HrpX - UniProtKB: Q3BW17 regulon and binding site collection of Xanthomonas campestris pv. vesicatoria str. 85-10


Sites are listed as curated.

TTCGCGGCGCGCGCGCCAGCTTCGT
TTCGCACACGCACCCTTGCATTCGC
TTCGCTTTGCATCGCTGCACTTCGT
TTCGGCCAAGCTTACGTCAACTCGC
TTCGTTTTTGGAGCGCCGCGTGCGG
TTCGTTTGCTGCGGCGGCGCTTCGT
TTCGCCAGCGAATTCCGATATTCGC
TTCGCCAGGCCATCCACACATTCGC
TTCGCCGGACCAGCTATCGCTTCGC
TTCGCCCATGACCATGCAGCTTCGC
TTCGCCAAAATAGTTCGTCGGCCAG

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

TTCGCGGCGCGCGCGCCAGCTTCGT
TTCGCACACGCACCCTTGCATTCGC
TTCGCTTTGCATCGCTGCACTTCGT
TTCGGCCAAGCTTACGTCAACTCGC
TTCGTTTTTGGAGCGCCGCGTGCGG
TTCGTTTGCTGCGGCGGCGCTTCGT
TTCGCCAGCGAATTCCGATATTCGC
TTCGCCAGGCCATCCACACATTCGC
TTCGCCGGACCAGCTATCGCTTCGC
TTCGCCCATGACCATGCAGCTTCGC
TTCGCCAAAATAGTTCGTCGGCCAG

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_007508.1 Q3BW17 dimer TTCGCGGCGCGCGCGCCAGCTTCGT +[600440:600464] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) XCV0536 , XCV0535
    ... ... XCV0536 XCV0535
    1127 16936021
    NC_007508.1 Q3BW17 dimer TTCGCACACGCACCCTTGCATTCGC +[2894865:2894889] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) XCV2568 , XCV2567 , XCV2566 , XCV2565
    ... ... XCV2568 XCV2567 XCV2566 XCV2565
    1127 16936021
    NC_007508.1 Q3BW17 dimer TTCGCTTTGCATCGCTGCACTTCGT -[3103540:3103564] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) XCV2729 , XCV2728
    ... ... XCV2729 XCV2728
    1127 16936021
    NC_007508.1 Q3BW17 dimer TTCGGCCAAGCTTACGTCAACTCGC +[3895036:3895060] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) XCV3407
    ... ... XCV3407
    1127 16936021
    NC_007508.1 Q3BW17 dimer TTCGTTTTTGGAGCGCCGCGTGCGG -[4351038:4351062] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) XCV3765 , XCV3764
    ... ... XCV3765 XCV3764
    1127 16936021
    NC_007508.1 Q3BW17 dimer TTCGTTTGCTGCGGCGGCGCTTCGT +[5101653:5101677] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) XCV4424 , XCV4425
    ... ... XCV4424 XCV4425
    1127 16936021
    NC_007508.1 Q3BW17 dimer TTCGCCAGCGAATTCCGATATTCGC +[477426:477450] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA affinity purification (ECO:0005629) hrcU (XCV0426) , hrcV (XCV0425) , hpaC (XCV0424) , hrcQ (XCV0423) , hrcR (XCV0422) , hrcS (XCV0421) , hpaA (XCV0420) , hrcD (XCV0419) , hrpD6 (XCV0418) , hrpE (XCV0417) , hpaB (XCV0416) , hpaE (XCV0415) , hrpB1 (XCV0427) , hrpB2 (XCV0428) , hrcJ (XCV0429) , hrpB4 (XCV0430) , hrcL (XCV0431) , hrcN (XCV0432) , hrpB7 (XCV0433) , hrcT (XCV0434) , hrcC (XCV0435)
    ... ... hrcU hrcV hpaC hrcQ hrcR hrcS hpaA hrcD hrpD6 hrpE hpaB hpaE hrpB1 hrpB2 hrcJ hrpB4 hrcL hrcN hrpB7 hrcT hrcC
    1127 16936021
    NC_007508.1 Q3BW17 dimer TTCGCCAGGCCATCCACACATTCGC -[477387:477411] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA affinity purification (ECO:0005629) hrcU (XCV0426) , hrcV (XCV0425) , hpaC (XCV0424) , hrcQ (XCV0423) , hrcR (XCV0422) , hrcS (XCV0421) , hpaA (XCV0420) , hrcD (XCV0419) , hrpD6 (XCV0418) , hrpE (XCV0417) , hpaB (XCV0416) , hpaE (XCV0415) , hrpB1 (XCV0427) , hrpB2 (XCV0428) , hrcJ (XCV0429) , hrpB4 (XCV0430) , hrcL (XCV0431) , hrcN (XCV0432) , hrpB7 (XCV0433) , hrcT (XCV0434) , hrcC (XCV0435)
    ... ... hrcU hrcV hpaC hrcQ hrcR hrcS hpaA hrcD hrpD6 hrpE hpaB hpaE hrpB1 hrpB2 hrcJ hrpB4 hrcL hrcN hrpB7 hrcT hrcC
    1127 16936021
    NC_007508.1 Q3BW17 dimer TTCGCCGGACCAGCTATCGCTTCGC -[473792:473816] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA affinity purification (ECO:0005629) - Experimental technique details Site directed mutagenesis (ECO:0005667) hpaC (XCV0424) , hrcQ (XCV0423) , hrcR (XCV0422) , hrcS (XCV0421) , hpaA (XCV0420) , hrcD (XCV0419) , hrpD6 (XCV0418) , hrpE (XCV0417) , hpaB (XCV0416) , hpaE (XCV0415)
    ... ... hpaC hrcQ hrcR hrcS hpaA hrcD hrpD6 hrpE hpaB hpaE
    1127 16936021
    NC_007508.1 Q3BW17 dimer TTCGCCCATGACCATGCAGCTTCGC -[470895:470919] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA affinity purification (ECO:0005629) hrcD (XCV0419) , hpaA (XCV0420) , hrpD6 (XCV0418) , hrpE (XCV0417) , hpaB (XCV0416) , hpaE (XCV0415)
    ... ... hrcD hpaA hrpD6 hrpE hpaB hpaE
    1127 16936021
    NC_007508.1 Q3BW17 dimer TTCGCCAAAATAGTTCGTCGGCCAG -[464990:465014] Experimental technique details Consensus search (ECO:0005624) hrpF (XCV0411) , XCV0410 , hpaF (XCV0409) , hpaG (XCV0408) , XCV0407 , XCV0412 , XCV0413 , xopF1 (XCV0414)
    ... ... hrpF XCV0410 hpaF hpaG XCV0407 XCV0412 XCV0413 xopF1
    1127 16936021

    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.

    TTCGCGGCGCGCGCGCCAGCTTCGT
    TTCGCACACGCACCCTTGCATTCGC
    TTCGCTTTGCATCGCTGCACTTCGT
    TTCGGCCAAGCTTACGTCAACTCGC
    TTCGTTTTTGGAGCGCCGCGTGCGG
    TTCGTTTGCTGCGGCGGCGCTTCGT
    TTCGCCAGCGAATTCCGATATTCGC
    TTCGCCAGGCCATCCACACATTCGC
    TTCGCCGGACCAGCTATCGCTTCGC
    TTCGCCCATGACCATGCAGCTTCGC
    TTCGCCAAAATAGTTCGTCGGCCAG

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

    TTCGCGGCGCGCGCGCCAGCTTCGT
    TTCGCACACGCACCCTTGCATTCGC
    TTCGCTTTGCATCGCTGCACTTCGT
    TTCGGCCAAGCTTACGTCAACTCGC
    TTCGTTTTTGGAGCGCCGCGTGCGG
    TTCGTTTGCTGCGGCGGCGCTTCGT
    TTCGCCAGCGAATTCCGATATTCGC
    TTCGCCAGGCCATCCACACATTCGC
    TTCGCCGGACCAGCTATCGCTTCGC
    TTCGCCCATGACCATGCAGCTTCGC
    TTCGCCAAAATAGTTCGTCGGCCAG
    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.