PvdS - UniProtKB: Q884G0 regulon and binding site collection of Pseudomonas syringae pv. tomato str. DC3000


Sites are listed as curated.

TTAATTACTGGCCCTCGCTAATCGTTCTT
TTAATTTTTCGACGTAGCGATACGTTCAA
TCTAAATATTTCCCCGCCAATTCGTTCTT
CTAATTATTTGCAGACGCCATCCGTTCTC
ATAAAAACATGCCAGACCGAGACGTTTAT
CTAAAAATTTTCGCCCGCGCTTCGTTTAA
CTAAATTTTTCGCCCATCCGCTCGTTCTC
CTAAATTTGTCAGCCGGTTTTACGTTCTA
CTAATTTTTCAGCCGCGAAGTACGTTCAA
TTGAATTAATTCTCCCGTCCGTCGTTCTC
CAAAATATTCCTACAGGAATCTCGTTCTC
TTAAATAATCGTTAATCGCTTTCGTTCTC
CTAAATTCCGGCCTGCATTTCTCGTTTAA
TAAATCACTGGAGGCACTCAAACGTTTAT
CTCAAGAAATCAACCACTTGAACGTTTTA

Sites are listed after the alignment process. For alignment of variable-length binding sites, LASAGNA is used.

TTAATTACTGGCCCTCGCTAATCGTTCTT
TTAATTTTTCGACGTAGCGATACGTTCAA
TCTAAATATTTCCCCGCCAATTCGTTCTT
CTAATTATTTGCAGACGCCATCCGTTCTC
ATAAAAACATGCCAGACCGAGACGTTTAT
CTAAAAATTTTCGCCCGCGCTTCGTTTAA
CTAAATTTTTCGCCCATCCGCTCGTTCTC
CTAAATTTGTCAGCCGGTTTTACGTTCTA
CTAATTTTTCAGCCGCGAAGTACGTTCAA
TTGAATTAATTCTCCCGTCCGTCGTTCTC
CAAAATATTCCTACAGGAATCTCGTTCTC
TTAAATAATCGTTAATCGCTTTCGTTCTC
CTAAATTCCGGCCTGCATTTCTCGTTTAA
TAAATCACTGGAGGCACTCAAACGTTTAT
CTCAAGAAATCAACCACTTGAACGTTTTA

For the selected transcription factor and species, the list of curated binding sites in the database are displayed below. Gene regulation diagrams show binding sites, positively-regulated genes, negatively-regulated genes, both positively and negatively regulated genes, genes with unspecified type of regulation.

    Genome TF TF conformation Site sequence Site location Experimental techniques Gene regulation Curations PMIDs
    NC_004578.1 Q884G0 not specified TTAATTACTGGCCCTCGCTAATCGTTCTT -[5573257:5573285] Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) azu (PSPTO_4923) , PSPTO_4924
    ... ... azu PSPTO_4924
    765 18363796
    NC_004578.1 Q884G0 not specified TTAATTTTTCGACGTAGCGATACGTTCAA +[2322442:2322470] Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) PSPTO_2137 , daT (PSPTO_2136)
    ... ... PSPTO_2137 daT
    765 18363796
    NC_004578.1 Q884G0 not specified TCTAAATATTTCCCCGCCAATTCGTTCTT +[2330473:2330501] Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) PSPTO_2147 , PSPTO_2148 , PSPTO_2149 , PSPTO_2150
    ... ... PSPTO_2147 PSPTO_2148 PSPTO_2149 PSPTO_2150
    765 18363796
    NC_004578.1 Q884G0 not specified CTAATTATTTGCAGACGCCATCCGTTCTC +[2306851:2306879] Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) PSPTO_2134 , PSPTO_2133 , pvsA (PSPTO_2135) , daT (PSPTO_2136) , PSPTO_2137
    ... ... PSPTO_2134 PSPTO_2133 pvsA daT PSPTO_2137
    765 18363796
    NC_004578.1 Q884G0 not specified ATAAAAACATGCCAGACCGAGACGTTTAT +[3717247:3717275] Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) PSPTO_3290
    ... ... PSPTO_3290
    765 18363796
    NC_004578.1 Q884G0 not specified CTAAAAATTTTCGCCCGCGCTTCGTTTAA +[2374230:2374258] Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) PSPTO_2161 , PSPTO_2160 , PSPTO_2159 , PSPTO_2158
    ... ... PSPTO_2161 PSPTO_2160 PSPTO_2159 PSPTO_2158
    765 18363796
    NC_004578.1 Q884G0 not specified CTAAATTTTTCGCCCATCCGCTCGTTCTC -[2367693:2367721] Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) PSPTO_2156 , PSPTO_2155 , PSPTO_2154 , pvdE (PSPTO_2153) , pvdP (PSPTO_5624)
    ... ... PSPTO_2156 PSPTO_2155 PSPTO_2154 pvdE pvdP
    765 18363796
    NC_004578.1 Q884G0 not specified CTAAATTTGTCAGCCGGTTTTACGTTCTA +[2367749:2367777] Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) pvdP (PSPTO_5624) , PSPTO_2156 , PSPTO_2155 , PSPTO_2154 , pvdE (PSPTO_2153)
    ... ... pvdP PSPTO_2156 PSPTO_2155 PSPTO_2154 pvdE
    765 18363796
    NC_004578.1 Q884G0 not specified CTAATTTTTCAGCCGCGAAGTACGTTCAA +[2329290:2329318] Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) PSPTO_2146 , PSPTO_2145 , PSPTO_2144 , PSPTO_2143 , PSPTO_2142 , PSPTO_2141 , PSPTO_2140 , PSPTO_2139 , PSPTO_2138
    ... ... PSPTO_2146 PSPTO_2145 PSPTO_2144 PSPTO_2143 PSPTO_2142 PSPTO_2141 PSPTO_2140 PSPTO_2139 PSPTO_2138
    765 18363796
    NC_004578.1 Q884G0 not specified TTGAATTAATTCTCCCGTCCGTCGTTCTC +[800052:800080] Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) PSPTO_0753
    ... ... PSPTO_0753
    765 18363796
    NC_004578.1 Q884G0 not specified CAAAATATTCCTACAGGAATCTCGTTCTC -[2329189:2329217] Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) PSPTO_2145 , PSPTO_2144 , PSPTO_2143 , PSPTO_2142 , PSPTO_2141 , PSPTO_2140 , PSPTO_2139 , PSPTO_2138 , PSPTO_2146
    ... ... PSPTO_2145 PSPTO_2144 PSPTO_2143 PSPTO_2142 PSPTO_2141 PSPTO_2140 PSPTO_2139 PSPTO_2138 PSPTO_2146
    765 18363796
    NC_004578.1 Q884G0 not specified TTAAATAATCGTTAATCGCTTTCGTTCTC -[2362155:2362183] Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Site directed mutagenesis (ECO:0005667) PSPTO_2152
    ... ... PSPTO_2152
    765 18363796
    NC_004578.1 Q884G0 not specified CTAAATTCCGGCCTGCATTTCTCGTTTAA -[2374175:2374203] Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) PSPTO_2160 , PSPTO_2159 , PSPTO_2158 , PSPTO_2161
    ... ... PSPTO_2160 PSPTO_2159 PSPTO_2158 PSPTO_2161
    765 18363796
    NC_004578.1 Q884G0 not specified TAAATCACTGGAGGCACTCAAACGTTTAT +[2341776:2341804] Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) PSPTO_2149 , PSPTO_2148 , PSPTO_2150
    ... ... PSPTO_2149 PSPTO_2148 PSPTO_2150
    765 18363796
    NC_004578.1 Q884G0 not specified CTCAAGAAATCAACCACTTGAACGTTTTA -[3353616:3353644] Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) PSPTO_2982 , PSPTO_2983
    ... ... PSPTO_2982 PSPTO_2983
    765 18363796

    All binding sites in split view are combined and a sequence logo is generated. Note that it may contain binding site sequences from different transcription factors and different species. To see individiual sequence logos and curation details go to split view.


    Sites are listed as curated.

    TTAATTACTGGCCCTCGCTAATCGTTCTT
    TTAATTTTTCGACGTAGCGATACGTTCAA
    TCTAAATATTTCCCCGCCAATTCGTTCTT
    CTAATTATTTGCAGACGCCATCCGTTCTC
    ATAAAAACATGCCAGACCGAGACGTTTAT
    CTAAAAATTTTCGCCCGCGCTTCGTTTAA
    CTAAATTTTTCGCCCATCCGCTCGTTCTC
    CTAAATTTGTCAGCCGGTTTTACGTTCTA
    CTAATTTTTCAGCCGCGAAGTACGTTCAA
    TTGAATTAATTCTCCCGTCCGTCGTTCTC
    CAAAATATTCCTACAGGAATCTCGTTCTC
    TTAAATAATCGTTAATCGCTTTCGTTCTC
    CTAAATTCCGGCCTGCATTTCTCGTTTAA
    TAAATCACTGGAGGCACTCAAACGTTTAT
    CTCAAGAAATCAACCACTTGAACGTTTTA

    Sites are listed after the alignment process. For alignment of variable-length binding sites, LASAGNA is used.

    TTAATTACTGGCCCTCGCTAATCGTTCTT
    TTAATTTTTCGACGTAGCGATACGTTCAA
    TCTAAATATTTCCCCGCCAATTCGTTCTT
    CTAATTATTTGCAGACGCCATCCGTTCTC
    ATAAAAACATGCCAGACCGAGACGTTTAT
    CTAAAAATTTTCGCCCGCGCTTCGTTTAA
    CTAAATTTTTCGCCCATCCGCTCGTTCTC
    CTAAATTTGTCAGCCGGTTTTACGTTCTA
    CTAATTTTTCAGCCGCGAAGTACGTTCAA
    TTGAATTAATTCTCCCGTCCGTCGTTCTC
    CAAAATATTCCTACAGGAATCTCGTTCTC
    TTAAATAATCGTTAATCGCTTTCGTTCTC
    CTAAATTCCGGCCTGCATTTCTCGTTTAA
    TAAATCACTGGAGGCACTCAAACGTTTAT
    CTCAAGAAATCAACCACTTGAACGTTTTA
    Download data in FASTA format.
    Download data in TSV (tab-separated-value) format. For each binding site, all sources of evidence (i.e. experimental techniques and publication information) are combined into one record.
    Download raw data in TSV format. All reported sites are exported individually.
    Download data in Attribute-Relation File Format (ARFF).
    Download Position-Specific-Frequency-Matrix of the motif in TRANSFAC format.
    Download Position-Specific-Frequency-Matrix of the motif in JASPAR format.
    Download Position-Specific-Frequency-Matrix of the motif in raw FASTA format. The matrix consists of four columns in the order A C G T.