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CIS-REGULATION

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  1. Region 'REG00001083'

Cis-regulatory Region

Name

Cirobu.REG.KH2012.C2.4472575-4475581|Fgf9/16/20

Short name

Fgf9/16/20 (-3008pb)

Region ID

REG00001083

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Izumi Oda-Ishii ()

Annotator

Marion Gueroult-Bellone (2017-09-03)

Curator

Marion Gueroult-Bellone (2018-03-13)

View position in WashU

Description

This region contains three Tcf7-binding sites that are critical for expression in the vegetal hemisphere domain. This regulatory region contains the entire 5 cis-regulatory region of Fgf9/16/20, (from -3008bp to the TSS in the article). Transcription start site is based on the start of the first exon of KH.C2.125.v1.A.nonSL4-1 transcript model.

Hierarchy of Regulatory Regions

Regulated gene(s)

KH2012:KH.C2.125 (FGF16; FGF20; FGF9)

Construct(s) made to test this region

CONS00001056: p.Cirobu.REG.KH2012.C2.4472575-4475581>GFP

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

4,472,5754,475,581

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 TCF/LEF n/a ttta [4,475,341 / 4,475,345] First of the 3 Tcf7 binding site located in FGF9/16/20 enhancer. Its mutation alone does not affect a lot the 219pb enhancer activity, but when both first and second Tcf7 binding sites are mutated, the enhancer is inactivated.
2 TCF/LEF n/a aaag [4,475,468 / 4,475,472] Second of the 3 Tcf7 binding site located in FGF9/16/20 enhancer. Its mutation alone does nearly anihilates the 219pb enhancer activity, and when associated to the mutation of another Tcf7 binding site, the enhancer is inactivated.
3 TCF/LEF n/a tttc [4,475,515 / 4,475,519] Third of the 3 Tcf7 binding site located in FGF9/16/20 enhancer. Its mutation alone does not affect the 219pb enhancer activity, but when it is associated with the mutation of the second Tcf7 binding site, the enhancer is inactivated.

Sequence

Aniseed Coordinates: [4,472,575 / 4,475,581] on scaffold KhC2

Sequence retrieved via the tool BLAST of Aniseed, thanks to the supporting information of the article (S4 Fig).

Show sequence

Length: 3,007


attaacgaccgttaatgcccacttttccatgaaagttgttatgtcttgtaggatgtcaga
aaaccgcacttacaggtgcctgctggtaacaactcttttgacttcatatatgacgtaccc
gggagtcaaaaaggccaattaccaaacggatgggtttccttaacttactttccgcaagtt
tggcaatttcaacaaaatcgattcggagaataactgtaaattagtggagtacgcggctcg
catcacccggtaggatatggacagtaaattttgtattttaacgaccgacagctcccagca
gaaccaagtgaaaaggagggcgatacaaaaactgcaccggttcttcataaaattctgttt
gtcttgtagttacatgcaccttgcgcgtatcggtgtttcagcgaaacttatttaccagct
ctttatgtcggagagaacacaaggcggactgatatcgactgtttgttctgatgcaaaatc
agaactgacccgtaacaggcttgaacacaaacaaacctaccgcacattctaaacgacctc
gcgcaaggcatcttcgtcaaacagcgatggcccgtgcgtcgaaagtgcaaatagaacatt
tgtttaggtgcttttcggattgagacgcgcgcgtgctgcgctgtctcgcagactattcgc
gatgccgataatattaacggcttagcggggaaaagtaaattcgtttcccgctgcgagcct
cgaattcactcgtaccaccttcgacagattttatgtttacgattctagaaagtaaactat
atgacgcggctgaagattccaaagcaacaacatcaatgtaaatattcaaaatatgacatc
acagttgacgtaatcagaatgtatcgggcatgaagtcagatttgtgatgtcgtttttaat
ttcggataattttaaattgaccgaaacaccccgaatctacccctttcatcatgaaaggga
ttcccgcggtggggtagggacatggttggtgagaaactgccagacttgggtgagatctgg
gcgtcgtatacaaatcttgtggggtcaaaaaactaagctgcccttctcaatccgaattac
gcatcggaatcattcgtcgggtgtgaggatccctatactgatgccgcgaccacagacgac
tccgtagtacatcaattatttcttacgggccaagatccaaataaggttaaaagttcccag
tataattagaaattacacgacggcttgtggggctggcttgatctactgatgtagtgatga
tcatcatgcgtcagcgtttggaatatgttgattcctacaaaccgcgcacatccctgaatc
agattcgatatattgcctccacccgcaactacggtttcctaacgtggacacgcacatacg
taacaaggtcggcggttagtcactaaagacaggtcggctcactgcttccgaccgactggt
ttaaatagggctcaacttggccgacattttcataactgtcgttgaggcatacgagtagga
taaggagctttaacgaattacaacgacagttccggaatatcgcgctcgtggctcttctcg
gcgcggtgcgtgtgaatctaatgagatcgcgttgtgttggaaaagtgctggtttcaatgg
tgaagttaaaagttcttaatgatagaagcgcgacaaaagtcgtcattaagtttcaaagca
aatacgtaacagtgtgaaaaatgtaaaactagatttaaagacgcggtgtagccaccgcat
ataacgtcataatggaactacgtcaaagccataattcgcacgcgaaaggtggcggtcgga
ccagctggccctaaatgcaagagccgaattatggggcaataacgaaatctagctattgtt
gaattcgattaagacatagttgcgttaaaagtaaatgctccgtcacagctataagaaccg
tagaacgtaaataataggtttaggggctaaagtgcgtgatacaccttcttatggcggcga
tataggggaagtcggttatttcggcaaaaaatattaacaacgttgagtagccatagccgg
taacctgaaccacgagaacattgtattgaattgcaacaatagagcatcccgttcgtggcg
agaaaaaggtggaaatcggtcgcgcgctgttctcgaaggcgagcacgaaaaagtttcgtt
tgaagaagttcggttcgcctcattcttcccatcattatcgccacgagcgacttttcatta
atcacatgcatttctaaactgctcggaagaggtaggttgtaaggcggcgagatatcggga
cagggaatgagatagaggtcgtaggaatgcactgtcggaatatgcaaactcgtaaagtcc
aaatagtgcattaaaatacttttataaaaaatattgtgggaaaagttggctagggtcaaa
acgttgtctcgtttttgattttgaaacgttcgcgccgcagtcttctataaaaaaagcttt
agaacagtagcgacttttcaaaaccaagtatagttgactcatggttgaagggatttgtaa
aattagccattgcatattacgtagttttaaacaatggccctttgacggcagaaggactct
gccttgagctaccaagtcgaaggtttaggcacgagaggcttaattctccttattgcagtt
agtgtaaacaacttttaagtagattttttataatcgcttcattgttaaacgcatatctga
aaattagcaacagtattcttatttggttcatgatctaacgttgtttttgcttttcatctt
aagttgtttacagcaattaagccgccatatagataactgtgcgcactggtcgtctgccca
tttttagatagccttcccagtgcttctgtactcgagattacgatcacaagcgtaagacgt
caagttcaccgacaaagataagaatcgcgacccacacaagtcactgccgccccttcttcg
tttctcgtcgtacacaaaagcagcgggaatcttgactcggagcatcactcttgaatcgcc
actcagc

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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