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CIS-REGULATION

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  1. Transcript 'KH2012:KH.S404.1.v3....' > 
  2. Region 'REG00000071'

Cis-regulatory Region

Name

Ci-Sna -465/codon 15

Short name

n/a

Region ID

REG00000071

Status

Curated

Origin

natural 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

Region extending from -465kb upstream of the start of cDNA AF002987 to codon 15 in exon 2. This region is the smallest that recapitulates the whole expression of Ci-Sna.

This region was named -465bp in the paper (Erives et al 1998).

Hierarchy of Regulatory Regions

Modification of Ci-Sna -1037/codon 15 by deletion

Regulated gene(s)

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

Construct(s) made to test this region

CONS00000061: pCi-Sna-465/codon 15::NLS-LacZ

Show in situ data
Overview of functional TF binding sites in this region

5,678,8185,680,582

Motif Name Binding Factor(s) Sequence Position in Region Comment
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: [5,678,818 / 5,680,582] on scaffold KhC3

JGI v1.0 assembly version of this region. Site E5 is not in the assembly.

Show sequence

Length: 1,765


ACTACAGCGCGCTTTGAAGCGTCCAAGCCGCCCGCTGAGCAGGGCGGATAGCTCGTTTGG
CACCTCGTCTGGCATCGTCCGCACTGTCAACCTTCTTCGTACAAACGTCCTCACCTGCCG
CGCAGGATTGCTTCATATGGCAGACCGAGTTGAGTGGGAAATCATATTCTGGTTGCTTCG
CTTATAGAGCTAGCTCACTAGAGACTAGAGTGTTGTGAATGATGAATCATTTGAATTAAG
CATTTTGTTTAGTTGATCAAATGAGTTTCAGTTTGATGTTCAGGACTGCTAAGTAATGCA
GTGAAAGGAATTCTAAAGTGATTATATTTAGAAATGGGCTATCAGTGCTTGATTACTGTT
GCAGGGTTATTTAAAAATGCAGTCGAACAGTCTAAGAAAGCTTAGCTATATTTGAAGGAT
TATGTATACTTATTTCATTAGAGCAATATTTTTTTTTTTATTTTAGACTTTTGGTACATA
TTCAAAATATCAAAATTCTCACTGTGAAATATATTACTGTGATTACATCATGACCTCCGT
CGAGCCCATGCTTTATCAAGGCAAGCACGCCGTTCAGAAAAATGAAGGTATATATGCAGT
CCTATTTATATTATAATTCATCGCGGCAATTGTTTCTCTTATAAAAATCAAACGCGATCA
TTTTAAATGTTGTAAACAGAGCAGATGCCTTTGTAAATATGCATCATCTTGTACCGAGAA
TCCAGCAGAATTTTCCATGAGACTTTCGTTCACGTAAAAGTTAAATTATTTTCGGAGGTT
ATTTGCGCACGGCGCGGTGTTGGAACTTTTCGCTAATCCGACTGTTTGTTTCCGCCTAAA
TTAATCACAAGTAACAGTTGCGATAAAACAAGGAAACGACTGGATCTCCCGCTGTTATAG
GATGCCACCTCGCACGTCAAACCCCACACATACCGTAACTTTTACCTAAATAATGGAAAT
GCAATTATTTAATTACCTGTGGAAGAATCCGGACTAAGCCGAGATTGCCTAATATAGTTA
GACAAGGTCCGGTCACTCGGGCTAAACATTCAAACAGGTGGTGCCTAAAATAGATGCGAG
CTGGTACCAAGTGTTTTGCTCGCACCGTTCCTCCCATGGGTGACTGGCTGGCTTTAAGGA
TGGAACGCTACCGATATAAGTTTGACGTAATCTCGGTCTGGATGAAAGCGTTGACAGCAC
TACCTGTTTGCACACTCGGCACAACTGCTGCTTATGGAAGTGAACTGCGGTTTCCCGATA
TGGAAACCGTATGGCTCAATAACAAATTATTTACGGCCCTCAGGACAGCCCGCCATGCAG
TCTGCACCATATTTTTAATCCTGGCTTTTGCCAAGACCAAATATTACAAAGTTAAATCTT
CTTTAGGCGAATCTACCCGTCCTTGCACTTTGAGTGGAGATGACAGTTTTTACTGCAGCG
GCGAATCAACAAATTCGACGTCATCTCCCACGTCATCCATTACGTCATCGCGTTCATGTG
GACCTGACAGCGACGAAGGTTTTCCGAGACAGGATGACCTGGATTTGCGTGACAAAGCCA
GCAAAAACTTGCAACATAGCGTTGAGCTTTTTTGCCCTATTAAGAGCAAGTCAGTTGATC
ATGATAACGATTTAATGCCTATGGATCTCTCGTGCAAAAAGAGAACTTTCCCAAAACAAA
ATTGCAAAACTGCTAGCATGCCTAAAACGAGCCCAACCATAAAATCAGAACCGATTGATG
ACTATCCAGCTTCACTTACACGCAA

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

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