BreR - UniProtKB: Q9KR96 regulon and binding site collection of Vibrio cholerae MJ-1236


Sites are listed as curated.

AAAGTAAACTCGTTGGTGTACTTT
AATGTACACCCGAAAGTTTACTTT
CATGTTAAACCAAGAGTTTAGTTT

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

AAAGTAAACTCGTTGGTGTACTTT
AAAGTAAACTTTCGGGTGTACATT
AAACTAAACTCTTGGTTTAACATG

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_012668.1 Q9KR96 not specified AAAGTAAACTCGTTGGTGTACTTT +[1784796:1784819] Experimental technique details Beta-gal reporter assay - 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 Motif-discovery (ECO:0005558) - Experimental technique details Site directed mutagenesis (ECO:0005667) VCD_002636 , VCD_002635 , VCD_002634 , VCD_002637 , VCD_002638 , VCD_002639
    ... ... VCD_002636 VCD_002635 VCD_002634 VCD_002637 VCD_002638 VCD_002639
    521 23144245
    NC_012668.1 Q9KR96 not specified AATGTACACCCGAAAGTTTACTTT -[1776047:1776070] Experimental technique details Beta-gal reporter assay - 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 Motif-discovery (ECO:0005558) - Experimental technique details Site directed mutagenesis (ECO:0005667) VCD_002628 , VCD_002627 , VCD_002629 , VCD_002630 , VCD_002631
    ... ... VCD_002628 VCD_002627 VCD_002629 VCD_002630 VCD_002631
    521 23144245
    NC_012668.1 Q9KR96 not specified CATGTTAAACCAAGAGTTTAGTTT -[1776218:1776241] Experimental technique details Beta-gal reporter assay - 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 Motif-discovery (ECO:0005558) - Experimental technique details Site directed mutagenesis (ECO:0005667) VCD_002628 , VCD_002627 , VCD_002629 , VCD_002630 , VCD_002631
    ... ... VCD_002628 VCD_002627 VCD_002629 VCD_002630 VCD_002631
    521 23144245

    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.

    AAAGTAAACTCGTTGGTGTACTTT
    AATGTACACCCGAAAGTTTACTTT
    CATGTTAAACCAAGAGTTTAGTTT

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

    AAAGTAAACTCGTTGGTGTACTTT
    AAAGTAAACTTTCGGGTGTACATT
    AAACTAAACTCTTGGTTTAACATG
    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.