Region from -2.6 kb upstream the +1 to the first 86 codons exhibits the complete staining pattern in late tailbud embryos including expression in the CNS, notochord, endoderm and occasionally in the mesenchyme. (the transcription start site is the nucleotide +1).

Anna Di Gregorio analysis:

Different cis regulatory elements in this region:

Region -2600 bp/-1770 bp mainly inhibits ectopic expression in the trunk epidermis.


Region -1770 bp/-1650 bp is responsible for normal expression in the ventral ependymal cells.


Region -1670 bp/-1630 bp is required for expression in notochord and endoderm.


Region -1650 bp/-1630 bp may contain a repressor element for excluding Ci-fkh expression from the lateral ependymal cells. This 20-bp region contains a T-box recognition sequence partially overlapping with a cluster of divergent Ci-Sna binding sites.



Region -1370 bp/-900 bp may contain a discrete CNS enhancer.


Region -610 bp/-550 bp contains a lateral CNS activator. Sequence analysis indicates the presence of a putative binding site for a Nkx-related factor.



There are two potential Ci-Fkh autoregulatory sites (one in region -1630/-1370 and the other in region -960/-900). Point mutations in one of these sites cause a general reduction in all aspects of the staining pattern, with reduced expression in gut, notochord and CNS.

Aniseed analysis (Nicolas Denans, unpublished data):

Is FOX site implicated in autoregulation of Ci-FoxA ?

There is an activator element in region -1030 bp/-1009 bp. Bioinformatic analysis allowed to identify a transcription factor site FOX in this element.
Experiment suggest that it is FOX site which is responsible of activity of element -1030 bp/-1009 bp.

Is the transcription factor GATAa actvator of region -1009 bp/-990 bp?

An activator element in A and a line should exist in region -1009 bp/ -984 bp. Bioinformatic analysis suggest that there are two sites GATA (sequence WGATA) in region -1009 bp/ -990 bp.

responsible factors of the activity in region -990 bp/-958bp and -860bp/-785bp ?

A reppressor element should exist in region -990 bp/-958bp for A and a line. Comparison with Ciona savignyi shows that there are two conserved regions in element -990 bp/-958bp . One of them should be a zinc finger transcription factor binding site.
Bioinformatics analysis reveal that in region -860bp/-785bp there are two orphan sequences well conserved in 10 vertebrates that should be transcription factor binding site (PF0125 et PF0090)

Modification of FoxAa -1715/173 by deletion

KH2012:KH.C11.313 (FOXA1; FOXA2; FOXA3)

CONS00000121: pFoxAa -1455/173::LacZ

4,404,5334,406,160

Aniseed Coordinates: [4,404,533 / 4,406,160] on scaffold KhC11

This sequence was found using a blast on the JGI site with the sequence includes in the publication listed bellow. The coordinates used here are the publication's coordinates.

Di Gregorio et al. (2001). The regulation of forkhead/HNF-3beta expression in the Ciona embryo. Dev. Biol. 229(1):31-43