- Clone 'cima814m12' >
- Transcript 'Boleac.CG.SB_v3.S241...' >
- Transcript 'KH2012:KH.C1.439.v1....' >
- Region 'REG00001114' >
- Region 'REG00001252'
Cis-regulatory Region
Name
Cirobu.REG.KH2012.C9:5648367-5648505_Fox1-3/Bra4mut|DDR1; DDR2; MUSK
Short name
DDR1/2_CRM24_139pb_Fox1-3/Bra4mut
Region ID
REG00001252
Status
Curated
Origin
engineered region from C. robusta formely Ciona int. type A
Type of Activity
regulatory_region
(enhancer)
Author
Diana S. José-Edwards (2017-09-09)
Annotator
Marion Gueroult-Bellone (2017-09-09)
Curator
Marion Gueroult-Bellone (2018-05-09)
Notochord activity of DDR1/2 139pb enhancer is abolished by the mutation of the fourth Brachyury and three Fox binding sites. But activity remains in the mesenchyme and tail muscles.
Modification of Cirobu.REG.KH2012.C9:5648367-5648505|DDR1; DDR2; MUSK by substitution
- Cirobu.REG.KH2012.C9:5648367-5650489|DDR1; DDR2; MUSK REG00001242 [ regulatory_region (extended_promoter) ]
- Cirobu.REG.KH2012.C9:5648367-5649375|DDR1; DDR2; MUSK REG00001243 [ regulatory_region (extended_promoter) ]
- Cirobu.REG.KH2012.C9:5648755-5649375|DDR1; DDR2; MUSK REG00001245 [ no_output ]
- Cirobu.REG.KH2012.C9:5648367-5648757|DDR1; DDR2; MUSK REG00001246 [ regulatory_region (enhancer) ]
- Cirobu.REG.KH2012.C9:5648367-5648505|DDR1; DDR2; MUSK REG00001247 [ regulatory_region (enhancer) ]
- Cirobu.REG.KH2012.C9:5648367-5648505_Fox1mut|DDR1; DDR2; MUSK REG00001248 [ regulatory_region (enhancer) ]
- Cirobu.REG.KH2012.C9:5648367-5648505_Bra4mut|DDR1; DDR2; MUSK REG00001249 [ regulatory_region (enhancer) ]
- Cirobu.REG.KH2012.C9:5648367-5648505_allBraMut|DDR1; DDR2; MUSK REG00001250 [ regulatory_region (enhancer) ]
- Cirobu.REG.KH2012.C9:5648367-5648505_Fox1/Bra4mut|DDR1; DDR2; MUSK REG00001251 [ regulatory_region (enhancer) ]
- Cirobu.REG.KH2012.C9:5648367-5648505_Fox1-3/Bra4mut|DDR1; DDR2; MUSK REG00001252 [ regulatory_region (enhancer) ]
- Cirobu.REG.KH2012.C9:5648367-5648505|DDR1; DDR2; MUSK REG00001247 [ regulatory_region (enhancer) ]
- Cirobu.REG.KH2012.C9:5649375-5650489|DDR1; DDR2; MUSK REG00001244 [ no_output ]
- Cirobu.REG.KH2012.C9:5648367-5649375|DDR1; DDR2; MUSK REG00001243 [ regulatory_region (extended_promoter) ]
CONS00001255: p.Cirobu.REG.KH2012.C9:5648367-5648505_Fox1-3/Bra4mut>LacZ
5,648,3675,648,505
Motif Name | Binding Factor(s) | Sequence | Position in Region | Comment | |
---|---|---|---|---|---|
1 | T-Box | n/a | tctcac | [5,648,369 / 5,648,375] | First Brachyury binding site of the Brachyury/Fox sites cluster contained in DDR1/2 139pb enhancer. Mutation of all four Brachyury sites strongly reduces enhancer activity in the notochord. |
2 | T-Box | n/a | gtgaca | [5,648,387 / 5,648,393] | Second Brachyury binding site of the Brachyury/Fox sites cluster contained in DDR1/2 139pb enhancer. Mutation of all four Brachyury sites strongly reduces enhancer activity in the notochord. |
3 | T-Box | n/a | gtgtga | [5,648,400 / 5,648,406] | Third Brachyury binding site of the Brachyury/Fox sites cluster contained in DDR1/2 139pb enhancer. Mutation of all four Brachyury sites strongly reduces enhancer activity in the notochord. |
4 | Fox | n/a | ccaaata | [5,648,449 / 5,648,456] | Fourth Fox binding site of the Brachyury/Fox sites cluster contained in DDR1/2 139pb enhancer. Mutation of the three other three Fox sites and of the fourth Brachyury site abolishes enhancer activity in the notochord. |
5 | Helix Turn Helix / Tryptophane clusters | n/a | attgaa | [5,648,477 / 5,648,483] | This Myb#2 binding site is located in the notochord-active enhancer of KH.C9.371. |
6 | ZnF_(C2H2) | n/a | ccacc | [5,648,492 / 5,648,497] | Sp1/Klf binding site located next to the Brachyury/Fox sites cluster contained in DDR1/2 139pb enhancer. |
Aniseed Coordinates: [5,648,367 / 5,648,505] on scaffold KhC9
The fourth Brachyury site and three Fox sites are mutated : Fox1 : tatttac is replaced by tgggcag Fox2 : gtaaata is replaced by tgcccgc Fox3 : ataaaca is replaced by cgcccca Bra4 : GTGTAA is replaced by TAATAA
aatctcacttacttgcgaaggtgacatcacccggtgtgacggatctcaaaccaggtttgg
gcagttcctcgttatgcccgccccaaatacagatcgcaaggctttgtcatattgaactct
gaaagccaccgctgttgcg