LuxO - UniProtKB: A7MVC2 regulon and binding site collection of Vibrio campbellii ATCC BAA-1116


Sites are listed as curated.

TTGCATTTTGCAA
TTGCATAATGCAA
TTGCAATTTGCAA
TTGCATTTTGCAA
TTGCAAAATGCGT
TTGCGATTTGCAA
TTGCAATATGCAT

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

TTGCATTTTGCAA
TTGCATTATGCAA
TTGCAATTTGCAA
TTGCATTTTGCAA
ACGCATTTTGCAA
TTGCGATTTGCAA
TTGCAATATGCAT

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_009784.1 A7MVC2 not specified TTGCATTTTGCAA -[1833586:1833598] Experimental technique details Ad-hoc quantitative phenotype observation (ECO:0005676) - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) VIBHAR_06697 , VIBHAR_06698
    ... ... VIBHAR_06697 VIBHAR_06698
    942 17234887
    NC_009784.1 A7MVC2 not specified TTGCATAATGCAA +[111092:111104] Experimental technique details Ad-hoc quantitative phenotype observation (ECO:0005676) - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) VIBHAR_04846
    ... ... VIBHAR_04846
    942 17234887
    NC_009784.1 A7MVC2 not specified TTGCAATTTGCAA -[555487:555499] Experimental technique details Ad-hoc quantitative phenotype observation (ECO:0005676) - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) VIBHAR_05322
    ... ... VIBHAR_05322
    942 17234887
    NC_009784.1 A7MVC2 not specified TTGCATTTTGCAA -[1833586:1833598] Experimental technique details Ad-hoc quantitative phenotype observation (ECO:0005676) - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) VIBHAR_06697 , VIBHAR_06698
    ... ... VIBHAR_06697 VIBHAR_06698
    942 17234887
    NC_009784.1 A7MVC2 not specified TTGCAAAATGCGT -[1833566:1833578] Experimental technique details Ad-hoc quantitative phenotype observation (ECO:0005676) - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) VIBHAR_06697 , VIBHAR_06698
    ... ... VIBHAR_06697 VIBHAR_06698
    942 17234887
    NC_009784.1 A7MVC2 not specified TTGCGATTTGCAA -[1081200:1081212] Experimental technique details Ad-hoc quantitative phenotype observation (ECO:0005676) - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) VIBHAR_05886 , VIBHAR_05885 , VIBHAR_05884 , VIBHAR_05883 , VIBHAR_05882
    ... ... VIBHAR_05886 VIBHAR_05885 VIBHAR_05884 VIBHAR_05883 VIBHAR_05882
    942 17234887
    NC_009784.1 A7MVC2 not specified TTGCAATATGCAT -[1081179:1081191] Experimental technique details Ad-hoc quantitative phenotype observation (ECO:0005676) - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) VIBHAR_05886 , VIBHAR_05885 , VIBHAR_05884 , VIBHAR_05883 , VIBHAR_05882
    ... ... VIBHAR_05886 VIBHAR_05885 VIBHAR_05884 VIBHAR_05883 VIBHAR_05882
    942 17234887

    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.

    TTGCATTTTGCAA
    TTGCATAATGCAA
    TTGCAATTTGCAA
    TTGCATTTTGCAA
    TTGCAAAATGCGT
    TTGCGATTTGCAA
    TTGCAATATGCAT

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

    TTGCATTTTGCAA
    TTGCATTATGCAA
    TTGCAATTTGCAA
    TTGCATTTTGCAA
    ACGCATTTTGCAA
    TTGCGATTTGCAA
    TTGCAATATGCAT
    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.