CtrA - UniProtKB: P0CAW8 regulon and binding site collection of Caulobacter crescentus CB15


Sites are listed as curated.

TTAAGATCTTTCTAA
TTAATAAGAAATTAA
TTAACGCTCTGTTAA
TTAAGCAACCGTTAA
CTAACGCCCTGTTAAC

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

CTTAAGATCTTTCTAA
CTTAATTTCTTATTAA
TTAACGCTCTGTTAAT
TTAACGGTTGCTTAAC
CTAACGCCCTGTTAAC

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_002696.2 P0CAW8 not specified TTAAGATCTTTCTAA +[4016751:4016765] Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Site directed mutagenesis (ECO:0005667) CC_3763 , CC_3762 , CC_3761
    ... ... CC_3763 CC_3762 CC_3761
    1021 10698954
    NC_002696.2 P0CAW8 not specified TTAATAAGAAATTAA +[4016772:4016786] Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Site directed mutagenesis (ECO:0005667) CC_3763 , CC_3762 , CC_3761
    ... ... CC_3763 CC_3762 CC_3761
    1021 10698954
    NC_002696.2 P0CAW8 not specified TTAACGCTCTGTTAA +[4016894:4016908] Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Site directed mutagenesis (ECO:0005667) CC_3763 , CC_3762 , CC_3761
    ... ... CC_3763 CC_3762 CC_3761
    1021 10698954
    NC_002696.2 P0CAW8 not specified TTAAGCAACCGTTAA +[205:219] Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Site directed mutagenesis (ECO:0005667) CC_0001 , CC_0002 , CC_0003 , coaE (CC_0004) , CC_0005 , CC_0006 , CC_0007
    ... ... CC_0001 CC_0002 CC_0003 coaE CC_0005 CC_0006 CC_0007
    1021 10698954
    NC_002696.2 P0CAW8 not specified CTAACGCCCTGTTAAC +[1207446:1207461] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Visual sequence inspection (nan) fliQ (CC_1075) , flhB (CC_1077) , fliR (CC_1076) , CC_1078
    ... ... fliQ flhB fliR CC_1078
    1027 8548829

    CtrA - UniProtKB: P0CAW8 regulon and binding site collection of Caulobacter crescentus NA1000


    Sites are listed as curated.

    TTAACGCTCTGTTAA
    TTGAAGTATGGTTAATGCCGG
    TCAACAAAAGACTAAA
    TTTACTGGCCATTAAG
    TTAACCGCCGATTAAC
    TGGTTAAGAACAAATAACG
    GTAAATACAAATAAACCAA
    TTAATGCCGGATTAA

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

    GTTAACGCTCTGTTAATCATGG
    CTTGAAGTATGGTTAATGCCGG
    TTTAGTCTTTTGTTGACCAAAG
    CTTAATGGCCAGTAAACAGCGA
    GTTAACCGCCGATTAACGATGG
    CGTTATTTGTTCTTAACCATGC
    GGTAAATACAAATAAACCAAAA
    CTTAATGCCGGATTAACCCTGT

    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_011916.1 P0CAW8 not specified TTAACGCTCTGTTAA +[4042876:4042890] Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Site directed mutagenesis (ECO:0005667) hemE (CCNA_03879) , hemH (CCNA_03878) , CCNA_03877
      ... ... hemE hemH CCNA_03877
      1020 12949109
      NC_011916.1 P0CAW8 not specified TTGAAGTATGGTTAATGCCGG +[2818599:2818619] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Visual sequence inspection (nan) fliX (CCNA_02664) , flgI (CCNA_02665) , CCNA_02666 , flbY (CCNA_02667)
      ... ... fliX flgI CCNA_02666 flbY
      1023 9555902
      NC_011916.1 P0CAW8 not specified TCAACAAAAGACTAAA -[3198953:3198968] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Visual sequence inspection (nan) pilA (CCNA_03043) , CCNA_03045 , CCNA_03044 , CCNA_03046
      ... ... pilA CCNA_03045 CCNA_03044 CCNA_03046
      1028 10880436
      NC_011916.1 P0CAW8 not specified TTTACTGGCCATTAAG -[3198796:3198811] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Visual sequence inspection (nan) pilA (CCNA_03043) , CCNA_03044 , CCNA_03045 , CCNA_03046
      ... ... pilA CCNA_03044 CCNA_03045 CCNA_03046
      1028 10880436
      NC_011916.1 P0CAW8 not specified TTAACCGCCGATTAAC -[2773206:2773221] Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Visual sequence inspection (nan) - Experimental technique details xylE reporter assay ftsZ (CCNA_02623) , CCNA_02622
      ... ... ftsZ CCNA_02622
      1029 9512521
      NC_011916.1 P0CAW8 not specified TGGTTAAGAACAAATAACG -[3198858:3198876] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Visual sequence inspection (nan) pilA (CCNA_03043) , CCNA_03044 , CCNA_03045 , CCNA_03046
      ... ... pilA CCNA_03044 CCNA_03045 CCNA_03046
      1026 10880436
      NC_011916.1 P0CAW8 not specified GTAAATACAAATAAACCAA -[3198839:3198857] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Visual sequence inspection (nan) pilA (CCNA_03043) , CCNA_03044 , CCNA_03045 , CCNA_03046
      ... ... pilA CCNA_03044 CCNA_03045 CCNA_03046
      1026 10880436
      NC_011916.1 P0CAW8 not specified TTAATGCCGGATTAA +[1085157:1085171] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Site directed mutagenesis (ECO:0005667) - Experimental technique details Visual sequence inspection (nan) fliO (CCNA_01003) , fliP (CCNA_01002) , flgB (CCNA_01004) , CCNA_01001 , flgC (CCNA_01005) , fliE (CCNA_01006)
      ... ... fliO fliP flgB CCNA_01001 flgC fliE
      1060 11133968

      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.

      TTAACGCTCTGTTAA
      TTAAGATCTTTCTAA
      TTAATAAGAAATTAA
      TTAACGCTCTGTTAA
      TTAAGCAACCGTTAA
      TTGAAGTATGGTTAATGCCGG
      TCAACAAAAGACTAAA
      TTTACTGGCCATTAAG
      TTAACCGCCGATTAAC
      TGGTTAAGAACAAATAACG
      GTAAATACAAATAAACCAA
      CTAACGCCCTGTTAAC
      TTAATGCCGGATTAA

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

      GTTAACGCTCTGTTAATCATGG
      CTTAAGATCTTTCTAACATATA
      CTTAATTTCTTATTAATATATG
      GTTAACGCTCTGTTAATCATGG
      GTTAACGGTTGCTTAACCACTT
      CTTGAAGTATGGTTAATGCCGG
      TTTAGTCTTTTGTTGACCAAAG
      CTTAATGGCCAGTAAACAGCGA
      GTTAACCGCCGATTAACGATGG
      CGTTATTTGTTCTTAACCATGC
      GGTAAATACAAATAAACCAAAA
      CCTAACGCCCTGTTAACCATAT
      CTTAATGCCGGATTAACCCTGT
      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.