H-NS - UniProtKB: Q9KSX6 regulon and binding site collection of Vibrio cholerae O395


Sites are listed as curated.

TCGATACCTT
TCGGTAAACC
CCGATAAAAA
TTGATCAATT
ATGATAAGTT
GCGTTAAAAT
GCATTAAATT
TGAATAAGTT
TCTGTCAATT
TACATAAATA

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

TCGATACCTT
TCGGTAAACC
CCGATAAAAA
TTGATCAATT
ATGATAAGTT
GCGTTAAAAT
GCATTAAATT
TGAATAAGTT
TCTGTCAATT
TACATAAATA

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_009456.1 Q9KSX6 other TCGATACCTT +[566154:566163] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) ctxA (VC0395_0512) , zot (VC0395_0511) , ace (VC0395_0510) , VC0395_0509 , cep (VC0395_0508) , rstB2 (VC0395_0507) , rstA1 (VC0395_0506) , VC0395_0505
    ... ... ctxA zot ace VC0395_0509 cep rstB2 rstA1 VC0395_0505
    502 21169492
    NC_009456.1 Q9KSX6 other TCGGTAAACC -[566198:566207] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) ctxA (VC0395_0512) , zot (VC0395_0511) , ace (VC0395_0510) , VC0395_0509 , cep (VC0395_0508) , rstB2 (VC0395_0507) , rstA1 (VC0395_0506) , VC0395_0505
    ... ... ctxA zot ace VC0395_0509 cep rstB2 rstA1 VC0395_0505
    502 21169492
    NC_009456.1 Q9KSX6 other CCGATAAAAA +[566204:566213] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) ctxA (VC0395_0512) , zot (VC0395_0511) , ace (VC0395_0510) , VC0395_0509 , cep (VC0395_0508) , rstB2 (VC0395_0507) , rstA1 (VC0395_0506) , VC0395_0505
    ... ... ctxA zot ace VC0395_0509 cep rstB2 rstA1 VC0395_0505
    502 21169492
    NC_009456.1 Q9KSX6 other TTGATCAATT +[566332:566341] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) ctxA (VC0395_0512) , zot (VC0395_0511) , ace (VC0395_0510) , VC0395_0509 , cep (VC0395_0508) , rstB2 (VC0395_0507) , rstA1 (VC0395_0506) , VC0395_0505
    ... ... ctxA zot ace VC0395_0509 cep rstB2 rstA1 VC0395_0505
    502 21169492
    NC_009456.1 Q9KSX6 other ATGATAAGTT +[566429:566438] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) ctxA (VC0395_0512) , zot (VC0395_0511) , ace (VC0395_0510) , VC0395_0509 , cep (VC0395_0508) , rstB2 (VC0395_0507) , rstA1 (VC0395_0506) , VC0395_0505 , VC0395_0513 , VC0395_0514
    ... ... ctxA zot ace VC0395_0509 cep rstB2 rstA1 VC0395_0505 VC0395_0513 VC0395_0514
    502 21169492
    NC_009457.1 Q9KSX6 other GCGTTAAAAT -[380910:380919] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) tcpA (VC0395_A0353) , tcpH (VC0395_A0352) , tcpP (VC0395_A0351) , tcpB (VC0395_A0354) , tcpQ (VC0395_A0355) , tcpC (VC0395_A0356) , tcpR (VC0395_A0357) , tcpD (VC0395_A0358) , tcpS (VC0395_A0359) , tcpT (VC0395_A0360) , tcpE (VC0395_A0361) , tcpF (VC0395_A0362)
    ... ... tcpA tcpH tcpP tcpB tcpQ tcpC tcpR tcpD tcpS tcpT tcpE tcpF
    503 21169492
    NC_009457.1 Q9KSX6 other GCATTAAATT +[380929:380938] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) tcpA (VC0395_A0353) , tcpH (VC0395_A0352) , tcpP (VC0395_A0351) , tcpB (VC0395_A0354) , tcpQ (VC0395_A0355) , tcpC (VC0395_A0356) , tcpR (VC0395_A0357) , tcpD (VC0395_A0358) , tcpS (VC0395_A0359) , tcpT (VC0395_A0360) , tcpE (VC0395_A0361) , tcpF (VC0395_A0362)
    ... ... tcpA tcpH tcpP tcpB tcpQ tcpC tcpR tcpD tcpS tcpT tcpE tcpF
    503 21169492
    NC_009457.1 Q9KSX6 other TGAATAAGTT +[380957:380966] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) tcpA (VC0395_A0353) , tcpH (VC0395_A0352) , tcpP (VC0395_A0351) , tcpB (VC0395_A0354) , tcpQ (VC0395_A0355) , tcpC (VC0395_A0356) , tcpR (VC0395_A0357) , tcpD (VC0395_A0358) , tcpS (VC0395_A0359) , tcpT (VC0395_A0360) , tcpE (VC0395_A0361) , tcpF (VC0395_A0362)
    ... ... tcpA tcpH tcpP tcpB tcpQ tcpC tcpR tcpD tcpS tcpT tcpE tcpF
    503 21169492
    NC_009457.1 Q9KSX6 other TCTGTCAATT +[381072:381081] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) tcpA (VC0395_A0353) , tcpH (VC0395_A0352) , tcpP (VC0395_A0351) , tcpB (VC0395_A0354) , tcpQ (VC0395_A0355) , tcpC (VC0395_A0356) , tcpR (VC0395_A0357) , tcpD (VC0395_A0358) , tcpS (VC0395_A0359) , tcpT (VC0395_A0360) , tcpE (VC0395_A0361) , tcpF (VC0395_A0362)
    ... ... tcpA tcpH tcpP tcpB tcpQ tcpC tcpR tcpD tcpS tcpT tcpE tcpF
    503 21169492
    NC_009457.1 Q9KSX6 other TACATAAATA +[381178:381187] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) tcpA (VC0395_A0353) , tcpH (VC0395_A0352) , tcpP (VC0395_A0351) , tcpB (VC0395_A0354) , tcpQ (VC0395_A0355) , tcpC (VC0395_A0356) , tcpR (VC0395_A0357) , tcpD (VC0395_A0358) , tcpS (VC0395_A0359) , tcpT (VC0395_A0360) , tcpE (VC0395_A0361) , tcpF (VC0395_A0362)
    ... ... tcpA tcpH tcpP tcpB tcpQ tcpC tcpR tcpD tcpS tcpT tcpE tcpF
    503 21169492

    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.

    TCGATACCTT
    TCGGTAAACC
    CCGATAAAAA
    TTGATCAATT
    ATGATAAGTT
    GCGTTAAAAT
    GCATTAAATT
    TGAATAAGTT
    TCTGTCAATT
    TACATAAATA

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

    TCGATACCTT
    TCGGTAAACC
    CCGATAAAAA
    TTGATCAATT
    ATGATAAGTT
    GCGTTAAAAT
    GCATTAAATT
    TGAATAAGTT
    TCTGTCAATT
    TACATAAATA
    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.