Cis-regulatory Region
Name
Ci-Trop -2993/6 delta -1393/-1093
Short name
n/a
Region ID
REG00000177
Status
Curated
Origin
engineered region from C. robusta formely Ciona int. type A
Type of Activity
regulatory_region
(extended_promoter)
Author
Anna Di Gregorio (2007-05-06)
Annotator
Clara Degos (2010-07-23)
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 : -3000bp/-1bp delta -1400bp/-1100bp
Modification of Ci-Trop -2993/6 by deletion
4,511,6924,514,690
| Motif Name | Binding Factor(s) | Sequence | Position in Region | Comment |
|---|
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.
Site deleted was replaced by "-".
Show sequence
Length: 2,998
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
AACGGACGTGACGTCACATCCGGATGGCATTTGGATCAGG--------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
---------------------------------------ATACCTACAGTGTCATACATA
CGTGCGTCTGTGAATACATTACCGCTTCCTGCACCATAGCTTTTGTATTGTATGATGATT
ACCTGAGAGTGCGGCAGTACGTAAGGACCGCTTGCCGCGTTATATCAACTGTTTCATTTC
GTTTCTTCCAGCGTCACATTTCAACAAATAAATTAATCAACTTTCGACGTATGCGAAATA
TTTGCCGAGTTCATAATGGCTGGCGAAGTTAGTTTTGTATTATATTTGATGAATAAGCAT
TCCGGTGTATTGTGTGACGACTACTTCCTAGTATTCTAGTTGAGCTCGGTGTATACAACG
TTTCTTTTGTTGTTATGGGACGCACAAGTGTTCGGGGCTGTACAGATTTCATTATTCAGC
CAGACAGAGAAACGGAGCGAAATGACGTCAGCTTTTAGAGCGGAATTTCGCTCATATGTT
TTGCCTCAAGTTGCAGAACGTTCGCATTTTTTCATGCGCGATCACTCGTGCGTGACTCAT
CTCTCCTCTAAAGTGATTTAAGAGCGAATAAAGCAAACCGTGTTAGGAGCCGCTAGCCAT
GAATGGTCTTGTTTTAGTTTCACGACTTGATACAAATAGAGACGCATTGAAATTCAGCAG
CAACAGTTAGTTTTCGGCAGTTGAGAGAGATCCTGCAGCTGTAAGCTATTAAATGTAAGT
TCAACCGATCGCTTTAAACGGAAAGTGCGTTTCAACAGAGCAAAACAGGAAGTGATATCA
CGGTTTAATGATTAATATGTGTAGGCTATTTTACTGTACATAAGTTGGCTGGTGTGTTTA
CAGTATCTTGTCACAGGTACGTCTTGAAGAGACAATTGCGCGAACTTTGTCGTTTCGTCG
CGGAAAAGTTAGTTGGCGACGTCGAACGGTTACGCCCTGTCGGTGGATTCTCGTTTTTAA
ACCAAACTTACGCTACGGCTGACTGGGTTACTGCGGCCTGTAAAAGCTCATAGGCGAGGT
AGCTTTCGGAGTATGTACAAATACGGCAAGTGAGCAGAAATTTGTCGCGTTTGAGAGAAT
AGCGTTGGTGTAGTTTTTAGGATGTGTCATACGGTGTTGTTTCATTTTGCAGAGATTA
