Abbreviation of experimental techniques

Input sequence : format

Please input only nucleotide sequences or Fasta format.
Ex.1)ATATGTGAT... or atgatccgt...
Ex.2)>Gene name..
ATGCCGTGAAATCGTCGATCG...

Binding factor

We use the same mean with transcription factor.

Regulated gene

If transcription factor regulates the operon, we described the first gene of the operon. We also have some operon information.

Sigma factor

In cace the references mentioned sigma factors, we described them.

Regulation

We described how transcrioption factors regulate the genes.
i.e. positive regulation (up regulation) / negative regulation (down regulation) / both / unknown

Absolute position

We recalculated the absolute position of each cis-element using NC_000964 sequence file.
ND : No Data.

Location

Location is counted from the transcription start site. Usually we show the reference data.

Binding sequence (cis-element)

We show not only cis-element but also nearby sequences.
Red characters or characters between braces [ex. {AGTC}] correspond to the exact binding sequence.
Bold face shows the transcription start site.

Abbreviations of Experimental Techniques Used

Abbrev.	Description
DB	Disruption of Binding Factor gene
DP	Deletion assay
FT	Footprinting assay (DNase I, DMS, etc.)
GS	Gel retardation assay
HB	Slot blot analysis
HM	Homology search
PE	Primer extension analysis
RO	Run-off transcription assay
S1	S1 mapping analysis (S1 nuclease transcript mapping)
SDM	Site-directed mutagenesis (Oligonucleotide-directed mutagenesis)
AR	DNA microarray and macroarray
ROMA	Run-off transcription followed by macroarray analysis
ND	No Data

Marks

mark	meaning
	It doesn't have orthologous gene.
	It has orthologous gene.
	It has orthologous gene and cis-element like sequence at the promoter region.

phylum	color	No. of species
Actinobacteria		4
Chlamydiae		2
Cyanobacteria		2
Firmicutes		12
Proteobacteria		24
Spirochaetes		2
othres		4
TOTAL		50

Go go Taxonomy

Phylogenetic profile

PHYLOGENETIC CONSERVATION STUDY
We've tried to display the results of an analysis into a systematic survey of the conservation of known cis-elements, as well as their binding factors, through available eubacterial genome sequences. To do this, we used the orthology information of the COG database and applied the above-mentioned weight matrices/consensus patterns to the upstream sequence of orthologous genes.