Aniseed - Cis-regulation

Region 'REG00001578'

Cis-regulatory Region

Name

Cirobu.REG.KhL96:471415-471527|Tbx2/3

Short name

Tbx2/3_115bp (José-Edwards 2013)

Region ID

REG00001578

Status

Curated

Origin

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

Type of Activity

inactive_region

Author

Diana S. José-Edwards (2023-02-23)

Annotator

Marion Gueroult-Bellone (2023-02-23)

Curator

Marion Gueroult-Bellone (2023-02-23)

View position in WashU

Description

Compared to its mother region (Tbx2/3_151bp), it lacks 2 T-box binding sites and is nota able anymore to drive gene expression.

Hierarchy of Regulatory Regions

Modification of Cirobu.REG.KhL96:471379-471527|Tbx2/3 by deletion

Cirobu.REG.KhL96:469627-471527|Tbx2/3 REG00001574 [ regulatory_region (enhancer) ]
- Cirobu.REG.KhL96:471236-471527|Tbx2/3 REG00001575 [ regulatory_region (enhancer) ]

Regulated gene(s)

KH2012:KH.L96.87 (TBX2; TBX3; TBX4)

Construct(s) made to test this region

CONS00001668: p.Cirobu.REG.KhL96:471415-471527>LacZ

Show in situ data

Overview of functional TF binding sites in this region

471,415471,527

	Motif Name	Binding Factor(s)	Sequence	Position in Region	Comment
1	T-Box	n/a	TTTCAC	[471,447 / 471,453]	1st of the 2 T-box binding sites ascertained from ChIP-chip data (Kubo et al., 2010), from the 151bp inactive upstream region of Tbx2/3.
2	T-Box	n/a	TAGCAC	[471,476 / 471,482]	2nd of the 2 T-box binding sites ascertained from ChIP-chip data (Kubo et al., 2010), from the 151bp inactive upstream region of Tbx2/3.

Sequence

Aniseed Coordinates: [471,415 / 471,527] on scaffold KhL96

This 115bp region is located in the 3rd intron of Tbx2/3. It is a cluster of 2 Ci-Bra and Ci-Tbx6b binding sites ascertained from ChIP-chip data. Primers used to amplify this region : 1823-1937 (115bp) F AtctagaGGCGAAATCTAACGCTAGATCAAC and Tbx2/3 intron #3 cluster R (Notochord CRM 1-1937) ATccatggGGAATGGGGATTACGGTAGTCGAC This region has no enhancer activity.

Show sequence

Length: 113

GGCGAAATCTAACGCTAGATCAACTGCGTGGCTTTCACATCTTTGGTGGTCGAGTAATAC
ATAGCACTAAACCGAAACAATTATTTTTCGTCGACTACCGTAATCCCCATTCC

Reference(s)

José-Edwards et al. (2013). Tbx2/3 is an essential mediator within the Brachyury gene network during Ciona notochord development. Development 140(11):2422-33