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CIS-REGULATION

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  1. Region 'REG00000120'

Cis-regulatory Region

Name

FoxAa -5600/173

Short name

n/a

Region ID

REG00000120

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Anna Di Gregorio (2006-10-29)

Annotator

Jonathan Luchino (2007-07-20)

Curator

Delphine Dauga (2010-02-28)

View position in WashU

Description

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Aniseed analysis (Nicolas Denans, unpublished data):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)


Hierarchy of Regulatory Regions

Regulated gene(s)

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

Construct(s) made to test this region

CONS00000239: pFoxAa -5600/173::LacZ

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

4,404,5334,410,390

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 Fox n/a TGTTT [4,409,193 / 4,409,197]

Sequence

Aniseed Coordinates: [4,404,533 / 4,410,390] on scaffold KhC11

This sequence was found using a blast on the JGI V1.0 with the sequence found in the publication. The coordinates used here are the publication's coordinates.

Show sequence

Length: 5,858


ACAAATGATATGATACGAAAATACAAATAAATAAACAAACAAAAGCACAAGGTTTAATAG
GACTATACACATATTTGAAAAGGTTGCGACTTGCAACCGTTATACGCCCATGTTAATTTA
TATTCAAACGTTATATTGTTGAATAAAATAAGTCCATTTTTAGGCAGCATCTGTTGCTGT
GGTTGAGGAGAAATGGCGCGCATGCGCACTGCGTTCTACCCATTAGTTTGGGTAAGTTAA
GTTACATTCATTCATTCATGGTATATGCCAATTCATGGTATATGCCAATTATCTTCAATA
TTAACATCCGACCCCTTTCAGGTTGTCGTCACTCCTAGCTCAGTGTAGGCGCGGTTTAGC
CGTGCATTTGGTCTTGCAGCAAGATCGTAGTTCCCTCCTGTTCCTTTAACGTTAATATCC
CTTTACCACCTAACCCCCTTTATCCTATTAACCGCGTTAGACACATTCCCAACACTGTCA
CACGAATGTTTAGCTTGCCGTGGTAAACCAGTTAACGAGTTAGTTTAGTTATGACGACAT
GATGACGTCACGATGACGAAGCACGAAACAAGAAGACACCACATACCCAAAGGGGTACAG
GGGAAATGTAACCGGGTCCTGCAGACGGAGAGGACGAAGGGAGTGGATGGAACACAAGCT
TCAGAACCAGTACGGTACAAATGGTAGTACTGGTACAAGGTGATGTCCAATATAGGCGGC
CATGGGCGCGTGGCATTTTTTAGGGGCGTCGCACTTTGTTGTATTATTTTTGTCGCTGGT
TACCCACCATGTGGTCCCCCTTTTGGGTCCCAGATGGTGGGGTACCAGTAACGCGCTAGG
CTAAACAACGCACGCACTCGCACGCACGCGCTCGCAAATACGCGCCGGAAGATTAAAGAC
GAAGAATAAAAGCAAAGACAAAGACAAACCTCCATCGTCCAATCCAAGAAGCAAAGATAT
CATACCCACACAGGGGGTTTAACTTAAGTATAACTTATTAATATTAACATTGTGTTGATA
CAGCCGCACCACACACCCCACACACAAACAACACAAATTGCCCATAGTGGTTCGGGCAAA
CCTTTTCCATTGCAATTCGCTGGTACCTTGTCGTGGTGCAGTGGCTTTAAAACCAAACCC
AGTGTAACCCTACATAACACAACATTCAATTATACATAGTATCTATTATGAATCTTTTCA
ATAACAGTACGAACTCAAATATTCTTCGTCGTATTAAAGTTGGCCAATTAATAACTGTAC
AAACATTTTCTAAAGAATGCAACTGTACAAACATTTAGACCATGTTTTCTCGTCGGGGGT
GTAGCTCAGATGGTAGAGCGCGCGCTTAGCATGCGCGAGGTACCGGGATCGATGCCCGGC
ACCTCCACATTTTTAACAATTAAATTAAGAGACTCTTGTTTTTTTTTTAAATATTGCGAT
CTTCGCGTTTTCGCAGAGGTAAATATATCTGTAGATATATACCTACCAAACGTGTTCTTG
TAGTAAAGAAATAAACCTTCCAACTGTGATCTGACGGTTATCACGATATTATTCCATTAG
ATATTATGCAAGAAATATTTTCTGGGAGTTTAGAAAATTCTGTTTTTATGGTGCCGTTAG
ATGTCGCCAATGCTACGTTCAAATTCATGTATTTTCGCGGCTAAGTCGGCAGTTTCCAAG
TCCCCGCCAATTTGTTAAGAAGCGAGTAAATACCTCCCGACACCGTAAGAAGTTTTATCA
ATGAAATAAAATTTAGTCACAAACATGCAAACGTATATTGCTCACACTAAAGTCGGGGTG
TCGACAAGGTAAAAAATACTTTGTTATAAAATGAATGCCGGAAAACGACAGTCATTAGGA
GTGTTCTATTCCATACACTGTGCGCCTGCTTACGAGTTAACACGTATGTAACTTTGTGAG
TAGGCTTGTATTTAAAGGATTCAAGTATGGCTGATAATTTATACCCGCCCCCCAAAAAAC
GTTAGAATAGATATTGACGGTTACAATGCAAATAGCGGCGTTTCGTTTAGAAATCTATGA
TTCCTGAATTGTCCAAACACCCTCCCATGTTTGCAAACATCCGTGTTTGGGAAACGGAAG
CAAAATACACCGGATGGCTTCCAACTTAAGTTTGACCTGTCCCGCCCACTACCGGTTGTT
TACTTTTCGCACTTTCGTTTTGATTCCAGCAGTGAAACTTTCTTCGCCGTCGCAGCGTCG
GATGCGAAAAACAATACGAATCTGGTACACTGGGGGACGTACTGCGTACACAGGTGCACG
CGAGATAGCGCAATGACGAATCGTCTCCTGACGTGCTCAATTTTGACCACTCTCCACCGC
TTTGTGTTTGTTGAGTAGAATATATTAGAGACCATTATTCCAAGAATTTTGTTGTTAAAG
CGCTTAATCAAATCAAACTAAAACACCTACCTTTCAAACGGCGAACCAATCACTTAATTC
TGTTCCTTGCTTTAGATAACGAATTGTAAAATCCAATACGAGACAGACGGGATTATGTTA
AACATCCCAACAATGTTTCAACACACAGCAGTGCATGACACCAAAGTATTATAATCTTTA
GTAAGGATTACTGTTTAACTACGCAGCTGTGGTGCTGCGGGATGACGTAGTATACAACGT
ATCGTTACGTCATAAAATAAATTAAACCGCTATAGATTACATCCAACACGCAGTTTGCCA
AAATCAAGCACAACAGGCGAATTAAAGTCAAGGACTCGTCGCCCCAGCCAATCAGCCCGT
ATATATGACGTCACTGATTAAAGCAAATATCTTGAAGCGTTGTGCAAATAAGCGCATGCT
CGCGGAGGTCAGAGCGGCGATAATTCAAACGCAAATCGCTGCCGCTCTCAGGCCAAACAG
GACCGTATAGTCTGCAGCCCTTTGAAGCAGTAGCCTTGTTTGGTGCCATTCTCTCATGCT
TGTGACGTTGCAACGGAATTCAATCCGAACAGCAAACACCAAGCGCTCCCAACCATTCAA
GTTTCGATTTGAACTTTTAAACGCAGCAGCAAAAATAGGACTCGCTATTGCGATTTTGCT
TCGAATATGTCGTCGTCATGGCCAATATATAACAGCTTATATATTGGAAAATATATTACT
TTGAATAATTTATAACCGTATGTGTACTTTATTTATTTTTTAAGTATTAGAATAAGGCGG
CAAACCGCTACCCATGTGTTGCTCAAAATAAATCTTTAAATTTGAACCCGTATCTTAATT
TTGCATCGCACGGAATTTAGGTGTTGATAATTTCCAAACTTTGATGTCAAATCAATTTCC
AATACTTTCATTAATACATCAAGAGTTACATTGATAACGCGCGCTTTATTAGAGTGTTAA
ATAAAACAAGTTCTAAATGACAAGACCAAGTCTTTAGAAATATCTAATGCACGTTTCTTA
TCAATGCATGATGAAACGCACCAAGTGCGACATTGGCGGGCCAGTGCAAAACGTCCCAGA
TAGGAAACGTGTGAAGCTTTCGTTCCGGCCGAAGTAGAGCGGCCTATTTTCACCAAGTCG
CAAATCATGTTTATTGTAATTAAACTATATCAAAATATCCCATGATGATTAACTAGGTGT
ATTTTCTGAACAATTTATAATAGAGTGGTGAAAACAAGACGAGTTGCAAATGTTTTTCCT
ATTTGGTTGTAAACAAAGAAATATTTACACGATCATACAACTATATTCTCATGATAAAAA
TATATTATTTTTGTTCAAACCCATCTTACCCCACAGTAGTATATTATGTAACATGTGTTT
ATGTAGTGGTAGAAAATATAAGTAACACTGTAACAAGATGTGTTGGTGCATCATCTATCA
TGTGTCTTTCACAATCCTTAAAAGTCTTACCATTGCACTTATTAAACTTTTTTTGAATTT
ATATTTTTTTAAATAAAAACAAGACTTAAATTTTAAAAGGAAATTGGTCTGTTAAGGTGC
TACATCCTATGCTTGATTGCTCCCAACATCGAGAGTAAATATTTGCGGTAGAATCAAACC
CGAACTCCCGCAGATCTGTAGACTTATTCCCGAGCAAAGTTCCCGGAGCCAAACTATGAT
GCTCCATTTTATTTTTTATTTTTTTAAATTAAATATTAAATAATACAAACTACTGAAATG
TGCGTTTAAAGTTATGAAATTATTCACATTTGTTTAAACCATTTAATTTGTTTGCATTCT
GTTAATTCACGCTGGTTATAAAGCATTTGGGACCTTTTACAAAGATAGCAAATTTGTATA
TATATAAAATTTCTCTTTCCATTTTACAATGTTTTTATTTGTAGAAACGACTTTTCATAT
AGTAAACCATTGTTTTAGTTTATGTATAAATGTATGCAAAGCCAACAACTTGATTTGTTG
ATTTGATATGGATCGCCTAAAAAGCAAACGTTTTGTATTTGGCCAAGAGTTTTCGGTTCG
TCGGACAAACTTATCGATATTTGAATATGTTTGCTGGGCTAATATATACTATAACAACAG
TCACTATAACAAACATTGCTATAGTGTATCTATTTGGATAACTTAACTGTGCAAATGTAT
TGTGTTACTATATGTTTTGGGAAGTGGGGAAAGTGGCCAGATGTTGACATTGAACGTAAA
TTAGAAGTGGCTGAATGCGCATCATTAGAAAGTTAAGTTTTGTTTGTTCACTGAGAAATG
ATAATGATATCAGTTGTACATATGGGCGGCACCGCTTTTAACGTGGGCTGCTGGTGGCGG
AAGGTGTTTCTAAAGCGAGTGGCCGCCGACGCTTGACCAGAGCCGTGGCGCGAAAAAGGG
GTTAGAGGGCGAGCACGTCTATGATAATGAGGAAAGAAGGAAAGTGGGCGCTACTCCAAA
GTCGGCATTCCGTCTTATAAGAGAGCTGGAATTTATTGGAAGCACAATTCAGTTTGTTCA
ATAGTGAACAGTGTAGTGGTTTCGTATTTAATTTAGATCTACATCTTACTTGAATTAGTA
TAGGTTTTCACTAAAGAGTCGAATTTAAATCGCAAGTATTTAACAGGTAATTGAGTTACT
TTTGCGAAATAGAACAATTGCTGGATGCAGTTAGCTTAGAAATACTTGCAGCCCTTGCAG
CCTAAAATTTGATTCAGAATTATTAAAGTTTTAAACTTTAACCGCAAGAGGTCGCCAAAT
ATTCAGTAGAATAAGCACAAAACTATTGCTGGTTAAATAGTGAGTGCTCCGTTACTACTT
GTTGTTTGCGTCCGGAGAGATTTGCGCTGAACCACGTCGACTTTAATTCAGGTGTCGATT
CAATTACCAGCTTTATTAGTTTTATTTACTTCAGCTAGGTGACTCAGAACTGGCTCAAGT
TGTATGTGGGGGGTAAGCAAGATTGTGTTGGGGTTACAATCCAGTTATACGCTTCGGTTA
ACTTAAAACACAATTTAGAATCTTGAAATTTAATATCCGAAAAACAGATTTGTAACAGGA
AGTTAATTCAGTAGCAAAGCGGAAACTTATCTTGACATATTTTCGTTATTTTCAGTTTTA
TATCTTTGACCAATAATTTCGCCGCCATTTTTTTCTTAAAATATCACGGCCAGTTTTTAA
CAAGTTATTTTTCTAGCTTTCTATTTGAAATATTATACACAACTGCTGCTGTAATTTCTG
AGAAAGCTTTTGAAATCGGATTACTTTTGCAAGTACAAAAATGATGTTGTCGTCTCCACC
GTCAAAGTACCAACCCTTCCAACAGTCTTATGCTACTGGTATGAACAATATGACCAACGG
TATGCAGCCTTCATACGTCAACCAGATGAACCCAATGTCGCTTACAGCTGCTGGCAACCA
GGTCGGATTTAACCAAGCTTTACCGCAAGGATATGGCG

Reference(s)

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

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