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CIS-REGULATION

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  1. Transcript 'Moocci.CG.ELv1_2.S17...' > 
  2. Clone 'cien178021' > 
  3. Region 'REG00001583'

Cis-regulatory Region

Name

Cirobu.REG.KhL96:471236-471527_Tbox6-7-mut|Tbx2/3

Short name

Tbx2/3_294bp_T6T7m (José-Edwards 2013)

Region ID

REG00001583

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 7th and 6th T-box binding sites neutralizes the notochord enhancer activity.

Hierarchy of Regulatory Regions

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

Regulated gene(s)

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

Construct(s) made to test this region

CONS00001673: p.Cirobu.REG.KhL96:471236-471527_Tbox6-7-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 GTGTTA [471,371 / 471,377] 5th of the 9 T-box binding sites ascertained from ChIP-chip data (Kubo et al., 2010), from the 294bp notochord enhancer of Tbx2/3. It's mutation alone increase the enhancer notochord activity and specificity. Mutated togeter with T-box5 and/or T-box7, it abrogates the notochord activity.
6 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.
7 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 6th and 7th T-box binding sites of the 294bp notochord enhancer of Tbx2/3 were mutated : GTG replaced by ata and CAC by tat respectively (in lowercase in the upper sequence). It is no longer active in notochord but strongly is in mesenchyme and tail muscles.

Show sequence

Length: 291


GTGGACAGACAGGGTAGTTAAATACGTTACAAAGTTCATTTGCCACCCAGCACAGTATTG
TACTTTATGACACTTGTGTTTATTCGTATAGTGGGACTAGTTATAAAATAAAACGGTTTA
TTCTCTGACACGTAAGTGTTAATCTATAAGCAATataACAAGAACAAATAAtatAAGGGG
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

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