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CIS-REGULATION

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  1. Region 'REG00001148'

Cis-regulatory Region

Name

Cirobu.REG.KH2012.C3:2806773-2807141|Efna.d

Short name

Efna.d (-360)

Region ID

REG00001148

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Izumi Oda-Ishii (2017-02-01)

Annotator

Marion Gueroult-Bellone (2017-09-03)

Curator

Marion Gueroult-Bellone (2018-03-13)

View position in WashU

Description

The 360pb region located upstream Efna.d TSS drives reporter expression specifically in the animal hemisphere. Compared to the 419pb minimal enhancer, it lacks a GATA binding site (only 3 left) and has lower activity.

Hierarchy of Regulatory Regions

Modification of Cirobu.REG.KH2012.C3:2806773-2807200|Efna.d by deletion

Regulated gene(s)

KH2012:KH.C3.716 (EFNA1; EFNA4; EFNA5)

Construct(s) made to test this region

CONS00001117: p.Cirobu.REG.KH2012.C3:2806773-2807141>GFP

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

2,806,7732,807,140

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 ZnF_(GATA) n/a ctatct [2,807,058 / 2,807,064] One of the 4 GATA4/5/6 (Gata.a) binding sites located on the 419pb upstream enhancer of KH.C3.716. When 3 or 4 of these TFBS are missing or mutated, the enhancer is inactive.
2 ZnF_(GATA) n/a ttatca [2,807,090 / 2,807,096] One of the 4 GATA4/5/6 (Gata.a) binding sites located on the 419pb upstream enhancer of KH.C3.716. When 3 or 4 of these TFBS are missing or mutated, the enhancer is inactive.
3 ZnF_(GATA) n/a ttatct [2,807,121 / 2,807,127] One of the 4 GATA4/5/6 (Gata.a) binding sites located on the 419pb upstream enhancer of KH.C3.716. When 3 or 4 of these TFBS are missing or mutated, the enhancer is inactive.

Sequence

Aniseed Coordinates: [2,806,773 / 2,807,140] on scaffold KhC3

Sequence obtained using Aniseed's Blast, thanks to the explanations in the article (Fig S7.A).

Show sequence

Length: 368


TTTAGGATctgaaaagtaaacacatatttagataactgaaatactataagcctttacttc
taaaaatcaaactggttgacatttattcttactgagcttgtggtattataaaatacaaac
gattagacgctatcaacttatttaatcgaactgcgttgaattcggtctcacgaaattgta
agctgcttactctgcgaaccgagatacactgatttgcggtagagagtcgaccgctataaa
gccacacaaattacggacttcttctcttttttcggtcgctgttcgctatctctcgtctga
ccaatcgagagtccagcttatcataatatttatgctcgcactcgtcccttatctgcttat
tagcttgg

Reference(s)

Oda-Ishii et al. (2016). A Maternal System Initiating the Zygotic Developmental Program through Combinatorial Repression in the Ascidian Embryo. PLoS Genet. 12(5):e1006045

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