Gene Networks Database
Gene Networks Database
Endo16 regulatory region
LOCUS Rr_ENDO16 2391 bp DNA INV 10-MAY-1998
DEFINITION Strongylocentrotus purpuratus Endo16, endoderm-specific marker gene, 5' regulatory region
DBSOURCE GENBANK: name S75835S1, accession S75835
KEYWORDS
SOURCE purple urchin embryo.
ORGANISM Strongylocentrotus purpuratus
Eukaryotae; mitochondrial eukaryotes; Metazoa; Echinodermata;
Echinozoa; Echinoidea; Euechinoidea; Echinacea; Echinoida;
Strongylocentrotidae; Strongylocentrotus.
REFERENCE 1 (bases 1 to 2391)
AUTHORS Yuh,C.H., Ransick,A., Martinez,P., Britten,R.J. and Davidson,E.H.
TITLE Complexity and organization of DNA-protein interactions in the
5'-regulatory region of an endoderm-specific marker gene in the sea
urchin embryo
JOURNAL Mech. Dev. 47 (2), 165-186 (1994)
MEDLINE 95110745
REMARK GeNet staff at the IHPC&DB created this entry from the original journal
articles. This sequence comes from Figures 1C [1] and 1A [2]
REFERENCE 2
AUTHORS Yuh,C.H. and Davidson,E.H.
TITLE Modular cis-regulatory organization of Endo16, a gut-specific gene of the
sea urchin embryo
JOURNAL Development 122, 1069-1082 (1996)
MEDLINE 96205031
REFERENCE 3
AUTHORS Yuh,C.H., Bolouri,H. and Davidson,E.H.
TITLE Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene
JOURNAL Science 279, 1896-1902 (1998)
MEDLINE
COMMENTS 2300 bp upstream of transcription start site suffice for correct
spatial and temporal expression of Endo16.CAT transgenes. At least 13
different DNA-binding proteins interact specifically with this region.
This interactions occur at 33 specific target binding sites, in addition
to ubiquitous SpGCF1 sites of which >20 have been identified [1]. The
cis-regulatory domain can be subdivided into six modules [2]. The most
proximal module, A, has two roles. It causes transcription to occur
in vegetal plate and archenteron, and its activity accounts quantitatively
for most of the expression up to the late gastrula stage. It is also
required to mediate the negative spatial control functions of modules E,
F and DC. Modules E and F individually repress ectopic expression in the
ectoderm surrounding the vedetal plate, and module DC represses ectopic
expression in the skeletogenic mesenchyme, but none of these repressor
modules operate in the absence of module A. Latter in development, the
relative importance of the positive activity of module A declines. At the
gastrula and pluteus stages, when expression of the Endo16 gene is
confined to midgut, its activity depends mainly on functions of module B,
which then drives expression to a new and higher per-cell level [2]. The
most distal module G, acts synergistically with both modules B and A when
linked to them, strondly increasing their level of expression. Module B
also acts synergistically with module A at the period when the latter
is dominant, earlier in development [2].
FEATURES Location/Qualifiers
source 1..2391
/organism="Strongylocentrotus purpuratus"
/db_xref="taxon:7668"
module G 152..415
/citation=[2]
module F 415..658
/citation=[2]
module E 658..1039
/citation=[2]
module D 1039..1281
/citation=[2]
module C 1281..1683
/citation=[2]
module B 1683..1979
/citation=[2]
module A 1979..2164
/citation=[2]
protein_bind 2065..2071
/citation=[3]
/site="CG1"
/evidence="gel shift assay"
/evidence="oligonucleotide gel shift competition"
/function="in concert with P site provides
the obligatory link between module A and
module B and mediates part of synergistic
enhancement of module B output"
/note="CG1, CG2, CG3 and CG4 sites bind the same protein"
protein_bind 2078..2084
/citation=[3]
/site="P"
/evidence="gel shift assay"
/evidence="oligonucleotide gel shift competition"
/function="in concert with CG1 site provides
the obligatory link between module A and
module B and mediates part of synergistic
enhancement of module B output"
protein_bind 2108..2113
/citation=[3]
/site="SpOtx"
/evidence="gel shift assay"
/evidence="oligonucleotide gel shift competition"
/function="mediates module A function and
alone suffices to generate endoderm expression"
protein_bind 2114..2123
/citation=[3]
/site="Z"
/evidence="gel shift assay"
/evidence="oligonucleotide gel shift competition"
/function="specifically is required for functional
interactions with module F (or either E or DC)"
protein_bind 2119..2125
/citation=[3]
/site="CG2"
/evidence="gel shift assay"
/evidence="oligonucleotide gel shift competition"
/function="appears to process positive outputs both from
module A and B; requires CG3 and CG4 functions"
/note="CG1, CG2, CG3 and CG4 sites bind the same protein"
protein_bind 2160..2165
/citation=[2,3]
/site="SpGCF1"
/evidence="gel shift assay"
/evidence="oligonucleotide gel shift competition"
/function="weak stimulation of transcription"
protein_bind 2175..2181
/citation=[3]
/site="CG3"
/evidence="gel shift assay"
/evidence="oligonucleotide gel shift competition"
/function="is directly involved in interactions between module A
and the adjaacent basic transcription machinery"
/note="CG1, CG2, CG3 and CG4 sites bind the same protein"
protein_bind 2202..2208
/citation=[3]
/site="CG4"
/evidence="gel shift assay"
/evidence="oligonucleotide gel shift competition"
/function="is directly involved in interactions between module A
and the adjaacent basic transcription machinery"
/note="CG1, CG2, CG3 and CG4 sites bind the same protein"
protein_bind 2213..2218
/citation=[2,3]
/site="SpGCF1"
/evidence="gel shift assay"
/evidence="oligonucleotide gel shift competition"
/function="weak stimulation of transcription"
protein_bind 2227..2234
/citation=[2,3]
/site="SpGCF1"
/evidence="gel shift assay"
/evidence="oligonucleotide gel shift competition"
/function="weak stimulation of transcription"
TATA 2252..2257
mRNA 2281
CDS 2307..
BASE COUNT 630 a 522 c 439 g 800 t
ORIGIN
1 tgggtcggtg acctaatttc ccttgttacg cagttttgta tatcggatat cgtgacatta
61 attttataat atatcatgac atttttgctg catattttgc ggtaccggaa gatggtgatt
121 ttaacatggg gataaagata ttgcatcaag atttgcacaa gctcttattc taatatccac
181 ccttgccccc cccccccatc tgctcccctc tcactccctg tttctttctt cgtcgtcgtt
241 cttcttattc gtcttctcct tttccccttt gtacatatcc ctttctttat cctctctctc
301 tctctctccc ccgtttccat ctacacctcc ctctgtttct gtttctgtat ctcactcttg
361 tttcttacac tgacccagtt cgcactccct ctttattttt ccttcaccca cactcgatct
421 ctctctctcc tgctctatat ctctctgtat atctgtctct atgtgtgtgt gggtgtgtgt
481 gtgtgtgtgt gtgtgcgtgc tctcacctca gcattcttgt ggggttttaa tgtgcgcttc
541 acatacccct tgtgaggcat tttactttgt ggggtaattt ttcaggaccc cacagagtaa
601 agtctttcaa atgactgtat attcggtgtc ctatgctgcg gggcattaga agtggtaccc
661 cataaatgac tttttgtgag cgtgtgctaa aacttgcaca cttttttatg ggtaacatcg
721 taagcacacc gccgggttgt tatcgccagg ttgtacatac cccactagta ggggaccaca
781 aggtatatct ggaacgcaca gaaatacccc acaatcaggt gccccacaaa ggccctgatg
841 tgagaatgcg tgtgtgcgcg tgtgtttgtg tgtgtgtctc tctctctctc tctctctctc
901 actctctaag tatatctatc tccttcccca ttttctcttt ccccctctga aatattgata
961 aaaagaatac ataatttggg ttttctgttg tacgcagaaa aacccctaaa tgtcgtattc
1021 tttcacaaat attcgacttc gaactcattt ccttgcagaa atgtgtctct aatcacatcc
1081 tcctaataca tttatgatac aattttattt tagggaaaat gttgtcgtca aaatgtatgg
1141 ggctcccaac gcttcaaagg ggctttaaag ttatcatatg aatgtaacct aaaccttctg
1201 aaaataatca tgatattggg cactgctggg atgattttat caatgaccaa accgtaactt
1261 ttgataaaat gtcattgcgc gtaaagtaga cgaccgcccc tcctcttcct cctttcgagt
1321 agttgatcct cccctccaaa aaaagtctta ttatgacgaa ataaataagt atgaatagta
1381 ttaggaacag atagtatctc gatacggagt cttgttgaat acaatgctta tacacgataa
1441 tgtggacgca ctttgcacac tgttatctat caaatttctt caaaagaaca tgtctagcat
1501 tgttttaccg acattaaaca gccagctttg gttgctaagt gtagtgcaga cggcggatcg
1561 ggtttaaagc atgaataaga tatgttttaa gtctttggtt ttctctaaac tgtgtgtgat
1621 aacagaagaa aattgatgtt ttagttacag gaacatattt tggagtaggt aacgggtatt
1681 ggtatactgg ctcctggtac actaatgtac acccacactc aaaacgtggc ttatggagaa
1741 ggggtttgga tttccaattc ggagttgttt ttgtatatca aataacaaat gaagagggca
1801 cttctaattc agaaatgtta tcatgaataa agactttaac tttgttggtt tttcaaatta
1861 attttggatg tttttcagtc gattccgatg agataaaacc ccgaatatac ctggaactga
1921 acgtcctttg tttccacgca agatttaatg cccgtaaaca caaacatctg acaaatgcat
1981 ttaaacttca tcaaacaatg taacaaaagc gtaatttcct cttaaatcgc ccttacttct
2041 aagaaacgtc gtaaatcgca acgtctcaaa aatattgacc aaaatgatca taccattatc
2101 atcgcgtagg attaagtgat taaactacca agtgattaca tcatctcaaa gttatcacat
2161 ccccgggtta aactgtttga gtttcgtctc ctgattgtgc tatcaaagac aaaggggtgt
2221 aactttaccc ccctcatcaa gagcggaggg ttaaatagag aaagactggt cgaggacagg
2281 tcataatatt gctaattttt gagacgatga tgaggttaaa tattttgctg ttcgcggttt
2341 tggccgtggc gcggtcaatg cccacaggta agaaatataa taattttaca a
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