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- Region 'REG00000179'
Cis-regulatory Region
Name
Ci-Trop -1355/6
Short name
n/a
Region ID
REG00000179
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)
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 : -1362bp/-1bp
Modification of Ci-Trop -1377/6 by deletion
4,511,6924,513,052
| Motif Name | Binding Factor(s) | Sequence | Position in Region | Comment |
|---|
Aniseed Coordinates: [4,511,692 / 4,513,052] 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: 1,361
GTGTTTACTTGCCAAAAGTAAGTAGTTCTCACGGGTTGGACGTTTTATCACTATCCTGTG
AAGTAGGCTTGGCAGCGCTTACAACTTTGAACACTGCTTTTATCTTACAGGTGGCTTGCA
GATTTGGAGGGTGACACTTTTATTGAAAGGATCTTACCCCTAGATCACGTTAGTGATTTT
GACGTCGCCTCCACCGATACCTGAGCGTCATTTCCGTGACGTCACACCTCCTAGACACCG
GTCCTTTATATCCATTAGCAGTATACCTACAGTGTCATACATACGTGCGTCTGTGAATAC
ATTACCGCTTCCTGCACCATAGCTTTTGTATTGTATGATGATTACCTGAGAGTGCGGCAG
TACGTAAGGACCGCTTGCCGCGTTATATCAACTGTTTCATTTCGTTTCTTCCAGCGTCAC
ATTTCAACAAATAAATTAATCAACTTTCGACGTATGCGAAATATTTGCCGAGTTCATAAT
GGCTGGCGAAGTTAGTTTTGTATTATATTTGATGAATAAGCATTCCGGTGTATTGTGTGA
CGACTACTTCCTAGTATTCTAGTTGAGCTCGGTGTATACAACGTTTCTTTTGTTGTTATG
GGACGCACAAGTGTTCGGGGCTGTACAGATTTCATTATTCAGCCAGACAGAGAAACGGAG
CGAAATGACGTCAGCTTTTAGAGCGGAATTTCGCTCATATGTTTTGCCTCAAGTTGCAGA
ACGTTCGCATTTTTTCATGCGCGATCACTCGTGCGTGACTCATCTCTCCTCTAAAGTGAT
TTAAGAGCGAATAAAGCAAACCGTGTTAGGAGCCGCTAGCCATGAATGGTCTTGTTTTAG
TTTCACGACTTGATACAAATAGAGACGCATTGAAATTCAGCAGCAACAGTTAGTTTTCGG
CAGTTGAGAGAGATCCTGCAGCTGTAAGCTATTAAATGTAAGTTCAACCGATCGCTTTAA
ACGGAAAGTGCGTTTCAACAGAGCAAAACAGGAAGTGATATCACGGTTTAATGATTAATA
TGTGTAGGCTATTTTACTGTACATAAGTTGGCTGGTGTGTTTACAGTATCTTGTCACAGG
TACGTCTTGAAGAGACAATTGCGCGAACTTTGTCGTTTCGTCGCGGAAAAGTTAGTTGGC
GACGTCGAACGGTTACGCCCTGTCGGTGGATTCTCGTTTTTAAACCAAACTTACGCTACG
GCTGACTGGGTTACTGCGGCCTGTAAAAGCTCATAGGCGAGGTAGCTTTCGGAGTATGTA
CAAATACGGCAAGTGAGCAGAAATTTGTCGCGTTTGAGAGAATAGCGTTGGTGTAGTTTT
TAGGATGTGTCATACGGTGTTGTTTCATTTTGCAGAGATTA
