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CIS-REGULATION

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  1. Transcript 'Moocul.CG.ELv1_2.S23...' > 
  2. Region 'REG00001523' > 
  3. Region 'REG00001384' > 
  4. Transcript 'Cisavi.CG.ENS81.R48....' > 
  5. Region 'REG00000661'

Cis-regulatory Region

Name

Ci-RhoD 565/989

Short name

n/a

Region ID

REG00000661

Status

Curated

Origin

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

Type of Activity

regulatory_region
(enhancer)

Author

Lionel Christiaen (2010-04-25)

Annotator

Clara Degos (2010-04-25)

Curator

Delphine Dauga (2010-05-05)

View position in WashU

Description

This region containing the second exon and most of the second intron is the minimal TVC enhancer.


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 448/990 by deletion

Regulated gene(s)

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

Construct(s) made to test this region

CONS00000642: pCi-RhoD 565/989 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]
5 Fox n/a TGTTTAT [896 / 902]
6 Fox n/a TGTTTGT [925 / 931]

Sequence

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

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
ATGTAACATATGACTAGTGTGTTCTGATGTGTGTTTATAATACAATAAACTAGCGCAAAC
TGTTTGTCCCATTATGTTTAGTCATATAGGTCATATGAGAGTAAATGAAGTGTAAACCAA
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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