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CIS-REGULATION

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  1. Transcript 'Moocul.CG.ELv1_2.S53...' > 
  2. Transcript 'Phfumi.CG.MTP2014.S7...' > 
  3. Region 'REG00000652'

Cis-regulatory Region

Name

Ci-RhoD -3406/83

Short name

n/a

Region ID

REG00000652

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Lionel Christiaen (2010-04-25)

Annotator

Clara Degos (2010-04-25)

Curator

Delphine Dauga (2010-05-03)

View position in WashU

Description

The complete cis regulatory region drives RhoD expression in notochord, TVC, muscles and mesenchyme. Here, the absence of the regulatory motifs (FoxF and Ets1/2) abolish expression in TVC and muscles.



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

Coordinates in the paper :-3472/+17

Hierarchy of Regulatory Regions

Modification of Ci-RhoD -3406/601 by deletion

Regulated gene(s)

KH2012:KH.C1.129 (RHOA; RHOB; RHOF)

Construct(s) made to test this region

CONS00000622: pCi-RhoD -3406/83::LacZ

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

7,848,7207,852,207

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

Sequence

Aniseed Coordinates: [7,848,720 / 7,852,207] on scaffold KhC1

Transcription start site is based on the start of the first exon of the KH transcript model.

Show sequence

Length: 3,488

CTCACGTCTCTAAAATAGATTTCTTGATTGTTCATATCGCGTTTAGAAAATATGGTGTAA
TATGCGCGAATCCCATCTTACCTCATGGTACTGCAAATCGCATAAGCGCTGTGACGTGGG
TAATAGGAATAATACAGCATTACAGTAACTAAACACCAGTGAAAAATTACTGTAAGCGTG
TTTGCTCCGGGCGTATTTGCTGCGAACAATGACGTCATTTGGTTTAATGTCTTGCGGCCT
TAGAAATCGTGCGTTTACTTTAGTTTAGCCCCAATTCAAATCTAACTTTTTAGCGAATTA
AAACTTTCGGTCGCTTAACTGGCATTGTGCGTGTTAACAAAATTTTAATACCCAAATCTT
AGGTCCCATGCCATGTCACGCTGTAGGACCTCTCAAGTAAAACAATAGAACTACTGACAG
TGTTTAGAAAGTCAAATAGATGCACAATTTTTCCGAAATCCTTTATAATTAATTTATTTA
TTCGCAACAAGAGACACGTTTAGGCGGTAGAGAGCAACTATACAACAAAATCATTATGTC
ACACATGCACTAACTTAACTCGTAAGCAGACACGAGGTGTATAAAAGCAAAACCTGGTTA
TTACCACTGCCGTTGCTCTGCCACGCGAAGATAAGTAAATTCCATTATTCTATAATTACA
GATACACAGGTAGTCTAAGAACTCCGGTAATGAACCGAATTTGGCTTAATTCCTAAGTCA
TGTGATAAGGATACAGAATATATGGGTTTCTAAAATTTGTTTTTTAAGCTATACCACCTA
CAAGTTGTCGTTATCCTAAATTTCAATTTAAAAACTTTACAGCGGTTTATCAAATTTATT
AGAATGAAGAATTTCAAATGTGTAGAATTGTATTGAGATATCTAAGAGAGCAACGTAAAC
ATAAAGTAAACAGATAACACCCAACTGTCGTTCACCAGAAATGCAAACACTCAGACCGCG
TTCCATATATAGTATGGTGGGGGAGATGGGACACTTTTTCATTCTATTTTCTCGTTCCAT
TTAGTAGTAAACAAAGAACACTTGAAGAAATATAAAAACCACATTCCCACAATTCCCATA
GACCGTTATTGTTAATTGTTTCACAATCAAAATATTTGGATAATATGTGCTAAAGGCGTC
CTATCTTCCCCCACAGTACTATAGTAGGGTGGGGAAGTTGGGCAACCTTTTTATTCCACT
TTATCGCCCCATTTGGTAGTAAACAAAGAACAGTCAAAGAATCGTTAAACCGTATCCTTA
CCGCTGGTAATTGTTCAAAACACGATCAAGATATTTAAATACTATATACGTTCTAATGTT
GTTTCGTTTTCTCCACCCTACTATATGTTATTAAAATTTGATTCTTCCTGTCTTTTCTAT
CATGAAGCAATATCATTGATGTTTATACTAACTCCAAATGTTCATGTATATGTATACATT
CATATGTTTTGCATATTTTTATATACAGAACCAATGTTAAATATACTGATATATATTTAC
TAATACATACCTATATAACAGTTATATAAACACCTATATACCCACTGTACCCAATAAATA
ATATATACATATACAGCATAAGTCTATTACACCACCTTTTAACAAATACACATATATTCG
TCTTAAGCCTGTCTTTACCAATAATACAGAGTACCCTTAAAACATGTTATCGTGTACCTC
ATCCTATCTCACTAGACGAGACATTTTACAGTAGAAACAAAATAAGCTCTGATTGTGTTT
CGGTTGCGACGAATGTTGCTACACCATGGTCTATTAATAAAGACGTGTCGGCTGTATAAT
AATGTAGTCTACACCACGGTCAATTAAATACGCCAAGTATGCTTATATAATACATTGAGT
AGGACAGTGGGCCATGTATACACAAATATATGGACTATTTATAAGTGGGTTAATGTGTGT
ATGTTGTTGCTAGTATATAGCTATTAGCAGTGTGATAAACGTATACAAGAATATTGCATC
TGCATTCGCCTTCCAGTCTGTTCCTGGATTCTTGTTTATGTTAAACAGTTCTACAAACCT
AAGGCACACAGCGCGTGCGTTCGTGCTGGTGTGTATAAAAACACGCCCTCATTGCGTAAA
CGCTTATTGACTGACAAGACCACAGTTTCCTGTGAGTTGCGCGAGTCTATATACTGCGGC
AAAAGACGTTAGAAGGCTGTGACCTGCTGGAAAGCCTTTGCCAGCTAACCTACCGTATCG
TATTTAGCGGCTAGTCTTTCAAGTCAAGTTGTACGAATCGTTTTAGTTGTATTCATACGT
CGCGAGCGGAGTTAATTATAGTGACAGATTTTTGAACTAAATGAACGTAGTTATAAATAT
TGTGAGTGAAATTCAAGCAGTAAGTGTATATAGTTAGAAGCATATGAAGTCATGGTGTAT
ACCATTTCGCAAAGTGTTAAAGAGGACAATTCAATACAGTCAACACGGTGTATAAAGTGC
CGAAGTATGGGTTTACACTATTTTAATATGGTTTGTGTGAGTTGTTGTACATTTAATTTT
TGAAATCAAGCTCACTGTACAGTTTGACGACTTGCGAATAGGTCGAACATGATTACATTT
TAGCCAGAATTAGTTATGAGTTTCATGGTTAATTTTACTATTTCCTAAACGCTGTCAATT
TACTGTGTATTATTAGATCTACTAGCAATAAAGTAATGCATTGCACGAGGGTTTAGTAAC
AAAAGCATGTTAATAACCGGGTTATAAATAACTCAGAACGTTTCGAAAATCGACATAGTG
ACTGGCCTACTATATCACCGAAGACGTAATAGACTATATATGCATAACACGCACATGCTT
TGCGCCATGTATATATATGATATTTGAATATAGATTTGATCACGCCGAAAGCTGTCCAGA
CTAAGAATGCTTACAAAGGTAAGTTTCAGACAGTTCTATAAAGTTACACCAGCGTTATAC
AAAGGATCTGTATGGCAACGTCAGACAATTTGCGTAACAGGAAGCAGAACTACTTGTTTC
TAACGTCACAGTCCCCTAGCGGCCTAGTGAATAACGGTGGCGAAAGATAGATAGTAAGTT
TTTTTTATTGTTTTATGTCCTTGGAGAGGTAAATAAATTAACTAGGAGATGATTGAAAAA
ACATTATTACGTCCACAATATGAGTATAGTATAGCATTGTAAGGTTGTATGTTTGAGTAA
GACTATCTAAAAAAGATAAAAAAGAGATGAAGTCTAGGATTTGTTTTTCTTTTTACAGCA
TTGTCGTTCAATTACCGCGTATATATGTATTTGTATTTTTAAAATTTAGCGTATATTTAG
CTGCATTTAAAGATAAAATGGGCTACTAAAGAATCCTCCCCAACTAACTGCTAGTCTAAA
TAGTATTCTTCACTACTGTAACAAAGTTGCATTTCTTCTTTTAGTGACTGGCATCACTTC
TTAGAATGTAGTTGCTAATTTTAACTTGTAAAGCCAAAACTATACACAAACAATGGAAAG
GATACCCA

Reference(s)

Christiaen et al. (2008). The transcription/migration interface in heart precursors of Ciona intestinalis. Science 320(5881):1349-52

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