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CIS-REGULATION

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  1. Region 'REG00000650'

Cis-regulatory Region

Name

Ci-RhoD -3406/1048

Short name

n/a

Region ID

REG00000650

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

This region drives RhoD expression in notochord, TVC, muscles and mesenchyme.



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

Coordinates in the paper : -3472/+982

Hierarchy of Regulatory Regions

Regulated gene(s)

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

Construct(s) made to test this region

CONS00000620: pCi-RhoD -3406/1048::LacZ

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

7,847,7547,852,207

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 Fox n/a tgtttgt [7,847,871 / 7,847,877]
2 Fox n/a tgtttat [7,847,900 / 7,847,906]
3 Ets n/a aggatc [7,848,001 / 7,848,006]
4 Ets n/a tggaag [7,848,043 / 7,848,048]
5 Fox n/a tgtttat [7,848,089 / 7,848,095]
6 Fox n/a tgtttga [7,848,180 / 7,848,186]

Sequence

Aniseed Coordinates: [7,847,754 / 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: 4,454


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
GATACCCAATGACGTCAAAGGTGCTTTCCCCGAGCAGCAACCCAAAATTAAATGTGTTAT
AGTTGGGGATGGTGGATGCGGTAAAACTTCAATGCTGGTTGTATATACGGAAGGCGAATT
CCCTGAAGTAAGTTTACGTTTAATTATAAACTTTTTTGTATAGTTGTCAGTTTCAATACA
AATATAGTGGGATGGGGAAAGATGGGACAACTTTAACACCTAATATCCAAATATTCTGGT
GGTGTTTTAAAGAATAAACAATGGTCTACGCCCTACGGGGTCGTAAGGATACGGTTTTAT
GATTCTTTGTATGTTCTTTGTTTACTACCAAATGGGACGAGAAAATCGAATGAAAAGGTG
TCCCATCTCCCCCCACCATACTATATATGACAGTCCGTATATATACTAGGGCGAGCAGGA
TAATTGGATAATATGTGCTAAAGGAATCCCATATCTTCCTTAACAGTACTATTTGGTATA
GTTTGCTTATACTAAATTTAATTAGCAACCCGCTGTTGTTCAAAGGTGTACACGCCCACG
GTGTTTGAGAATTACAGCAGAGAGGTGGAATTAAATCGAAAGAAGGCGGTGCTAACATTG
TGGGATACGGCGGGTATATATTAGTACATACGTGTTTATGCAAGACATCGTAGGCTTGTT
GACTTAGTTTCGGTTAGCATGGAAGTGTAGTCTATGTTCTACGTGGGTTATGTTCTTGTC
GAGGATCTGGGATTAGGGCTAAATTCAGCCTATTATTACCACAACATTCAGACTGCTTTT
GTAGGTCCAAATGTAACATATGACTAGTGTGTTCTGATGTGTGTTTATAATACAATAAAC
TAGCGCAAACTGTTTGTCCCATTATGTTTAGTCATATAGGTCATATGAGAGTAAATGAAG
TGTAAACCAAATGTTTACTTGTACCAGGTCAGGAAGATTATGACCGGCTTCGACCTCTCT
CTTACAACAACGCA

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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