CcpA regulon and binding site collection in Streptococcus lutetiensis 033

CcpA - UniProtKB: S5RJF3 regulon and binding site collection of Streptococcus lutetiensis 033

Sites are listed as curated.

TGAAAGCGATTTATC

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

TGAAAGCGATTTATC

Motif structure	Inverted repeat
GC-content	33.33%
Regulatory mode	Activation	Repression	Dual	Not specified
Regulatory mode	100%	0%	0%	0%
TF conformation	Monomer	Dimer	Tetramer	Other	Not specified
TF conformation	0%	0%	0%	0%	100%
Binding site type	Motif-associated	Variable-motif-associated	Non-motif-associated
Binding site type	1	0	0

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_021900.1	S5RJF3	not specified	TGAAAGCGATTTATC	+[776749:776763]	Experimental technique details qRT-PCR [RNA] (ECO:0001808) qRT-PCR [RNA] - ECO:0001808 Quantitative Reverse-Transcription PCR is a modification of PCR in which RNA is first reverse transcribed into cDNA and this is amplified measuring the product (qPCR) in real time. It therefore allows one to analyze transcription by directly measuring the product (RNA) of a gene's transcription. If the gene is transcribed more, the starting product for PCR is larger and the corresponding volume of amplification is also larger. - Experimental technique details Visual sequence inspection (nan) Visual sequence inspection - nan Visual inspection of promoter region to identify putative binding sites based on previous knowledge	KE3_0819 , KE3_0820 , KE3_0818 , KE3_0817 , KE3_0816 , KE3_0815	875	18565772

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.

TGAAAGCGATTTATC

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

TGAAAGCGATTTATC

To generate the weblogo, aligned binding sites are used.

	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.