SITECON¶
SITECON — is a program package for recognition of potential transcription factor binding sites basing on the data about conservative conformational and physicochemical properties revealed on the basis of the binding sites sets analysis.
To cite SITECON use the following article:
“Oshchepkov D.Y., Vityaev E.E., Grigorovich D.A., Ignatieva E.V., Khlebodarova T.M.SITECON: a tool for detecting conservative conformational and physicochemical properties in transcription factor binding site alignments and for siterecognition. //Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W208-12.”
UGENE version of SITECON provides a tool for recognition of potential binding sites for over 90 types of transcription factors. Also UGENE version of SITECON provides a tool for recognition of potential binding sites basing site alignment proposed by user. For the detailed method description see the original SITECON site.
Data about used context-dependent conformational and physicochemical properties are available in the PROPERTY Database.
SITECON Searching Transcription Factors Binding Sites¶
To search transcription factor binding sites in a DNA sequence select the Analyze ‣ Search TFBS with SITECON... context menu item.
In the appeared search dialog you must select a file with TFBS profile. The profiles supplied with UGENE are placed in the $UGENE/data/sitecon_models folder.
After the profile is loaded the threshold-filter is populated with values read from profile. You can use the filter to remove low-scoring regions from the result.
The regions found by SITECON algorithm can be saved as annotations to the DNA sequence in the Genbank format.
Every SITECON profile supplied with UGENE contains complete information about calibration settings provided to UGENE team by the author of SITECON.
The original TFBS alignments used to calculate profiles can be requested directly from the author of SITECON.
Types of SITECON Models¶
Eukaryotic¶
| Name | Description |
|---|---|
| CEBP_a | CCAAT-enhancer-binding protein_alpha |
| CEBP_all | CCAAT-enhancer-binding proteins |
| CLOCK | Circadian Locomotor Output Cycles Kaput |
| cMyc_can | Myc (c-Myc) is a regulator gene that codes for a transcription factor. A mutated version of Myc is found in many cancers. |
| CRE | Cyclic AMP response element |
| E2F1 | Transcription factor E2F1 is a protein that in humans is encoded by the E2F1 gene. |
| E2F1/DP1sel1 | E2F factors bind to DNA as homodimers or heterodimers in association with dimerization partner DP1. |
| EGR1 | Early growth response protein 1 |
| EKLf | Erythroid Kruppel-like Factor |
| ER2 | Estrogen receptor beta |
| GATA_all | GATA transcription factors are a family of transcription factors characterized by their ability to bind to the DNA sequence “GATA” |
| GATA-1 | GATA-binding factor 1 |
| GATA-2 | GATA-binding protein 2 |
| GATA-3 | Trans-acting T-cell-specific transcription factor GATA-3 |
| HMG-1 | High-mobility group protein 1 |
| HNF-1 | Hepatocyte nuclear factor 1 |
| HNF-3 | Hepatocyte nuclear factor 3 |
| HNF-4 | Hepatocyte nuclear factor 4 |
| IRF | Interferon regulatory factors |
| isre | Interferon stimulation response element |
| MyoD | MyoD belongs to a family of proteins known as myogenic regulatory factors (MRFs) |
| MyOGsel3 | Myogenin |
| NF-1 | Neurofibromin 1 |
| NF-E2 | Transcription factor NF-E2 45 kDa subunit is a protein that in humans is encoded by the NFE2 gene. |
| NFATp | Pre-existing component of the NFAT(Nuclear factor of activated T-cells) transcription complex. |
| NFkB_all | Nuclear factor kappa-light-chain-enhancer of activated B cells |
| NFkB_hetero | The p50 (NFKB1)/p65 (RELA) heterodimer is the most abundant form of NF-kB |
| NFkB_ homo | The c-Rel protein is a member of the NF-kB family of transcription factors and contains a Rel homology domain |
| Nfy | Nuclear transcription factor Y |
| Nrf2 | Nuclear factor (erythroid-derived 2)-like 2 |
| Oct-1 | Octamer transcription factor 1 |
| Oct_all | Octamer transcription factors |
| p53 | Protein 53 |
| PPRF | Paramedian pontine reticular formation |
| Pu1 | Is a protein that in humans is encoded by the SPI1 gene |
| setCREB | cAMP response element-binding |
| setCREBzag | cAMP response element-binding |
| SRE_san | Serum response element |
| SRF | Serum response factor |
| STAT1 | Signal Transducer and Activator of Transcription 1 |
| STAT | Signal Transducer and Activator of Transcription |
| TTF1 | Thyroid transcription factor 1 |
| USF | Upstream stimulatory factors |
| yy1 | Is a protein that in humans is encoded by the YY1 gene |
Prokaryotic¶
| Name | Description |
|---|---|
| AgaR | N-acetylgalactosamine repressor, AgaR, negatively controls the expression of the aga gene cluster |
| AgaC | AgaC is the Enzyme IIC domain of a predicted N-acetylgalactosamine-transporting PEP-dependent phosphotransferase system |
| ArcA | ArcA transcriptional dual regulator |
| ArgR | ArgR complexed with L-arginine represses the transcription of several genes involved in biosynthesis and transport of arginine, transport of histidine, and its own synthesis and activates genes for arginine catabolism. |
| CpxR | DNA-binding response regulator in two-component regulatory system with CpxA |
| Crp | cAMP receptor protein |
| CysB | Cysteine B |
| CytR | Cytidine Regulator |
| DeoR | Deoxyribose Regulator |
| DnaA | DnaA is the linchpin element in the initiation of DNA replication in E. coli. |
| FadR | Fatty acid degradation Regulon |
| fis | Factor for inversion stimulation |
| FlhDC | Operon that encodes two transcriptional regulators |
| Fnr | FNR is the primary transcriptional regulator that mediates the transition from aerobic to anaerobic growth through the regulation of hundreds of genes. |
| Frur | Fructose repressor |
| FUR | Ferric Uptake Regulation |
| GALR | Galactose repressor |
| GALS | Galactose isorepressor |
| GLPR | sn-Glycerol-3-phosphate repressor |
| GNTP | Is a member of the GntP family transporters |
| HNS | Histone-like nucleoid structuring protein |
| ICLR | Isocitrate lyase Regulator |
| IHF | Integration host factor |
| ISCR1 | Iron-sulfur cluster Regulator 1 |
| ISCR3 | Iron-sulfur cluster Regulator 3 |
| LEXA | LexA represses the transcription of several genes involved in the cellular response to DNA damage or inhibition of DNA replication |
| Lrp | Leucine-responsive regulatory protein |
| MALT | Maltose regulator |
| MARA | Multiple antibiotic resistance |
| MELR | Melibiose regulator |
| MEtJ | MetJ represses the expression of genes involved in biosynthesis and transport of methionine |
| MetR1 | MetR participates in controlling several genes involved in methionine biosynthesis [ Weissbach91 ] and a gene involved in protection against nitric oxide |
| MLC | DgsA, better known as Mlc, “makes large colonies,” is a transcriptional dual regulator that controls the expression of a number of genes encoding enzymes of the Escherichia coli phosphotransferase (PTS) and phosphoenolpyruvate (PEP) systems |
| MODE | Molybdate-responsive transcription factor |
| NAC | Nitrogen assimilation control |
| NAGC_new2 | N-acetylglucosamine |
| NANR | N-acetyl-neuraminic acid regulator |
| NARL2 | Nitrate/nitrite response regulator NarL |
| NARL | Nitrate/nitrite response regulator NarL |
| NARP | Nitrate/nitrite response regulator NarP |
| NIRC | NirC is a nitrite transporter which is a member of the FNT family of formate and nitrite transporters |
| OmpC | OmpC is a member of the GMP family |
| OxyR | Oxidative stress regulator |
| PHOB | PhoB is a dual transcription regulator that activates expression of the Pho regulon in response to environmental Pi |
| PHOP | Member of the two-component regulatory system phoQ/phoP involved in adaptation to low Mg2+ environments and the control of acid resistance genes |
| PurR | PurR dimer controls several genes involved in purine nucleotide biosynthesis and its own synthesis |
| RcsB_1 | Regulator capsule synthesis B |
| RcsB_2 | Regulator capsule synthesis B |
| Rob2 | Right origin-binding protein |
| ROB | Right origin-binding protein |
| soxS | SoxS is a dual transcriptional activator and participates in the removal of superoxide and nitric oxide and protection from organic solvents and antibiotics |
| TORR | TorR response regulator |
| TRPR | Tryptophan (trp) transcriptional repressor |
| TyrR | Tyrosine repressor |