Aniseed - Cis-regulation

Cis-regulatory Region

Name

Ci-Rora -658/-539

Short name

n/a

Region ID

REG00000443

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Hélène Auger (2009-04-07)

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 AS2 in the paper.

Hierarchy of Regulatory Regions

Modification of Ci-Rora -678/-421 by deletion

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

CONS00000422: pCi-Rora -658/-539 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
1	Fox	n/a	TGTTT	[2,731,887 / 2,731,891]
2	Fox	n/a	tgttt	[2,731,934 / 2,731,938]
3	Fox	n/a	tgttt	[2,731,949 / 2,731,953]
4	Fox	n/a	aaaca	[2,731,972 / 2,731,976]
5	Fox	n/a	TGTTT	[2,731,991 / 2,731,995]

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.

Show sequence

Length: 119

ACGTTGTTTGCTCAGAAGAGCCGAAACAAGCATTACGGTGTCGTCGTGTTTGCATTTGGC
GTGTTTAATTGATAGCGCCATTCGCGAGTCTAAAGACGCGAAAGATAATGTTTTGCTTG

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