RicR - UniProtKB: O07434 regulon and binding site collection of Mycobacterium tuberculosis H37Rv


Sites are listed as curated.

CTACCCCTATAGGGTAT
ATACCCCCGGGTGGTAT
ATACCCGTATAGGGTAT
ATACCCCGCTGGGGTAC
ATACCCCATAGGGGTAT

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

CTACCCCTATAGGGTAT
ATACCACCCGGGGGTAT
ATACCCGTATAGGGTAT
ATACCCCGCTGGGGTAC
ATACCCCTATGGGGTAT

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_000962.3 O07434 not specified CTACCCCTATAGGGTAT +[944298:944314] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA affinity purification (ECO:0005629) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Site directed mutagenesis (ECO:0005667) - Experimental technique details Visual sequence inspection (nan) lpqS (Rv0847) , Rv0846c
    ... ... lpqS Rv0846c
    1116 21166899
    NC_000962.3 O07434 not specified ATACCCCCGGGTGGTAT +[3315201:3315217] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) Rv2963 , Rv2962c , purU (Rv2964)
    ... ... Rv2963 Rv2962c purU
    1116 21166899
    NC_000962.3 O07434 not specified ATACCCGTATAGGGTAT -[218620:218636] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) mymT (Rv0186A) , Rv0187 , Rv0188
    ... ... mymT Rv0187 Rv0188
    1116 21166899
    NC_000962.3 O07434 not specified ATACCCCGCTGGGGTAC +[221784:221800] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) Rv0190 , ilvD (Rv0189c) , Rv0191 , Rv0192 , Rv0192A
    ... ... Rv0190 ilvD Rv0191 Rv0192 Rv0192A
    1116 21166899
    NC_000962.3 O07434 not specified ATACCCCATAGGGGTAT +[1934020:1934036] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) PPE23 (Rv1706c) , PPE22 (Rv1705c) , cycA (Rv1704c) , Rv1703c
    ... ... PPE23 PPE22 cycA Rv1703c
    1116 21166899

    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.

    CTACCCCTATAGGGTAT
    ATACCCCCGGGTGGTAT
    ATACCCGTATAGGGTAT
    ATACCCCGCTGGGGTAC
    ATACCCCATAGGGGTAT

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

    CTACCCCTATAGGGTAT
    ATACCACCCGGGGGTAT
    ATACCCGTATAGGGTAT
    ATACCCCGCTGGGGTAC
    ATACCCCTATGGGGTAT
    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.