Login
Help

CIS-REGULATION

Submit your Data

  1. Region 'REG00000649' > 
  2. Region 'REG00000773' > 
  3. Region 'REG00000763' > 
  4. Region 'REG00000564' > 
  5. Region 'REG00000769'

Cis-regulatory Region

Name

Short name

n/a

Region ID

REG00000769

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Ryosuke Koyano (2010-06-21)

Annotator

Clara Degos (2010-07-22)

Curator

Delphine Dauga (2010-07-09)

View position in WashU

Description

1113-bp-genomic DNA fragment containing the Ci-RAR promoter region in which region from -953bp to -218bp and region from -972bp to -963bp were deleted.


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

- "A site" (TTAATTATAT), with a potential binding site for Msbx transcription factor.

- "B site" (TTTGTTGCATCGTTA), with a potential binding site for Sox proteins.
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 delta -953/-218 by deletion

Regulated gene(s)

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

Construct(s) made to test this region

CONS00000733: pCi-RAR -1113/1 delta -953/-218 & delta -972/-963::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. The deleted sequence was replaced by "-".

Show sequence

Length: 1,113

AGCTTTGCGATCTGGTAAACGTCCTTTTGTTTTGTAACAATTAAATTTTACCAGACAATG
GTTTAGTTTTCAGACGAAGTAATTATCGAAAGAAGTACAGTTCGCAATGGTTTTGTTGCA
TCGTTAAGAGTTAATTATAT----------ACATGGATGG--------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
--------------------------------------------------------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

Back to Top