Aniseed - Cis-regulation

Cis-regulatory Region

Name

Ci-Sna -482/-168

Short name

n/a

Region ID

REG00000070

Status

Curated

Origin

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

Type of Activity

regulatory_region
(enhancer)

Author

Albert Erives (2006-10-01)

Annotator

Daniel Sobral (2007-11-09)

Curator

Delphine Dauga (2010-02-26)

View position in WashU

Description

This sequence goes from -482 to -168 upstream of the start of cDNA AF002987. It recapitulates very weak expression of Ci-sna in the primary muscle and full expression in the trunk mesenchyme.

This region is named 314bp in the paper (Erives et al 1998).

Hierarchy of Regulatory Regions

Modification of Ci-Sna -672/-168 by deletion

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

CONS00000060: pCi-Sna -482/-168 pBra Syn::NLS-LacZ

Show in situ data

Overview of functional TF binding sites in this region

5,678,8015,679,114

	Motif Name	Binding Factor(s)	Sequence	Position in Region
1	T-Box	n/a	TTTGGCACCT	[5,678,873 / 5,678,882]
2	bHLH	n/a	CACCTG	[5,678,929 / 5,678,934]
3	bHLH	n/a	CATATG	[5,678,951 / 5,678,956]
4	bHLH	n/a	CATTTG	[5,679,045 / 5,679,050]
5	bHLH	n/a	CAAATG	[5,679,075 / 5,679,080]

Sequence

Aniseed Coordinates: [5,678,801 / 5,679,114] on scaffold KhC3

JGI v1.0 version of the region.

Show sequence

Length: 314

GTTGAGAGCAAGAAGACACTACAGCGCGCTTTGAAGCGTCCAAGCCGCCCGCTGAGCAGG
GCGGATAGCTCGTTTGGCACCTCGTCTGGCATCGTCCGCACTGTCAACCTTCTTCGTACA
AACGTCCTCACCTGCCGCGCAGGATTGCTTCATATGGCAGACCGAGTTGAGTGGGAAATC
ATATTCTGGTTGCTTCGCTTATAGAGCTAGCTCACTAGAGACTAGAGTGTTGTGAATGAT
GAATCATTTGAATTAAGCATTTTGTTTAGTTGATCAAATGAGTTTCAGTTTGATGTTCAG
GACTGCTAAGTAAT

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