RdgB - UniProtKB: Q47588 regulon and binding site collection of Pectobacterium carotovorum subsp. carotovorum PCC21


Sites are listed as curated.

TTTTATTAAACTCGATTAATAAGC
AATACTTAAACTCCTTTAAAATCATA
TTTTTCTAAAACAGATTAAAAGCCGC
GTTTTCTAATTCACTTTAAAATCGTT
TTTTATTAAACTCGATTAATAAGCTT

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

TTTTATTAAACTCGATTAATAAGCTT
AATACTTAAACTCCTTTAAAATCATA
TTTTTCTAAAACAGATTAAAAGCCGC
GTTTTCTAATTCACTTTAAAATCGTT
TTTTATTAAACTCGATTAATAAGCTT

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_018525.1 Q47588 dimer TTTTATTAAACTCGATTAATAAGC +[1604141:1604164] Experimental technique details CAT reporter gene assays (ECO:0005617) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) PCC21_014030
    ... ... PCC21_014030
    1133 9084157
    NC_018525.1 Q47588 not specified AATACTTAAACTCCTTTAAAATCATA +[1803920:1803945] Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) PCC21_015820 , PCC21_015830 , PCC21_015840 , PCC21_015850 , PCC21_015860
    ... ... PCC21_015820 PCC21_015830 PCC21_015840 PCC21_015850 PCC21_015860
    1134 18689515
    NC_018525.1 Q47588 not specified TTTTTCTAAAACAGATTAAAAGCCGC +[1806364:1806389] Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) PCC21_015870 , PCC21_015880 , PCC21_015890 , PCC21_015900 , PCC21_015910
    ... ... PCC21_015870 PCC21_015880 PCC21_015890 PCC21_015900 PCC21_015910
    1134 18689515
    NC_018525.1 Q47588 not specified GTTTTCTAATTCACTTTAAAATCGTT +[1809510:1809535] Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) PCC21_015920 , PCC21_015930
    ... ... PCC21_015920 PCC21_015930
    1134 18689515
    NC_018525.1 Q47588 not specified TTTTATTAAACTCGATTAATAAGCTT +[1604141:1604166] Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) PCC21_014030
    ... ... PCC21_014030
    1134 18689515

    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.

    TTTTATTAAACTCGATTAATAAGC
    AATACTTAAACTCCTTTAAAATCATA
    TTTTTCTAAAACAGATTAAAAGCCGC
    GTTTTCTAATTCACTTTAAAATCGTT
    TTTTATTAAACTCGATTAATAAGCTT

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

    TTTTATTAAACTCGATTAATAAGCTT
    AATACTTAAACTCCTTTAAAATCATA
    TTTTTCTAAAACAGATTAAAAGCCGC
    GTTTTCTAATTCACTTTAAAATCGTT
    TTTTATTAAACTCGATTAATAAGCTT
    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.