SypG - UniProtKB: Q5DYQ0 regulon and binding site collection of Vibrio fischeri ES114


Sites are listed as curated.

TTCTCATTCTGCAAA
TTCTCAATTTGAGAA
TTCTCAAAATGAGAA
TTCTCAATTTGAGAA
TTCTCAATTTGCAAT
TTCTCAATTTGAAAA
TTCTCATATTGATTC

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

TTCTCATTCTGCAAA
TTCTCAATTTGAGAA
TTCTCATTTTGAGAA
TTCTCAATTTGAGAA
TTCTCAATTTGCAAT
TTCTCAATTTGAAAA
GAATCAATATGAGAA

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_006841.2 Q5DYQ0 not specified TTCTCATTCTGCAAA +[1149437:1149451] Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) - Experimental technique details Beta-gal reporter assay - Experimental technique details ChIP-PCR (ECO:0005620) - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details Site directed mutagenesis (ECO:0005667) sypA (VF_A1020) , VF_A1019 , VF_A1018 , sypB (VF_A1021) , sypC (VF_A1022) , sypD (VF_A1023) , sypE (VF_A1024) , sypF (VF_A1025) , sypG (VF_A1026) , sypH (VF_A1027)
    ... ... sypA VF_A1019 VF_A1018 sypB sypC sypD sypE sypF sypG sypH
    842 24097942
    NC_006841.2 Q5DYQ0 not specified TTCTCAATTTGAGAA +[1160038:1160052] Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) - Experimental technique details Beta-gal reporter assay - Experimental technique details ChIP-PCR (ECO:0005620) - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details Site directed mutagenesis (ECO:0005667) sypI (VF_A1028) , sypJ (VF_A1029) , sypK (VF_A1030) , sypL (VF_A1031) , sypM (VF_A1032) , sypN (VF_A1033) , sypO (VF_A1034)
    ... ... sypI sypJ sypK sypL sypM sypN sypO
    842 24097942
    NC_006841.2 Q5DYQ0 not specified TTCTCAAAATGAGAA +[1165441:1165455] Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) - Experimental technique details Beta-gal reporter assay - Experimental technique details ChIP-PCR (ECO:0005620) - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details Site directed mutagenesis (ECO:0005667) sypM (VF_A1032) , sypN (VF_A1033) , sypO (VF_A1034)
    ... ... sypM sypN sypO
    842 24097942
    NC_006841.2 Q5DYQ0 not specified TTCTCAATTTGAGAA +[1168988:1169002] Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) - Experimental technique details Beta-gal reporter assay - Experimental technique details ChIP-PCR (ECO:0005620) - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details Site directed mutagenesis (ECO:0005667) sypP (VF_A1035) , sypQ (VF_A1036) , sypR (VF_A1037)
    ... ... sypP sypQ sypR
    842 24097942
    NC_006841.2 Q5DYQ0 not specified TTCTCAATTTGCAAT -[1149456:1149470] Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) VF_A1019 , VF_A1018 , sypA (VF_A1020) , sypB (VF_A1021) , sypC (VF_A1022) , sypD (VF_A1023) , sypE (VF_A1024) , sypF (VF_A1025) , sypG (VF_A1026) , sypH (VF_A1027)
    ... ... VF_A1019 VF_A1018 sypA sypB sypC sypD sypE sypF sypG sypH
    842 24097942
    NC_006841.2 Q5DYQ0 not specified TTCTCAATTTGAAAA +[134907:134921] Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) VF_A0120 , VF_A0119 , VF_A0118 , VF_A0117 , VF_A0121
    ... ... VF_A0120 VF_A0119 VF_A0118 VF_A0117 VF_A0121
    842 24097942
    NC_006841.2 Q5DYQ0 not specified TTCTCATATTGATTC -[635041:635055] Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) VF_A0550 , VF_A0549
    ... ... VF_A0550 VF_A0549
    842 24097942

    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.

    TTCTCATTCTGCAAA
    TTCTCAATTTGAGAA
    TTCTCAAAATGAGAA
    TTCTCAATTTGAGAA
    TTCTCAATTTGCAAT
    TTCTCAATTTGAAAA
    TTCTCATATTGATTC

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

    TTCTCATTCTGCAAA
    TTCTCAATTTGAGAA
    TTCTCATTTTGAGAA
    TTCTCAATTTGAGAA
    TTCTCAATTTGCAAT
    TTCTCAATTTGAAAA
    GAATCAATATGAGAA
    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.