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CIS-REGULATION

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  1. Region 'REG00000348' > 
  2. Molecular Tool 'FGF8/17/18-MO (Imai 2009)' > 
  3. Molecular Tool 'BMP2/4-MO (Imai 2009)' > 
  4. EST 'AV677935' > 
  5. Region 'REG00000148'

Cis-regulatory Region

Name

Ci-RAR -549/281

Short name

n/a

Region ID

REG00000148

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Fujiwara team (2007-01-19)

Annotator

Clara Degos (2010-07-22)

Curator

Delphine Dauga (2010-06-28)

View position in WashU

Description

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


Hierarchy of Regulatory Regions

Modification of Ci-RAR -814/-226 by deletion

Regulated gene(s)

KH2012:KH.C9.580 (RARA; RARB; RARG)

Construct(s) made to test this region

CONS00000139: pRAR -549/281::LacZ

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

3,688,5093,689,338

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 bHLH n/a CACGTG [-252 / -247]
2 bHLH n/a CAACTG [-225 / -220]

Sequence

Aniseed Coordinates: [3,688,509 / 3,689,338] on scaffold KhC9

Sequence obtained by cutting the base region with the restriction enzyme SacII (Fujiwara, 2005). ANISEED coordinates may differ from the coordinates defined in the publication because of polymorphisms.

Show sequence

Length: 830


GGTCACTGGTGAGGGAAGGCAGAAGCTGCTATGTATTGTTTGGAAATTCGCTGCGCAGGA
AATCGCTAATAAAAGCTTGATATTTTCCACGATAGGACTTGCGATAAGGTTAAGCCATGG
TAAACTGCAACGTGCGTTCTTCCCACGTTACTACACTTATAGAGCGTTATGCGAGACGCC
GAATTCGGTTGCTGCAATATAGTAATGTTGCCACGTAGAAAGATTTTGTAGATACAAAAA
GAGCTTTTAAATTTTGAGAGTCTAGACAGTAAAGTGTCAAGCTATTGCATTTAGTGCCAC
GTGTTATTACTGTCAGGAATGTAACAACTGCTTGCTAACAGGGGTCAACTGCGTGATAAT
CTTCTGTTGAGCTTGAAGAGAGTATTCGTCACCTAATCACGTTTAAACTGTCGTCACTAT
AGCTGGTAGTTTATCACTGTAGTTGCTTTTTTCCTGGTAAGCACTTCAGCTTAAAGAACA
ACATTGGCAGCCGCCCAAAATGTAACGTAACATCCGAAATGTCGTTTTAACGTTTTCATA
TCGTTGCAGTTTGTTCTAGTTAATTAGTACAAAGCATTGAGCTTCCAGCAAGCAACTTGT
TTTATTGTGGTGTCAGTATCAGCGTGATAGCGTTGTTGAACTCTGCGTGAATACTATAGC
ATGATGAACGTTATGGAGTTTCAAGAACAATGGAGAAACCGAATGAATGGAATCTTGAGC
GACATGTTTCATCCTACATCTACAATATGCGATGCTATGACTGGCATGCCACGTTCGCAT
AATACAATGGCATCTATGATAGATTCCCCGCCACCGTTACAGAATCTGAC

Reference(s)

Fujiwara et al. (2005). Promoter activity of the retinoic acid receptor gene in the Ciona intestinalis embryo. Dev. Dyn. 232(4):1124-30

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