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CIS-REGULATION

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  1. Clone 'ciad054k15' > 
  2. Clone 'cien114116' > 
  3. Clone 'cien49171' > 
  4. Clone 'ciht009f24' > 
  5. Region 'REG00001559'

Cis-regulatory Region

Name

Cirobu.REG.KH2012.L59:1807-2057|Zic-r.b

Short name

Zic-r.b -251bp (Imai 2016)

Region ID

REG00001559

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Kaoru S. Imai (2022-11-28)

Annotator

Marion Gueroult-Bellone (2022-11-28)

Curator

Marion Gueroult-Bellone (2022-11-28)

View position in WashU

Description

This 250bp DNA sequence is located directly upstream of Zic-r.b (KhL59.1) transcription start site. This cis-regulatory element is active in the marginal cells: NN (notochord and nerve chord, A6.2 and A6.4), aMM (Muscle, mesenchyme and notochord, B6.2) and pMM (Muscle and mesenchyme, B6.4) lineages at the 32-cell stage.

Hierarchy of Regulatory Regions

Modification of Cirobu.REG.KH2012.L59:1807-2086|Zic-r.b by deletion

Regulated gene(s)

KH2012:KH.L59.1 (ZIC2; ZIC3; ZIC4)

Construct(s) made to test this region

CONS00001643: p.Cirobu.REG.KH2012.L59:1807-2057>LacZ

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

1,8072,056

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 Fox n/a AACA [1,813 / 1,817] Conserved putative GATA binding site. When the 3 Fox sites are mutated, the enhancer activity of this region is strongly reduced.
2 ZnF_(GATA) n/a TTATCT [1,828 / 1,834] Conserved putative GATA binding site. When the 3 GATA sites are mutated, the enhancer activity of this region is strongly reduced.
3 ZnF_(GATA) n/a TTATCT [1,837 / 1,843] Conserved putative GATA binding site. When the 3 GATA sites are mutated, the enhancer activity of this region is strongly reduced.
4 Fox n/a TATTTATT [1,844 / 1,852] Conserved putative GATA binding site. When the 3 Fox sites are mutated, the enhancer activity of this region is strongly reduced.
5 ZnF_(GATA) n/a TTATCG [1,930 / 1,936] Conserved putative GATA binding site. When the 3 GATA sites are mutated, the enhancer activity of this region is strongly reduced.
6 Fox n/a AACAACA [2,028 / 2,035] Conserved putative GATA binding site. When the 3 Fox sites are mutated, the enhancer activity of this region is strongly reduced.

Sequence

Aniseed Coordinates: [1,807 / 2,056] on scaffold KhL59

KH coordinates given by the authors. Part of this region (KhL59:1799-2064) is higly conserved with Ciona savignyi and higly similar to the usptream regions of the 3 other Zic-r.b copies from Ciona robusta genome (KhL59.12, KhS816.1 and S816.4).

Show sequence

Length: 250


TTTCGTAACACAATGACTTAATTATCTTCTTTATCTTTATTTATTTGACTTCCGATCGCC
CGTCGCTTTCCCATGCGCACGTGGTTCGACCCCCCACCTCCGAAATTTACATCGCGAAGG
TAATTATCGTGTCGATCGCTCGTCTCGCGGTACTTTTGGCACGCTTTCGCTCGTGCCTGT
CTACGCAAGGTTTACCTATGGCACTTTCTCTACGTGAAGTCAACAACAAGTTACACATTG
CAGAGTGGTT

Reference(s)

Imai et al. (2016). Antagonism between β-catenin and Gata.a sequentially segregates the germ layers of ascidian embryos. Development 143(22):4167-4172

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