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CIS-REGULATION

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  1. Region 'REG00001576'

Cis-regulatory Region

Name

Cirobu.REG.KhL96:471236-471407|Tbx2/3

Short name

Tbx2/3_172bp (José-Edwards 2013)

Region ID

REG00001576

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 #7, 8 and 9. 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

CONS00001666: p.Cirobu.REG.KhL96:471236-471407>LacZ

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

471,236471,407

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 T-Box n/a TGCCAC [471,276 / 471,282] 1st of the 6 T-box binding sites ascertained from ChIP-chip data (Kubo et al., 2010), from the 172bp notochord enhancer of Tbx2/3.
2 T-Box n/a TGACAC [471,303 / 471,309] 2nd of the 6 T-box binding sites ascertained from ChIP-chip data (Kubo et al., 2010), from the 172bp enhancer of Tbx2/3.
3 T-Box n/a GTGGGA [471,326 / 471,332] 3rd of the 6 T-box binding sites ascertained from ChIP-chip data (Kubo et al., 2010), from the 172bp notochord enhancer of Tbx2/3.
4 T-Box n/a TGACAC [471,361 / 471,367] 4th of the 6 T-box binding sites ascertained from ChIP-chip data (Kubo et al., 2010), from the 172bp notochord enhancer of Tbx2/3.
5 T-Box n/a GTGTTA [471,371 / 471,377] 5th of the 6 T-box binding sites ascertained from ChIP-chip data (Kubo et al., 2010), from the 172bp enhancer of Tbx2/3.
6 T-Box n/a GTGACA [471,390 / 471,396] 6th of the 6 T-box binding sites ascertained from ChIP-chip data (Kubo et al., 2010), from the 172bp enhancer of Tbx2/3.

Sequence

Aniseed Coordinates: [471,236 / 471,407] on scaffold KhL96

This 172bp region is located in the 3rd intron of Tbx2/3. It is a cluster of 6 Ci-Bra and Ci-Tbx6b binding sites ascertained from ChIP-chip data. Primers used to amplify this region : (294bp) F: AtctagaGTGGACAGACAGGGTAGTTAAATAC and (172bp) R: TAccatggGTTATTTGTTCTTGTCACA This region is weakly active in the notochord, in tail muscles and in the sensory vesicle.

Show sequence

Length: 172


GTGGACAGACAGGGTAGTTAAATACGTTACAAAGTTCATTTGCCACCCAGCACAGTATTG
TACTTTATGACACTTGTGTTTATTCGTATAGTGGGACTAGTTATAAAATAAAACGGTTTA
TTCTCTGACACGTAAGTGTTAATCTATAAGCAATGTGACAAGAACAAATAAC

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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