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CIS-REGULATION

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  1. Transcript 'KH2012:KH.C3.481.v1....' > 
  2. Region 'REG00001292'

Cis-regulatory Region

Name

Cirobu.REG.KH2012.L13:47071-47600_Bra2mut|KH.L13.2

Short name

KH.L13.2_CRM9_530pb_Bra2mut

Region ID

REG00001292

Status

Curated

Origin

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

Type of Activity

regulatory_region
(enhancer)

Author

Diana S. José-Edwards (2018-03-01)

Annotator

Marion Gueroult-Bellone (2018-03-01)

Curator

Marion Gueroult-Bellone (2018-03-01)

View position in WashU

Description

This 530pb sequence, located in the upstream region of KH.L13.2, drives no reporter gene expression in notochord but is active in mesenchyme and tail muscles. It contains 4 Myb, 3 E-box and 3 Brachyury putative binding sites. Compared to the active WT enhancer, it lacks the second Brachyury binding site.

Hierarchy of Regulatory Regions

Modification of Cirobu.REG.KH2012.L13:47071-47600|KH.L13.2 by deletion

Regulated gene(s)

KH2012:KH.L13.2 (CORIN; HSPG2; LRP2)

Construct(s) made to test this region

CONS00001311: p.Cirobu.REG.KH2012.L13:47071-47600_Bra2mut>LacZ

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

47,07147,600

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 bHLH n/a acctg [47,071 / 47,076] This putative E-box binding site is located in the upstream 530pb enhancer of KH.L13.2.
2 Helix Turn Helix / Tryptophane clusters n/a taacgg [47,122 / 47,128] This is one of the 3 Myb#3 binding sites located in the notochord-active enhancer of KH.C13.2.
3 Helix Turn Helix / Tryptophane clusters n/a attgaa [47,131 / 47,137] This Myb#2 binding site is located in the notochord-active enhancer of KH.C13.2.
4 T-Box n/a tatcac [47,249 / 47,255] This putative Brachyury binding site is located in the upstream 530pb enhancer of KH.L13.2.
5 Helix Turn Helix / Tryptophane clusters n/a ccgttg [47,301 / 47,307] This is one of the 3 Myb#3 binding sites located in the notochord-active enhancer of KH.C13.2.
6 Helix Turn Helix / Tryptophane clusters n/a ccgtta [47,371 / 47,377] This is one of the 3 Myb#3 binding sites located in the notochord-active enhancer of KH.C13.2.
7 bHLH n/a caactg [47,386 / 47,392] This putative E-box binding site is located in the upstream 530pb enhancer of KH.L13.2.
8 T-Box n/a tctcac [47,481 / 47,487] This putative Brachyury binding site is located in the upstream 530pb enhancer of KH.L13.2. When this TFBS (3rd of 4 Brachyury binding sites) is mutated, the 530pb enhancer is still active in the notochord and its tail muscle activity is increased.
9 T-Box n/a gtgata [47,551 / 47,557] This putative Brachyury binding site is located in the upstream 530pb enhancer of KH.L13.2.
10 bHLH n/a caaatg [47,591 / 47,597] This putative E-box binding site is located in the upstream 530pb enhancer of KH.L13.2.

Sequence

Aniseed Coordinates: [47,071 / 47,600] on scaffold KhL13

The second brachyury binding site is mutated : TCGCAC replaced by TCGTCT.

Show sequence

Length: 530


acctggtatatgctggaataatgaacatatttaactcatattcatttgaaataacggcct
attgaatttaaagcgataattgccctttaagagctcacgtccataacgcttattgcctct
ccatctttggaactgactctgtacataaagtggcttcaactaaaacctatttaaaatcta
tcactttactgagaagagtcaaagacgaacattggccgggaagtgggtgaccgttgaatc
cggcttatccacgctggctgacttaccagatcgcttattaactttttaactccattacgt
ccgttatcaagctgacaactggcgcgaatggaatcgtaactctatatatattataactca
atctaccgagacgacgggttatcgaagaaaaacattcttgtctggcactctctcacctaa
gtgccttataaggagttagtctctcgacttagtaaaaagtaactaacgtcgctgcgaaga
gtgatactggagtaacaatgactcattaagccgcgataaccaaatgctac

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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