Aniseed - Cis-regulation

Cis-regulatory Region

Name

Ci-Rorb -330/113

Short name

n/a

Region ID

REG00000448

Status

Curated

Origin

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

Type of Activity

regulatory_region
(RNApol_II_core_promoter)

Author

Hélène Auger (2009-06-29)

Annotator

Clara Degos (2010-07-23)

Curator

Delphine Dauga (2010-02-24)

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 BS2/3 in the paper. This construct recapitulates the endogenous expression of Ci-Rorb.

Hierarchy of Regulatory Regions

Modification of Ci-Rorb -596/113 by deletion

Ci-RORb -1649bp/4353bp REG00000445 [ regulatory_region (extended_promoter) ]

Regulated gene(s)

KH2012:KH.C8.737 (MUSK; ROR1; ROR2)

Construct(s) made to test this region

CONS00000610: pCi-Rorb -330/113::LacZ

Show in situ data

Overview of functional TF binding sites in this region

2,707,9052,708,347

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

Sequence

Aniseed Coordinates: [2,707,905 / 2,708,347] on scaffold KhC8

Sequence from JGI Version 1 thanks to the primers described in the paper.

Show sequence

Length: 443

ATGTGTGTTGACTTTGCAGCGCGTCTAATCGCCAATAGCGATAACGTAATGAGATCCGAC
TGCGGCTCTAATTAGCGCGGACACGGGCGAGAGATATTGCCTTTTTCCTACATTTCGTGC
CCCACTCCGTAAAAGCGTTTGCGCTTTTCTATCACTATACAGTCGAATAAGTGAAACGTG
AGCGCGGTTGCTTGTTATGACTTTCTGCTTATAATTACTACTTTAATGATTTCGAAATTA
GCTCCTTTGCCAGGAGAAGCAAGATAATTGCGTGAGATTTAAGTGTACGTCTGGTTTCCA
GTATTACACGTATGTATCCTATCTTGCAGAATATTTTAAGGAAGTATTTTAAAGTACAAG
TGTTCGGACAAGACAGAAAGTATCAAAAATCAAAGTGTTGCGGATATTGACGGAAATGAA
AAGACACCATCTGTTATGGAGTC

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