311,070 / 311,303] on scaffold KhL65

This sequence was retrieved using ANISEED Blast tool, thanks to the information provided in FigS3.d and TableS5 of Jose-Edwards et al. 2015.

Show sequence

Length: 234


gatatctcgtgtgtgtctggtacatctcaatttaacagcctcgacaccaacgccttacat
gcgtttgtaagttcgcttcgcaacctatttaacaaaccggtgtaaatataacatctgtag
gtgttatatttagagtcacatggcggcgtacacgcctggtgttattttggtaaataaaac
ttaacgtttcaagcaaaaggtaaactgtagaatatagtaggttggggtaagtcg

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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