RutR - UniProtKB: P0ACU2 regulon and binding site collection of Escherichia coli str. K-12 substr. MG1655


Sites are listed as curated.

ATCGCCATCAGGTTGG
ATGACAAATTCGACAA
ATGACCATGATTTCGT
ATGACCATTGCGCCAG
CACACCAGTTGGTCAA
CCAACCATTCGGTCAA
CTGACCAATCGGTCAC
TAGACCGACTGGTCTA
TGGACCAAACAGTCTG
TGGACTAAACGGTCAA
TTAACTGTCTGGTCGG
TTGACCACACGGTCCA
TTGACCAGCCATTCCA
TTGACCATACGGTAAA
TTGACCATTTGGTCCA
TTGACTACCTGGTCAA
TTGACTGGCTGGTCAG
TTTACCATCTGGTCAT
TTTACCACCTGGTCCG

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

ATCGCCATCAGGTTGG
ATGACAAATTCGACAA
ATGACCATGATTTCGT
ATGACCATTGCGCCAG
CACACCAGTTGGTCAA
TTGACCGAATGGTTGG
CTGACCAATCGGTCAC
TAGACCAGTCGGTCTA
CAGACTGTTTGGTCCA
TTGACCGTTTAGTCCA
TTAACTGTCTGGTCGG
TTGACCACACGGTCCA
TTGACCAGCCATTCCA
TTGACCATACGGTAAA
TTGACCATTTGGTCCA
TTGACTACCTGGTCAA
TTGACTGGCTGGTCAG
ATGACCAGATGGTAAA
TTTACCACCTGGTCCG

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_000913.2 P0ACU2 dimer ATCGCCATCAGGTTGG +[2510537:2510552] Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) mntH (b2392) , ypeC (b2390) , nupC (b2393)
    ... ... mntH ypeC nupC
    102 18515344
    NC_000913.2 P0ACU2 dimer ATGACAAATTCGACAA +[623770:623785] Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) fepB (b0592) , entS (b0591) , entC (b0593) , entE (b0594) , entB (b0595) , entA (b0596) , entH (b0597)
    ... ... fepB entS entC entE entB entA entH
    102 18515344
    NC_000913.2 P0ACU2 dimer ATGACCATGATTTCGT +[3578820:3578835] Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) yhhX (b3440) , yhhW (b3439) , ryhB (b4451)
    ... ... yhhX yhhW ryhB
    102 18515344
    NC_000913.2 P0ACU2 dimer ATGACCATTGCGCCAG +[4603502:4603517] Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) fhuF (b4367) , bglJ (b4366) , yjjQ (b4365) , yjjZ (b4567) , leuV (b4368) , leuP (b4369) , leuQ (b4370)
    ... ... fhuF bglJ yjjQ yjjZ leuV leuP leuQ
    102 18515344
    NC_000913.2 P0ACU2 dimer CACACCAGTTGGTCAA +[139549:139564] Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) gcd (b0124) , cueO (b0123) , hpt (b0125) , can (b0126)
    ... ... gcd cueO hpt can
    102 18515344
    NC_000913.2 P0ACU2 dimer CCAACCATTCGGTCAA +[3198035:3198050] Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) ygiF (b3054) , glnE (b3053) , rfaE (b3052) , ygiM (b3055)
    ... ... ygiF glnE rfaE ygiM
    102 18515344
    NC_000913.2 P0ACU2 dimer CTGACCAATCGGTCAC +[1272883:1272898] Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) ychN (b1219) , chaC (b1218) , ychO (b1220) , narL (b1221) , narX (b1222)
    ... ... ychN chaC ychO narL narX
    102 18515344
    NC_000913.2 P0ACU2 dimer TAGACCGACTGGTCTA +[1724016:1724031] Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) ydhL (b1648) , ydhF (b1647) , nemR (b1649) , nemA (b1650)
    ... ... ydhL ydhF nemR nemA
    102 18515344
    NC_000913.2 P0ACU2 dimer TGGACCAAACAGTCTG +[2718339:2718354] Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) yfiQ (b2584) , yfiP (b2583) , pssA (b2585) , yfiM (b2586) , kgtP (b2587)
    ... ... yfiQ yfiP pssA yfiM kgtP
    102 18515344
    NC_000913.2 P0ACU2 dimer TGGACTAAACGGTCAA +[1073342:1073357] Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) rutA (b1012) , rutB (b1011) , rutC (b1010) , rutD (b1009) , rutE (b1008) , rutF (b1007) , rutG (b1006) , rutR (b1013) , putA (b1014)
    ... ... rutA rutB rutC rutD rutE rutF rutG rutR putA
    102 18515344
    NC_000913.2 P0ACU2 dimer TTAACTGTCTGGTCGG +[535237:535252] Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) hyi (b0508) , gcl (b0507) , glxR (b0509)
    ... ... hyi gcl glxR
    102 18515344
    NC_000913.2 P0ACU2 dimer TTGACCACACGGTCCA +[1015568:1015583] Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) fabA (b0954) , rmf (b0953) , ycbZ (b0955)
    ... ... fabA rmf ycbZ
    102 18515344
    NC_000913.2 P0ACU2 dimer TTGACCAGCCATTCCA +[2371543:2371558] Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) pmrD (b2259) , arnF (b2258) , arnE (b4544) , arnT (b2257) , arnD (b2256) , arnA (b2255) , arnC (b2254) , arnB (b2253) , menE (b2260) , menC (b2261) , menB (b2262) , menH (b2263) , menD (b2264)
    ... ... pmrD arnF arnE arnT arnD arnA arnC arnB menE menC menB menH menD
    102 18515344
    NC_000913.2 P0ACU2 dimer TTGACCATACGGTAAA +[4419509:4419524] Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) ulaB (b4194) , ulaA (b4193) , ulaC (b4195) , ulaD (b4196) , ulaE (b4197) , ulaF (b4198)
    ... ... ulaB ulaA ulaC ulaD ulaE ulaF
    102 18515344
    NC_000913.2 P0ACU2 dimer TTGACCATTTGGTCCA +[29358:29373] Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) dapB (b0031) , carA (b0032) , carB (b0033)
    ... ... dapB carA carB
    102 18515344
    NC_000913.2 P0ACU2 dimer TTGACTACCTGGTCAA +[3211864:3211879] Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) rpoD (b3067) , dnaG (b3066) , mug (b3068)
    ... ... rpoD dnaG mug
    102 18515344
    NC_000913.2 P0ACU2 dimer TTGACTGGCTGGTCAG +[3994559:3994574] Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) xerC (b3811) , yigA (b3810) , dapF (b3809) , yifL (b4558) , yigB (b3812)
    ... ... xerC yigA dapF yifL yigB
    102 18515344
    NC_000913.2 P0ACU2 dimer TTTACCATCTGGTCAT +[3221531:3221546] Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) ebgA (b3076) , ebgR (b3075) , ebgC (b3077)
    ... ... ebgA ebgR ebgC
    102 18515344
    NC_000913.2 P0ACU2 dimer TTTACCACCTGGTCCG +[1822680:1822695] Experimental technique details ChIP-chip (ECO:0006007) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Northern blot (ECO:0005653) ves (b1742) , cho (b1741) , spy (b1743)
    ... ... ves cho spy
    103 18515344

    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.

    ATCGCCATCAGGTTGG
    ATGACAAATTCGACAA
    ATGACCATGATTTCGT
    ATGACCATTGCGCCAG
    CACACCAGTTGGTCAA
    CCAACCATTCGGTCAA
    CTGACCAATCGGTCAC
    TAGACCGACTGGTCTA
    TGGACCAAACAGTCTG
    TGGACTAAACGGTCAA
    TTAACTGTCTGGTCGG
    TTGACCACACGGTCCA
    TTGACCAGCCATTCCA
    TTGACCATACGGTAAA
    TTGACCATTTGGTCCA
    TTGACTACCTGGTCAA
    TTGACTGGCTGGTCAG
    TTTACCATCTGGTCAT
    TTTACCACCTGGTCCG

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

    ATCGCCATCAGGTTGG
    ATGACAAATTCGACAA
    ATGACCATGATTTCGT
    ATGACCATTGCGCCAG
    CACACCAGTTGGTCAA
    TTGACCGAATGGTTGG
    CTGACCAATCGGTCAC
    TAGACCAGTCGGTCTA
    CAGACTGTTTGGTCCA
    TTGACCGTTTAGTCCA
    TTAACTGTCTGGTCGG
    TTGACCACACGGTCCA
    TTGACCAGCCATTCCA
    TTGACCATACGGTAAA
    TTGACCATTTGGTCCA
    TTGACTACCTGGTCAA
    TTGACTGGCTGGTCAG
    ATGACCAGATGGTAAA
    TTTACCACCTGGTCCG
    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.