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CIS-REGULATION

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  1. Region 'REG00000799'

Cis-regulatory Region

Name

Ci-Nut1 -123/94 ZicL2 mutated 3

Short name

n/a

Region ID

REG00000799

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Kotaro Shimai (2010-06-30)

Annotator

Clara Degos (2011-08-11)

Curator

Delphine Dauga (2011-08-11)

View position in WashU

Description

Region upstream of Ci-Nut1 from -123bp to +94bp. This region can drive expression in neural tube. This region is the minimal region driving neural tube expression.

Three putative regulatory motifs were present in this region : 2 ZicL binding sites and one Fox binding site. Here the second putative ZicL binding site was mutated in all bases : GTCGCTTTG => GTCGATTTT. This region was named ZicL2(m59) in the paper, and these mutations have no effect on neural tube expression.

Transcription start site is based on the start of the first exon of the KH transcript model.

Be carefull the coordinates in the paper may be different from ANISEED coordinates.

Hierarchy of Regulatory Regions

Modification of Ci-Nut1 -123/94 by substitution

Regulated gene(s)
n/a
Construct(s) made to test this region

CONS00000762: pCi-Nut1 -123/94 ZicL2 mutated 3 pVenus::EGFP

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

1,413,7951,414,011

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 ZnF_(C2H2) n/a CATGCTGTG [-74 / -66]
2 Fox n/a TGTATTGTTT [-63 / -54]

Sequence

Aniseed Coordinates: [1,413,795 / 1,414,011] on scaffold KhC14

Transcription start site is based on the start of the first exon of the KH transcript model.

Show sequence

Length: 217


TTCACTGCGTTGTCTAAATCCATGCGAAACAACAAAATAAGTCGCAAGACATGCTGTGCG
TGTATTGTTTTTTTGAAACCCCGTCGATTTTTGAAAATCTGGTTGATTATTTTTTCGTAC
CAGTTTTACAGTTTAAATACGACTGTGCTTCAGTTTTTGTTAGTATTGAGTTGTACACTA
TATCAACAACATGGAAATTGATTTTGGATTTGCAAGA

Reference(s)

Shimai et al. (2010). Upstream regulatory sequences required for specific gene expression in the ascidian neural tube. Zool. Sci. 27(2):76-83

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