Search a Pattern against Cyanobacterial genomic regions
Model: Mismatches

StressElementOrganismCis elementRegulated geneBinding factorFunctionReference
HeatCIRCABacillus subtilisTTAGCACTCN{9}GAGTGCTAAdnaK and groESL operonsHrcAnegative regulation on Heat shock8113175
Light, HeatCIRCASynechocystis PCC6803TTAGCACTCN{9}GAGTGCTAAgroEHrcALight and heat response17434494
Light, HeatK-boxSynechocystis PCC6803GTTCGGNNANCCNNACgroEHrcALight and heat response17434494
Light, HeatN-boxSynechocystis PCC6803GATCTAgroEHrcALight and heat response17434494
light HLR1 Synechocystis PCC6803 [GT]TTACA[TA][TA] hliB RpaB 17294172
light Synechocystis PCC6803 RWWTRGGYNNYY pedR 17035238
light HLR1 Synechocystis PCC6803 AAAACAATtcTTTACATA PsaE RpaB 19074384
co Synechocystis PCC6803 AAACCTTGACATTN{5}AATGTTAAGGTTT corT corR 10692354
heat inverted repeat (IR) Thermosynechococcus elongatus ACAAgcAAATTTagTTGT hspA 12270139
ox inverted repeat sequence Synechocystis PCC6803 ATAATTAT PerR 15150218
ox perR box Synechocystis PCC6803 ATAATTATTCTATCTAATA PerR 15150218
ox perR box Synechocystis PCC6803 ATAATTATTCTATCTAATA ahpC PerR 15150218
co2 Synechocystis PCC6803 ATCN{9}GAT slr0040, slr0041, slr0043, and slr0044 CbbR 11222586
light Synechocystis PCC6803 CAACN{6}GTTG SufR 17827500
fe Pseudomonas aeruginosa CGAGGAA and CGTGGAT, 8626326
Synechocystis PCC6803 CTAN{9}CTA lexA LexA-related protein 18555801
Synechocystis PCC6803 CTAN{9}CTA crhR LexA-related protein 18555801
green light Nostoc punctiforme ATCC 29133 CTTTNCNATTTCTTTNCNATTT CcaR 20404166
n-box GATCTA groESL1 17434494
light HLR1 Synechocystis PCC6803 GTAACAATaaTTAAAAAT PsaAB RpaB 19074384
nitrogen Synechocystis PCC6803-coccus GTAN{8}TAC nir NtcA- 8026471
nitrogen Synechocystis PCC6803 GTAN{8}TAC sll1423 NtcA- 11161053
light HLR1 Synechocystis PCC6803 GTTACAGTtcTTGACAAA PsaD RpaB 19074384
light HLR1 Synechocystis PCC6803 GTTACGATtaTTTACAAT PsaFJ RpaB 19074384
k-box GTTCGGNNANCCNNAC groESL1 17434494
heat/light K-box and N-box Synechocystis PCC6803 GTTCGGNNANCCNNAC and GATCTA HrcA 17434494
light HLR1 Synechocystis PCC6803 GTTGCAATacTTAACAAA PsaK RpaB 19074384
circadian timing Synechococcus elongatus PCC 7942 LxxxExxxL, LR, and TxxGxGY kaiA, kaiB, and kaiC RpaA 16882723
phosphate Synechocystis PCC6803 PyTTAAPyPy[TA] phoA, sphX, and pstS SphR 14707128
- Anabaena RGTACNNNDGTWCB LexA 17630298
light Synechocystis PCC6803 RWWTRGGYNNYY hlL PedR 17035238
light Synechocystis PCC6803 RWWTRGGYNNYY chlN PedR 17035238
light Synechocystis PCC6803 RWWTRGGYNNYY chlB PedR 17035238
light Synechocystis PCC6803 RWWTRGGYNNYY slr1957 PedR 17035238
light Synechocystis PCC6803 RWWTRGGYNNYY ndhD2 PedR 17035238
light Synechocystis PCC6803 RWWTRGGYNNYY rpe PedR 17035238
light Synechocystis PCC6803 RWWTRGGYNNYY PedR 17035238
bacillus RWWTRGGYNNYY sigK GerE 11418558
Anabaena sp. PCC 7120 TATGAAAAGAATATGAGAA mntH ManR 12417709, 15063797 ,15604770,15742142
ox Synechocystis PCC6803 TCAATGN{10}ATCAAT Sll1594 Sll1594 11136465
ox Synechocystis PCC6803 TCAATGN{10}ATCAAT slr1727 Sll1594 11136465
lignt, salt Synechocystis PCC6803 TCAATGN{10}ATCAAT Sll1594 11136465
osmotic Synechocystis PCC6803 TCAATGN{10}ATCAAT sll1594, slr1727 11136465
arsenic Synechocystis PCC6803 TCATN{7}TTTG ArsR 12949088
light Synechocystis PCC6803 TGTGAN{6}TCACA Crp 12085767
light Synechocystis PCC6803 TGTGAN{6}TCACA slr1667 Crp 12085767
ox Synechocystis PCC6803 TGTTCCTCCTAACATCGG sll1621 Type 2 peroxiredoxins like 15047877
ox Synechocystis PCC6803 AGTCTATCTAGCTTAACA sll1621 Type 2 peroxiredoxins like 15047877
nitrogen Synechocystis PCC6803 TN{11}A NtcB 11566981
h2o2 Synechocystis PCC6803 TTN{5}AAC abrB2 22865847
heat CIRCE Synechocystis PCC6803 TTAGCACTCN{9}GAGTGCTAA groESL1 17434494
light, low CO2 conditions CbbR binding motif Synechocystis PCC6803 TTAN{7}TAA psbAII CmpR 15101988
light, low CO2 conditions CbbR binding motif Synechocystis PCC6803 TTAN{8}TAA psbAIIi CmpR 15101988
light HLR1 Synechocystis PCC6803 TTCAAATTctGTTACATC PsaC RpaB 19074384
light L Box F. diplosiphon TTGCACAN{4}TTGCACA RcaC 18346116 via 20833804
light L box Fremyella diplosiphon TTGCACANNNNTTGCACA RcaC 20833804
nitrogen Synechococcus sp. PCC 7942 ttGTAaacaatcacTACa (or) tGTAgcacccgtagCa nblA NblR 11532155
light HLR1 Synechocystis PCC6803 TTTAAAAAaaTTCATTAA PsaL RpaB 19074384

Organism Database :
Number of sequences matched :
Query time :

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Search Type Character Meaning Examples
Peptide Searches IFVLWMAGCYP
Exact match DQGT
J Any hydrophobic residue (IFVLWMAGCY) AAAAAAJJ
O Any hydrophilic residue (TSHEDQNKR) TTTTTTOO
X or . Any amino acid DXXXNW..VSK
Nucleotide searches ACTGU Exact match ACCGGCGTAA
R Any purine base (AG) AAGGCCGGRRRR
Y Any pyrimidine base (CT) CCCATAYYGGYY
W A or T
M A or C
K G or T
V A or C or G CCGG...WHW.{3,5}HWH...CCGG
H A or C or T
D A or G or T
B C or G or T
N or X or . Any base ATGCTNNNNATCG
All searches: [ ] A subset of elements
[TC] = T or C
[^ ] An excluded subset of elements
[^TA] = not T or A,
(matches nucleotides C or G)
( ) Specifies a sub-pattern
{m,n} {m} = exactly m times
{m,} = at least m times
{,m} = 0 to m times
{m,n} = between m and n times
< Constrains pattern to N-terminus or 5' end <MNTD (pep)
<ATGX{6,10}RTTRTT (nuc)
> Constrains pattern to C-terminus or 3' end sbgz> (pep)
yattrtga> (nuc)

Species selected---
Rows selected------

Sequence will appear here!

Bioinformatics Lab | National Facility for Marine Cyanobacteria