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CIS-REGULATION

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  1. Region 'REG00000092'

Cis-regulatory Region

Name

Ci-Bra -3500/17 first codons

Short name

n/a

Region ID

REG00000092

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Joseph C. Corbo (2005-05-30)

Annotator

Delphine Dauga (2008-04-01)

Curator

Delphine Dauga (2011-11-14)

View position in WashU

Description

Region from -483 bp upstream the +1 to the first 17 codons is the minimal enhancer which drives the entire Ci-Bra expression (the transcription start site is the nucleotide +1).

This region contains three essential cis-regulatory elements.

Region - 483 bp/- 348 bp : negative response that keeps the enhancer off in ectopic mesodermal lineage (muscles and mesenchyme). This region contains three copies of a conserved 15 bp sequence motif. It is currently unclear whether this repeat is important for repression.

Region -348 bp/ - 237 bp : it contains one, or possibly two, Su(H) binding sites. Removal of these sites significantly decreases expression in the notochord.

Region - 237 bp/- 71 bp : it contains important element for activation in the mesenchyme and muscles. This region contains three E-box sequences. Progressive truncations that remove these sequences lead to a sequential loss of expression in ectopic mesodermal lineage.

Hierarchy of Regulatory Regions

Regulated gene(s)

KH2012:KH.S1404.1 (TBX19; TBX6; TBXT)

Construct(s) made to test this region

CONS00000084: pBra -3500/17 first codons::LacZ

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

2,7716,344

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 ZnF_(C2H2) n/a tctggtgtt [5,941 / 5,949]
2 Su(H) n/a cttcccacg [6,010 / 6,018]
3 Su(H) n/a aatgggaaa [6,025 / 6,033]
4 ZnF_(C2H2) n/a acacttggt [6,049 / 6,057]
5 bHLH n/a cacttg [6,050 / 6,055]
6 ZnF_(C2H2) n/a caaggtgtt [6,082 / 6,090]
7 ZnF_(C2H2) n/a ccagctgtg [6,095 / 6,103]
8 bHLH n/a cagctg [6,096 / 6,101]
9 ZnF_(C2H2) n/a cacagctgg [6,140 / 6,148]
10 bHLH n/a cagctg [6,142 / 6,147]
11 ZnF_(C2H2) n/a accacctac [6,154 / 6,162]

Sequence

Aniseed Coordinates: [2,771 / 6,344] on scaffold KhS1404

This sequence was found using a blast on the JGI V1.0 using sequences included in Corbo et al. (1997 and 1998), Fujiwara et al. (1998) and Yagi et al (2004). Motifs were also deduced from these four articles. Coordinates from Yagi et al. were taken as reference.

Show sequence

Length: 3,574


GCCCCACTTACCCCTTTTCTATCGGGGGGGAACACCAGTCTTGCATTACGTCATCAACCT
ACGTCAGTGATGAGTCACGTGCACAATATGGCTGCCCAGGTGTTCGCTGTCGAGCATAAA
TATCGTTCTCAACTCGTAAGTTGGTTTGAACATTTATACAATCAAGAATATTCATCAAAG
TTTGTTTAGAATTTAACGCGAAAGCTCGAAGCCGAGAACGAAAGTTTAAAAGCTTCTGAA
CAAGCCATGTGCCGGAGGCTAAATGAGGTAAGAGATTTTGCTTATAAGTTGTTCGGTGGA
GATTTAATATGAGATTAATGTTTAGGTTGGAGTGGCTGGGGACGAAATAATTGGTGGTGC
ATCGGTGAGTTGAAGCGCCCACGTGCGGTTCATGGGATTTAAGTTTTTTTTGTTTTAGAC
TCACAGTTTATTCGAGAAATTGTCGAAAACTGAAGAGCGCGTGCGCAGTCTGGAGAGGGA
ACTTGCGCAGTACCGTAGTGCGCATGCACGTGAAAGATGCGCACGAGAACGCCTTGAAGC
AGAAAGAGAGAAAATGCAAAATATTCTTGGTCGTATTGAAACGTCTACGTCATTCAATGA
TGACGTCATTGTTAGCAAACAAGTATGTATTGAAGTCATATGGTTATCGATTTGATGGCG
CCTCTTTTTAAACTTTATTTTTTCAGACCGAAAAAAGTGAAACACACATGACGTCAGCAG
TTGCTGACGTCAAACCATACGTCACACACCACGTGAATAAAACATCAATGTCTCTCAAGC
GAATAAATTCACCTCTGGATTTATCGGGTACGTAATGATGACGTAAATAAACGACATCGA
TGATGTAATATTGGTAACGATGACGTAACAATCTTTACAGTTGAGGCTACGTCATCGAAA
AACCGGAAATCATCTTTCGACCAATCACGAGATACCACGTGGTCGGAAGATTTTTTAACA
AATCGACGTCATAGCAACGTGACGTCACCACCAACGTTTCGAGTGATTCCTATGACGTCA
CAAGAGGAAAAGCCGTCATCGCGATCTTCATGCTCCAGTGATTCAACCACCTCACGTGAT
TCCTATCGAGGTCGCTCTTTATCGCCGCCCCAGCGCTCATCTCATCTTGCTTCTCATAGA
AATACAATACAAGTTACGTGACTATCGTCGCCCAATGACAAACCGTAGTTTCTTTTCCCG
CCAAATTCAAAGATTTGTTCCAAACCAATCACACAACGCTACGTCATCGTTTTTCTAATT
TTCAAATAAAAACTTTTTTGCGATTTTAACAAAGACGTCTTCTTTGTTACAATGAGTCTT
ATTGTTACAAGTACCATCGAGTAACGACGATTGTTCCGTCATAACGAGCATAGTCAGCCG
TTCAATATGAATGTAGCATCCTGTTGTGATGTTTATTGTACAAGTTGTAGGATCTGGTAT
CTCAGTTTCCTGAGACCTGGTGATTCTGTTCCATTCAAGAAACCGAAACTAATTCTACCG
CTGGGTGTCGCTAAGATATTAATTGGTAATTAATGTTATTTATAATTAATTGGATCGTAA
TGAAAATGTTCGCAGCTACTGTGGTAATAATACTCGATTGTCTTGCATTGTTTTGTCAAA
CAATGGGCATGACGTCGCCGCCGCCATCTTTCCTGGGAAGCCCGGGATTTCCCCTCTGGA
TATCTTTGCTGGTAATCCCCCATTTAAGCGACGTTCCCGGTTTAACTTTCTTTTTATTCC
AGTTTATTTTCTCGGGTTGCTGCAACGTTGTGGCTTTTAAACGAAATTCGAGATTCACGG
TAAGTCCATGGTTTGTAAAAATTGTAACTATGACGTAACAAGCGAACTGTTGCTAGACCG
CCATCGCGTTCGGATCTTCTTGTCTTTCAACAATCGTGATTGTCGTTCTTCTCTGTGTCG
TCACAATGGCAGTAGCGGAAGAAGTAATTGTGTTAATGTTGTTATATTATGTCGTAACAA
AGATATATTGTAGTTATCATTCTATCAATTGTCACATAAAGGCGTTGGTGTCGTCATCTC
TTCGATAATATGTTTGCTGGTACTTTCCCTTCTTGCTGTGACGTCATCATCATCGCTTCT
TTGTTACGTAGCTCTGACGTCACACGACGATCGTTGGTTTACCGACAGGGTAAGCCCCTT
TTGTAGTTACGCTTAATCTAACATCGGTTCATGCAGGGAACACAATGCGACTCCACAGCG
CCGTCTACCGGTGGCCACGAATGTGCCAGCCTAACTATTCCATCCAACAAACCAGCCTTC
GTTTTCTACGCTCCTTCAGATGAAGCGGCGAAATATACGTCAGCGTTTCGTGACGTCATT
AGGGGACTGGAAACCAAAGGTTTGTGGTTTGAATATTATTCTTGTTTGGTTAATATTCTT
GTTTTTAGACAAACTCGACCGAGAGTTTGATGACGTCAAGACACCGGGTAGGTTGATATT
ATGACGTCATTAATGCGTGGCGCCACAAAATTAGATATCTTTCTAGATTCGAGCGAAGAC
GGGGTAGCAGTTATTGAAGTAGACGGACAACCCCTGCCGGGGAATTACCTGCATAGTACT
TAAGCTCTTATGACGTAATAATGGACCTTACAAAAGAACAAACAATTAATATATAAGAAT
TCGGCTTATGACGAAATAATGTAAACGTCAAATTATTGTGACATTTATTATTGCGTCATT
GAGGTTTTGTCGCCCACTCGCGAAACGTCAGGCAATTAGTTTCCTTGTTTACGGAACAAA
CGACTGCGGGGGTGCGAATTGTGACGTCATCAATCAAACTAAAAAGGGGAGTTGTGACGC
AATAATAAAGTAATTTTCAAATGCGATTGTTATGTAATAAAAAAGGAAAAAATAATGAAC
ATAATTATTCGTTTCTTCGACTGCGACAGCGAAGATAAAATTAATTAAAACAACAAAGAG
AACGAAATTTGCAACAAGACGACAGTCGATAAAACACGATGAGTAGAAACTACTTGAGTA
AAAGTGTCAAATAAAACAAAAAATGAAAAAAACACACCCAACGTACAATAAAACTTACGG
CAAATTGTAGTTAAAATTCATAATTACAAAACAATAAAGATCATATAAACAAAATATTAA
AGATCATATTAACAATATAATATAGATCATATTAATAGCGACAAACCTTATCTGGTGTTA
CGTCACAATACAAACAAAATATTTCGACATGTCAATCAAAATCGGAAACCAAGTTTCAAC
TTCCCACGCAAGACAATGGGAAAGTAACACGTCACAATACACTTGGTGACGTCATATCAC
TAAAACAAACACAAGGTGTTCGATCCAGCTGTGAAAGTAAACATAGAGCGCCACCACACG
AGCAACCCTCACAGCTGGATGCCACCACCTACGGCGCACTTTCAACAAACATAAAATTTC
AAAAAGAAGAAGTTATGACGTCACAATCCTGTATAAACTTGCACCCGAGTGTGATTTGGA
GGCAGAATGTTTTCGAAGCTCAGTGCGAGTTACAAACCTATAATGACGTCATCAGATAGT
AAGTTAGCAGGTATGACGTCATCAGAATCAATTG

Reference(s)

Yagi et al. (2004). A zinc finger transcription factor, ZicL, is a direct activator of Brachyury in the notochord specification of Ciona intestinalis. Development 131(6):1279-88

Corbo et al. (1997). Characterization of a notochord-specific enhancer from the Brachyury promoter region of the ascidian, Ciona intestinalis. Development 124(3):589-602

Fujiwara et al. (1998). The snail repressor establishes a muscle/notochord boundary in the Ciona embryo. Development 125(13):2511-20

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