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CIS-REGULATION

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  1. Transcript 'KH2012:KH.C8.269.v2....' > 
  2. Clone 'cien111534' > 
  3. Transcript 'KH2012:KH.C2.821.v1....' > 
  4. Region 'REG00001359' > 
  5. Region 'REG00001335'

Cis-regulatory Region

Name

Cirobu.REG.KH2012.S345:67958-69408|KH.S345.4

Short name

n/a

Region ID

REG00001335

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.S345.4 (KH.S345.4)

Construct(s) made to test this region

CONS00001355: p.Cirobu.REG.KH2012.S345:67958-69408>LacZ

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

67,95869,385

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 ZnF_(C2H2) n/a ggtgg [68,529 / 68,534] This the first of the 4 Sp1/Klf binding sites located in the notochord-active enhancer of KH.S345.4. Deletion of the region containing this binding site, or its mutation inhibits enhancer activity in the notochord.
2 bHLH n/a caagtg [68,545 / 68,551] This the first of the 3 E-box binding sites located in the notochord-active enhancer of KH.S345.4.
3 ZnF_(C2H2) n/a ccacc [68,600 / 68,605] This is one of the 4 Sp1/Klf binding sites located in the notochord-active enhancer of KH.S345.4.
4 bHLH n/a caaatg [68,617 / 68,623] This is one of the 3 E-box binding sites located in the notochord-active enhancer of KH.S345.4.
5 ZnF_(C2H2) n/a ggtgg [68,702 / 68,707] This is one of the 4 Sp1/Klf binding sites located in the notochord-active enhancer of KH.S345.4.
6 T-Box n/a tggcc [68,742 / 68,747] This Brachyury binding site is located in the notochord-active enhancer of KH.S345.4. Its mutation does not affect enhancer activity in the notochord.
7 Helix Turn Helix / Tryptophane clusters n/a attgaa [68,786 / 68,792] This Myb#2 binding site is located in the notochord-active enhancer of KH.S345.4. Its deletion does not affect enhancer activity in the notochord.
8 ZnF_(C2H2) n/a ggtgg [68,808 / 68,813] This is one of the 4 Sp1/Klf binding sites is located in the notochord-active enhancer of KH.S345.4. Its deletion does not affect enhancer activity in the notochord.

Sequence

Aniseed Coordinates: [67,958 / 69,385] on scaffold KhS345

This 1450bp sequence, located in the upstream region of KH.S345.4, drives reporter gene expression in notochord. It contains a cluster of 3 E-box, 4 Sp1/Klf, 1 Myb#2 and 1 Brachyury putative binding sites. This sequence was retrieved using ANISEED Blast tool, thanks to the information provided in FigS1.c and TableS5 of Jose-Edwards et al. 2015.

Show sequence

Length: 1,428


acgcgtattggccgccatgataacgttgccaaattagtagcgagggagagcgcgaaacgt
cattgaaaggtgatacgcgagacggccgttctaacgctggccggtattcgccgacctgac
cttggcgatagtggccgataatgccgagctctcggatgctcacagcggcaagtttattgt
attacgataacggggcgatacgggggtaggtagcccataatactggggcaagtaaaatca
cgttctcaagtctcaccactaactggcgcggttgcatggcggaagaatctggccggatgc
tgaaactcggcctccccaattcaattagggggcgatttccgcggttgttctagaaaaggc
tttttcacacgtacctctgctttaagacggaggcatttcgagttagttgctgataaaagc
aagctggatgaaaacgttagtagaaacgggttagaaactgaggtaagccacctcaagcca
ttatcaaaaggcgaaggctctaaagagtgggggggctacctaccgtaagctgcatggcgc
cggggcaaaagcgcaccaaaacaaactagccggtggataggcagggccaagtgcctggcc
atccttgcaagaagggccacgtactagatggccgcccgaaggccacctcaagccattatc
aaatggcaaaggctctaaagagtgggggctacctaccgtaagctgcatggcgccggggca
aaagcgcaccaaaacaaactagccggtggataggccgggcctgcaagaagggccaggtac
tagatggcacgcccgaaggccacacagccaagaacaagtcataagacgattgaacgatgg
ccaggcactaggtggccgcccgaaagccaaacagccaagaacaagtcataagacgattga
acataatcgatccagttgggtgtgatgcacaccttcataagatatacatgtaaggatgga
tcgcgccaggtaaagcggtagcttgaaaactgtaaaagccatcgatagccaaatgcctcg
tcaactaattagtgacgcgcatgaatggattaccgagattcccgctgtccctatctagcg
aaaccacagccaagggaacgaacgggcttggcannnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn

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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