Gene Networks Database
Gene Networks Database
CyIIIa actin gene regulatory domain
LOCUS Rr_SPCYIIIA 2350 bp DNA INV 15-JUN-1993
DEFINITION Strongylocentrotus purpuratus TZ2 CyIIIa actin gene regulatory
domain.
DBSOURCE GENBANK: name SUSCYIIIA, accession M64573
KEYWORDS actin.
SOURCE S.purpuratus DNA.
ORGANISM Strongylocentrotus purpuratus
Eukaryotae; mitochondrial eukaryotes; Metazoa; Echinodermata;
Echinozoa; Echinoidea; Euechinoidea; Echinacea; Echinoida;
Strongylocentrotidae; Strongylocentrotus.
REFERENCE 1 (sites)
AUTHORS Calzone,F.J., Theze,N., Thiebaud,P., Hill,R.L., Britten,R.J. and
Davidson,E.H.
TITLE Developmental appearance of factors that bind specifically to
cis-regulatory sequences of a gene expressed in the sea urchin
embryo
JOURNAL Genes Dev. 2, 1074-1088 (1988)
MEDLINE 89053046
REFERENCE 2 (bases 1 to 2350)
AUTHORS Theze,N., Calzone,F.J., Thiebaud,P., Hill,R.L., Britten,R.J. and
Davidson,E.H.
TITLE Sequences of the CyIIIa actin gene regulatory domain bound
specifically by sea urchin embryo nuclear proteins
JOURNAL Mol. Reprod. Dev. 25, 110-122 (1990)
MEDLINE 90180426
REFERENCE 3 (function)
AUTHORS Kirchhamer,C.V., Davidson,E.H.
TITLE Spatial and temporal information processing in the sea urchin embryo:
modular and intramodular organization of the CyIIIa gene cis-regulatory
system
JOURNAL Development 122, 333-348 (1996)
MEDLINE 96152227
REFERENCE 4 (function)
AUTHORS Kirchhamer,C.V., Yuh,C.-H. and Davidson,E.H.
TITLE Modular cis-regulatory organization of developmentally expressed genes:
two genes transcribed tettitorially in the sea urchin embryo, and additional
examples
JOURNAL Proc. Natl. Acad. Sci. USA 93, 9322-9328 (1996)
MEDLINE 96382464
COMMENTS 2.3 kb of DNA sequence extending upstream of the CyIIIa transcription
start site is necessary and sufficient for correct spatial, temporal and
quantitatively accurate expression of CyIIIa.CAT transgenes. Embryonoc
expression of CyIIIa gene is controlled through interactions with at
least 9 different transcription factors that bind at over 20 specific
sites [1,2]. CyIIIa regulatory system consists of three complex modules.
The proximal module (PM) interprets the specification functions by which the
oral and aboral ectoderm (AE) and vegetal territories are established, and its
function is to activate the CyIIIa gene in the AE late in
cleavage [3,4]. This module is largely responsible for the whole early
pattern of CyIIIa expression. The major positive input to the PM is yet
uncharacterized P1 factor, which is active throughout the ectoderm.
Expression is confined to the AE by the negatively acting
SpP3A2 factor, which must become functional specifically in the oral ectoderm (OE)
lineages [3]. The other positively acting factors SpOct, SpTEF1, CTF,
that bind to the PM determine the level of expression and convey temporal
information [3]. The middle module (MM) assumes the major role in controlling
CyIIIa expression from the gastrula stage onward, driving the rate of
expression to higher levels as the AE differntiates. The major positive input
is provided by the SpRunt. Two different negatively acting factors, SpZ12-1
and SpMyb are required to confine expression to AE from the gastrula stage
onward. The distal module of CyIIIA gene increases the output of either
or both of PM and MM and contains clustered SpGCF1 sites. The PM and MM
display at least three forms of interdependence: (i) some of the positively
acting factors of the proximal module, particularly the CTF and the SpTEF1
boost the output of the middle module if their target sites also present
in the construct. (ii) Some site in the PM, yet undefined is necessary
for MM function in synthetic transgenes. (iii) The SpRunt1 interaction
in the MM boosts the output of the PM early in development [3,4].
COMMENTS There is additional binding site for SpP3A2 factor in between
SpZ12-1 and CTF-factor binding sites (i.e. in the region 1282 -
1620, which can be located at 1456 -1464 (identified by sequence
inspection). This site is located in proximal module.
There are several additional sites for SpGCF1 factor binding:
one -in between CTF-factor and SpTEF1 (1790 - 1798 by sequence
inspection), and two other around SpMyb factor binding site.
FEATURES Location/Qualifiers
source 1..2350
/organism="Strongylocentrotus purpuratus"
/db_xref="taxon:7668"
/dev_stage="Embryo"
/germline
protein_bind 10..23
/bound_moiety="SpGCF1"
/evidence=experimental
protein_bind 189..201
/citation=[1]
/bound_moiety="SpGCF1"
/evidence=experimental
protein_bind 259..279
/citation=[1]
/bound_moiety="SpGCF1"
/evidence=experimental
protein_bind 406..416
/citation=[1]
/bound_moiety="SpGCF1"
/evidence=experimental
protein_bind 411..420
/citation=[1]
/bound_moiety="SpGCF1"
/evidence=experimental
protein_bind 427..447
/citation=[1]
/bound_moiety="SpGCF1"
/evidence=experimental
protein_bind 456..466
/citation=[1]
/bound_moiety="SpGCF1quot;
/evidence=experimental
protein_bind 476..500
/citation=[1]
/bound_moiety="SpGCF1"
/evidence=experimental
protein_bind 899..916
/citation=[1]
/bound_moiety="SpRunt1"
/evidence=experimental
protein_bind 1024..1086
/citation=[1]
/bound_moiety="SpMyb"
/evidence=experimental
protein_bind 1240..1260
/citation=[1]
/bound_moiety="SpZ12-1"
/evidence=experimental
protein_bind 1274..1282
/citation=[1]
/bound_moiety="SpZ12-1"
/evidence=experimental
protein_bind 1620..1635
/citation=[1]
/bound_moiety="CTF(CCAAT-factor)"
/evidence=experimental
protein_bind 1963..1986
/citation=[1]
/bound_moiety="SpTEF-1"
/evidence=experimental
protein_bind 2080..2104
/citation=[1]
/bound_moiety="SpP3A2"
/evidence=experimental
protein_bind 2119..2135
/citation=[1]
/bound_moiety="SpOct"
/evidence=experimental
protein_bind 2202..2235
/citation=[1]
/bound_moiety="SpGCF1"
/evidence=experimental
protein_bind 2237..2264
/citation=[1]
/bound_moiety="SpGCF1"
/evidence=experimental
protein_bind 2265..2274
/citation=[1]
/bound_moiety="P1"
/evidence=experimental
protein_bind 2308..2321
/citation=[1]
/bound_moiety="P1"
/evidence=experimental
BASE COUNT 699 a 527 c 432 g 692 t
ORIGIN
1 ctgcagcttt ctcagaaccc cgcatcgtat atacattccc ataaacacac acacacattc
61 acacaaaatg taactttttt aatacttaaa acacaattat cattctttga tgtacagcac
121 atagttgaca caaaggggat gcttttagaa tagttgaaaa caccgtgctt tctgtgagag
181 ggaatgaccc tgatccccga cccatacaca catgcaaaca tccaggacgt agataagggg
241 gcagtgtgaa tatgtgcacc cctccccccc ccctccccca accatcaaat gataagaaaa
301 tatacagaaa ggtgaaagtg gagaggagga aatgtaacgt aaaatgaata tgctatcttc
361 cccacaccct cccatgtaac ttcgcatttt atccatcggg taagattgat cccctccccc
421 acctcaccct cccccccccc cccctcctac taaacctgag cccctcaatg cctggaccca
481 cgttacgcca ttttacgcac tttccggccg tttttattag accctatact cgtaatgtaa
541 aagggttttg cagccatgtt atttttcacg tatatctaat gtgtttttcg gggaaaaact
601 tgacaaagtt actccctgtg gataaatttc ctaatttgcg ggtcctagtt ttagttactt
661 atgacaaaca aattatgaaa agcaaaatat taaggtaaaa tacaggaata acataaagag
721 gtctcaaggt tttgaacagt tgaaatgttg ttaaattaca tctcacaaac aactgtataa
781 aataatttaa aataagtaga cacacggaga gattgtggga catgtcgaac actcctctgc
841 agacccttgt gtcagatgca aggattttat acgaaatcta tcagaacaga cgcaggccgg
901 ttgtggtcat ggttttaaaa gtagaaagtt tgggtcattt tgcggttgtc cgacatttgc
961 tcctgctaaa attgccttgc atcaatttca tactcacact ttgttcttga cttcaatcct
1021 tgacccaaca atatatctaa ccgttaccct taacctaacc ttaaagccaa atgtaactct
1081 aaccccgatc cctcgtatgt gacttaataa agacagccgc aaggaccatt ttcgtaatgt
1141 aaccagattt aatgcataag tctttgtgaa gtgcctcaat acatattata tcattcgcct
1201 cataagaata acaacgtttc aatagtcaga atgcacggta catgttgcta ggtaggtcaa
1261 gccatattgt ttgtcctacc tggcaacaac taatgtatgc cgttcggatt ttgtctattg
1321 aaatactatt attcttatca ggtgaatgaa attttttatt gaggcacctc actattaaag
1381 aattatgcat taaatttggt tacattacga aactggccta ttggaggagg agtaagcatc
1441 ttacaaatcg tacggcggcg cacaaatgcg gggttcgcct gatctgggcc tcttatggcg
1501 gcggaaagat taagtatgta agaaataagt aatgcatgga tctcacatga atacaaaagc
1561 aaccggcaca agggaatgga cttaaagagc tagcgagaat cattcaacca taatggaaac
1621 tctgattgga ccacggtgaa tgggatatac tgagctactt taaaaggagt atttaattca
1681 ggttatgcac gctctggtgg tatgaggttt caataggcca gacgttatag gaaagattgc
1741 gattgaagac tcccaagaaa aaggtaacaa tggagcgata aaattgtttc tcccctttga
1801 gttaatgctt tttgtcatgc ctaattatac ctcggtgatg ctcggtcaca ccgcctaaac
1861 gattctatac cccctccaaa ctgagccatt taagcttaat cctattttgg tcccgtactg
1921 gccaacagta tgtagacgcc taagtttatt attgcattgt cattcattgt cgcgacatac
1981 ttgtagttag ctttttattc ctccttactt tctttgggta ttagctgcga agcttatcta
2041 ttggcctcgt tgtcacattt gtttttaaaa agaataaatg aagcgcaaac aaactttatt
2101 aagcaaaaaa gcaccgaatc tcatttgcat atccttttca atgcattcct tatctgccct
2161 gaggcgctac gatgtgtcta aattgtctcc ttatttggtc aaaaccctgg acataactct
2221 cgcttggggg tctttgtcca aggaaggggt agtacattac ttggtccccc acagtatcat
2281 ttcactctcg accaagcaat caagcaggtg gtgtcatcca gttctctttc tcttctctct
2341 ctaactcggt
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