Aniseed - Cis-regulation

Cis-regulatory Region

Name

Ci-Sna -650/87 E5 mutated

Short name

n/a

Region ID

REG00000064

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Albert Erives (2006-10-01)

Annotator

Patrick Lemaire (2007-11-06)

Curator

Delphine Dauga (2010-02-26)

View position in WashU

Description

The sequence below extends from -650 to +87 bp of the start of cDNA AF002987. The E5 site is mutated. Note that in the JGI version of the sequence, this E5 site is not present, which fits with the fact that deletion of E5 in the construct has not obvious effect.

This region is named Ci-sna AC - 3 in the paper (Erives et al 1998).

Hierarchy of Regulatory Regions

Modification of Ci-Sna -650/87 by substitution

Ci-Sna -3200/codon 15 REG00000051 [ regulatory_region (extended_promoter) ]

Regulated gene(s)

KH2012:KH.C3.751 (SNAI1; SNAI2; SNAI3)

Construct(s) made to test this region

CONS00000051: pCi-Sna -650/87 E5 mutated::NLS-LacZ

Show in situ data

Overview of functional TF binding sites in this region

5,678,6335,679,369

	Motif Name	Binding Factor(s)	Sequence	Position in Region
1	bHLH	n/a	CAACTG	[5,678,683 / 5,678,688]
2	T-Box	n/a	GATCCCACCT	[5,678,737 / 5,678,746]
3	bHLH	n/a	CAACTG	[5,678,786 / 5,678,791]
4	T-Box	n/a	TTTGGCACCT	[5,678,873 / 5,678,882]
5	bHLH	n/a	CACCTG	[5,678,929 / 5,678,934]
6	bHLH	n/a	CATATG	[5,678,951 / 5,678,956]
7	bHLH	n/a	CATTTG	[5,679,045 / 5,679,050]
8	bHLH	n/a	CAAATG	[5,679,075 / 5,679,080]

Sequence

Aniseed Coordinates: [5,678,633 / 5,679,369] on scaffold KhC3

JGI v1.0 version of the region. The E5 site is missing.

Show sequence

Length: 737

CAGAAGATCGGTGTGTTTTGCTGGACAAATATTGAGAAAATCTGTGGCGACAACTGTGGT
CTGATTTACAGGCGAGTTGGACGGAGTTGACAGGTCGCGAAAGCGATCCCACCTTCGTGT
CTGGGTTTCGAGGTGCCGCCCGTCGTGCAGTAGCAACTGTGCGGTCAAGTTGAGAGCAAG
AAGACACTACAGCGCGCTTTGAAGCGTCCAAGCCGCCCGCTGAGCAGGGCGGATAGCTCG
TTTGGCACCTCGTCTGGCATCGTCCGCACTGTCAACCTTCTTCGTACAAACGTCCTCACC
TGCCGCGCAGGATTGCTTCATATGGCAGACCGAGTTGAGTGGGAAATCATATTCTGGTTG
CTTCGCTTATAGAGCTAGCTCACTAGAGACTAGAGTGTTGTGAATGATGAATCATTTGAA
TTAAGCATTTTGTTTAGTTGATCAAATGAGTTTCAGTTTGATGTTCAGGACTGCTAAGTA
ATGCAGTGAAAGGAATTCTAAAGTGATTATATTTAGAAATGGGCTATCAGTGCTTGATTA
CTGTTGCAGGGTTATTTAAAAATGCAGTCGAACAGTCTAAGAAAGCTTAGCTATATTTGA
AGGATTATGTATACTTATTTCATTAGAGCAATATTTTTTTTTTTATTTTAGACTTTTGGT
ACATATTCAAAATATCAAAATTCTCACTGTGAAATATATTACTGTGATTACATCATGACC
TCCGTCGAGCCCATGCT

Reference(s)

Erives et al. (1998). Lineage-specific regulation of the Ciona snail gene in the embryonic mesoderm and neuroectoderm. Dev. Biol. 194(2):213-25