TorR - UniProtKB: Q8EHJ3 regulon and binding site collection of Shewanella oneidensis MR-1


Sites are listed as curated.

TTCATAATTTTTCATA
TTCATACTTTTTCATA
TTCATATTCATTCATA

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

TTCATAATTTTTCATA
TTCATACTTTTTCATA
TTCATATTCATTCATA

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_004347.2 Q8EHJ3 dimer TTCATAATTTTTCATA -[1286243:1286258] Experimental technique details EMSA (ECO:0001807) - Experimental technique details qPCR [quantitative real-time] (ECO:0005660) - Experimental technique details Site directed mutagenesis (ECO:0005667) - Experimental technique details Visual sequence inspection (nan) torE (SO_1234) , torC (SO_1233) , torA (SO_1232) , torD (SO_1231) , SO_1236
    ... ... torE torC torA torD SO_1236
    996 15231782
    NC_004347.2 Q8EHJ3 dimer TTCATACTTTTTCATA -[1276179:1276194] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details qPCR [quantitative real-time] (ECO:0005660) torR (SO_1228) , SO_1227
    ... ... torR SO_1227
    996 15231782
    NC_004347.2 Q8EHJ3 dimer TTCATATTCATTCATA +[4896427:4896442] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details qPCR [quantitative real-time] (ECO:0005660) torF (SO_4694) , vmeA (SO_4693) , vmeB (SO_4692)
    ... ... torF vmeA vmeB
    996 15231782

    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.

    TTCATAATTTTTCATA
    TTCATACTTTTTCATA
    TTCATATTCATTCATA

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

    TTCATAATTTTTCATA
    TTCATACTTTTTCATA
    TTCATATTCATTCATA
    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.