Region from -483 bp upstream the +1 to the first 17 codons is the minimal enhancer which drives the entire Ci-Bra expression (the transcription start site is the nucleotide +1).

This region contains three essential cis-regulatory elements.

Region - 483 bp/- 348 bp : negative response that keeps the enhancer off in ectopic mesodermal lineage (muscles and mesenchyme). This region contains three copies of a conserved 15 bp sequence motif. It is currently unclear whether this repeat is important for repression.

Region -348 bp/ - 237 bp : it contains one, or possibly two, Su(H) binding sites. Removal of these sites significantly decreases expression in the notochord.

Region - 237 bp/- 71 bp : it contains important element for activation in the mesenchyme and muscles. This region contains three E-box sequences. Progressive truncations that remove these sequences lead to a sequential loss of expression in ectopic mesodermal lineage.

Modification of Ci-Bra -483/17 first codons by substitution

KH2012:KH.S1404.1 (TBX19; TBX6; TBXT)

CONS00000096: pBra -483/17 first codons ZicLb2 mutated::LacZ

5,7886,344

Aniseed Coordinates: [5,788 / 6,344] on scaffold KhS1404

This sequence was found using a blast on the JGI V1.0 using sequences included in Corbo et al. (1997 and 1998), Fujiwara et al. (1998) and Yagi et al (2004). Motifs were also deduced from these four articles. Coordinates from Yagi et al. were taken as reference.
ZicLb2 binding site was mutated.

Yagi et al. (2004). A zinc finger transcription factor, ZicL, is a direct activator of Brachyury in the notochord specification of Ciona intestinalis. Development 131(6):1279-88