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CIS-REGULATION

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  1. Clone 'cien194742' > 
  2. Region 'REG00000449' > 
  3. Clone 'cien95818' > 
  4. Clone 'cien110993' > 
  5. Region 'REG00000767'

Cis-regulatory Region

Name

Ci-RAR -1113/1 delta -1016/-218

Short name

n/a

Region ID

REG00000767

Status

Curated

Origin

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

Type of Activity

inactive_region

Author

Ryosuke Koyano (2010-06-21)

Annotator

Clara Degos (2010-06-28)

Curator

Delphine Dauga (2010-06-28)

View position in WashU

Description

1113-bp-genomic DNA fragment containing the Ci-RAR promoter region in which region from 1016bp to -218bp was deleted.


The region contains two important elements essential for dorsal midline epidermis (DME) expression:

- A element (TTAATTATAT). Ci-Msbx can bind this element.

- B element (TTTGTTGCATCGTTA). Ci-SoxB1 can bind this element.

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



Hierarchy of Regulatory Regions

Modification of Ci-RAR -1113/1 by deletion

Regulated gene(s)

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

Construct(s) made to test this region

CONS00000731: pCi-RAR -1113/1 delta -1016/-218::LacZ

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

3,688,7903,689,902

Motif Name Binding Factor(s) Sequence Position in Region Comment

Sequence

Aniseed Coordinates: [3,688,790 / 3,689,902] on scaffold KhC9

ANISEED coordinates may differ from the coordinates defined in the publication because of polymorphisms. Coordinates were based on the first exon on the KH transcript model.
The deleted sequence was replaced by '-'.

Show sequence

Length: 1,113

AGCTTTGCGATCTGGTAAACGTCCTTTTGTTTTGTAACAATTAAATTTTACCAGACAATG
GTTTAGTTTTCAGACGAAGTAATTATCGAAAGAAGTA-----------------------
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--------------------------------------------------------TGCT
AACAGGGGTCAACTGCGTGATAATCTTCTGTTGAGCTTGAAGAGAGTATTCGTCACCTAA
TCACGTTTAAACTGTCGTCACTATAGCTGGTAGTTTATCACTGTAGTTGCTTTTTTCCTG
GTAAGCACTTCAGCTTAAAGAACAACATTGGCAGCCGCCCAAAATGTAACGTAACATCCG
AAATGTCGTTTTAACGTTTTCATATCGTTGCAG

Reference(s)

Koyano et al. (2009). Transcriptional regulation of the retinoic acid receptor in the dorsal midline epidermis in the Ciona intestinalis embryo. Dev. Growth Differ. 51(9):777-86

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