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CIS-REGULATION

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  1. Region 'REG00000804'

Cis-regulatory Region

Name

Short name

n/a

Region ID

REG00000804

Status

Curated

Origin

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

Type of Activity

regulatory_region
(complex_region)

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, named -119bp or Ci-Nut Minimal Enhancer (Ci-NutME) in the paper. This region can drive expression in neural tube. This region is the minimal region driving neural tube expression. A part of this region (from -123bp to +14bp, named -119/-3 in the paper) was added upstream of the region. This region was named NutME +(-119/-3) in the paper.

Three putative regulatory motifs were present in this region : 2 ZicL binding sites and one Fox binding site.
As a part of Ci-NutME was repeated, all the binding sites were present twice.

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 insertion

Regulated gene(s)

KH2012:KH.C14.4 (ADRB2; P2RY12; RGR)

Construct(s) made to test this region

CONS00000767: pCi-Nut1 -123/94 & -123/14 added 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]
3 ZnF_(C2H2) n/a GTCGCTTTG [-41 / -33]
4 ZnF_(C2H2) n/a CATGCTGTG [63 / 71]
5 Fox n/a TGTATTGTTT [74 / 83]
6 ZnF_(C2H2) n/a GTCGCTTTG [96 / 104]

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.
Sequence was found thanks to the primers used in the paper.

Show sequence

Length: 353


TTCACTGCGTTGTCTAAATCCATGCGAAACAACAAAATAAGTCGCAAGACATGCTGTGCG
TGTATTGTTTTTTTGAAACCCCGTCGCTTTGTGAAAATCTGGTTGATTATTTTTTCGTAC
CAGTTTTACAGTTTAATTCACTGCGTTGTCTAAATCCATGCGAAACAACAAAATAAGTCG
CAAGACATGCTGTGCGTGTATTGTTTTTTTGAAACCCCGTCGCTTTGTGAAAATCTGGTT
GATTATTTTTTCGTACCAGTTTTACAGTTTAAATACGACTGTGCTTCAGTTTTTGTTAGT
ATTGAGTTGTACACTATATCAACAACATGGAAATTGATTTTGGATTTGCAAGA

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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