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CIS-REGULATION

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  1. Transcript 'Phmamm.CG.MTP2014.S7...' > 
  2. Region 'REG00000675'

Cis-regulatory Region

Name

Ci-RhoD 565/989 FoxF3/4 mutated

Short name

n/a

Region ID

REG00000675

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 +989bp of the RhoD/F gene, containing the second exon. The third and fourth FoxF site were mutated and RhoD expression is lost.



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

CONS00000637: pCi-RhoD 565/989 FoxF3/4 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 Fox n/a TGTTTAT [707 / 713]
3 Ets n/a TGGAAG [754 / 759]
4 Ets n/a AGGATC [796 / 801]

Sequence

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

The two FoxF sites were mutated (TGTT->TGGT).
Transcription start site is based on the start of the first exon of the KH transcript model.

Show sequence

Length: 424


ACTAAATTTAATTAGCAACCCGCTGTTGTTCAAAGGTGTACACGCCCACGGTGTTTGAGA
ATTACAGCAGAGAGGTGGAATTAAATCGAAAGAAGGCGGTGCTAACATTGTGGGATACGG
CGGGTATATATTAGTACATACGTGTTTATGCAAGACATCGTAGGCTTGTTGACTTAGTTT
CGGTTAGCATGGAAGTGTAGTCTATGTTCTACGTGGGTTATGTTCTTGTCGAGGATCTGG
GATTAGGGCTAAATTCAGCCTATTATTACCACAACATTCAGACTGCTTTTGTAGGTCCAA
ATGTAACATATGACTAGTGTGTTCTGATGTGTGGTTATAATACAATAAACTAGCGCAAAC
TGGTTGTCCCATTATGTTTAGTCATATAGGTCATATGAGAGTAAATGAAGTGTAAACCAA
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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