Aniseed - Cis-regulation

Cis-regulatory Region

Name

Ci-Rora -658/-539 Fox mutated

Short name

n/a

Region ID

REG00000638

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Hélène Auger (2010-02-24)

Annotator

Clara Degos (2010-07-23)

Curator

Delphine Dauga (2010-02-26)

View position in WashU

Description

Transcription start site is based on the start of the first exon of the KH transcript model. Construct used to test this sequence is named Mutated Rora_AS2 enhancer in the paper.

Hierarchy of Regulatory Regions

Modification of Ci-Rora -658/-539 by substitution

Ci-Rora -4493/-421 REG00000441 [ regulatory_region (extended_promoter) ]
- Ci-Rora -678/-421 REG00000442 [ regulatory_region (extended_promoter) ]
  - Ci-Rora -658/-539 REG00000443 [ regulatory_region (extended_promoter) ]
    - Ci-Rora -658/-539 Fox mutated REG00000638 [ regulatory_region (extended_promoter) ]
  - Ci-Rora -545/-423 REG00000444 [ regulatory_region (RNApol_II_core_promoter) ]

Regulated gene(s)

KH2012:KH.C8.101 (MUSK; ROR1; ROR2)

Construct(s) made to test this region

CONS00000609: PCi-Rora -658/-539 Fox mutated pFog::LacZ

Show in situ data

Overview of functional TF binding sites in this region

2,731,8812,731,999

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

Sequence

Aniseed Coordinates: [2,731,881 / 2,731,999] on scaffold KhC8

Sequence from JGI Version 1 thanks to the primers described in the paper. The Fox motifs were mutated (TGtTT -> TGcTT).

Show sequence

Length: 119

ACGTTGCTTGCTCAGAAGAGCCGTGCTTAGCATTACGGTGTCGTCGTGCTTGCATTTGGC
GTGCTTAATTGATAGCGCCATTCGCGAGTCTAAAGACGCGAAAGATAATGCTTTGCTTG

Reference(s)

Auger et al. (2009). Similar regulatory logic in Ciona intestinalis for two Wnt pathway modulators, ROR and SFRP-1/5. Dev. Biol. 329(2):364-73