OmpR - UniProtKB: Q7CFX0 regulon and binding site collection of Yersinia pestis biovar Microtus str. 91001


Sites are listed as curated.

AAAACATTTTATTACATTTA
AAAACATTTTATTACATTTA
ATAAATACTTGTTGCAATTT
TTTACATTTTGTAACACATA
TTTAAATGTTGTAACAATTT
TTAACACTTAAATTCATTTT
CATACTCTGCGTAACATTTT
AGCACAGTTTATTACATCTC
GATCAGTTTTGTAACATTTG
GATCAGTTTTGTAACATTTG
TTTACCCATGATTTCATCTT
TGTACTCAACGTATCATCTA
AATAAGCTTTGTAACAATTT
GAAATTCTTTGTTACATGAA

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

AAAACATTTTATTACATTTA
AAAACATTTTATTACATTTA
ATAAATACTTGTTGCAATTT
TTTACATTTTGTAACACATA
TTTAAATGTTGTAACAATTT
TTAACACTTAAATTCATTTT
CATACTCTGCGTAACATTTT
AGCACAGTTTATTACATCTC
GATCAGTTTTGTAACATTTG
GATCAGTTTTGTAACATTTG
TTTACCCATGATTTCATCTT
TGTACTCAACGTATCATCTA
AATAAGCTTTGTAACAATTT
GAAATTCTTTGTTACATGAA

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_005810.1 Q7CFX0 not specified AAAACATTTTATTACATTTA +[3259503:3259522] Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) YP_2927 , bglX2 (YP_2934) , YP_2933 , malG5 (YP_2932) , malF5 (YP_2931) , ugpB4 (YP_2930) , purR10 (YP_2929) , YP_2928 , yapF (YP_2924) , YP_2925 , YP_2926
    ... ... YP_2927 bglX2 YP_2933 malG5 malF5 ugpB4 purR10 YP_2928 yapF YP_2925 YP_2926
    971 21345178
    NC_005810.1 Q7CFX0 not specified AAAACATTTTATTACATTTA +[3259503:3259522] Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) YP_2926 , bglX2 (YP_2934) , YP_2933 , malG5 (YP_2932) , malF5 (YP_2931) , ugpB4 (YP_2930) , purR10 (YP_2929) , YP_2928 , YP_2927 , yapF (YP_2924) , YP_2925
    ... ... YP_2926 bglX2 YP_2933 malG5 malF5 ugpB4 purR10 YP_2928 YP_2927 yapF YP_2925
    971 21345178
    NC_005810.1 Q7CFX0 not specified ATAAATACTTGTTGCAATTT -[980677:980696] Experimental technique details Beta-gal reporter assay - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) ompC1 (YP_0916)
    ... ... ompC1
    971 21345178
    NC_005810.1 Q7CFX0 not specified TTTACATTTTGTAACACATA +[1275636:1275655] Experimental technique details Beta-gal reporter assay - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) ompC2 (YP_1182)
    ... ... ompC2
    971 21345178
    NC_005810.1 Q7CFX0 not specified TTTAAATGTTGTAACAATTT +[1956987:1957006] Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) phoP (YP_1764) , phoQ (YP_1763) , YP_1762
    ... ... phoP phoQ YP_1762
    971 21345178
    NC_005810.1 Q7CFX0 not specified TTAACACTTAAATTCATTTT +[2015863:2015882] Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) ampD3 (YP_1812)
    ... ... ampD3
    971 21345178
    NC_005810.1 Q7CFX0 not specified CATACTCTGCGTAACATTTT +[2947521:2947540] Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) sfcA2 (YP_2657)
    ... ... sfcA2
    971 21345178
    NC_005810.1 Q7CFX0 not specified AGCACAGTTTATTACATCTC -[611334:611353] Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) rplU (YP_0571) , ispB (YP_0570) , rpmA (YP_0572) , rhaT3 (YP_0573) , obgE (YP_0574)
    ... ... rplU ispB rpmA rhaT3 obgE
    971 21345178
    NC_005810.1 Q7CFX0 not specified GATCAGTTTTGTAACATTTG +[3402375:3402394] Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) hcp7 (YP_3069) , YP_3068 , YP_3067 , YP_3066 , YP_3065
    ... ... hcp7 YP_3068 YP_3067 YP_3066 YP_3065
    971 21345178
    NC_005810.1 Q7CFX0 not specified GATCAGTTTTGTAACATTTG +[3402375:3402394] Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) YP_3068 , YP_3067 , YP_3066 , YP_3065 , hcp7 (YP_3069)
    ... ... YP_3068 YP_3067 YP_3066 YP_3065 hcp7
    971 21345178
    NC_005810.1 Q7CFX0 not specified TTTACCCATGATTTCATCTT -[3791961:3791980] Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) cysM2 (YP_3381) , hutU (YP_3380) , hutH (YP_3379) , apt2 (YP_3382) , rhaT14 (YP_3383) , accC1 (YP_3384)
    ... ... cysM2 hutU hutH apt2 rhaT14 accC1
    971 21345178
    NC_005810.1 Q7CFX0 not specified TGTACTCAACGTATCATCTA -[3793502:3793521] Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) apt2 (YP_3382) , rhaT14 (YP_3383) , accC1 (YP_3384)
    ... ... apt2 rhaT14 accC1
    971 21345178
    NC_005810.1 Q7CFX0 not specified AATAAGCTTTGTAACAATTT +[149307:149326] Experimental technique details Beta-gal reporter assay - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details PSSM site search (ECO:0005659) ompR (YP_0137) , envZ (YP_0138)
    ... ... ompR envZ
    971 21345178
    NC_005810.1 Q7CFX0 not specified GAAATTCTTTGTTACATGAA -[2583293:2583312] Experimental technique details Beta-gal reporter assay - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) ompX (YP_2321) , rhaT11 (YP_2322) , rimI1 (YP_2323) , tam (YP_2324)
    ... ... ompX rhaT11 rimI1 tam
    971 21345178

    OmpR - UniProtKB: Q7CFX0 regulon and binding site collection of Yersinia pseudotuberculosis YPIII


    Sites are listed as curated.

    TTACTTTTTAAATTTT
    CTAACATTTTGTAAGAAAT

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

    TTTACTTTTTAAATTTTTA
    ATTTCTTACAAAATGTTAG

    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_010465.1 Q7CFX0 monomer TTACTTTTTAAATTTT +[1936372:1936387] Experimental technique details Beta-gal reporter assay - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Site directed mutagenesis (ECO:0005667) YPK_1745 , YPK_1746 , YPK_1744
      ... ... YPK_1745 YPK_1746 YPK_1744
      28 19643764
      NC_010465.1 Q7CFX0 monomer CTAACATTTTGTAAGAAAT +[1936550:1936568] Experimental technique details Beta-gal reporter assay - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Site directed mutagenesis (ECO:0005667) YPK_1745 , YPK_1746 , YPK_1744
      ... ... YPK_1745 YPK_1746 YPK_1744
      29 19643764

      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.

      TTACTTTTTAAATTTT
      CTAACATTTTGTAAGAAAT
      AAAACATTTTATTACATTTA
      AAAACATTTTATTACATTTA
      ATAAATACTTGTTGCAATTT
      TTTACATTTTGTAACACATA
      TTTAAATGTTGTAACAATTT
      TTAACACTTAAATTCATTTT
      CATACTCTGCGTAACATTTT
      AGCACAGTTTATTACATCTC
      GATCAGTTTTGTAACATTTG
      GATCAGTTTTGTAACATTTG
      TTTACCCATGATTTCATCTT
      TGTACTCAACGTATCATCTA
      AATAAGCTTTGTAACAATTT
      GAAATTCTTTGTTACATGAA

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

      TTTTACTTTTTAAATTTTTA
      TATTTCTTACAAAATGTTAG
      TAAATGTAATAAAATGTTTT
      TAAATGTAATAAAATGTTTT
      AAATTGCAACAAGTATTTAT
      TATGTGTTACAAAATGTAAA
      AAATTGTTACAACATTTAAA
      AAAATGAATTTAAGTGTTAA
      AAAATGTTACGCAGAGTATG
      GAGATGTAATAAACTGTGCT
      CAAATGTTACAAAACTGATC
      CAAATGTTACAAAACTGATC
      AAGATGAAATCATGGGTAAA
      TAGATGATACGTTGAGTACA
      AAATTGTTACAAAGCTTATT
      TTCATGTAACAAAGAATTTC
      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.