Aniseed - Cis-regulation

Cis-regulatory Region

Name

Ci-Trop -2993/6

Short name

n/a

Region ID

REG00000174

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Anna Di Gregorio (2007-05-06)

Annotator

Jonathan Luchino (2007-05-06)

Curator

Delphine Dauga (2010-04-07)

View position in WashU

Description

A 3 kb region of Ci-trop 5-flanking sequence was characterized via electroporation of lacZ fusion genes into fertilized Ciona eggs.

-A minimal, 114 bp enhancer (between -1,4 kb and -1,3 kb) was identified that is sufficient to direct the expression of a heterologous promoter in the notochord. DNA binding assay indicate that this enhancer contains two sets of low affinity Brachyury half-sites, which are bound in vitro by a GST/Ci-bra fusion protein.

-The region between -1,3 kb to -1 bp drives expression in the tail epidermis and in the trunk mesenchyme that is normally silenced by negative control elements between -1,4 kb and -1,3 kb.

Be careful, coordinates in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.

Coordinates in the paper : -3000bp/-1bp

Hierarchy of Regulatory Regions

Ci-Trop -2993/6 REG00000174 [ regulatory_region (extended_promoter) ]

Regulated gene(s)

KH2012:KH.C7.260 (TPM1; TPM3; TPM4)

Construct(s) made to test this region

CONS00000166: pTrop -2996/6::LacZ

Show in situ data

Overview of functional TF binding sites in this region

4,511,6924,514,690

	Motif Name	Binding Factor(s)	Sequence	Position in Region	Comment

Sequence

Aniseed Coordinates: [4,511,692 / 4,514,690] on scaffold KhC7

This sequence was found using a blast on the JGI site with the fragment of sequence given in the publication "Regulation of Ci-tropomyosin-like, a Brachyury target gene in the ascidian, Ciona intestinalis" Di Gregorio A, Levine M. Development. 1999 Dec;126(24):5599-609.

Show sequence

Length: 2,999

CCGATAGCATACATCTAACCCTGCTGACTAAGGATCCTGACAACTTATTGCTTCTATGGA
GCCAACACGGTGGCGTGGGAAGATGGAAACAGGTTCAAATCAGTCTAAATTTCACCGGCT
CGTCGAGGTTGCGGTTTACAGGCCAGGTTTTCCTAGCAGAGCAAATTCGGTCGCTATACA
ATGTGTACCGACTTCGAAATATTAAGATCCTACCATCATGTATGATAAGCGGTCGGTTTT
ATAATTCCCGCGGCGTATATAAACCCGGCGCCTCGCCGTACTCAAATTTCAAATGTGGCT
GGATAAGCCTGGATTCGGTTTGGGTCCCGGAGGTACAACTTTCTATTATGACAACGAATC
GTAGTAGCCTTGATTGGGAAGTCAAAGCCACGTTTATTTCCAACACTGGGTTCAACGTAT
GCGTCTATAAAGCGTCGTATAGCAAGCACGGCTGGACGAGCACTGACATAGCAGTGTACT
GGGAGTTGAGTAAAGCTTCGAACAGCCAATCTCTAAACTACACAAAATCAAACGTTTCGG
TTTCCTCCGCTCCCAACAGTTGGAGCACAGTGGAACCAGTTTGTTCCGGTTCATACCGGT
GTGTACAAACCAGCATCTGCATCCCGAATGGACTTGTTTGCAATGGTTTGGATGATTGTC
CTGCCGGGGACGACGAGTTTCAAGCGTGTGGGGAAGCGACATCTTTTGTCTTTGCGGTCG
TTTCGGCATCCACCGCCGGTGTATTCGCCATTCTGTTCCTTTATCTTTATTACGTCAGAA
TTCAGTTACTCGACAACGACATCTACGGCGAGAATTTCGACTCCGAAGACCGACGGTATA
TTGAACTGCTTGAAACTGCGATCGCAAACACCAAATGCTCAAAGCGAGAGGCCAAAATCG
CCGTGGGCGTCCACCAAGACCGAAGCAGCATTGACAATAGCAGTCTGTGACATCACAATA
GACGTGTTGTGTCTCGCGAAACAAATAAAACGAAAATTCGCAAACTCTTAATAAATGCAT
CAATTCATGCCTGCTCTTTTTTCGTCACCTTTTATGGCAAGTTATATTTTTCGTTTTCAG
TTTCCGTCCAAACTACGACTTTATTCGTTCGCCCACAAAGCACTTGACCGGATTGAACTG
GTTAGAACTGGCTGCAGTTTTACCTCGACAAGACACTTCCACAATAGGCGAGGTATTTGT
CATTTAAAAATCGTGCGTTTTTACTCAATTACCGCCATAAATACAACGTTGCTCTATTAC
GTAATCTTCAGACGTGTGATTATTACGTCACAATACGCACAAGTGATCAAGAAGACGCCG
GTACAACGGCCCAGGTCTACGTCATTCTTACCGGAAGTGCGGGAGACAGCGGAAAAAGAT
GGCTCGTGACGTCATCGAATGGTGATGACGTCAGTTTCCGACCGGGCAATGAACTTAAGT
TTACATTCACCAGTGTAAACGTTGGCACCATAAAAGAGGTATGTCACTGTGTTTTACCCT
TACACGAAATACACCGATCGTGTTTTTAAATTTTGAATTTCTCAGCTTGTGATTGGCCAC
AACGGACGTGACGTCACATCCGGATGGCATTTGGATCAGGTCACCGTCTCTTCGTCTCTC
GCACCCGGCACCTCTTTCGTGTTTACTTGCCAAAAGTAAGTAGTTCTCACGGGTTGGACG
TTTTATCACTATCCTGTGAAGTAGGCTTGGCAGCGCTTACAACTTTGAACACTGCTTTTA
TCTTACAGGTGGCTTGCAGATTTGGAGGGTGACACTTTTATTGAAAGGATCTTACCCCTA
GATCACGTTAGTGATTTTGACGTCGCCTCCACCGATACCTGAGCGTCATTTCCGTGACGT
CACACCTCCTAGACACCGGTCCTTTATATCCATTAGCAGTATACCTACAGTGTCATACAT
ACGTGCGTCTGTGAATACATTACCGCTTCCTGCACCATAGCTTTTGTATTGTATGATGAT
TACCTGAGAGTGCGGCAGTACGTAAGGACCGCTTGCCGCGTTATATCAACTGTTTCATTT
CGTTTCTTCCAGCGTCACATTTCAACAAATAAATTAATCAACTTTCGACGTATGCGAAAT
ATTTGCCGAGTTCATAATGGCTGGCGAAGTTAGTTTTGTATTATATTTGATGAATAAGCA
TTCCGGTGTATTGTGTGACGACTACTTCCTAGTATTCTAGTTGAGCTCGGTGTATACAAC
GTTTCTTTTGTTGTTATGGGACGCACAAGTGTTCGGGGCTGTACAGATTTCATTATTCAG
CCAGACAGAGAAACGGAGCGAAATGACGTCAGCTTTTAGAGCGGAATTTCGCTCATATGT
TTTGCCTCAAGTTGCAGAACGTTCGCATTTTTTCATGCGCGATCACTCGTGCGTGACTCA
TCTCTCCTCTAAAGTGATTTAAGAGCGAATAAAGCAAACCGTGTTAGGAGCCGCTAGCCA
TGAATGGTCTTGTTTTAGTTTCACGACTTGATACAAATAGAGACGCATTGAAATTCAGCA
GCAACAGTTAGTTTTCGGCAGTTGAGAGAGATCCTGCAGCTGTAAGCTATTAAATGTAAG
TTCAACCGATCGCTTTAAACGGAAAGTGCGTTTCAACAGAGCAAAACAGGAAGTGATATC
ACGGTTTAATGATTAATATGTGTAGGCTATTTTACTGTACATAAGTTGGCTGGTGTGTTT
ACAGTATCTTGTCACAGGTACGTCTTGAAGAGACAATTGCGCGAACTTTGTCGTTTCGTC
GCGGAAAAGTTAGTTGGCGACGTCGAACGGTTACGCCCTGTCGGTGGATTCTCGTTTTTA
AACCAAACTTACGCTACGGCTGACTGGGTTACTGCGGCCTGTAAAAGCTCATAGGCGAGG
TAGCTTTCGGAGTATGTACAAATACGGCAAGTGAGCAGAAATTTGTCGCGTTTGAGAGAA
TAGCGTTGGTGTAGTTTTTAGGATGTGTCATACGGTGTTGTTTCATTTTGCAGAGATTA

Reference(s)

Di Gregorio et al. (1999). Regulation of Ci-tropomyosin-like, a Brachyury target gene in the ascidian, Ciona intestinalis. Development 126(24):5599-609