Aniseed - Cis-regulation

Cis-regulatory Region

Name

Ci-Sna -650/87 E7/E6/E5 mutated

Short name

n/a

Region ID

REG00000061

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 (2011-11-14)

View position in WashU

Description

The region extends from -650bp to +87 bp of the start of cDNA AF002987. Mutation of the E7, E6 and E5 sites from AC core E-boxes to TT-core E-boxes leads to a strong decrease in the activity of the region.

This region is named Ci-sna AC-6 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

CONS00000048: pCi-Sna -650/87 E7/E6/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	T-Box	n/a	GATCCCACCT	[5,678,737 / 5,678,746]
2	T-Box	n/a	TTTGGCACCT	[5,678,873 / 5,678,882]
3	bHLH	n/a	CACCTG	[5,678,929 / 5,678,934]
4	bHLH	n/a	CATATG	[5,678,951 / 5,678,956]
5	bHLH	n/a	CATTTG	[5,679,045 / 5,679,050]
6	bHLH	n/a	CAAATG	[5,679,075 / 5,679,080]

Sequence

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

JGI version 1.0 version of the sequence, in which sites E7, E6 and E5 were mutated from CAACTG to a TT core E-box site: CATTTG. Note that the E5 mutation cannot be seen on the JGI assembly, as this site does not exist.

Show sequence

Length: 737

CAGAAGATCGGTGTGTTTTGCTGGACAAATATTGAGAAAATCTGTGGCGACATTTGTGGT
CTGATTTACAGGCGAGTTGGACGGAGTTGACAGGTCGCGAAAGCGATCCCACCTTCGTGT
CTGGGTTTCGAGGTGCCGCCCGTCGTGCAGTAGCATTTGTGCGGTCAAGTTGAGAGCAAG
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