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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