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CIS-REGULATION

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  1. Region 'REG00001361'

Cis-regulatory Region

Name

Cirobu.REG.KH2012.C1:9941324-9941487_Myb1-2Mut|C6ST-like7

Short name

n/a

Region ID

REG00001361

Status

Curated

Origin

engineered 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 164bp sequence, located in the downstream region of KH.C1.738, drives reporter gene expression in mesenchyme but not in notochord. It contains 3 Fox, 2 Brachyury and 2 Myb#1 putative binding sites. Compared to the notochord-active WT enhancer, it lacks the second Myb#1 binding site.

Hierarchy of Regulatory Regions

Modification of Cirobu.REG.KH2012.C1:9941324-9941487|C6ST-like7 by deletion

Regulated gene(s)

KH2012:KH.C1.738 (CHST1; CHST3; CHST6)

Construct(s) made to test this region

CONS00001381: p.Cirobu.REG.KH2012.C1:9941324-9941487_Myb1-2Mut>LacZ

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

9,941,3249,941,487

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 T-Box n/a ttccac [9,941,332 / 9,941,338] This is one of the 2 Brachyury binding sites located in the notochord-active enhancer of KH.C1.738 (C6ST-like7).
2 Helix Turn Helix / Tryptophane clusters n/a taac [9,941,352 / 9,941,356] This is one of the 3 Myb#1 binding sites located in the notochord-active enhancer of KH.C1.738 (C6ST-like7).
3 T-Box n/a gtgata [9,941,357 / 9,941,363] This is one of the 2 Brachyrury binding sites located in the notochord-active enhancer of KH.C1.738 (C6ST-like7).
4 Fox n/a tgtttac [9,941,384 / 9,941,391] This is one of the 3 Fox binding sites located in the notochord-active enhancer of KH.C1.738 (C6ST-like7).
5 Fox n/a tatttac [9,941,433 / 9,941,440] This is one of the 3 Fox binding sites located in the notochord-active enhancer of KH.C1.738 (C6ST-like7).
6 Helix Turn Helix / Tryptophane clusters n/a gtta [9,941,444 / 9,941,448] This is one of the 3 Myb#1 binding sites located in the notochord-active enhancer of KH.C1.738 (C6ST-like7). Deletion of this first Myb#1 BS does not affect enhancer activity.
7 Fox n/a tatttac [9,941,450 / 9,941,457] This is one of the 3 Fox binding sites located in the notochord-active enhancer of KH.C1.738 (C6ST-like7). Deletion of this first Fox BS does not affect enhancer activity.

Sequence

Aniseed Coordinates: [9,941,324 / 9,941,487] on scaffold KhC1

The second Myb#1 binding site is mutated. TAAC replaced by GCCC. This sequence was retrieved using ANISEED Blast tool, thanks to the information provided in FigS1.f and TableS5 of Jose-Edwards et al. 2015.

Show sequence

Length: 164


ccctcgcattccacattctcgttttcattaacagtgataatgcctatctcgaaaactcta
tgtttactcttaggaatgGCCcaagtatctgcgagaagtaatcagacggtatttactgac
gttaaatatttacaaaaggccttgcaatctaggattctctagag

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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