Aniseed - Cis-regulation

Cis-regulatory Region

Name

Cirobu.REG.KhL96:471236-471527_Tbox5-6-7-mut|Tbx2/3

Short name

Tbx2/3_294bp_T5T6T7m (José-Edwards 2013)

Region ID

REG00001585

Status

Curated

Origin

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

Type of Activity

regulatory_region
(enhancer)

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

Mutation of the 5th, 6th and 7th T-box binding sites abrogates its notochord enhancer activity.

Hierarchy of Regulatory Regions

Modification of Cirobu.REG.KhL96:471236-471527|Tbx2/3 by substitution

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

CONS00001675: p.Cirobu.REG.KhL96:471236-471527_Tbox5-6-7-mut>LacZ

Show in situ data

Overview of functional TF binding sites in this region

471,236471,526

	Motif Name	Binding Factor(s)	Sequence	Position in Region	Comment
1	T-Box	n/a	TGCCAC	[471,276 / 471,282]	1st of the 9 T-box binding sites ascertained from ChIP-chip data (Kubo et al., 2010), from the 294bp notochord enhancer of Tbx2/3.
2	T-Box	n/a	TGACAC	[471,303 / 471,309]	2nd of the 9 T-box binding sites ascertained from ChIP-chip data (Kubo et al., 2010), from the 294bp notochord enhancer of Tbx2/3.
3	T-Box	n/a	GTGGGA	[471,326 / 471,332]	3rd of the 9 T-box binding sites ascertained from ChIP-chip data (Kubo et al., 2010), from the 294bp notochord enhancer of Tbx2/3.
4	T-Box	n/a	TGACAC	[471,361 / 471,367]	4th of the 9 T-box binding sites ascertained from ChIP-chip data (Kubo et al., 2010), from the 294bp notochord enhancer of Tbx2/3.
5	T-Box	n/a	TTTCAC	[471,446 / 471,452]	8th of the 9 T-box binding sites ascertained from ChIP-chip data (Kubo et al., 2010), from the 294bp notochord enhancer of Tbx2/3.
6	T-Box	n/a	TAGCAC	[471,475 / 471,481]	9th of the 9 T-box binding sites ascertained from ChIP-chip data (Kubo et al., 2010), from the 294bp notochord enhancer of Tbx2/3.

Sequence

Aniseed Coordinates: [471,236 / 471,526] on scaffold KhL96

The 5th, 6th and 7th T-box binding sites of the 294bp notochord enhancer of Tbx2/3 were mutated : GTG replaced by ata or CAC by tat (in lowercase in the upper sequence). It is no longer active in notochord, only weakly in mesenchyme and tail muscles.

Show sequence

Length: 291

GTGGACAGACAGGGTAGTTAAATACGTTACAAAGTTCATTTGCCACCCAGCACAGTATTG
TACTTTATGACACTTGTGTTTATTCGTATAGTGGGACTAGTTATAAAATAAAACGGTTTA
TTCTCTGACACGTAAataTTAATCTATAAGCAATataACAAGAACAAATAAtatAAGGGG
CGAAATCTAACGCTAGATCAACTGCGTGGCTTTCACATCTTTGGTGGTCGAGTAATACAT
AGCACTAAACCGAAACAATTATTTTTCGTCGACTACCGTAATCCCCATTCC

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