SoxR - UniProtKB: Q8P6Y4 regulon and binding site collection of Xanthomonas campestris pv. campestris str. ATCC 33913


Sites are listed as curated.

CCTCAACCAAGGTTGAGG
CCTCAACCATGCTTTAGG

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

CCTCAACCAAGGTTGAGG
CCTCAACCATGCTTTAGG

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_003902.1 Q8P6Y4 not specified CCTCAACCAAGGTTGAGG -[3344463:3344480] Experimental technique details EMSA (ECO:0001807) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Site directed mutagenesis (ECO:0005667) - Experimental technique details Visual sequence inspection (nan) soxR (XCC2831) , XCC2830 , XCC2829 , XCC2832
    ... ... soxR XCC2830 XCC2829 XCC2832
    630 22056938
    NC_003902.1 Q8P6Y4 not specified CCTCAACCATGCTTTAGG -[368605:368622] Experimental technique details EMSA (ECO:0001807) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) XCC0300
    ... ... XCC0300
    630 22056938

    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.

    CCTCAACCAAGGTTGAGG
    CCTCAACCATGCTTTAGG

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

    CCTCAACCAAGGTTGAGG
    CCTCAACCATGCTTTAGG
    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.