Clp - UniProtKB: Q4UZF6 regulon and binding site collection of Xanthomonas campestris pv. campestris str. 8004


Sites are listed as curated.

AACGGTGCGCTTCACCGCACCC

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

AACGGTGCGCTTCACCGCACCC

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_007086.1 Q4UZF6 not specified AACGGTGCGCTTCACCGCACCC -[4241630:4241651] Experimental technique details EMSA (ECO:0001807) - Experimental technique details GUS reporter gene assay (ECO:0005641) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) XC_3573 , XC_3575
    ... ... XC_3573 XC_3575
    628 18175178

    Clp - UniProtKB: Q4UZF6 regulon and binding site collection of Xanthomonas campestris pv. campestris str. ATCC 33913


    Sites are listed as curated.

    CGATGTGATCGGTGCGGCAATG
    TTCTGTGGGGACGATCACACCA
    CGTGCACATCGACACA
    GGCGATCGGCATCACG
    CGTGGATCTGCGCACT
    TGAGCGGTCAGTCACA
    CGCGACGTGCTTCGCA

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

    CGATGTGATCGGTGCGGCAATG
    TGGTGTGATCGTCCCCACAGAA
    GCGCGTGCACATCGACACATCG
    AAGCGTGATGCCGATCGCCCCG
    CCACGTGGATCTGCGCACTTGG
    ATTTGTGACTGACCGCTCAGCC
    AGTTGCGAAGCACGTCGCGGAT

    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_003902.1 Q4UZF6 not specified CGATGTGATCGGTGCGGCAATG +[4194908:4194929] Experimental technique details Beta-gal reporter assay - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Site directed mutagenesis (ECO:0005667) - Experimental technique details Visual sequence inspection (nan) engXCA (XCC3521) , ybaR (XCC3520)
      ... ... engXCA ybaR
      599 15955530
      NC_003902.1 Q4UZF6 not specified TTCTGTGGGGACGATCACACCA +[4194935:4194956] Experimental technique details Beta-gal reporter assay - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Site directed mutagenesis (ECO:0005667) - Experimental technique details Visual sequence inspection (nan) engXCA (XCC3521) , ybaR (XCC3520)
      ... ... engXCA ybaR
      599 15955530
      NC_003902.1 Q4UZF6 not specified CGTGCACATCGACACA +[768481:768496] Experimental technique details Beta-gal reporter assay - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Visual sequence inspection (nan) pel (XCC0644)
      ... ... pel
      600 19601664
      NC_003902.1 Q4UZF6 not specified GGCGATCGGCATCACG +[3932757:3932772] Experimental technique details Beta-gal reporter assay - Experimental technique details EMSA (ECO:0001807) XCC3315
      ... ... XCC3315
      607 23137357
      NC_003902.1 Q4UZF6 monomer CGTGGATCTGCGCACT -[4118219:4118234] Experimental technique details Beta-gal reporter assay - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Visual sequence inspection (nan) peh-1 (XCC3459)
      ... ... peh-1
      608 18310017
      NC_003902.1 Q4UZF6 not specified TGAGCGGTCAGTCACA +[3237952:3237967] Experimental technique details Beta-gal reporter assay - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Visual sequence inspection (nan) XCC2731 , XCC2730
      ... ... XCC2731 XCC2730
      609 21237626
      NC_003902.1 Q4UZF6 not specified CGCGACGTGCTTCGCA -[1514003:1514018] Experimental technique details Beta-gal reporter assay - Experimental technique details EMSA (ECO:0001807) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) XCC1294 , XCC1293 , XCC1292
      ... ... XCC1294 XCC1293 XCC1292
      632 22002465

      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.

      CGATGTGATCGGTGCGGCAATG
      TTCTGTGGGGACGATCACACCA
      CGTGCACATCGACACA
      GGCGATCGGCATCACG
      CGTGGATCTGCGCACT
      TGAGCGGTCAGTCACA
      AACGGTGCGCTTCACCGCACCC
      CGCGACGTGCTTCGCA

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

      CGATGTGATCGGTGCGGCAATG
      TGGTGTGATCGTCCCCACAGAA
      GCGCGTGCACATCGACACATCG
      AAGCGTGATGCCGATCGCCCCG
      CCACGTGGATCTGCGCACTTGG
      ATTTGTGACTGACCGCTCAGCC
      GGGTGCGGTGAAGCGCACCGTT
      AGTTGCGAAGCACGTCGCGGAT
      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.