Login
Help

CIS-REGULATION

Submit your Data

  1. Region 'REG00001577'

Cis-regulatory Region

Name

Cirobu.REG.KhL96:471379-471527|Tbx2/3

Short name

Tbx2/3_151bp (José-Edwards 2013)

Region ID

REG00001577

Status

Curated

Origin

natural 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

Compared to its mother sequence (Tbx2/3_294bp), it lacks T-box binding sites #1 to 5. Its activity is strongly reduced.

Hierarchy of Regulatory Regions

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

Regulated gene(s)

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

Construct(s) made to test this region

CONS00001667: p.Cirobu.REG.KhL96:471379-471527>LacZ

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

471,379471,527

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 T-Box n/a GTGACA [471,390 / 471,396] 1st of the 4 T-box binding sites ascertained from ChIP-chip data (Kubo et al., 2010), from the 151bp enhancer of Tbx2/3.
2 T-Box n/a TAACAC [471,404 / 471,410] 2nd of the 4 T-box binding sites ascertained from ChIP-chip data (Kubo et al., 2010), from the 151bp enhancer of Tbx2/3.
3 T-Box n/a TTTCAC [471,447 / 471,453] 3rd of the 4 T-box binding sites ascertained from ChIP-chip data (Kubo et al., 2010), from the 151bp enhancer of Tbx2/3.
4 T-Box n/a TAGCAC [471,476 / 471,482] 4th of the 4 T-box binding sites ascertained from ChIP-chip data (Kubo et al., 2010), from the 151bp enhancer of Tbx2/3.

Sequence

Aniseed Coordinates: [471,379 / 471,527] on scaffold KhL96

This 151bp region is located in the 3rd intron of Tbx2/3. It is a cluster of 4 Ci-Bra and Ci-Tbx6b binding sites ascertained from ChIP-chip data. Primers used to amplify this region : 1787-1937 (151bp) F AtctagaCTATAAGCAATGTGACAAG and Tbx2/3 intron #3 cluster R (Notochord CRM 1-1937) ATccatggGGAATGGGGATTACGGTAGTCGAC This region is weakly active in the notochord and in tail muscles.

Show sequence

Length: 149


CTATAAGCAATGTGACAAGAACAAATAACACGAAGGGGCGAAATCTAACGCTAGATCAAC
TGCGTGGCTTTCACATCTTTGGTGGTCGAGTAATACATAGCACTAAACCGAAACAATTAT
TTTTCGTCGACTACCGTAATCCCCATTCC

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

Back to Top