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CIS-REGULATION

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  1. Transcript 'KH2012:KH.C1.133.v2....' > 
  2. Transcript 'Mooccu.CG.ELv1_2.S20...' > 
  3. Region 'REG00000619' > 
  4. Transcript 'Moocul.CG.ELv1_2.S10...' > 
  5. Region 'REG00001352'

Cis-regulatory Region

Name

Cirobu.REG.KH2012.C12:711845-714190|CbpD,CbpE,CbpN

Short name

n/a

Region ID

REG00001352

Status

Curated

Origin

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

Type of Activity

regulatory_region
(complex_region)

Author

Diana S. José-Edwards (2018-05-08)

Annotator

Marion Gueroult-Bellone (2018-05-08)

Curator

Marion Gueroult-Bellone (2018-05-08)

View position in WashU

Description

Hierarchy of Regulatory Regions

Regulated gene(s)

KH2012:KH.C12.16 (CPD; CPE; CPN1)

Construct(s) made to test this region

CONS00001372: p.Cirobu.REG.KH2012.C12:711845-714190>LacZ

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

711,845714,190

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 Fox n/a acaaaca [712,452 / 712,459] This is one of the 3 Fox binding sites located in the notochord-active enhancer of KH.C12.16.
2 Fox n/a acaaata [712,465 / 712,472] This is one of the 3 Fox binding sites located in the notochord-active enhancer of KH.C12.16.
3 Fox n/a acaata [712,480 / 712,486] This is one of the 3 Fox binding sites located in the notochord-active enhancer of KH.C12.16.
4 Helix Turn Helix / Tryptophane clusters n/a ccgttg [712,519 / 712,525] This Myb#3 binding site is located in the notochord-active enhancer of KH.C12.16. Mutation or deletion of this binding site inhibits enhancer activity in the notochord.

Sequence

Aniseed Coordinates: [711,845 / 714,190] on scaffold KhC12

This 2356bp sequence, located in the downstream region of KH.C12.16, drives reporter gene expression in notochord. It contains a cluster of 3 Fox and 1 Myb#3 putative binding sites. This sequence was retrieved using ANISEED Blast tool, thanks to the information provided in FigS1.e and TableS5 of Jose-Edwards et al. 2015.

Show sequence

Length: 2,346


aatcactgtgacgcaataaagacagcattgttgacagccgagttaaatccaagcaacctt
tacatccggtcatctcgtcaacttcgagcgatcgcgctgccgtaaaccaacattatgacg
tcataaagacacgtcggtcactcaaaattgtgagaaccgcgttaaaaactgcgaggcaga
tatataggcagaaggcgataaagagtcacatcaacgaaaaatcgaaaattgtatttacat
aaagatgctcggatgtaattttttacttcagcagctcaatttcacgcgacttttcagaag
ctgttctggtttttaaaactttgttggtagctttagattacatttgagcatttttatcaa
aacacaaattttgatttttcgttggtatgctcctttaagttttctcgcatattttaacga
ctttactaccatatatcacgcatcgtcaatcatgcgtgtctgaagtgcgatgacaattgt
gacgtaacacaggccacttaatgttgacgagttaaacctttgtgtggtttgttgggtcgc
gtggaatgcgtcgagctcttccccaatgtacattgtgacatcacatatatgcgttgtgac
gtcatatacaaacaacaagaacaaatagtgacgtaacaatacaaatatcgagtaaattcg
acgtcacggttgaaccgttgtgtggataagttaaccatgacgtcaccggtataaaggtaa
tgcggtgacgtcacagataagatgaaagtcttcaacgcgaatataaaacttctggcatca
atttccggacgacgccattccaactcccgcgggacgtcctatgtgacgtcatacaccact
atttaaccgttagcggtgaagggaagattgtaacttgttttatcctcgcgtggcaggcca
acgacagtctttatagcacgaatgttcggtttcgtacacgtcatgcctgcttacgaatta
caacgtatatgtaactttgtgggtaataaaaagtctgttttctcttttttgatttttttt
tttggttgtggaataaatgaatgtgcacgtagtgaaaacgtgattaccaggtggaagttg
cagctttccgtgattaatccccttgtcatccaagttgggagtggcacggaattcacacaa
cccctcatcgataacaaatcacttactgtattgtgacgtggcacaacatacaatagaata
taagcacgtgacttttagcccatcacaaaaatattcaggatattttataaaatacacacg
cgactaaatgtgcggtttatattcggtaaaggccgttctttacacacacgctatttttag
gcgacaccaaaatagaatgtcgtttgtcgttatttcctgtcgctctttcgtcaatttttt
tttttttaaaaaaaaaaaataacgaaaagggggggaaaaaattcccccgtagctataacg
acgaatggagataatataatacagattcgcgttgtcacgatctattcaagcatttcttcg
taagtaacaaaagtcatatttaagttgtattcgattaaactattacagtgtggcataaag
tatggtgtgaaatgctgcaacctttttggagcgattataataagttatacgaaactatca
gcattgctacataagataatgctgtagtagcattgcgcaaacgccagcaaatacatcaaa
caaacctcagtgtaggtaagttgggtttgggtgaagataaacgttcaaacatatacgatg
gttaagtgtggagggttggtcacgaatggatggaaatacgtgttgcttgctcggggttac
ggggtgtgccgcattccacgcttacccggcaaatacaaaacacttccctagtttatataa
caacatagcgtgtcagtgtcactcttaacattgaagagatgcctagaatttcgagtccgc
agatgcttgaatgctatcgcaagaggcgtggggtttaaggttcaaaacccgtgcaggtga
caacaaactaatttatctgtcacgtgttggtaaatgaggttgaaggctaagggttaaccg
ggttcgaacctatctgaggtaaacaaacagactcaacgtcacatagagaagaaaattaat
tatttgtgacgtcaaggggacttgggcaatattaaacatttctagtggtacttagcaaca
cttgtaagctgaacaaaccacggtcggaaatatgcgtaatatgggaagctgataatggtc
gtttaattaagggttaatattcgctgaattttgtttattcaaaagatagttttgtgacga
tagaatcaacgagcgctttcagtctgtgacgtaacaaacggtcattattacgatatgatt
gttgca

Reference(s)

José-Edwards et al. (2015). Brachyury, Foxa2 and the cis-Regulatory Origins of the Notochord. PLoS Genet. 11(12):e1005730

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