CodY - UniProtKB: Q18BE1 regulon and binding site collection of Clostridium difficile 630


Sites are listed as curated.

AATTCTCTGAAACAC
AAGTTTTTGATATTT
AATTAACAGAATCTT
AATCTTTATACAATT

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

AATTCTCTGAAACAC
AAATATCAAAAACTT
AATTAACAGAATCTT
AATTGTATAAAGATT

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_009089.1 Q18BE1 not specified AATTCTCTGAAACAC +[1795171:1795185] Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) hisZ (CD630_15470) , CD630_15461 , CD630_15460 , hisG (CD630_15480) , hisC (CD630_15490) , hisB (CD630_15500) , hisH (CD630_15510) , hisA (CD630_15520) , hisF (CD630_15530) , hisI (CD630_15540)
    ... ... hisZ CD630_15461 CD630_15460 hisG hisC hisB hisH hisA hisF hisI
    476 20709897
    NC_009089.1 Q18BE1 not specified AAGTTTTTGATATTT -[2714014:2714028] Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) CD630_23440 , cat1 (CD630_23430) , sucD (CD630_23420) , CD630_23450
    ... ... CD630_23440 cat1 sucD CD630_23450
    476 20709897
    NC_009089.1 Q18BE1 not specified AATTAACAGAATCTT +[1059844:1059858] Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) glgC (CD630_08820) , CD630_08810 , CD630_08800 , glgD (CD630_08830) , glgA (CD630_08840) , glgP (CD630_08850) , CD630_08860
    ... ... glgC CD630_08810 CD630_08800 glgD glgA glgP CD630_08860
    476 20709897
    NC_009089.1 Q18BE1 not specified AATCTTTATACAATT +[1059853:1059867] Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) glgC (CD630_08820) , CD630_08810 , CD630_08800 , glgD (CD630_08830) , glgA (CD630_08840) , glgP (CD630_08850) , CD630_08860
    ... ... glgC CD630_08810 CD630_08800 glgD glgA glgP CD630_08860
    476 20709897

    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.

    AATTCTCTGAAACAC
    AAGTTTTTGATATTT
    AATTAACAGAATCTT
    AATCTTTATACAATT

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

    AATTCTCTGAAACAC
    AAATATCAAAAACTT
    AATTAACAGAATCTT
    AATTGTATAAAGATT
    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.