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CIS-REGULATION

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  1. Region 'REG00000673'

Cis-regulatory Region

Name

Ci-RhoD 565/989 FoxF2/3 mutated

Short name

n/a

Region ID

REG00000673

Status

Curated

Origin

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

Type of Activity

regulatory_region
(enhancer)

Author

Lionel Christiaen (2010-04-28)

Annotator

Clara Degos (2010-07-12)

Curator

Delphine Dauga (2010-05-05)

View position in WashU

Description

Region from +565bp to +989 of the RhoD/F gene, containing the second exon.

The second and third FoxF sites were mutated -> decrease of RhoD expression.


Be careful, coordinates in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.

Coordinates in the paper : +498/+922

Hierarchy of Regulatory Regions

Modification of Ci-RhoD 565/989 by substitution

Regulated gene(s)

KH2012:KH.C1.129 (RHOA; RHOB; RHOF)

Construct(s) made to test this region

CONS00000635: pCi-RhoD 565/989 FoxF2/3 mutated pFOG::LacZ

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

7,847,8147,848,237

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 Fox n/a TGTTTGA [616 / 622]
2 Ets n/a TGGAAG [754 / 759]
3 Ets n/a AGGATC [796 / 801]
4 Fox n/a TGTTTAT [896 / 902]

Sequence

Aniseed Coordinates: [7,847,814 / 7,848,237] on scaffold KhC1

The two FoxF sites were mutated (TGTTTAT->TGGTTAT).

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

Show sequence

Length: 424


ACTAAATTTAATTAGCAACCCGCTGTTGTTCAAAGGTGTACACGCCCACGGTGTTTGAGA
ATTACAGCAGAGAGGTGGAATTAAATCGAAAGAAGGCGGTGCTAACATTGTGGGATACGG
CGGGTATATATTAGTACATACGTGGTTATGCAAGACATCGTAGGCTTGTTGACTTAGTTT
CGGTTAGCATGGAAGTGTAGTCTATGTTCTACGTGGGTTATGTTCTTGTCGAGGATCTGG
GATTAGGGCTAAATTCAGCCTATTATTACCACAACATTCAGACTGCTTTTGTAGGTCCAA
ATGTAACATATGACTAGTGTGTTCTGATGTGTGTTTATAATACAATAAACTAGCGCAAAC
TGGTTATCCCATTATGTTTAGTCATATAGGTCATATGAGAGTAAATGAAGTGTAAACCAA
ATGT

Reference(s)

Christiaen et al. (2008). The transcription/migration interface in heart precursors of Ciona intestinalis. Science 320(5881):1349-52

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