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CIS-REGULATION

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  1. Transcript 'KH2012:KH.C2.598.v1....' > 
  2. Region 'REG00001291'

Cis-regulatory Region

Name

Cirobu.REG.KH2012.L13:47071-47600_Bra3mut|KH.L13.2

Short name

KH.L13.2_CRM9_530pb_Bra3mut

Region ID

REG00001291

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 reporter gene expression in notochord, CNS, mesenchyme and tail muscles. It contains 4 Myb, 3 E-box and 3 Brachyury putative binding sites. Compared to the WT fragment, it lacks one Brachyury binding site.

Hierarchy of Regulatory Regions

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

Regulated gene(s)

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

Construct(s) made to test this region

CONS00001310: p.Cirobu.REG.KH2012.L13:47071-47600_Bra3mut>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 T-Box n/a gtgcga [47,273 / 47,279] This putative Brachyury binding site is located in the upstream 530pb enhancer of KH.L13.2. When this TFBS (2nd of 4 Brachyury binding sites) is mutated, the 530pb enhancer is no longer active in the notochord.
6 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.
7 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.
8 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.
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

Third brachyury putative binding site is mutated. TCTCAC replaced by TCTtct.

Show sequence

Length: 530


acctggtatatgctggaataatgaacatatttaactcatattcatttgaaataacggcct
attgaatttaaagcgataattgccctttaagagctcacgtccataacgcttattgcctct
ccatctttggaactgactctgtacataaagtggcttcaactaaaacctatttaaaatcta
tcactttactgagaagagtcaagtgcgaacattggccgggaagtgggtgaccgttgaatc
cggcttatccacgctggctgacttaccagatcgcttattaactttttaactccattacgt
ccgttatcaagctgacaactggcgcgaatggaatcgtaactctatatatattataactca
atctaccgagacgacgggttatcgaagaaaaacattcttgtctggcactctcttctctaa
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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