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CIS-REGULATION

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  1. Region 'REG00001146'

Cis-regulatory Region

Name

Cirobu.REG.KH2012.C3:2806773-2809874|Efna.d

Short name

Efna.d (-3318)

Region ID

REG00001146

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Izumi Oda-Ishii (2017-02-01)

Annotator

Marion Gueroult-Bellone (2017-09-03)

Curator

Marion Gueroult-Bellone (2018-03-13)

View position in WashU

Description

The 3.3kb region located upstream Efna.d TSS drive strong reporter expression in the animal hemisphere and weak expression in the vegetal hemisphere. It contains 4 GATA binding sites.

Hierarchy of Regulatory Regions

Regulated gene(s)

KH2012:KH.C3.716 (EFNA1; EFNA4; EFNA5)

Construct(s) made to test this region

CONS00001115: p.Cirobu.REG.KH2012.C3:2806773-2809874>GFP

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

2,806,7732,809,874

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 ZnF_(GATA) n/a ctatct [2,807,059 / 2,807,065] One of the 4 GATA4/5/6 (Gata.a) binding sites located on the 419pb upstream enhancer of KH.C3.716. When 3 or 4 of these TFBS are missing or mutated, the enhancer is inactive.
2 ZnF_(GATA) n/a ttatca [2,807,091 / 2,807,097] One of the 4 GATA4/5/6 (Gata.a) binding sites located on the 419pb upstream enhancer of KH.C3.716. When 3 or 4 of these TFBS are missing or mutated, the enhancer is inactive.
3 ZnF_(GATA) n/a ttatct [2,807,122 / 2,807,128] One of the 4 GATA4/5/6 (Gata.a) binding sites located on the 419pb upstream enhancer of KH.C3.716. When 3 or 4 of these TFBS are missing or mutated, the enhancer is inactive.
4 ZnF_(GATA) n/a tgataa [2,807,166 / 2,807,172] One of the 4 GATA4/5/6 (Gata.a) binding sites located on the 419pb upstream enhancer of KH.C3.716. When 3 or 4 of these TFBS are missing or mutated, the enhancer is inactive.

Sequence

Aniseed Coordinates: [2,806,773 / 2,809,874] on scaffold KhC3

Sequence retrieved via the tool BLAST of Aniseed, thanks to the supporting information of the article (S7 Fig.)

Show sequence

Length: 3,102


TTTAGGATctgaaaagtaaacacatatttagataactgaaatactataagcctttacttc
taaaaatcaaactggttgacatttattcttactgagcttgtggtattataaaatacaaac
gattagacgctatcaacttatttaatcgaactgcgttgaattcggtctcacgaaattgta
agctgcttactctgcgaaccgagatacactgatttgcggtagagagtcgaccgctataaa
gccacacaaattacggacttcttctctttttttcggtcgctgttcgctatctctcgtctg
accaatcgagagtccagcttatcataatatttatgctcgcactcgtcccttatctgctta
ttagcttggcgcccacgatttgcagagtattggtgataacggtattgtgtccgtgtgcaa
tattgcaattgcagcgacgaaagtcaaacattgcttactgtacccaaacctgagcgattt
caatacattaagtcccaatacatcaatgtcaacgactttgggctcaaacaaacggacttg
tctggcattagttctagtgtattaaatatgataaattacaccttataaggaacacttctt
attgctaatgtggtagcgttcatgatcgcctgacgtcagaaattaatcttatttctgcaa
acaagcagcttcgagctacgatataattcgcaacctatcaagatgatttattaccgaagc
gattttgccgaatcgtgaagatttccactcggcaaaacgagacagtatttgtccagccat
tgactcaattcttggtcaaattgactcacactaagccaccaaacatgctacgacaagctg
tcaccataacacaaaatattaaatgggccgtctgttataataccttgcctacaatccagg
tgcacttggtcgttagcgaagtcgaggacttatttggaagtgaaagtttaattaaaacaa
gaacggattcggcgaagtaaactttaagcaaaggatcaattcattcgagtagtggtctcc
cttagacgcttttctcactgagccttccttcaattcgttttggattcgttacttcccgaa
cgccaaatcacgggcaaatctcaaacgggaattgtacacaacggatgcgagatacaaagg
aggcctctgtgttccgcttgtattgatccagtataactacccggggttaacaatggtcga
tttacgcaactctttatatttctatgatggtactttttcatatcccggtttgttttgttt
tcggtgacgaccttccaaggaccaagacttcaatttcgttgcgtattgcggctcggcaga
aacttggccaattattatgcgaaagcacaagatagatcggttttccgctatggatattta
aacattcaattactcatcctttggcgtgagtattattttaataaagatttcacgcttatg
atcatatttttaaataatcaataattaaacgaaacttttgaaactagttttttctccttt
atagcgccacgtactggtaaattgtagcgtaaaacataattttttgccgaatctaattat
tggaaaacggttcaatattatcgaggtaacatattttgcatgcgcgagtcagattcgaac
cttgtctccttatcaccaattaactcacgactgcagtcagttatcataataacacgtgat
tcagctggcgacgaaattcgttgcgtgcaagttaaaataatgcactggcgtctgtaatat
atttacactttggtctgcattggtttttcgtctgtctcatattttatggatttcgcattc
attatagagaattaccttttaggcacctaacgacgcattaaaataagcaaacattgcaag
ttctcattttaaaaaggtaaaagtgattgcgaaacataccaattgcaactatccaaatcg
aagctgtgcttatttgcagctattagtgtcttgttgattccctgatatgatgtttttcga
aatgtcacattgaaactcgacccggcttaacagttataaaggccaacgaacgaccctttt
gttccggtgtattcaaattattataaagatcttttatcagcgacacgatcattcacacta
accgtgtttattacagttctgaatacggaccatcaggcactggttgtcgtgagagctaaa
ccgcaaaacgtcacttgtcaaagtgaaaggtcgtaacagtgtcctggtttgaatttgcat
cgattttagatgttatggtcggggaagtgtgtatcgatgtctagagaggtctaagatgac
atttaagcgtaaaggtaactttgccaaacagagcgttttgtttctcacctctacatttgc
ttgctcccattgtaaaatatataatggcggttttcagggaattgtgtttattctacgagt
tagttgccccctttcgtggccttaatggtgacaaatcaattttggcagcggtgctaaaaa
ttaacaacgcggaaaactatctaaaaattctttgcctccaagattgaacccaattacgca
caagatcccatacggcgacgtgtgcagttcaatgagcgccgccaaacacattgaacaata
aatcgtaaagtagtttactgcttatagaaacaaaatgaaaccttaattcgttggcgtgta
actgcagtcacgcactcgaagaattgcatgcgtctcacgggcgacacaagatagcgaata
gctagtatctgggcgacgtggtaattgctgataaaactgcacgataagcgacaacgaaat
ccgaccaaaattgttcggagatatgtaagcctgataggctcgtgaggttttaggtggttg
gatattttgtttgcatatacgtcggtcatgatatttaatttagtggcaattaggatctaa
gttttaacagttaaacagggtgtgcctatctagcacagcctaaataggtcgaaattggtt
aaatgtctaactcttatgtgtagtttagggttaaatgtacgtacctttttgtatatatga
cctaattgtttaagcaattacatctgtgtacaattcattaataagaatagatatacgtgc
gtttggtttcattataaatgctgttaaactttcgacttgatt

Reference(s)

Oda-Ishii et al. (2016). A Maternal System Initiating the Zygotic Developmental Program through Combinatorial Repression in the Ascidian Embryo. PLoS Genet. 12(5):e1006045

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