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CIS-REGULATION

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  2. Region 'REG00000370' > 
  3. Transcript 'Moocci.CG.ELv1_2.S45...' > 
  4. Region 'REG00000053'

Cis-regulatory Region

Name

Ci-Sna -3000/-68

Short name

n/a

Region ID

REG00000053

Status

Curated

Origin

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

Type of Activity

regulatory_region
(complex_region)

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 starts 3.2kb upstream from the start of cDNA AF002987 and extends up to position -68.
It directs expression of a pbra-beta-galactosidase reporter gene in a pattern that is very similar to the endogenous gene (Tail muscles, trunk mesenchyme, TVCs and sensory vesicle and lateral ependymal cells). In addition A-line notochord expression is detected.

This region was named 3.0kb in the paper (Erives et al 1998).

Hierarchy of Regulatory Regions

Modification of Ci-Sna -3200/codon 15 by deletion

Regulated gene(s)

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

Construct(s) made to test this region

CONS00000038: pCi-Sna -3000/-68 pBra anti::NLS-LacZ

CONS00000037: pCi-Sna -3000/-68 pBra syn::NLS-LacZ

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

5,676,0835,679,220

Motif Name Binding Factor(s) Sequence Position in Region Comment
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: [5,676,083 / 5,679,220] on scaffold KhC3

JGI v1.0 version of this region. E-box site E5 is absent from this sequence, replaced by a different E-box.

Show sequence

Length: 3,138


ATAATAAAATACGTAAAGGATTTTTTGATACGGACCAATTTGCGAATCCGCAAGGACTGT
AAAGTATAGGATAGAGGTTGATATATGAATAATAAGTGCTATTTTGTACACCTCATCAGA
GAAATGGCTAACTGTAACTTGCGATAAATTCTTTCGCAGTTTACGGTGTATCGTGGGCTT
TAATAAACAATGCACCTGTTTAAAACCGGCGTTCTGTATAGCGCCTATCACATTACCACG
CCTCGTGTGTCTTTACCCAAGAGACGTATATTTCAATCACTTAACGGCTTAATTCGAAAC
CGAGCAAGTGTTATGGTTAGATACGTCATGTTTCTAATGCAAGGGTATTTTAATCTATAT
CTCTATATACTATTAATAGACAATCATTATTCCTATGTAGTTAGAATTTCATCACATTCA
GTATTTTATTTGTATATAAGCCATCTTTGATTTTAAAATAATTTTATTGCCGCCTTAGCC
GAGAGCAAACTAATAACTGGACTTTAAACGATACGTCACTCGTTACGGATTTTTTCCAGA
CTATATTAAAGTGACGTCAGTGAAATGAATGCATGCGCGTGTCGCACTTTGTTATTTAAT
GACGTAATCTTGATGCGGCCACATAGATTAATGGGTGCACCGAGTACTTTCATCATACCA
GGCGTCCGGTGCCGAAGCAACAGGCGGCTAACCGAAATAGAACAACGACCAGCAGGAGCG
AGCCAACAACTGTTACCGAAGCGGTCCACTTAATCCCGGGACACGCGCGAACTGTACGCG
ACAAATATCAAAATATAAACAACGGCATTCAACTATTAATATTGCGCCTTTGGTTACGTT
CAACCGAGTTTTAAAAACCTGTCACATTTTTAAACTGAAGGCTGTCTGTATAGTCATCGA
AAGAATATCCCACGACCCAGCGTGCACACTTGGCCCGTATAACCTTCCGTTTGTGTTGGT
TTTTATTCCGAATACTCCAAATGATTGTAGCGCCGGGATACCTTAGTTGGCTTAGTACAC
CGATAGCAGACCGCCCCTCCACGAAATACAGACACTCTGTTTGTCACCAGTGTTCTATCA
ACTGTCTCGTTTAGCTACGGTGTACACATGCTTCTACATACGTTCCGCGGGTGTCTATTG
TTGCCCTTGTCCTTACAGTGCGTCTAGAGTAAACTAACCAAGATACGATTGCGTATACCG
GGACAATAGGATAACATTTGCACGGAGACACGTGGTCAACTATACGAGGCACGTAACCGC
AGGGCACTACCAAAGTCCGGTTATTTAAGTTTATATTTTTGCCTAGCCGTCGAAAAAACA
TGCATATATTAAAATTAATAAAACCGTTTATTCTCTATATCGTACATTGGTTATGAGCGC
TTTAGCACCAAAATATAACGAGTTCTATAAACGCAGTTAAATTCAATTGATTTTACCTTA
CCAGCAGGCAGTTTCTCTCCACAAACATTTAAGCCTCATTCCTAACGTGCGGGAATTCTC
CTCATCCGATAGAAACATATTAGTGTACGGACACTTCTCCATTCTTTGACAATGTGGTGA
CAGGGGAATATCATTTACGACAGTGCGAAGCGTCTCCTTTACCGAATAAACCTCATGATT
CTAACATTAAAGTCGTTGCAATAGGTACGGATATTCTAAAATTGAAACTATGCACAATCA
CGGGTATACCATATATATATATAGTAGGGTGGGAAAAATAGGACACCATTTTATTCTATT
TTCTCGTCCCATTTTGTAGAAAACAAGGAACATTTAAAGAATTATAAAACCGTATCCGTA
CGACTACCATAGACCGTTGTAAATTGTTTAAACACGATCAAGATATTTGGATATTATGTG
CTAACGGTGTCTCATCTACCCCCACCCTATTATAACACCGAACGTTAAAAATTCATTGCA
CCGAATGTTCCACCGTTTTAGTGTATTAGCGGATTCAGAATGTCGCACGCGTTCAAAGCG
ACCCAGTACCTATTGGTGTCAATTAACACCATTTTGGATCGAATTTTCGGATGAGCCTTT
GTGTGAAAATTAGCGGTTCACTCTGCCGGCCATCCTCAGGTTGAGATAACGCATCTATCG
CAAAGTAGCAGCTGAAGTGAAGACTTGCGATCGGAGAGAATTTAATTTCGATATTTTTAT
TTGCATTGATTTACAAAAATATTTATACAGTTTTTGATTTTGAAAACAATAGAGTAGGGT
GGGGGAAAATGGGATACCCTTTCATTCTATTTCCTTGTTCCATTTAGTAGTAAACAAAGA
CCTTTTCAGAGAATTATAAAACCGTATTCTCACGACTCCCACAGCCCTTTGTTAATTATT
TAAAACATGATTAGAATATTTAAATATAATGTCCCAAAGATGCCCCATCTTCCGCCACAG
TACTATACTTGAAAAATATATTGTTCTGCCCCTGAAATAGGAACTTTAGGGGGAGATTTT
TCTTACGCACATGATAAATTAATATGTTGTTACCGATAAATTGTAGATACTTAAAATGAA
AAGGTCGCAATTGTATTTACCATTATAAAACAGAAGATCGGTGTGTTTTGCTGGACAAAT
ATTGAGAAAATCTGTGGCGACAACTGTGGTCTGATTTACAGGCGAGTTGGACGGAGTTGA
CAGGTCGCGAAAGCGATCCCACCTTCGTGTCTGGGTTTCGAGGTGCCGCCCGTCGTGCAG
TAGCAACTGTGCGGTCAAGTTGAGAGCAAGAAGACACTACAGCGCGCTTTGAAGCGTCCA
AGCCGCCCGCTGAGCAGGGCGGATAGCTCGTTTGGCACCTCGTCTGGCATCGTCCGCACT
GTCAACCTTCTTCGTACAAACGTCCTCACCTGCCGCGCAGGATTGCTTCATATGGCAGAC
CGAGTTGAGTGGGAAATCATATTCTGGTTGCTTCGCTTATAGAGCTAGCTCACTAGAGAC
TAGAGTGTTGTGAATGATGAATCATTTGAATTAAGCATTTTGTTTAGTTGATCAAATGAG
TTTCAGTTTGATGTTCAGGACTGCTAAGTAATGCAGTGAAAGGAATTCTAAAGTGATTAT
ATTTAGAAATGGGCTATCAGTGCTTGATTACTGTTGCAGGGTTATTTAAAAATGCAGTCG
AACAGTCTAAGAAAGCTT

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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