RhpR - UniProtKB: Q883X4 regulon and binding site collection of Pseudomonas syringae pv. tomato str. DC3000


Sites are listed as curated.

GTATCCGTATCGATAC
GTATCAACCTGGGTAC
GTATCGCGCCGCTTAC
GTATCGCCGCTGCTAC
GTATCACCCCGGACAC
GTAACACAGACGATAC

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

GTATCCGTATCGATAC
GTACCCAGGTTGATAC
GTAAGCGGCGCGATAC
GTAGCAGCGGCGATAC
GTGTCCGGGGTGATAC
GTAACACAGACGATAC

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.

Site sequence Experimental techniques Gene regulation Curations PMIDs
GTATCCGTATCGATAC Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details Northern blot (ECO:0005653) - Experimental technique details Site directed mutagenesis (ECO:0005667) - Experimental technique details Visual sequence inspection (nan) PSPTO_2223 , PSPTO_2222 , PSPTO_2224
... ... PSPTO_2223 PSPTO_2222 PSPTO_2224
642 20521955
GTATCAACCTGGGTAC Experimental technique details ChIP-PCR (ECO:0005620) - Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details Northern blot (ECO:0005653) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) PSPTO_2767
... ... PSPTO_2767
642 20521955
GTATCGCGCCGCTTAC Experimental technique details ChIP-PCR (ECO:0005620) - Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details Northern blot (ECO:0005653) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) PSPTO_2036 , folE-2 (PSPTO_2035) , PSPTO_2034
... ... PSPTO_2036 folE-2 PSPTO_2034
642 20521955
GTATCGCCGCTGCTAC Experimental technique details ChIP-PCR (ECO:0005620) - Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details Northern blot (ECO:0005653) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) PSPTO_3477 , PSPTO_3478
... ... PSPTO_3477 PSPTO_3478
642 20521955
GTATCACCCCGGACAC Experimental technique details ChIP-PCR (ECO:0005620) - Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details Northern blot (ECO:0005653) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) PSPTO_0536 , tRNA-Met-1 (PSPTO_t02) , PSPTO_0535
... ... PSPTO_0536 tRNA-Met-1 PSPTO_0535
642 20521955
GTAACACAGACGATAC Experimental technique details ChIP-PCR (ECO:0005620) - Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details Northern blot (ECO:0005653) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) PSPTO_0897 , PSPTO_0898
... ... PSPTO_0897 PSPTO_0898
642 20521955

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.

GTATCCGTATCGATAC
GTATCAACCTGGGTAC
GTATCGCGCCGCTTAC
GTATCGCCGCTGCTAC
GTATCACCCCGGACAC
GTAACACAGACGATAC

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

GTATCCGTATCGATAC
GTACCCAGGTTGATAC
GTAAGCGGCGCGATAC
GTAGCAGCGGCGATAC
GTGTCCGGGGTGATAC
GTAACACAGACGATAC
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.