This application incorporates by reference co-pending provisional application Ser. No. 60/388,315 filed Jun. 14, 2002, Ser. No. 60/361,073 filed Mar. 1, 2002, and Ser. No. 60/346,898 filed Jan. 11, 2002.
FIELD OF THE INVENTION The invention relates to the field of assays for the detection of factors that modulate gene expression. Specifically, the invention relates to reporter constructs and methods for identifying agents that modulate the expression of the INGAP gene.
BACKGROUND OF THE INVENTION Islet neogenesis gene associated protein (INGAP protein) has been identified as a pancreatic acinar cell protein that can induce islet cell neogenesis from progenitor cells resident in the pancreas in a manner that recapitulates islet development during normal embryogenesis. INGAP is unique in its ability to stimulate growth and differentiation of islets of Langerhans from precursor cells associated with pancreas. These islets evolve a mature insulin secretory profile capable of responding to perturbations in blood glucose in a physiologic manner. This potential anti-diabetic therapeutic has been shown to demonstrate homology across several species and to exert a biological response.
Pancreatic islet cell mass is lost in type 1 diabetes mellitus, a disease in which a progressive autoimmune reaction results in the selective destruction of insulin-producing β-cells. In type 2 diabetes mellitus, so-called adult-onset disease, but also increasingly a condition in young overweight people, the β-cell mass may be reduced by as much as 60% of normal. The number of functioning β-cells in the pancreas is of critical significance for the development, course, and outcome of diabetes. In type I diabetes, there is a reduction of β-cell mass to less than 2% of normal. Even in the face of severe insulin resistance as occurs in type II diabetes, the development of diabetes only occurs if there is inadequate compensatory increase in β-cell mass. Thus, the development of either of the major forms of diabetes can be regarded as a failure of adaptive β-cell growth and a subsequent deficiency in insulin secretion. Stimulating the growth of islets and β-cells from precursor cells, known as islet neogenesis, is an attractive approach to the amelioration of diabetes. There is need in the art for methods to identify agents that can modulate the expression of INGAP, whether in animals or in cultured cells.
BRIEF SUMMARY OF THE INVENTION It is an object of the invention to provide a reporter construct containing the 5′-regulatory region from mammalian INGAP gene.
It is another object of the invention to provide methods for identifying agents which modulate INGAP expression.
It is another object of the invention to provide a nucleic acid or fragment of INGAP 5′-regulatory region.
It is another object of the invention to provide methods for increasing INGAP expression.
It is another object of the invention to provide a kit for modulating INGAP expression.
These and other objects of the invention are provided by one or more of the embodiments described below.
In one aspect of the invention a reporter construct is provided. The reporter construct comprises a regulatory region nucleotide sequence and a nucleotide sequence encoding a detectable product. In one aspect of the invention, the reporter construct is provided in a vector. The regulatory region nucleotide sequence is linked to the nucleotide sequence encoding a detectable product. The regulatory region nucleotide sequence may comprise one or more fragments of 5′ regulatory region of the INGAP genomic sequence, SEQ ID NO: 23, or it may comprise the entire length of the 5′ regulatory region. In one embodiment of the reporter construct, a promoter element is interposed between the regulatory region nucleotide sequence and the nucleotide sequence encoding a detectable product. The promoter element may be selected from the promoter elements present in the INGAP regulatory sequence. Alternatively, the promoter element present in the vector comprising the reporter construct may be used. The detectable product encoded by the said nucleotide sequence encoding a detectable product could be either a nucleic acid or a protein. The detectable product need not be the INGAP gene nucleic acid or protein.
In another embodiment of the invention, a method identifying agents that modulate INGAP expression is provided. The method comprises contacting a cell with a test agent, wherein the cell comprises a reporter construct of the present invention. Expression of the detectable nucleic acid or protein product in the cell is determined. A test agent is identified as a modulator of INGAP expression if the test agent modulates expression of the detectable product in the cell.
In another embodiment of the invention, an isolated nucleic acid comprising the genomic sequence of the hamster INGAP gene (SEQ ID NO: 2), or a fragment thereof is provided.
According to another embodiment of the invention, an in vitro method for identifying agents that modulate INGAP expression is provided. The method comprises contacting a test agent with a reporter construct of the present invention in a cell-free system that allows for transcription and translation of a nucleotide sequence. Expression of the detectable product is determined. The substance is identified as a modulator of INGAP expression if the test substance modulates expression of the detectable product.
According to another embodiment of the invention, an in vitro method for identifying an agent that modulate INGAP expression is provided. The method comprises contacting a test agent with a nucleic acid of the invention. Binding of the test agent to the nucleic acid is determined. The test agent is identified as a modulator of INGAP expression if the test agent binds to the nucleic acid.
According to another embodiment of the invention a method for increasing INGAP expression is provided. An effective amount of a factor that stimulates INGAP expression directly or indirectly, for example cytokines, chemokines, growth factors, or pharmacological agents, is administered to a mammal in need of increased INGAP expression.
According to another embodiment of the invention a kit for modulating INGAP expression is provided. The kit comprises a modulator of INGAP expression and instructions for using the modulator of INGAP expression to modulate INGAP expression.
According to another embodiment of the invention a method for modulating INGAP expression in a mammal to treat a disease state related to reduced islet cell function is provided. The method comprises the step of administering to the mammal an effective amount of a modulator of INGAP expression whereby the level of INGAP expression in the mammal is modified.
All documents cited are, in relevant part, incorporated herein by reference; the citation of any document is not to be construed as an admission that it is prior art with respect to the present invention.
BRIEF DESCRIPTION OF EE DRAWINGS FIG. 1 shows the annotation of the hamster INGAP gene structure. The boundaries of introns 1-5 are listed in Table 1.
FIG. 2 shows an overview of the 5′-regulatory region of the hamster INGAP gene (nucleotides 1-3137 of SEQ ID NO: 2) showing many well known and well-characterized transcription factor binding sites. The minimal promoter element contains the regions noted with an underline (CAAT-box, TATA-box, and GC-box).
FIG. 3 shows a schematic of many well known and well-characterized transcription factor-binding sites for nucleotides 1-3123 of the 5′-regulatory region (SEQ ID NO: 1) of the hamster INGAP gene. Table 3 further describes these transcription factor-binding sites.
FIG. 4 shows the predicted transcription start sites within the 5′-regulatory region (SEQ ID NO: 1) of the hamster INGAP gene (SEQ ID NO: 2). The predicted start site is indicated by a boldface nucleotide. The start and end nucleotide numbers are indicated for the promoter sequence. The numbers refer to nucleotide numbers of the hamster INGAP gene (SEQ ID NO: 2)
FIG. 5 shows the adapter primer structure and sequence used in gene walking. Adapter primer 1 (AP1) and adapter primer 2 (AP2) are shown.
FIGS. 6 and 7 show the strategy for reconstructing the hamster INGAP gene. The hamster INGAP gene was reconstructed using the technique of gene walking. Shown are the fragments and the gene specific primers (GSP1 and GSP2) used in PCR amplification for gene walking. Fragments were joined together using unique restriction enzyme sites within each fragment. The nucleotide sequences of the individual primers are listed in Table 2.
FIG. 8 shows the fragments of INGAP 5′-regulatory region, which were cloned into pβGal-basic upstream of a β-galactosidase reporter gene. The labels on the left refer to the nucleotide fragments of SEQ ID NO: 23 which were cloned upstream of pβGal-basic.
FIG. 9A shows reporter activity in human embryonic kidney cells (293T) transfected with a reporter construct that contains various fragments of the 5′-regulatory region (SEQ ID NO: 23) of hamster INGAP DNA cloned upstream of a β-galactosidase reporter gene (pβGal-basic), or in a reporter construct which contains no INGAP DNA. The cells are stimulated with phorbol myristate acetate. Promoter activity is assessed by determining the level of β-galactosidase present in the cell using a β-galactosidase luminescent assay.
FIG. 9B shows reporter activity in human embryonic kidney cells (293T) transfected with a reporter construct that contains nucleotides 2030 to 3137 of the 5′-regulatory region (SEQ ID NO: 23) of hamster INGAP cloned upstream of a β-galactosidase reporter gene, or in a reporter construct which contains no INGAP DNA. The cells are stimulated with leukemia inhibitory factor. Promoter activity is assessed by determining the level of β-galactosidase present in the cell using a β-galactosidase luminescent assay.
FIG. 10 shows the reporter activity in human embryonic kidney cells (293T) transfected with a reporter construct that contains different fragments (see FIG. 8) of the 5′-regulatory region of hamster INGAP cloned upstream of a β-galactosidase reporter gene. The cells are stimulated with phorbol myristate acetate. Concentrations of PMA used are 6 ng/ml, 17 ng/ml, 50 ng/ml, 100 ng/ml, or 300 ng/ml. Promoter activity is assessed by determining the level of β-galactosidase present in the cell using a β-galactosidase luminescent assay.
FIG. 11 shows reporter activity in human embryonic kidney cells (293T) transfected with a reporter construct that contains different fragments (see FIG. 8) of the 5′-regulatory region of hamster INGAP cloned upstream of a β-galactosidase reporter gene. The cells are stimulated with human leukemia inhibitory factor (hLIF). Concentrations of hLIF used are 1 ng/ml, 10 ng/ml, or 30 ng/ml. Promoter activity was assessed by determining the level of β-galactosidase present in the cell using a β-galactosidase luminescent assay.
FIG. 12 shows RNA analysis for INGAP gene upregulation in rat amphicrine pancreatic cells, AR42J, treated with cytokine IL-6 or untreated. Total RNA is probed by Northern analysis for INGAP gene.
DETAILED DESCRIPTION OF THE INVENTION Definitions It must be noted that as used herein and in the appended claims, the singular forms “a”, “an”, and “the” include plural references unless the context clearly dictates otherwise.
The term “promoter” is used to define the region of a gene at which initiation and rate of transcription are controlled. It contains the site at which RNA polymerase binds and also sites for the binding of regulatory proteins, e.g. transcription factors, repressors, etc. In order to differentiate between the transcription initiation site and other sites that modulate rate of transcription, promoter region is generally subdivided into “minimal promoter element” and “regulatory region”. The term “minimal promoter element” or sometimes simply referred to as “promoter” therefore may include TATA box, GC-rich sequence and CAAT box; while “regulatory region” is usually a long stretch of nucleotide sequence where transcription factors and other factors bind. Most eukaryotic genes have long regulatory regions where many different transcription factors bind. The expression or the lack of expression of a given gene in a given cell type, tissue, organ, or an organism is governed by the interactions that take place on its regulatory region.
The term “transcription factor” is used to describe the proteins that bind short stretches of DNA in the regulatory regions of a gene. Transcription factors may interact with each other as well as RNA polymerase. Thus, transcription factors may bind hormones or second messengers, DNA, RNA, other transcription factors, or other proteins. They may activate or inhibit transcription of a given gene. Transcription factors are also sometimes referred to as “enhancers” or “repressors”. Transcription factor binding sites can be used to identify agents that bind to the 5′-regulatory region of the gene and modulate the gene's expression.
The term “reporter” is used to describe a coding sequence attached to a heterologous promoter or enhancer elements and whose product, either nucleic acid or protein, is easily detected and is quantifiable. Some common reporter genes include β-galactosidase (lacZ), chloramphenicol acetyltransferase (cat), β-glucuronidase (GUS), and green fluorescent protein (GFP).
A “reporter construct” is a piece of nucleic acid that includes a promoter element and a reporter gene housed in a suitable vector plasmid DNA. Regulatory region nucleotide sequences may be cloned 5′ of the promoter element to determine if they contain transcription factor binding sites. The reporter construct-containing vector is introduced into a cell that contains many transcription factors. Activation of the reporter gene by transcription factors may be monitored by detection and quantification of the product of the reporter gene.
The term “agent” is used here to essentially describe any means to modulate INGAP expression. Agent may be a chemical compound, a biological agent, or a physical force, a mechanical contraption, or any combinations thereof.
INGAP Promoter and Regulatory Region It is a discovery of the present inventors that INGAP gene is regulated by a 5′-regulatory region that is susceptible to modulation by many known transcription factors, including PMA and LIF.
It is a further discovery of the present invention that the 5′-regulatory region nucleotide sequence of the INGAP gene may be used in screening assays to identify agents capable of modulating the INGAP gene expression. These modulating agents have potential as therapeutic agents for treating pathological conditions including, but not limited to, diabetes mellitus, both type 1 and type 2, endocrine and non-endocrine hypoplasia, hypertrophy, adenoma, neoplasia, and nesidioblastosis.
Mammalian INGAP, like most genes, has a 5′-regulatory region followed by introns and exons. The sequence of a mammalian (Hamster sp.) INGAP gene is provided as SEQ ID NO: 2. FIG. 1 details the relative location of the 5′-regulatory region, the introns and the exons of the hamster INGAP gene. The boundaries of introns 1-5 and the location of the TATA-box and the poly-A signal are listed in Table 1.
TABLE 1
Position In INGAP Gene
Description (SEQ ID NO: 2)
TATA-Box 3094
INTRON 1 3150-3426
INTRON 2 3508-4442
INTRON 3 4562-4735
INTRON 4 4874-5459
INTRON 5 5587-5843
Poly-A Signal 6098-6103
The nucleotide sequence of the 5′-regulatory region including the promoter elements of mammalian INGAP, is shown partially in SEQ ID NO: 1, and completely in SEQ ID NO: 2 and 23 (nucleotides 1-3137 of SEQ ID NO: 2). Nucleotides 1-3120 of SEQ ID NO: 1 are identical to nucleotides 1-3120 of SEQ ID NO: 2 and SEQ ID NO: 23. An overview of the 5′-regulatory region is shown in FIG. 2. Representative transcription enhancer/repressor binding sites are shown also in FIG. 2. Predicted transcription enhancer/repressor binding sites for nucleotides 1-3123 of the 5′-regulatory region are shown in FIG. 3. Table 3 at the end of the specification details these transcription factors and their binding sites, and their locations in the regulatory region. Potential transcription factor binding analysis was done using MatInspector professional, which is a bioinformatics software that utilizes a library of matrix descriptions for transcription factor binding sites to locate matches in sequences of unlimited length (Quandt, K., Frech, K., Karas, H., Wingender, E., Werner, T. (1995) Nucleic Acids Res. 23, 4878-4884).
Table 3 lists predicted binding proteins (Further Information) based upon their classification into functionally similar matrix families (Family/matrix). The DNA sequence predicted to bind the protein (Sequence), whether sense or antisense DNA (Str) and location of the sequence in SEQ ID NO: 2, (Position) are listed. Further the similarity to the consecutive highest conserved nucleotides of a matrix (Core sim.) and similarity to all nucleotides in that matrix (Matrix sim.) along with the optimized value (Opt) defined in a way that a minimum number of matches is found in non-regulatory test sequences are also listed. Details to the algorithms used in MatInspectorprofessional™ is referenced:
OPT: This matrix similarity is the optimized value defined in a way that a minimum number of matches are found in non-regulatory test sequences (i.e. with this matrix similarity the number of false positive matches is minimized). This matrix similarity is used when the user checks “Optimized” as the matrix similarity threshold for MatInspector professional™.
Family: Each matrix belongs to a so-called matrix family, where functionally similar matrices are grouped together, eliminating redundant matches by MatInspector professional™ professional (if the family option was selected). E.g. the matrix family V$NFKB includes 5 similar matrices for NFkappaB (V$NFKAPPAB.01, V$NFKAPPAB.02, V$NFKAPPAB.03, V$NFKAPPAB50.01, V$NFKAPPAB65.01) as well as 1 matrix for the NFkappaB related factor c-Rel (V$CREL.01).
Matrix: The MatInspector professional™ matrices have an identifier that indicates one of the following seven groups: vertebrates (V$), insects (I$), plants (P$), fungi (F$), nematodes (N$), bacteria (B$), and other functional elements (0$); followed by an acronym for the factor the matrix refers to, and a consecutive number discriminating between different matrices for the same factor. Thus, V$OCT1.02 indicates the second matrix for vertebral Oct-1 factor.
Core Sim: The “core sequence” of a matrix is defined as the (usually 4) consecutive highest conserved positions of the matrix. The core similarity is calculated as described here. The maximum core similarity of 1.0 is only reached when the highest conserved bases of a matrix match exactly in the sequence. More important than the core similarity is the matrix similarity which takes into account all bases over the whole matrix length.
Matrix Sim: The matrix similarity is calculated as described here. A perfect match to the matrix gets a score of 1.00 (each sequence position corresponds to the highest conserved nucleotide at that position in the matrix), a “good” match to the matrix usually has a similarity of >0.80. Mismatches in highly conserved positions of the matrix decrease the matrix similarity more than mismatches in less conserved regions.
Another aspect of the invention provides for a reporter construct. Reporter constructs contain a 5′ regulatory region nucleotide sequence fragment of SEQ ID NO: 23 (e.g., an enhancer and/or repressor binding site containing region), a promoter element (which may or may not be from INGAP regulatory region nucleotide sequence, SEQ ID NO: 23), and a reporter gene. The 5′-regulatory region nucleotide sequence is positioned upstream of the reporter gene. In order to determine the identity of various transcription factors that bind the 5′ regulatory region nucleotide sequence and to elucidate their binding locations within the 5′ regulatory nucleotide sequence of the INGAP gene, the region may be mapped using deletion analysis. One or more fragments of the regulatory region nucleotide sequence may be initially analyzed for their responses to various transcription factor activators. Once, a region of interest is determined, further fine mapping may be carried out where DNA from different locations within the regulatory region could be combined to make a more robust, and responsive reporter construct. DNA sequences, such as INGAP 5′-regulatory region DNA or a fragment thereof, can be manipulated by methods well known in the art. Examples of such techniques include, but are not limited to, polymerase chain reaction (PCR), restriction enzyme endonuclease digestion, ligation, and gene walking. Cloning fragments of DNA, such as 5′-regulatory regions is well known in the art.
Another approach to quantify the expression levels of a gene is to measure transcription of the gene. PCR-ELISA may be used to capture transcripts onto a solid phase using biotin or digoxigenin-labelled primers, oligonucleotide probes (oligoprobes) or directly after incorporation of the digoxigenin into the transcripts (Watzinger, F. and Lion, T. (2001) Nucleic Acids Res., 29, e52). Once captured, the transcripts can be detected using an enzyme-labeled avidin or anti-digoxigenin reporter molecule similar to a standard ELISA format Another approach is to employ real-time PCR to detect the transcript of the reporter gene (Mackay, I. M. and Nitsche, A., Nucleic Acids Res. 2002 Mar. 15; 30(6), 1292-305). In real-time PCR fluorogenic nucleotides are used and progress of the transcript is monitored in real-time as the polymerase transcribes the reporter gene.
The promoter element in the reporter construct may or may not be from the same gene as the 5′-regulatory region. As an example, the enhancer/repressor region from the INGAP 5′-regulatory region, or a fragment of the enhancer/repressor region from the INGAP 5′-regulatory region, may be cloned upstream of a heterologous minimal promoter element, e.g., the minimal CMV promoter (Boshart et al., 1985) and the promoters for TK (Nordeen, 1988), IL-2, and MMTV.
Transcription of a gene begins around the minimal promoter. FIG. 4 shows the predicted transcription start sites for mammalian INGAP gene (SEQ ID NO: 2). SEQ ID NO: 2 was analyzed using “Neural Network Promoter Prediction” program designed by Martin Reese to identify eukaryotic promoter recognition elements such as TATA-box, GC-box, CAAT-box, and the transcription start site. These promoter elements are present in various combinations separated by various distances in sequence. The program is available on the Internet and is located at http://www.fruitfly.org/seq_tools/promoter.html.
The reporter construct can be used to identify agents that modulate, either alone or in combination, the expression of INGAP. Some such agents may modulate expression of INGAP by binding to the regulatory region directly while others may regulate expression of transcription factors that bind to the INGAP regulatory region.
The reporter construct can be transfected into a host cell in vitro, or in vivo through the pancreatic duct, either transiently or stably, and a test agent introduced to the assay system. Examples of test agents include, but are not limited to organic and inorganic chemical agents, carbohydrates, proteins, oligonucleotides, cholecystokinin, mechanically induced pressure, and agents which cause a pancreatic duct obstruction. Expression of the reporter gene product can be determined by an assay appropriate for the reporter gene employed. Examples of such assays include, but are not limited to a luminescent assay for β-galactosidase or luciferase, an enzymatic assay for chloramphenicol acetyl transferase, and fluorescence detection for fluorescent proteins. Such assays are well known in the art, and a skilled artisan will be able to select an appropriate assay for the chosen reporter. A test agent is identified as a modulator of INGAP expression if the test agent modulates expression of the reporter gene product. Preferably the level of increase or decrease is at least 50%, 100%, 200%, 500%, or 1000%, but any statistically significant change can be an indicator of modulatory activity. A skilled artisan may also determine reporter gene product expression in untreated cells, and in treated and untreated cells transfected with a promoter-less reporter gene only. Such determinations can be used to determine background levels of expression.
Test agents can also be obtained by fractionating pancreatic secretion fluids. A pancreatic duct obstruction can be used as an exemplary method of harvesting pancreatic secretion fluids. The pancreatic secretion fluids can be fractionated by methods well known in the art. Examples include high-pressure liquid chromatography (HPLC), size exclusion chromatography, hydrophobic interacting columns, and density gradient centrifugation. Individual fractions can be tested for agents that modulate reporter gene expression using a method described herein. The individual fractions can be further fractionated to identify agents that modulate reporter gene expression. The identified test agents can be used to modulate the expression of INGAP.
A host cell can be any cell suitable for transfection and maintenance in a suitable assay system. Examples of suitable cells include, but are not limited to, mammalian cells, human cells, mouse cells, rat cells, monkey cells, dog cells, bovine cells, and porcine cells. Preferably the cells used will be human cells. The cells could be either transformed cells line or primary cells. Whole organ explants may also be used where the regulation may be monitored over many different cell types. Many methods exist in the art for transfecting or infecting cells with reporter construct DNA. Such methods include, but are not limited to, lipofection, electroporation, calcium phosphate precipitation, DEAE dextran, gene guns, and modified viral techniques (e.g., recombinant adenovirus or recombinant retrovirus). The skilled artisan can readily choose a method suitable for use with a given cell type and assay system.
The reporter construct can also be introduced in vivo directly into cells of the pancreas. Examples of methods to introduce the reporter construct into pancreatic cells in vivo include pancreatic duct retrograde perfusion and in vivo electroporation (Mir, 2001). The reporter construct encodes a reporter gene product that is readily measured in vivo. A test agent can be administered systemically or locally, and N expression of the reporter gene in vivo can be determined by an assay appropriate for the particular reporter employed. Examples of such include a fluorescence assay for green fluorescent protein.
Methods for identifying agents that modulate INGAP expression can also be accomplished in vitro. The reporter construct can be contacted with a test agent in vitro under conditions sufficient for transcription and/or translation of the reporter gene. Components such as rabbit reticulocyte lysates or wheat germ extracts can be utilized for such a method. Subsequently, the expression level of the Reporter gene can be determined as described above utilizing an appropriate assay for a given reporter gene. A test agent is identified as a modulator of INGAP expression if the test agent modulates expression of the reporter gene. Threshold levels of change can be set by the practitioner as discussed above.
A test agent can alternatively be contacted with an isolated and purified INGAP 5′-regulatory DNA molecule and one can determine if the test agent binds to the DNA molecule. Test agents can be a chemical agent, a protein, or a nucleic acid. Appropriate INGAP 5′-regulatory DNA molecules would include nucleotides 1-6586 of SEQ ID NO: 2, the 5′-regulatory region DNA (SEQ ID NO: 1, or SEQ ID NO: 23), or any fragment of the 5′-regulatory region, preferably a fragment which contains one or more enhancer/repressor binding sites. Methods to determine binding of the test agent to the fragment of DNA are well known in the art, e.g., electrophoretic mobility shift assay (EMSA). See for example Sambrook et al., MOLECULAR CLONING: A LABORATORY MANUAL, 2d ed., 1989, at pages 9.50-9.51. Fragments of the 5′-regulatory region can be obtained by methods well known in the art using the disclosed sequence (SEQ ID NO: 2). Examples of such methods include, PCR, restriction enzyme digestion, and chemical synthesis. Any fragment of DNA within the 5′-regulatory region (SEQ ID NO: 1, or 23) can be used. The exact location that an agent binds can be determined for example by utilizing smaller fragments to map precisely the binding site for the test agent. Test agents that bind in the assay can be further tested in other assays that require modulatory activity.
An agent that causes an increase or decrease in reporter gene expression can be used as a modulator of INGAP expression. The modulator can be administered to a mammal in need of such modulation. Examples of mammals that may need INGAP expression modulation are those with reduced pancreatic function, in particular reduced islet cell function. Such mammals include those who have diabetes mellitus, impaired glucose tolerance, impaired fasting glucose, hyperglycemia, obesity, and pancreatic insufficiency.
An agent that is identified as a modulator of INGAP expression can be supplied in a kit to treat diseases associated with reduced islet cell function. The kit would comprise in single or divided containers, in single or divided doses a modulator of INGAP expression. Written instructions may be included for using the modulator of INGAP expression. The instructions may simply refer a reader to another location such as a website or other information source.
Agents that cause an increase in reporter gene expression can be used to increase INGAP expression to treat a disease state related to reduced islet cell function. Agents that cause a decrease in reporter gene expression can be used to decrease INGAP expression to treat a disease state related to hyperactivity of islet cells or a disease where reduced INGAP expression is desirable. Examples of such agents include, but are not limited to, PMA, LIF, interleukin-6, Oncostatin M, and ciliary neurotropic factor. Agents can be administered by any number of routes including, but not limited to, oral, intravenous, intramuscular, intra-arterial, intramedullary, intrathecal, intraventricular, transdermal, subcutaneous, intraperitoneal, intranasal, parenteral, topical, sublingual, rectal, or pancreatic duct retrograde perfusion. Agents for oral administration can be formulated using pharmaceutically acceptable carriers well known in the art in dosages suitable for oral administration. Such carriers enable the pharmaceutical compositions to be formulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions, and the like, for ingestion by the mammal. Agents for intravenous, intramuscular, intra-arterial, transdermal, and subcutaneous injections can be formulated using pharmaceutically acceptable carriers well known in the art in dosages suitable for injection into the mammal. Agents for intranasal, topical, and rectal administration can be formulated using pharmaceutically acceptable carriers well known in the art in dosages suitable for surface administration to the mammal. Mammals in need of an increase in INGAP expression include for example, mammals with diabetes mellitus, impaired glucose tolerance, impaired fasting glucose, hyperglycemia, obesity, and pancreatic insufficiency. Mammals in need of a decrease in INGAP expression include for example, mammals with hypoglycemia.
The following examples are offered by way of illustration and do not limit the invention disclosed herein.
EXAMPLES Example 1 Hamster INGAP Genomic Sequence and Structure The hamster INGAP genomic sequence and structure was determined by gene walking (Clontech) and DNA sequencing. Gene walking is a method for walking upstream toward a promoter or downstream in genomic DNA from a known sequence, such as cDNA. This method utilizes four uncloned, adapter-ligated genomic fragment libraries. The manufacturer's recommended protocol is followed with one notable exception; hamster genomic DNA was used to create the uncloned, adapter-ligated genomic fragment libraries.
To create uncloned, adapter ligated genomic fragment libraries, genomic DNA was purified from hamster cells. Four separate aliquots were thoroughly digested with PvuII, StuI, DraI, or EcoRV. Following digestion, inactivation of the restriction enzymes, and dephosphorylation, each separate pool of DNA fragments was ligated to an adapter, see FIG. 5. The adapter was phosphorylated to provide the requisite phosphate group for a ligation reaction. Also note that the 3-prime side of the short adapter contains an amine group to prevent the adapters from forming concatamers.
Two gene specific primers (GSP1 and GSP2) were designed for each region of known sequence (i.e., the exons of the INGAP gene). See FIG. 6 for fragment location and GSP1 and GSP2 location. The gene specific primers were designed as reverse PCR primers for all fragments except fragments 1—2 and 14—5. The gene specific primers for fragments 1—2 and 14—5 were designed as forward primers. Adapter primer 1 (AP1) and adapter primer 2 (AP2) (FIG. 5) were forward PCR primers for all fragments except fragments 1—2 and 14—5, which were reverse PCR primers. The outer gene specific primer (GSP1) was used with adapter primer 1 in a PCR reaction. To increase specificity, a second, nested PCR was set up using the inner gene specific primer (GSP2) and adapter primer 2. A small aliquot of the first reaction served as template for the second reaction. Gene specific PCR primers utilized for gene walking are listed in Table 2 and the strategy used to build the INGAP genomic sequence is shown in FIGS. 6 and 7. The arrowheads in FIG. 6 represent the adapter primers (AP1 and AP2), while the circles represent the gene specific primers (GSP1 and GSP2).
TABLE 2
NAME (LOCATION) SEQUENCE
INGEN 21_3 5′-ACAAGCAATCTAGAGATGG-3′
(1464, 1482) (SEQ ID NO: 3)
INGEN 19_3 5′-GTTCAGCTATGTTCATAGCAGGG-3′
(1401, 1423) (SEQ ID NO: 4)
INGEN 16_3 5′-GTCTGTATGACTGTGTGGGAAG-3′
(1855, 1876) (SEQ ID NO: 5)
INGEN 15_3 5′-GCACTTGAACTCAATGGCTC-3′
(1929, 1948) (SEQ ID NO: 6)
INGEN 14_3 5′-GAACCACCTGACATGGGTGATG-3′
(2147, 2168) (SEQ ID NO: 7)
INGEN 13_3 5′-GGGCATCGTATCATCTGGTTACAG-3′
(2177, 2200) (SEQ ID NO: 8)
INGEN 8_3 5′-GGTTCAAAAAAGCTGCTTCAAC-3′
(2544, 2565) (SEQ ID NO: 9)
INGEN 7_3 5′-GGAATAGCTGCAATTTATGCCCAT-3′
(2666, 2689) (SEQ ID NO: 10)
INGEN 4_3 5′-CTTAGGAACATTCAGGCAGCCTCCTG-3′
(2833, 2858) (SEQ ID NO: 11)
INGEN 3_3 5′-GTTGCCCTCTGCCACGTGTCAAGTTC-3′
(2866, 2891) (SEQ ID NO: 12)
INGEN 2_3 5′-CATCCAAGACATCCTACAGAGGGTCAT-3′
(3444, 3470) (SEQ ID NO: 13)
INGEN 1_3 5′-CCCAAGAAAGGAACATCAGGCAGGAAA-3′
(3475, 3501) (SEQ ID NO: 14)
INGEN 2_2 5′-CCAAATGAGTGCTTCCCTGAA-3′
(3330, 3350) (SEQ ID NO: 15)
INGEN 1_2 5′-GCAGCACTCTGAAACTCAGTAGAGTT-3′
(3241, 3266) (SEQ ID NO: 16)
INGEN 14_5 5′-GCTGCTGACCGTGGTTATTG-3′
(5544, 5563) (SEQ ID NO: 17)
INGEN 13_5 5′-ACACTACCCAACGGAAGTGGATG-3′
(5463, 5485) (SEQ ID NO: 18)
INGAP1_1L 5′-TTTCCTGCCTGATGTTCC-3′
(3475, 3492) (SEQ ID NO: 19)
INGAP1_1R 5′-TCATACTTGCTTCCTTGTCC-3′
(5957, 5976) (SEQ ID NO: 20)
INGAP2_1L 5′-CTTCACGTATAACCTGTCC-3′
(4470, 4488) (SEQ ID NO: 21)
INGAP2_1R 5′-ATTAGAACTGCCCTAGACC-3′
(5905, 5923) (SEQ ID NO: 22)
The PCR fragments were sequenced to determine the nucleotide sequence of the INGAP 5′-regulatory region, the introns, the intron/exon junctions, and the 3-prime polyadenylation regions. The nucleotide sequence of hamster INGAP genomic DNA is shown in SEQ ID NO: 2.
Example 2 Cloning Hamster INGAP 5′-Regulatory Region Fragment into a Reporter Construct To construct the INGAP 5′-regulatory region, individual PCR fragments were joined together at unique restriction sites located within two adjoining fragments. FIGS. 6 and 7 detail the strategy used to piece the INGAP 5′-regulatory region together. Fragments 8—3 and 2—3 were joined at a unique SphI site; 14—3 and 8—3 were joined at a unique BbsI site; 16—3 and 14—3 were joined at a unique PstI site. The nucleotide sequence of hamster INGAP 5′-regulatory region DNA is shown in SEQ D NO: 1 and 23 in the sequence listing.
The hamster INGAP 5′-regulatory region or a fragment of the 5′-regulatory region was cloned into a reporter plasmid, pβGal-Basic (Clontech). The 5′-regulatory region or fragments were cloned utilizing the unique XmaI site from the gene walking adapter primer and a unique BglII site located at the 3-prime side of the regulatory region. FIG. 8 details the fragments cloned into pβGal-Basic. The sizes of the fragments are indicated to the right of the fragments and are expressed as the number of nucleotides of the fragment.
Example 3 Assay System to Screen for Factors that Modulate the Expression of INGAP Promoter analysis of INGAP identified a number of potential promoter-proximal regulatory sites including the consensus transcription factor binding sites; cAMP response element (CRE), AP-1 and STAT. Promoter-fragment reporter-gene constructs were transiently transfected into 293T cells and co-transfection of secretory alkaline phosphatase was used to normalize for transfection efficiency.
Reporter constructs containing INGAP 5′-regulatory region fragments 2—3sP (SEQ ID NO: 37), 2—3dP (SEQ ID NO: 38), 2—3pP (SEQ ID NO: 36), 14—3P (SEQ ID NO: 34), 16—3P (SEQ ID NO: 31), or 19—3P (SEQ 11D NO: 23) were transfected into human cells. The pβGal-Basic plasmid without the hamster INGAP DNA was also transfected into human cells as a control to measure the level of endogenous reporter activity. Two days following transfection, the cells were treated with PMA for 24 hours or were untreated. To determine the level of promoter activity, the amount of β-galactosidase gene product was determined using a luminescent assay for β-galactosidase. FIG. 9A shows that construct 14—3P activated the INGAP expression the most, followed by 2—3pP, and 16—3P.
Reporter construct containing INGAP 5′-regulatory region DNA nucleotides 2030 to 3120 was transfected into human cells. The pβGal-Basic plasmid without the hamster INGAP DNA was also transfected into human cells as a control to measure the level of endogenous reporter activity. Two days following transfection, the cells were treated with LIF for 24 hours or were untreated. To determine the level of promoter activity, the amount of β-galactosidase gene product was determined using a luminescent assay for β-galactosidase. FIG. 9B shows the results. LIF was determined to increase the activity of the 5′-regulatory region of mammalian INGAP. Forskolin (an activator of cAMP/CREB/CRE) did not modulate gene expression (data not shown).
It is important to note that when present in human cells, the hamster INGAP 5′-regulatory region is transactivated by the human transcription factors. Thus, linked to a reporter gene, the 5′-regulatory region of hamster INGAP creates a sensitive assay system to screen for factors that modulate the expression of INGAP.
Example 4 Determination of Approximate Location of PMA and LIF-Mediated Transcription Factor Binding in the 5′-Regulatory Region To map the approximate location of PMA-initiated or LIF-initiated transcription factor binding different fragments of the hamster INGAP 5′-regulatory region were cloned into pβGal-Basic. See FIG. 8. The fragments cloned into the reporter construct were 2—3sP (SEQ ID NO: 37), 2—3dP (SEQ ID NO: 38), 2—3pP (SEQ ID NO: 36), 14—3P (SEQ ID NO: 34), 16—3P (SEQ ID NO: 31), or 19—3P (SEQ ID NO: 23). The reporter constructs were transfected into human cells. Two days following transfection, the cells were treated with different concentrations of PMA or LIF for 24 hours. The concentrations of PMA used were 6 ng/ml, 17 ng/ml, 50 ng/ml, 100 ng/ml, or 300 ng/ml. The concentrations of LIF used were 1 ng/ml, 10 ng/ml, or 30 ng/ml. To determine the level of promoter activity, the amount of β-galactosidase gene product was determined using a luminescent assay for β-galactosidase. FIGS. 10 and 11 show the results for PMA and LIF treatment, respectively. Both PMA and LIF activated the cell reporter constructs. The exact location of the DNA contact sites can be narrowed further by cloning smaller fragments of the hamster INGAP 5′-regulatory region and by site directed mutations or deletions.
Example 5 RNA Analysis of INGAP Gene Upregulation To determine if INGAP RNA levels increase after stimulation with a cytokine that signals through STAT, rat amphocrine pancreatic cells, AR42J were treated with IL-6 (1000 U/ml) for 24 hours. Total RNA was extracted from the treated and untreated cells using techniques well known in the art, e.g., using TRIZOL® reagent.
Equal amounts of total RNA (10 μg) were loaded in 2.5% formaldehyde gel and electrophoresed for 4 hours at 70V with a constant circulation of the buffer using a circulating pump. The gel was photographed and washed with water twice at room temperature and soaked in 20×SSC. The gel was transferred to a nylon membrane (Amersham) in 20×SSC overnight following a standard procedure. The membrane was washed with 20×SSC to remove any agar that might have attached to the membrane and baked for 4 hours at 80° C.
One hundred nanograms of hamster INGAP cDNA was labeled using Random Prime Labeling kit (Roche-BMB) and alpha-P32 dCTP (ICN). Approximately 20 million counts were used for hybridization in 20 ml hybridization buffer following the standard procedure at 42° C. for overnight. The blot was washed as follows: 2-times at room temperature with 2×SSC for 10 minutes each; 2-times at 42° C. with 2×SSC for 10 minutes each; 2-times at 55° C. with 1×SSC for 10 minutes each. The membrane was exposed to the film (XOMAT-Kodak) and kept at −80° C. overnight before developing.
Treatment with IL-6 caused an increase in INGAP gene expression (FIG. 12). These data demonstrate that extracellular factors that elevate AP-1-binding transcription factors and STAT-binding transcription factors are involved in the regulation of INGAP gene expression. These studies suggest that it is feasible to enhance INGAP expression as a means of inducing islet neogenesis.
While particular embodiments of the present invention have been illustrated and described, it would be obvious to those skilled in the art that various other changes and modifications can be made without departing from the spirit and scope of the invention. It is therefore intended to cover in the appended claims all such changes and modifications that are within the scope of this invention.
TABLE 3
Position Core Matrix
Family/matrix Further Information Opt. from-to anchor Str. sim. sim. Sequence
V$LEFF/LEF1.01 TCF/LEF-1, involved in the 0.86 12-28 20 (+) 1.000 0.900 ggaccatCAAAgtctgt
Wnt signal transduction
pathway
V$MITF/MIT.01 MIT (microphthalmia 0.81 22-40 31 (+) 1.000 0.823 agtctgtCATGtcatttgg
transcription factor) and TFE3
V$OCT1/OCT1.05 octamer-binding factor 1 0.90 27-41 34 (+) 0.833 0.904 gTCATgtcatttggg
V$TCFF/TCF11.01 TCF11/KCR-F1/Nrf1 1.00 32-38 35 (+) 1.000 1.000 GTCAttt
homodimers
V$MYOF/MYOGNF1.01 Myogenin/nuclear factor 1 or 0.71 25-53 39 (+) 1.000 0.735 ctgtcatgtcatTTGGgggagggcctatg
related factors
V$ZBPF/ZBP89.01 Zinc finger transcription factor 0.93 36-48 42 (−) 1.000 0.982 gccctCCCCcaaa
ZBP-89
V$SP1F/GC.01 GC box elements 0.88 38-52 45 (+) 0.876 0.898 tgggGGAGggcctat
V$PERO/PPARA.01 PPAR/RXR heterodimers 0.70 44-64 54 (−) 0.884 0.708 acagaggagggcATAGgccct
V$PAX5/PAX9.01 zebrafish PAX9 binding sites 0.78 43-71 57 (−) 0.800 0.811 cagataCACAgaggagggcataggccctc
V$TBPF/ATATA.01 Avian C-type LTR TATA box 0.81 68-84 76 (−) 1.000 0.987 tgctattTAAGcccaga
V$HMTB/MTBF.01 muscle-specific Mt binding 0.90 76-84 80 (−) 1.000 0.932 tgctATTTa
site
V$OCT1/OCT1.06 octamer-binding factor 1 0.80 74-88 81 (−) 0.750 0.865 ggtatgctATTTaag
V$BRNF/BRN2.01 POU factor Brn-2 (N-Oct 3) 0.91 89-105 97 (+) 1.000 0.970 tccataggAAATgggct
V$HMTB/MTBF.01 muscle-specific Mt binding 0.90 108-116 112 (−) 1.000 0.953 tggaATTTg
site
V$OCT1/OCT1.05 octamer-binding factor 1 0.90 106-120 113 (−) 0.944 0.917 tATATggaatttggg
V$HNF6/HNF6.01 Liver enriched Cut - 0.82 108-122 115 (+) 0.833 0.885 caaatTCCAtatatg
Homeodomain transcription
factor HNF6 (ONECUT)
V$SRFF/SRF.02 serum response factor 0.83 110-128 119 (+) 1.000 0.862 aattCCATatatgcactag
V$OCTP/OCT1P.01 octamer-binding factor 1, 0.86 114-126 120 (+) 1.000 0.903 ccatatATGCact
POU-specific domain
V$MYOF/MYOGNF1.01 Myogenin/nuclear factor 1 or 0.71 171-199 185 (+) 0.857 0.740 ctggtcttttagCTGGcacccatccatat
related factors
V$NF1F/NF1.02 Nuclear factor 1 (CTF1) 0.81 181-199 190 (+) 1.000 0.812 agcTGGCacccatccatat
V$CLOX/CDPCR3HD.01 cut-like homeodomain protein 0.94 187-203 195 (−) 0.929 0.940 ctgaatatgGATGggtg
V$MYOF/MYOGNF1.01 Myogenin/nuclear factor 1 or 0.71 181-209 195 (−) 0.785 0.767 aaccctctgaatATGGatgggtgccagct
related factors
V$OCTP/OCT1P.01 octamer-binding factor 1, 0.86 192-204 198 (+) 0.980 0.907 atccatATTCaga
POU-specific domain
V$CREB/TAXCREB.02 Tax/CREB complex 0.71 202-222 212 (−) 0.750 0.721 ttgaacTGAAccaaaccctct
V$HOXF/EN1.01 Homeobox protein engrailed 0.77 210-226 218 (−) 0.782 0.823 aacaTTGAactgaacca
(en-1)
V$BARB/BARBIE.01 barbiturate-inducible element 0.88 230-244 237 (−) 1.000 0.894 ttatAAAGctgagga
V$TBPF/TATA.01 cellular and viral TATA box 0.90 230-246 238 (−) 1.000 0.910 agttaTAAAgctgagga
elements
V$BARB/BARBIE.01 barbiturate-inducible element 0.88 252-266 259 (−) 1.000 0.902 agtgAAAGcagagag
V$MYT1/MYT1.01 MyT1 zinc finger transcription 0.75 272-284 278 (−) 0.750 0.756 craCAGTtgacct
factor involved in primary
neurogenesis
V$SMAD/SMAD4.01 Smad4 transcription factor 0.94 304-312 308 (+) 1.000 0.940 GTCTtgact
involved in TGF-beta signaling
V$HOXF/CRX.01 Cone-rod homeobox- 0.94 312-328 320 (−) 1.000 0.960 gagggATTAgaaaagga
containing transcription factor/
otx-like homeobox gene
V$ECAT/NFY.01 nuclear factor Y (Y-box 0.90 337-351 344 (−) 1.000 0.906 ggaatCCAAtygtag
binding factor)
V$HOXF/PTX1.01 Pituitary Homeobox 1 (Ptx1) 0.79 337-353 345 (+) 0.789 0.802 ctacraTTGGattccat
V$FKHD/FREAC2.01 Fork head RElated ACtivator-2 0.84 362-378 370 (−) 1.000 0.897 tacagcTAAAcactgag
V$MINI/MUSCLE_INI.02 Muscle Initiator Sequence 0.86 401-419 410 (−) 0.840 0.865 gagcctTCATccagtagct
V$MOKF/MOK2.01 Ribonucleoprotein associated 0.74 409-429 419 (−) 1.000 0.746 tgtcatcttagagCCTTcatc
zinc finger protein MOK-2
(mouse)
V$ZFIA/ZID.01 zinc finger with interaction 0.85 414-426 420 (+) 1.000 0.861 agGCTCtaagatg
domain
V$CART/XVENT2.01 Xenopus homeodomain factor 0.82 418-434 426 (+) 0.750 0.837 tcTAAGatgacaattaa
Xvent-2; early BMP signaling
response
V$OCT1/OCT1.04 octamer-binding factor 1 0.80 421-435 428 (+) 0.807 0.840 aaGATGacaattaag
V$HOMS/S8.01 Binding site for S8 type 0.97 426-434 430 (+) 1.000 0.994 gacaATTAa
homeodomains
V$NKXH/NKX25.02 homeo domain factor Nkx- 0.88 424-436 430 (−) 1.000 1.000 cctTAATtgtcat
2.5/Csx, tinman homolog low
affinity sites
V$CREB/CREBP1.01 cAMP-responsive element 0.80 425-445 435 (−) 0.766 0.808 cgacgattACCTtaattgtca
binding protein 1
V$COMP/COMP1.01 COMP1, cooperates with 0.76 434-454 444 (−) 0.750 0.768 aatgaggATCGacgattacct
myogenic proteins in
multicomponent complex
V$HOXF/HOX1-3.01 Hox-1.3, vertebrate 0.83 444-460 452 (+) 1.000 0.886 cgatcctcATTAtagtg
homeobox protein
V$ETSF/GABP.01 GABP: GA binding protein 0.85 454-470 462 (+) 1.000 0.868 tatagtGGAAgggcttc
V$LEFF/LEF1.01 TCF/LEF-1, involved in the 0.86 463-479 471 (+) 1.000 0.904 agggcttCAAAggcagt
Wnt signal transduction
pathway
V$STAT/STAT6.01 STAT6: signal transducer and 0.84 464-482 473 (−) 0.758 0.867 gagacTGCCtttgaagccc
activator of transcription 6
V$GATA/GATA1.03 GATA-binding factor 1 0.95 490-502 496 (−) 1.000 0.971 ttcaGATAggcag
V$SRFF/SRF.01 serum response factor 0.66 487-505 496 (−) 0.757 0.672 atgttcaGATAggcagtag
V$EVI1/EVI1.04 Ecotropic viral integration site 0.77 493-509 501 (−) 0.800 0.824 gGAAAtgttcagatagg
1 encoded factor
V$AP4R/TH1E47.01 Thing1/E47 heterodimer, TH1 0.93 509-525 517 (+) 1.000 0.951 cctaatgCCAGatgtct
bHLH member specific
expression in a variety of
embryonic tissues
V$AP4R/ Tal-1beta/ITF-2 heterodimer 0.85 512-528 520 (+) 1.000 0.852 aatgcCAGAtgtctctt
TAL1BETAITF2.01
V$NEUR/NEUROD1.01 DNA binding site for 0.83 514-526 520 (−) 1.000 0.851 gagaCATCtggca
NEUROD1 (BETA-2/E47
dimer)
V$MEF2/MEF2.05 MEF2 0.96 518-540 529 (−) 1.000 0.984 aggataggttTAAAgagacatct
V$EVI1/EVI1.04 Ecotropic viral integration site 0.77 523-539 531 (−) 1.000 0.774 gGATAggtttaaagaga
1 encoded factor
V$MEF2/AMEF2.01 myocyte enhancer factor 0.80 521-543 532 (+) 1.000 0.813 tgtctcttTAAAcctatcctggc
V$TBPF/MTATA.01 Muscle TATA box 0.84 524-540 532 (+) 1.000 0.877 ctcttTAAAcctatcct
V$HOXF/HOX1-3.01 Hox-1.3, vertebrate 0.83 543-559 551 (+) 1.000 0.845 ctcccttcATTAaggta
homeobox protein
V$PDX1/ISL1.01 Pancreatic and intestinal lim- 0.82 543-563 553 (−) 1.000 0.834 gagatacctTAATgaagggag
homeodomain factor
V$OCT1/OCT1.05 octamer-binding factor 1 0.90 556-570 563 (+) 0.944 0.926 gGTATctcatttttt
V$CIZF/NMP4.01 NMP4 (nuclear matrix protein 0.97 562-572 567 (−) 1.000 0.972 gcAAAAaatga
4)/CIZ (Cas-interacting zinc
finger protein)
V$EVI1/EVI1.01 Ecotropic viral integration site 0.72 569-585 577 (−) 0.764 0.720 ggaaCAGAggagagcaa
1 encoded factor
V$AP1F/AP1.01 AP1 binding site 0.95 582-602 592 (−) 0.881 0.964 aaaactgaATCAgtggnggaa
V$PIT1/PIT1.01 Pit1, GHF-1 pituitary specific 0.86 589-599 594 (+) 1.000 0.886 actgATTCagt
pou domain transcription
factor
V$AP1F/AP1.01 AP1 binding site 0.95 586-606 596 (+) 0.850 0.956 nccactgaTTCAgtttttctg
V$VMYB/VMYB.01 v-Myb 0.90 593-603 598 (−) 0.876 0.910 aaaAACTgaat
V$CIZF/NMP4.01 NMP4 (nuclear matrix protein 0.97 595-605 600 (−) 1.000 0.975 agAAAAactga
4)/CIZ (Cas-interacting zinc
finger protein)
V$GREF/PRE.01 Progesterone receptor binding 0.84 604-622 613 (+) 1.000 0.875 ctgatccctctTGTTctcc
site
V$GKLF/GKLF.01 Gut-enriched Krueppel-like 0.91 632-646 639 (−) 1.000 0.971 gaaaaagagaAGGGa
factor
V$CIZF/NMP4.01 NMP4 (nuclear matrix protein 0.97 637-647 642 (−) 1.000 0.987 ggAAAAagaga
4)/CIZ (Cas-interacting zinc
finger protein)
V$NFAT/NFAT.01 Nuclear factor of activated T- 0.97 640-650 645 (−) 1.000 0.982 ggagGAAAaag
cells
V$MAZF/MAZ.01 Myc associated zinc finger 0.90 649-661 655 (−) 1.000 0.910 ggtgGAGGgaagg
protein (MAZ)
V$EGRF/WT1.01 Wilms Tumor Suppressor 0.88 658-672 665 (−) 1.000 0.932 gggggTGGGagggtg
V$ZBPF/ZBP89.01 Zinc finger transcription factor 0.93 663-675 669 (+) 1.000 0.972 tcccaCCCCcatg
ZBP-89
V$IRFF/IRF2.01 interferon regulatory factor 2 0.80 702-716 709 (−) 1.000 0.815 aggaagggGAAAggg
V$BRNF/BRN2.01 POU factor Brn-2 (N-Oct 3) 0.91 746-762 754 (−) 1.000 0.911 aaaataggAAATaagga
V$ETSF/PU1.01 Pu.1 (Pu120) Ets-like 0.86 746-762 754 (−) 1.000 0.883 aaaataGGAAataagga
transcription factor identified
in lymphoid B-cells
V$EVI1/EVI1.04 Ecotropic viral integration site 0.77 750-766 758 (−) 0.760 0.792 aGAGAaaataggaaata
1 encoded factor
V$EVI1/EVI1.05 Ecotropic viral integration site 0.80 755-771 763 (−) 0.763 0.817 cccccagagaaAATAgg
1 encoded factor
V$ZBPF/ZBP89.01 Zinc finger transcription factor 0.93 764-776 770 (−) 1.000 0.934 ccacaCCCCcaga
ZBP-89
V$FAST/FAST1.01 FAST-1 SMAD interacting 0.81 769-783 776 (+) 0.983 0.894 gggtgtgGATTttat
protein
V$TBPF/TATA.02 Mammalian C-type LTR TATA 0.89 771-787 779 (−) 1.000 0.942 caccaTAAAatccacac
box
V$PAX5/PAX9.01 zebrafish PAX9 binding sites 0.78 781-809 795 (−) 0.866 0.813 aacataTGCAcagaagggcttccaccata
V$OCT1/OCT.01 Octamer binding site 0.79 793-807 800 (−) 1.000 0.790 catATGCacagaagg
(OCT1/OCT2 consensus)
V$OCTP/OCT1P.01 octamer-binding factor 1, 0.86 798-810 804 (−) 1.000 0.910 caacatATGCaca
POU-specific domain
V$SRFF/SRF.01 serum response factor 0.66 797-815 806 (+) 0.757 0.666 ctgtgcaTATGttgtctta
V$EVI1/EVI1.05 Ecotropic viral integration site 0.80 802-818 810 (−) 0.750 0.828 caataagacaaCATAtg
1 encoded factor
V$CLOX/CDP.01 cut-like homeodomain protein 0.75 803-819 811 (−) 1.000 0.776 ccAATAagacaacatat
V$EVI1/EVI1.02 Ecotropic viral integration site 0.83 807-823 815 (−) 1.000 0.836 tcaaccaatAAGAcaac
1 encoded factor
V$ECAT/NFY.02 nuclear factor Y (Y-box 0.91 810-824 817 (−) 1.000 0.960 atcaaCCAAtaagac
binding factor)
V$HAML/AML3.01 Runt-related transcription 0.84 811-825 818 (+) 1.000 0.844 tcttatTGGTtgata
factor 2/CBFA1 (core-
binding factor, runt domain,
alpha subunit 1)
V$PCAT/CAAT.01 cellular and viral CCAAT box 0.90 813-823 818 (−) 1.000 0.943 tcaaCCAAtaa
V$GATA/GATA.01 GATA binding site 0.95 818-830 824 (+) 1.000 0.956 ggttGATAaataa
(consensus)
V$HNF1/HNF1.02 Hepatic nuclear factor 1 0.76 818-834 826 (+) 0.757 0.791 gGTTGataaataaagca
V$HOXT/ Homeobox protein MEIS1 0.79 823-835 829 (−) 0.750 0.797 gTGCTttatttat
MEIS1_HOXA9.01 binding site
V$ECAT/NFY.01 nuclear factor Y (Y-box 0.90 837-851 844 (+) 1.000 0.912 gttgtCCAAtaggga
binding factor)
V$FKHD/FREAC2.01 Fork head RElated ACtivator-2 0.84 844-860 852 (+) 0.750 0.843 aataggGAAAcaagata
V$EVI1/EVI1.06 Ecotropic viral integration site 0.83 846-862 854 (+) 1.000 0.960 tagggaaacaAGATagg
1 encoded factor
V$GATA/GATA1.01 GATA-binding factor 1 0.96 853-865 859 (+) 1.000 0.970 acaaGATAggtgg
V$PCAT/ACAAT.01 Avian C-type LTR CCAAT box 0.86 856-866 861 (−) 0.750 0.867 cccaCCTAtct
V$XBBF/RFX1.01 X-box binding protein RFX1 0.89 909-927 918 (−) 1.000 0.929 ggatcacatgGCAAccctc
V$EBOX/MYCMAX.02 c-Myc/Max heterodimer 0.92 912-928 920 (−) 0.895 0.936 aggatCACAtggcaacc
V$MITF/MIT.01 MIT (microphthalmia 0.81 911-929 920 (+) 1.000 0.863 gggttgcCATGtgatccta
transcription factor) and TFE3
V$ETSF/PU1.01 Pu.1 (Pu120) Ets-like 0.86 927-943 935 (+) 1.000 0.950 ctaggaGGAAttgacac
transcription factor identified
in lymphoid B-cells
V$OCT1/OCT1.06 octamer-binding factor 1 0.80 932-946 939 (−) 1.000 0.800 catgtgtcAATTcct
V$TALE/TGIF.01 TG-interacting factor 1.00 936-942 939 (−) 1.000 1.000 tGTCAat
belonging to TALE class of
homeodomain factors
V$MITF/MIT.01 MIT (microphthalmia 0.81 935-953 944 (−) 1.000 0.835 ccattctCATGtgtcaatt
transcription factor) and TFE3
v$OCT1/OCT1.04 octamer-binding factor 1 0.80 941-955 948 (+) 0.846 0.800 caCATGagaatgggg
V$GATA/GATA.01 GATA binding site 0.95 962-974 968 (+) 1.000 0.998 gaaaGATAagtcc
(consensus)
V$SRFF/SRF.01 serum response factor 0.66 968-986 977 (−) 1.000 0.672 atattttTATAaggactta
V$CDXF/CDX2.01 Cdx-2 mammalian caudal 0.84 970-988 979 (−) 1.000 0.867 atatattTTTAtaaggact
related intestinal transcr.
factor
V$FKHD/XFD2.01 Xenopus fork head domain 0.89 972-988 980 (+) 1.000 0.894 tccttaTAAAaatatat
factor 2
V$MEF2/MEF2.01 myogenic enhancer factor 2 0.74 970-992 981 (+) 1.000 0.740 agtccttaTAAAaatatatatta
V$TBPF/TATA.01 cellular and viral TATA box 0.90 973-989 981 (+) 1.000 0.963 ccttaTAAAaatatata
elements
V$CART/CART1.01 Cart-1 (cartilage 0.84 978-994 986 (−) 1.000 0.870 acTAATatatattttta
homeoprotein 1)
V$CART/CART1.01 Cart-1 (cartilage 0.84 985-1001 993 (−) 1.000 0.855 caTAATtactaatatat
homeoprotein 1)
V$SATB/SATB1.01 Special AT-rich sequence- 0.93 985-1001 993 (−) 1.000 0.943 cataattacTAATatat
binding protein 1,
predominantly expressed in
thymocytes, binds to matrix
attachment regions (MARs)
V$BRNF/BRN3.01 POU transcription factor Brn-3 0.78 987-1003 995 (−) 1.000 0.816 cccATAAttactaatat
V$CLOX/CDP.01 cut-like homeodomain protein 0.75 987-1003 995 (−) 0.757 0.765 ccCATAattactaatat
V$HOMS/S8.01 Binding site for S8 type 0.97 992-1000 996 (+) 1.000 0.989 agtaATTAt
homeodomains
V$NKXH/DLX1.01 DLX-1, −2, and −5 binding 0.91 990-1002 996 (−) 1.000 0.976 ccatAATTactaa
sites
V$HOXF/HOX1-3.01 Hox-1.3, vertebrate 0.83 989-1005 997 (−) 1.000 0.886 aacccataATTActaat
homeobox protein
V$PDX1/PDX1.01 Pdx1 (IDX1/IPF1) pancreatic 0.74 988-1008 998 (−) 1.000 0.775 attaacccaTAATtactaata
and intestinal homeodomain
TF
V$FKHD/XFD3.01 Xenopus fork head domain 0.82 998-1014 1006 (+) 0.826 0.844 tatgggttAATAattaa
factor 3
V$HNF1/HNF1.01 hepatic nuclear factor 1 0.78 1000-1016 1008 (−) 0.755 0.857 aCTTAattattaaccca
V$HNF1/HNF1.01 hepatic nuclear factor 1 0.78 1002-1018 1010 (+) 1.000 0.966 gGTTAataattaagtca
V$PAX4/PAX4.01 Pax-4 paired domain protein, 0.97 1005-1015 1010 (+) 1.000 0.972 taatAATTaag
together with PAX-6 involved
in pancreatic development
V$HOMS/S8.01 Binding site for S8 type 0.97 1007-1015 1011 (−) 1.000 0.995 cttaATTAt
homeodomains
V$HOXF/HOX1-3.01 Hox-1.3, vertebrate 0.83 1003-1019 1011 (−) 1.000 0.873 ctgacttaATTAttaac
homeobox protein
V$NKXH/DLX1.01 DLX-1, −2, and −5 binding 0.91 1005-1017 1011 (+) 1.000 0.988 taatAATTaagtc
sites
V$RBIT/BRIGHT.01 Bright, B cell regulator of IgH 0.92 1005-1017 1011 (+) 1.000 0.931 taataATTAagtc
transcription
V$TBPF/ATATA.01 Avian C-type LTR TATA box 0.81 1005-1021 1013 (+) 1.000 0.881 taataatTAAGtcagag
V$CREB/CREBP1.01 cAMP-responsive element 0.80 1004-1024 1014 (−) 0.766 0.819 tagctctgACTTaattattaa
binding protein 1
v$RORA/RORA2.01 RAR-related orphan receptor 0.82 1007-1023 1015 (+) 0.750 0.874 ataattaAGTCagagct
alpha2
V$PCAT/CAAT.01 cellular and viral CCAAT box 0.90 1022-1032 1027 (+) 0.856 0.928 ctagCCATtaa
V$NKXH/NKX25.02 homeo domain factor Nkx- 0.88 1022-1034 1028 (−) 1.000 0.903 tctTAATggctag
2.5/Csx, tinman homolog low
affinity sites
V$CREB/HLF.01 hepatic leukemia factor 0.84 1022-1042 1032 (−) 0.770 0.842 ctagtGTTTcttaatggctag
V$HOXF/HOX1-3.01 Hox-1.3, vertebrate 0.83 1056-1072 1064 (+) 1.000 0.891 gcttcataATTAatata
homeobox protein
V$HOMS/S8.01 Binding site for S8 type 0.97 1061-1069 1065 (−) 1.000 0.995 attaATTAt
homeodomains
V$NKXH/DLX1.01 DLX-1, −2, and −5 binding 0.91 1059-1071 1065 (+) 1.000 0.988 tcatAATTaatat
sites
V$RBIT/BRIGHT.01 Bright, B cell regulator of IgH 0.92 1059-1071 1065 (+) 1.000 0.952 tcataATTAatat
transcription
V$BRNF/BRN2.01 POU factor Brn-2 (N-Oct 3) 0.91 1058-1074 1066 (+) 1.000 0.945 ttcataatTAATatagt
V$OCT1/OCT1.06 octamer-binding factor 1 0.80 1060-1074 1067 (−) 1.000 0.885 actatattAATTatg
V$HOXF/HOX1-3.01 Hox-1.3, vertebrate 0.83 1061-1077 1069 (−) 1.000 0.854 gatactatATTAattat
homeobox protein
V$OCT1/OCT1.06 octamer-binding factor 1 0.80 1079-1093 1086 (+) 0.750 0.875 tgtatgttCATTtgg
V$FAST/FAST1.01 FAST-1 SMAD interacting 0.81 1080-1094 1087 (+) 0.850 0.887 gtatgttCATTtggg
protein
V$RREB/RREB1.01 Ras-responsive element 0.79 1081-1095 1088 (−) 1.000 0.816 cCCCAaatgaacata
binding protein 1
V$E2FF/E2F.02 E2F, involved in cell cycle 0.84 1085-1099 1092 (−) 1.000 0.849 tcagcccCAAAtgaa
regulation, interacts with Rb
p107 protein
V$CREB/TAXCREB.01 Tax/CREB complex 0.81 1091-1111 1101 (+) 1.000 0.828 tggggcTGACacagttctggg
V$AP1F/VMAF.01 v-Maf 0.82 1092-1112 1102 (+) 1.000 0.833 ggggcTGACacagttctggga
V$MYT1/MYT1.01 MyT1 zinc finger transcription 0.75 1123-1135 1129 (+) 0.750 0.791 aggAAGAytactt
factor involved in primary
neurogenesis
V$CLOX/CLOX.01 Clox 0.81 1136-1152 1144 (−) 0.804 0.820 cctacaATCCatgtacc
V$HNF4/HNF4.01 Hepatic nuclear factor 4 0.82 1156-1172 1164 (−) 1.000 0.864 atagagCAAAggactac
V$LEFF/LEF1.01 TCF/LEF-1, involved in the 0.86 1157-1173 1165 (−) 1.000 0.907 catagagCAAAggacta
Wnt signal transduction
pathway
V$PERO/PPARA.01 PPAR/RXR heterodimers 0.70 1157-1177 1167 (−) 1.000 0.700 tagacatagagcAAAGgacta
V$CLOX/CLOX.01 Clox 0.81 1173-1189 1181 (+) 0.804 0.831 gtctaaATCCatatatg
V$HNF6/HNF6.01 Liver enriched Cut - 0.82 1175-1189 1182 (+) 0.833 0.929 ctaaaTCCAtatatg
Homeodomain transcription
factor HNF6 (ONECUT)
V$SRFF/SRF.02 serum response factor 0.83 1177-1195 1186 (+) 1.000 0.851 aaatCCATatatgaatgag
V$CLOX/CDPCR3.01 cut-like homeodomain protein 0.75 1180-1196 1188 (−) 1.000 0.761 actcattcatatATGGa
V$PIT1/PIT1.01 Pit1, GHF-1 pituitary specific 0.86 1186-1196 1191 (−) 1.000 0.919 actcATTCata
pou domain transcription
factor
V$HMTB/MTBF.01 muscle-specific Mt binding 0.90 1196-1204 1200 (−) 0.807 0.901 tggtATGTa
site
V$FKHD/HFH8.01 HNF-3/Fkh Homolog-8 0.92 1200-1216 1208 (−) 1.000 0.922 gaaagayAAACatggta
V$E4FF/E4F.01 GLI-Krueppel-related 0.82 1223-1235 1229 (−) 0.789 0.898 gtgAGGTaacccc
transcription factor, regulator
of adenovirus E4 promoter
V$CREB/HLF.01 hepatic leukemia factor 0.84 1221-1241 1231 (+) 1.000 0.854 atgggGTTAcctcactcagga
V$VBPF/VBP.01 PAR-type chicken vitellogenin 0.86 1226-1236 1231 (+) 1.000 0.903 gTTACctcact
promoter-binding protein
V$OCT1/OCT.01 Octamer binding site 0.79 1259-1273 1266 (−) 0.758 0.870 cgcAGGCaaatgaat
(OCT1/OCT2 consensus)
V$STAT/STAT6.01 STAT6: signal transducer and 0.84 1261-1279 1270 (+) 0.758 0.850 tcattTGCCtgcgaatttt
activator of transcription 6
V$CDXF/CDX2.01 Cdx-2 mammalian caudal 0.84 1270-1288 1279 (+) 1.000 0.869 tgcgaatTTTAagattcca
related intestinal transcr.
factor
V$SORY/SOX9.01 SOX (SRY-related HMG box) 0.90 1280-1296 1288 (−) 1.000 0.990 taaaaCAATggaatctt
V$FKHD/HFH2.01 HNF-3/Fkh Homolog 2 0.93 1285-1301 1293 (−) 1.000 0.931 aggaataaAACAatgga
V$CDXF/CDX2.01 Cdx-2 mammalian caudal 0.84 1286-1304 1295 (+) 1.000 0.865 ccattgtTTTAttcctctg
related intestinal transcr.
factor
V$OCTB/TST1.01 POU-factor Tst-1/Oct-6 0.87 1288-1302 1295 (−) 0.894 0.876 gaggAATAaaacaat
V$PDX1/ISL1.01 Pancreatic and intestinal lim- 0.82 1298-1318 1308 (+) 1.000 0.824 tcctctgagTAATactccatt
homeodomain factor
V$SORY/SOX9.01 SOX (SRY-related HMG box) 0.90 1308-1324 1316 (−) 1.000 0.925 ttacaCAATggagtatt
V$CREB/HLF.01 hepatic leukemia factor 0.84 1310-1330 1320 (−) 0.901 0.920 ggtacATTAcacaatggagta
V$VBPF/VBP.01 PAR-type chicken vitellogenin 0.86 1315-1325 1320 (−) 1.000 0.871 aTTACacaatg
promoter-binding protein
V$CEBP/CEBPB.01 CCAAT/enhancer binding 0.94 1313-1331 1322 (+) 0.929 0.955 tccattgtGTAAtgtacca
protein beta
V$PDX1/ISL1.01 Pancreatic and intestinal lim- 0.82 1313-1333 1323 (+) 1.000 0.859 tccattgtgTAATgtaccaca
homeodomain factor
V$HAML/AML1.01 runt-factor AML-1 1.00 1323-1337 1330 (−) 1.000 1.000 aaaatgTGGTacatt
V$GREF/ARE.01 Androgene receptor binding 0.80 1323-1341 1332 (+) 0.750 0.819 aatgtaccacaTTTTctcc
site
V$TEAF/TEF1.01 TEF-1 related muscle factor 0.84 1343-1355 1349 (+) 1.000 0.896 taCATTcttcagt
V$CMYB/CMYB.01 c-Myb, important in 0.99 1352-1360 1356 (+) 1.000 0.990 caGTTGagg
hematopoesis, cellular
equivalent to avian
myoblastosis virus oncogene
v-myb
V$AP4R/TH1E47.01 Thing1/E47 heterodimer, TH1 0.93 1378-1394 1386 (−) 1.000 0.932 gcaatagCCAGaacctg
bHLH member specific
expression in a variety of
embryonic tissues
V$CP2F/CP2.01 CP2 0.90 1384-1394 1389 (−) 1.000 0.945 gcaatagCCAG
V$CHOP/CHOP.01 heterodimers of CHOP and 0.90 1386-1398 1392 (−) 1.000 0.951 attTGCAatagcc
C/EBPalpha
V$CEBP/CEBP.02 C/EBP binding site 0.85 1385-1403 1394 (+) 1.000 0.853 tggctattGCAAataaccc
V$MEF2/HMEF2.01 myocyte enhancer factor 0.76 1384-1406 1395 (+) 1.000 0.809 ctggctattgcAAATaaccctgc
V$OCT1/OCT1.03 octamer-binding factor 1 0.85 1388-1402 1395 (+) 1.000 0.889 ctattgcAAATaacc
V$HMTB/MTBF.01 muscle-specific Mt binding 0.90 1394-1402 1398 (−) 1.000 0.900 ggttATTTg
site
V$CLOX/CDPCR3.01 cut-like homeodomain protein 0.75 1422-1438 1430 (+) 0.975 0.761 acatatgtcattATTGt
V$OCT1/OCT1.05 octamer-binding factor 1 0.90 1423-1437 1430 (+) 0.944 0.938 cATATgtcattattg
V$HOXF/HOX1-3.01 Hox-1.3, vertebrate 0.83 1423-1439 1431 (+) 1.000 0.836 catatgtcATTAttgta
homeobox protein
V$PDX1/PDX1.01 Pdx1 (IDX1/IPF1) pancreatic 0.74 1423-1443 1433 (−) 1.000 0.889 ttcatacaaTAATgacatatg
and intestinal homeodomain
TF
V$SORY/SOX5.01 Sox-5 0.87 1426-1442 1434 (−) 1.000 0.870 tcataCAATaatgacat
V$OCT1/OCT1.05 octamer-binding factor 1 0.90 1444-1458 1451 (−) 0.944 0.914 aATATgtaaaacaga
V$CREB/E4BP4.01 E4BP4, bZIP domain, 0.80 1443-1463 1453 (−) 1.000 0.856 tttaaaatatGTAAaacagat
transcriptional repressor
V$VBPF/VBP.01 PAR-type chicken vitellogenin 0.86 1449-1459 1454 (+) 1.000 0.886 tTTACatattt
promoter-binding protein
V$TBPF/MTATA.01 Muscle TATA box 0.84 1455-1471 1463 (+) 1.000 0.841 tatttTAAAccatctct
V$PBXF/PBX1.01 homeo domain factor Pbx-1 0.78 1469-1481 1475 (−) 1.000 0.783 caagCAATctaga
V$COMP/COMP1.01 COMP1, cooperates with 0.76 1467-1487 1477 (+) 1.000 0.765 tctctagATTGcttgtaatat
myogenic proteins in
multicomponent complex
V$SORY/SOX5.01 Sox-5 0.87 1478-1494 1486 (−) 1.000 0.997 tttaaCAATattacaag
V$FKHD/FREAC2.01 Fork head RElated ACtivator-2 0.84 1485-1501 1493 (+) 1.000 0.885 tattgtTAAAcatagag
V$PDX1/ISL1.01 Pancreatic and intestinal lim- 0.82 1495-1515 1505 (+) 1.000 0.839 catagagagTAATaatgctat
homeodomain factor
V$HOXF/HOX1-3.01 Hox-1.3, vertebrate 0.83 1499-1515 1507 (−) 1.000 0.872 atagcattATTActctc
homeobox protein
V$PDX1/PDX1.01 Pdx1 (IDX1/IPF1) pancreatic 0.74 1498-1518 1508 (−) 0.826 0.843 tttatagcaTTATtactctct
and intestinal homeodomain
TF
V$CART/XVENT2.01 Xenopus homeodomain factor 0.82 1502-1518 1510 (+) 1.000 0.829 agTAATaatgctataaa
Xvent-2; early BMP signaling
response
V$CDXF/CDX2.01 Cdx-2 mammalian caudal 0.84 1507-1525 1516 (−) 1.000 0.906 tttaattTTTAtagcatta
related intestinal transcr.
factor
V$MEF2/MEF2.05 MEF2 0.96 1505-1527 1516 (+) 1.000 0.983 aataatgctaTAAAaattaaaaa
V$HNF1/HNF1.01 hepatic nuclear factor 1 0.78 1510-1526 1518 (−) 0.755 0.805 tTTTAatttttatagca
V$OCT1/OCT1.06 octamer-binding factor 1 0.80 1511-1525 1518 (+) 1.000 0.832 gctataaaAATTaaa
V$TBPF/TATA.02 Mammalian C-type LTR TATA 0.89 1510-1526 1518 (+) 1.000 0.991 tgctaTAAAaattaaaa
box
V$NKXH/MSX.01 Homeodomain proteins MSX- 0.97 1514-1526 1520 (−) 1.000 0.989 tttTAATttttat
1 and MSX-2
V$RBIT/BRIGHT.01 Bright, B cell regulator of IgH 0.92 1515-1527 1521 (+) 1.000 0.944 taaaaATTAaaaa
transcription
V$MEF2/AMEF2.01 myocyte enhancer factor 0.80 1514-1536 1525 (+) 1.000 0.807 ataaaaatTAAAaataatgataa
V$EVI1/EVI1.02 Ecotropic viral integration site 0.83 1526-1542 1534 (+) 1.000 0.872 aataatgatAAGAaaga
1 encoded factor
V$GATA/GATA1.02 GATA-binding factor 1 0.99 1528-1540 1534 (+) 1.000 0.993 taatGATAagaaa
V$GATA/GATA3.02 GATA-binding factor 3 0.91 1537-1549 1543 (+) 1.000 0.931 gaaAGATcctata
V$GATA/GATA3.02 GATA-binding factor 3 0.91 1559-1571 1565 (+) 1.000 0.915 tacAGATgaaaat
V$OCT1/OCT1.02 octamer-binding factor 1 0.82 1561-1575 1568 (+) 0.763 0.867 cagATGAaaatttag
V$CEBP/CEBPB.01 CCAAT/enhancer binding 0.94 1567-1585 1576 (+) 0.985 0.964 aaaatttaGAAAtacttta
protein beta
V$PLZF/PLZF.01 Promyelocytic leukemia zink 0.86 1574-1588 1581 (−) 0.958 0.866 agcTAAAgtatttct
finger (TF with nine Krueppel-
like zink fingers)
V$PAX3/PAX3.01 Pax-3 paired domain protein, 0.76 1587-1599 1593 (−) 1.000 0.763 TCGTcagtggtag
expressed in embryogenesis,
mutations correlate to
Waardenburg Syndrome
V$CREB/ATF.01 activating transcription factor 0.90 1588-1608 1598 (+) 1.000 0.923 taccacTGACgaaatttgtat
V$AP4R/TH1E47.01 Thing1/E47 heterodimer, TH1 0.93 1614-1630 1622 (−) 1.000 0.959 tttaattCCAGacattc
bHLH member specific
expression in a variety of
embryonic tissues
V$NKXH/MSX.01 Homeodomain proteins MSX- 0.97 1619-1631 1625 (−) 1.000 0.977 cttTAATtccaga
1 and MSX-2
V$RBIT/BRIGHT.01 Bright, B cell regulator of IgH 0.92 1620-1632 1626 (+) 1.000 0.923 ctggaATTAaaga
transcription
V$OCTB/TST1.01 POU-factor Tst-1/Oct-6 0.87 1620-1634 1627 (+) 1.000 0.898 ctggAATTaaagaaa
V$NKXH/DLX3.01 Distal-less 3 homeodomain 0.91 1628-1640 1634 (−) 1.000 0.915 cagTAATttcttt
transcription factor
V$GREF/PRE.01 Progesterone receptor binding 0.84 1628-1646 1637 (+) 1.000 0.922 aaagaaattacTGTTcttt
site
V$TBPF/TATA.01 cellular and viral TATA box 0.90 1636-1652 1644 (−) 1.000 0.934 ttataTAAAgaacagta
elements
V$FKHD/XFD2.01 Xenopus fork head domain 0.89 1637-1653 1645 (−) 1.000 0.890 attataTAAAgaacagt
factor 2
V$TBPF/TATA.01 cellular and viral TATA box 0.90 1638-1654 1646 (−) 0.891 0.923 tattaTATAaagaacag
elements
V$CREB/E4BP4.01 E4BP4, bZIP domain, 0.80 1638-1658 1648 (−) 0.769 0.856 ctattattatATAAagaacag
transcriptional repressor
V$PDX1/ISL1.01 Pancreatic and intestinal lim- 0.82 1644-1664 1654 (+) 1.000 0.836 tttatataaTAATagactgta
homeodomain factor
V$COMP/COMP1.01 COMP1, cooperates with 0.76 1648-1668 1658 (+) 0.791 0.760 tataataATAGactgtaaaat
myogenic proteins in
multicomponent complex
V$TBPF/TATA.02 Mammalian C-type LTR TATA 0.89 1658-1674 1666 (+) 1.000 0.912 gactgTAAAatggcaac
box
V$IRFF/ISRE.01 interferon-stimulated 0.81 1662-1676 1669 (+) 0.750 0.817 gtaaaatgGCAActt
response element
V$XBBF/RFX1.01 X-box binding protein RFX1 0.89 1660-1678 1669 (+) 1.000 0.907 ctgtaaaatgGCAActttt
V$MYT1/MYT1.02 MyT1 zinc finger transcription 0.88 1667-1679 1673 (−) 1.000 0.882 taaAAGTtgccat
factor involved in primary
neurogenesis
V$OCT1/OCT1.06 octamer-binding factor 1 0.80 1683-1697 1690 (+) 1.000 0.878 tatttgctAATTcac
V$AP1F/TCF11MAFG.01 TCF11/MafG heterodimers, 0.81 1681-1701 1691 (−) 0.777 0.865 tcctgTGAAttagcaaatatt
binding to subclass of AP1
sites
V$NKXH/MSX2.01 Muscle segment homeo box 0.95 1687-1699 1693 (+) 1.000 0.969 tgCTAAttcacag
2, homologue of Drosophila
(HOX 8)
V$FAST/FAST1.01 FAST-1 SMAD interacting 0.81 1687-1701 1694 (−) 0.850 0.866 tcctgtgAATTagca
protein
V$PBXC/ Binding site for a Pbx1/Meis1 0.76 1686-1702 1694 (+) 0.750 0.788 ttgctaatTCACaggat
PBX1_MEIS1.03 heterodimer
V$CIZF/NMP4.01 NMP4 (nuclear matrix protein 0.97 1699-1709 1704 (−) 1.000 0.973 agAAAAaatcc
4)/CIZ (Cas-interacting zinc
finger protein)
V$STAT/STAT6.01 STAT6: signal transducer and 0.84 1702-1720 1711 (−) 1.000 0.908 agatgTTCCaaagaaaaaa
activator of transcription 6
V$AP4R/ Tal-1beta/E47 heterodimer 0.87 1710-1726 1718 (−) 1.000 0.919 ttgttCAGAtgttccaa
TAL1BETAE47.01
V$SORY/HMGIY.01 HMGI(Y) high-mobility-group 0.92 1720-1736 1728 (+) 1.000 0.953 tgaacaAATTtccctta
protein I (Y), architectural
transcription factor organizing
the framework of a nuclear
protein-DNA transcriptional
complex
V$MYT1/MYT1.01 MyT1 zinc finger transcription 0.75 1723-1735 1729 (+) 0.750 0.757 acaAATTtccctt
factor involved in primary
neurogenesis
V$SRFF/SRF.01 serum response factor 0.66 1728-1746 1737 (+) 1.000 0.771 tttccctTATAtgaatcac
V$HOXF/HOXA9.01 Member of the vertebrate 0.87 1731-1747 1739 (−) 1.000 0.908 agtGATTcatataaggg
HOX - cluster of homeobox
factors
V$HOXT/ Homeobox protein MEIS1 0.79 1734-1746 1740 (−) 1.000 0.797 gTGATtcatataa
MEIS1_HOXA9.01 binding site
V$PIT1/PIT1.01 Pit1, GHF-1 pituitary specific 0.86 1737-1747 1742 (−) 1.000 0.912 agtgATTCata
pou domain transcription
factor
V$AP1F/AP1.01 AP1 binding site 0.95 1734-1754 1744 (+) 0.881 0.958 ttatatgaATCActtacattt
V$VBPF/VBP.01 PAR-type chicken vitellogenin 0.86 1746-1756 1751 (+) 1.000 0.860 cTTACattttt
promoter-binding protein
V$FAST/FAST1.01 FAST-1 SMAD interacting 0.81 1757-1771 1764 (+) 0.850 0.829 gcctgttCATTtaaa
protein
V$HOXF/EN1.01 Homeobox protein engrailed 0.77 1759-1775 1767 (−) 1.000 0.832 gtttTTTAaatgaacag
(en-1)
V$TBPF/MTATA.01 Muscle TATA box 0.84 1763-1779 1771 (+) 1.000 0.853 tcattTAAAaaactgca
V$ETSF/ETS2.01 c-Ets-2 binding site 0.86 1774-1790 1782 (+) 1.000 0.866 actgcAGGAaagttgtg
V$MYT1/MYT1.02 MyT1 zinc finger transcription 0.88 1780-1792 1786 (+) 1.000 0.891 ggaAAGTtgtgat
factor involved in primary
neurogenesis
V$GFI1/GFI1.01 Growth factor independence 1 0.97 1782-1796 1789 (−) 1.000 1.000 ataAATCacaacttt
zinc finger protein acts as
transcriptional repressor
V$TBPF/TATA.01 cellular and viral TATA box 0.90 1784-1800 1792 (−) 1.000 0.931 cattaTAAAtcacaact
elements
V$BRNF/BRN2.01 POU factor Brn-2 (N-Oct 3) 0.91 1786-1802 1794 (−) 1.000 0.933 tgcattatAAATcacaa
V$HOXT/ Homeobox protein MEIS1 0.79 1788-1800 1794 (+) 1.000 0.924 gTGATttataatg
MEIS1_HOXA9.01 binding site
V$MEF2/AMEF2.01 myocyte enhancer factor 0.80 1783-1805 1794 (−) 0.866 0.827 agttgcatTATAaatcacaactt
V$OCTB/TST1.01 POU-factor Tst-1/Oct-6 0.87 1787-1801 1794 (+) 0.894 0.898 tgtgATTTataatgc
V$HOXF/HOXA9.01 Member of the vertebrate 0.87 1787-1803 1795 (+) 1.000 0.971 tgtGATTtataatgcaa
HOX - cluster of homeobox
factors
V$BRNF/BRN2.01 POU factor Brn-2 (N-Oct 3) 0.91 1788-1804 1796 (+) 1.000 0.916 gtgatttaTAATgcaac
V$PARF/DBP.01 Albumin D-box binding 0.84 1791-1805 1798 (+) 0.884 0.891 atttaTAATgcaact
protein
V$OCT1/OCT1.02 octamer-binding factor 1 0.82 1795-1809 1802 (+) 1.000 0.861 ataATGCaactgcac
V$FKHD/FREAC2.01 Fork head RElated ACtivator-2 0.84 1816-1832 1824 (+) 1.000 0.910 cagtctTAAAcaatgct
V$SORY/SOX5.01 Sox-5 0.87 1821-1837 1829 (+) 1.000 0.992 ttaaaCAATgctaacca
V$AREB/AREB6.04 AREB6 (Atp1a1 regulatory 0.98 1837-1849 1843 (+) 1.000 0.981 actgtGTTTcagc
element binding factor 6)
V$MYT1/MYT1.02 MyT1 zinc finger transcription 0.88 1848-1860 1854 (−) 1.000 0.889 gggAAGTttatgc
factor involved in primary
neurogenesis
V$RBPF/RBPJK.01 Mammalian transcriptional 0.84 1851-1865 1858 (−) 1.000 0.878 tgtgTGGGaagttta
repressor RBP-Jkappa/CBF1
V$OCT1/OCT1.02 octamer-binding factor 1 0.82 1875-1889 1882 (+) 0.763 0.826 actATGAaaacacat
V$FKHD/FREAC4.01 Fork head RElated ACtivator-4 0.78 1875-1891 1883 (+) 1.000 0.786 actatgaaAACAcatgc
V$EBOX/MYCMAX.02 c-Myc/Max heterodimer 0.92 1880-1896 1888 (+) 0.895 0.920 gaaaaCACAtgcttaaa
V$PAX6/PAX6.01 Pax-6 paired domain protein 0.75 1880-1898 1889 (−) 0.773 0.791 cctttAAGCatgtgttttc
V$IRFF/IRF3.01 Interferon regulatory factor 3 0.86 1891-1905 1898 (+) 1.000 0.874 cttaaaggCAAAtct
(IRF-3)
V$HNF1/HNF1.02 Hepatic nuclear factor 1 0.76 1895-1911 1903 (−) 0.858 0.782 aGGTAaagatttgcctt
V$FKHD/FREAC2.01 Fork head RElated ACtivator-2 0.84 1898-1914 1906 (−) 1.000 0.853 ctgaggTAAAgatttgc
V$E4FF/E4F.01 GLI-Krueppel-related 0.82 1902-1914 1908 (−) 0.789 0.830 ctgAGGTaaagat
transcription factor, regulator
of adenovirus E4 promoter
V$CREB/CREBP1.01 cAMP-responsive element 0.80 1900-1920 1910 (+) 0.766 0.820 aaatctttACCTcagttaact
binding protein 1
V$VBPF/VBP.01 PAR-type chicken vitellogenin 0.86 1905-1915 1910 (+) 1.000 0.862 tTTACctcagt
promoter-binding protein
V$MYT1/MYT1.01 MyT1 zinc finger transcription 0.75 1912-1924 1918 (−) 0.750 0.775 gaaTAGTtaactg
factor involved in primary
neurogenesis
V$HNF1/HNF1.01 hepatic nuclear factor 1 0.78 1913-1929 1921 (+) 1.000 0.811 aGTTAactattccatag
V$PCAT/CAAT.01 cellular and viral CCAAT box 0.90 1928-1938 1933 (+) 0.856 0.925 agagCCATtga
V$HNF6/HNF6.01 Liver enriched Cut - 0.82 1929-1943 1936 (−) 1.000 0.873 tgaacTCAAtggctc
Homeodomain transcription
factor HNF6 (ONECUT)
V$PXRF/PXRCAR.01 Halfsite of PXR (pregnane X 0.98 1935-1945 1940 (−) 1.000 0.980 ctTGAActcaa
receptor)/RXR resp. CAR
(constitutive androstane
receptor)/RXR heterodimer
binding site
V$RARF/RTR.01 Retinoid receptor-related 0.81 1934-1952 1943 (+) 1.000 0.854 attgagtTCAAgtgcattt
testis-associated receptor
(GCNF/RTR)
V$HOXF/EN1.01 Homeobox protein engrailed 0.77 1936-1952 1944 (+) 0.782 0.813 tgagTTCAagtgcattt
(en-1)
V$NKXH/NKX25.01 homeo domain factor Nkx- 1.00 1939-1951 1945 (+) 1.000 1.000 gttcAAGTgcatt
2.5/Csx, tinman homolog,
high affinity sites
V$GATA/GATA3.02 GATA-binding factor 3 0.91 1953-1965 1959 (+) 1.000 0.928 agaAGATataatg
V$TBPF/TATA.01 cellular and viral TATA box 0.90 1968-1984 1976 (−) 0.891 0.912 atataTATAtggccata
elements
V$SRFF/SRF.01 serum response factor 0.66 1969-1987 1978 (+) 1.000 0.777 atggccaTATAtatatata
V$CLOX/CDPCR3.01 cut-like homeodomain protein 0.75 1972-1988 1980 (−) 1.000 0.806 atatatatatatATGGc
V$PAX1/PAX1.01 Pax1 paired domain protein, 0.61 2016-2034 2025 (−) 0.750 0.675 CTGTgctgatatatatata
expressed in the developing
vertebral column of mouse
embryos
V$TBPF/ATATA.01 Avian C-type LTR TATA box 0.81 2019-2035 2027 (+) 0.750 0.827 atatataTCAGcacagt
V$GFI1/GfI1B.01 Growth factor independence 1 0.82 2021-2035 2028 (+) 1.000 0.904 ataTATCagcacagt
zinc finger protein Gfi-1B
V$NRSF/NRSF.01 neuron-restrictive silencer 0.69 2025-2045 2035 (+) 1.000 0.704 atcAGCAcagtggaaacagtt
factor
V$NFAT/NFAT.01 Nuclear factor of activated T- 0.97 2033-2043 2038 (+) 1.000 0.970 agtgGAAAcag
cells
V$AREB/AREB6.04 AREB6 (Atp1a1 regulatory 0.98 2034-2046 2040 (−) 1.000 0.991 taactGTTTccac
element binding factor 6)
V$HNF1/HNF1.01 hepatic nuclear factor 1 0.78 2036-2052 2044 (−) 1.000 0.798 tGTTAttaactgtttcc
V$FKHD/XFD3.01 Xenopus fork head domain 0.82 2038-2054 2046 (+) 0.826 0.824 aaacagttAATAacatt
factor 3
V$PDX1/PDX1.01 Pdx1 (IDX1/IPF1) pancreatic 0.74 2036-2056 2046 (+) 1.000 0.749 ggaaacagtTAATaacatttt
and intestinal homeodomain
TF
V$OCT1/OCT1.01 octamer-binding factor 1 0.77 2050-2064 2057 (−) 1.000 0.863 taTATGctaaaatgt
V$TBPF/TATA.01 cellular and viral TATA box 0.90 2053-2069 2061 (−) 0.891 0.908 tagtaTATAtgctaaaa
elements
V$ETSF/GABP.01 GABP: GA binding protein 0.85 2080-2096 2088 (+) 1.000 0.897 gaggctGGAAgggggct
V$BEL1/BEL1.01 Bel-1 similar region (defined 0.78 2083-2105 2094 (+) 1.000 0.787 gctggaagggggcTCAGcagtta
in Lentivirus LTRs)
V$VMYB/VMYB.01 v-Myb 0.90 2097-2107 2102 (−) 0.876 0.901 attAACTgctg
V$GREF/ARE.01 Androgene receptor binding 0.80 2106-2124 2115 (+) 0.750 0.840 atagcacatacTATTcttc
site
V$PDX1/PDX1.01 Pdx1 (IDX1/IPF1) pancreatic 0.74 2137-2157 2147 (+) 0.782 0.747 gtttggtttTCATcacccatg
and intestinal homeodomain
TF
V$MYOD/MYOD.02 myoblast determining factor 0.98 2154-2168 2161 (−) 1.000 0.988 gaacCACCtgacatg
V$GATA/GATA1.03 GATA-binding factor 1 0.95 2169-2181 2175 (−) 1.000 0.958 tacaGATAgaaat
V$AP4R/ Tal-1beta/E47 heterodimer 0.87 2179-2195 2187 (+) 1.000 0.924 gtaacCAGAtgatacga
TAL1BETAE47.01
V$OAZF/ROAZ.01 Rat C2H2 Zn finger protein 0.73 2204-2220 2212 (−) 0.750 0.762 agGTACccaaggggact
involved in olfactory neuronal
differentiation
V$GATA/GATA1.01 GATA-binding factor 1 0.96 2217-2229 2223 (−) 1.000 0.960 aggtGATAgaggt
V$MYOD/E47.02 TAL1/E47 dimers 0.93 2220-2234 2227 (−) 1.000 0.939 atagCAGGtgataga
V$LTUP/TAACC.01 Lentiviral TATA upstream 0.71 2225-2247 2236 (+) 0.759 0.710 cacctgctattctCACCaaaga
element
V$RREB/RREB1.01 Ras-responsive element 0.79 2239-2253 2246 (+) 1.000 0.805 aCCCAaagacacaca
binding protein 1
V$OCT1/OCT1.05 octamer-binding factor 1 0.90 2251-2265 2258 (−) 0.944 0.904 tGTATgtgagtgtgt
V$OCT1/OCT1.02 octamer-binding factor 1 0.82 2282-2296 2289 (+) 1.000 0.854 tgcATGCacatagtt
V$COUP/COUP.01 COUP antagonizes HNF-4 by 0.81 2284-2298 2291 (−) 0.977 0.855 tGAACtatgtgcatg
binding site competition or
synergizes by direct protein —
protein interaction with HNF-4
V$MEF2/MEF2.01 myogenic enhancer factor 2 0.74 2290-2312 2301 (+) 0.750 0.767 catagttcAAAAaataaaatttt
V$CDXF/CDX2.01 Cdx-2 mammalian caudal 0.84 2296-2314 2305 (−) 1.000 0.896 ttaaaatTTTAttttttga
related intestinal transcr.
factor
V$MYT1/MYT1.01 MyT1 zinc finger transcription 0.75 2301-2313 2307 (−) 0.750 0.798 taaAATTttattt
factor involved in primary
neurogenesis
V$NFAT/NFAT.01 Nuclear factor of activated T- 0.97 2314-2324 2319 (+) 1.000 0.991 aaagGAAAaaa
cells
V$CIZF/NMP4.01 NMP4 (nuclear matrix protein 0.97 2317-2327 2322 (+) 1.000 0.977 ggAAAAaaagc
4)/CIZ (Cas-interacting zinc
finger protein)
V$GATA/GATA3.02 GATA-binding factor 3 0.91 2326-2338 2332 (−) 1.000 0.946 aaaAGATttgagc
V$HMTB/MTBF.01 muscle-specific Mt binding 0.90 2351-2359 2355 (−) 1.000 0.901 aggaATTTt
site
V$NOLF/OLF1.01 olfactory neuron-specific 0.82 2350-2372 2361 (+) 0.806 0.820 taaaatTCCTatgagtgtgtgat
factor
V$PDX1/PDX1.01 Pdx1 (IDX1/IPF1) pancreatic 0.74 2363-2383 2373 (−) 0.782 0.753 tactgacttTGATcacacact
and intestinal homeodomain
TF
V$GATA/GATA3.02 GATA-binding factor 3 0.91 2395-2407 2401 (−) 1.000 0.942 cacAGATtatacc
V$NFAT/NFAT.01 Nuclear factor of activated T- 0.97 2406-2416 2411 (+) 1.000 0.971 tgtgGAAAaca
cells
V$OCTP/OCT1P.01 octamer-binding factor 1, 0.86 2433-2445 2439 (+) 0.980 0.879 ctcagtATTCaca
POU-specific domain
V$MITF/MIT.01 MIT (microphthalmia 0.81 2438-2456 2447 (−) 1.000 0.827 ctactttCATGtgtgaata
transcription factor) and TFE3
V$PAX8/PAX8.01 PAX 2/5/8 binding site 0.88 2441-2453 2447 (−) 0.850 0.952 cttTCATgtgtga
V$TBPF/ATATA.01 Avian C-type LTR TATA box 0.81 2451-2467 2459 (+) 1.000 0.838 aagtagcTAAGaataaa
V$GATA/GATA3.02 GATA-binding factor 3 0.91 2462-2474 2468 (−) 1.000 0.960 aatAGATtttatt
V/$CLOX/CLOX.01 Clox 0.81 2462-2478 2470 (+) 0.806 0.819 aataaaATCTattcatc
V$HNF6/HNF6.01 Liver enriched Cut — 0.82 2464-2478 2471 (+) 0.785 0.846 taaaaTCTAttcatc
Homeodomain transcription
factor HNF6 (ONECUT)
V$PIT1/PIT1.01 Pit1, GHF-1 pituitary specific 0.86 2468-2478 2473 (+) 1.000 0.890 atctATTCatc
pou domain transcription
factor
V$AP4R/ Tal-1beta/ITF-2 heterodimer 0.85 2469-2485 2477 (−) 1.000 0.881 aaaaaCAGAtgaataga
TAL1BETAITF2.01
V$CIZF/NMP4.01 NMP4 (nuclear matrix protein 0.97 2477-2487 2482 (−) 1.000 0.981 ggAAAAacaga
4)/CIZ (Cas-interacting zinc
finger protein)
V$NFAT/NFAT.01 Nuclear factor of activated T- 0.97 2480-2490 2485 (−) 1.000 0.976 taagGAAAaac
cells
V$STAT/STAT.01 signal transducers and 0.87 2479-2497 2488 (−) 1.000 0.872 aggattttaaGGAAaaaca
activators of transcription
V$TBPF/TATA.02 Mammalian C-type LTR TATA 0.89 2484-2500 2492 (+) 1.000 0.897 actgagtcAACActgta
box
V$FKHD/XFD3.01 Xenopus fork head domain 0.82 2501-2517 2509 (−) 1.000 0.880 actgagtcAACActgta
factor 3
V$AP1F/AP1.01 AP1 binding site 0.95 2500-2520 2510 (−) 1.000 0.984 accactgaGTCAacactgtag
V$AP1F/AP1.01 AP1 binding site 0.95 2504-2524 2514 (+) 0.964 0.984 agtgttgaCTCAgtggttgct
V$PCAT/CAAT.01 cellular and viral CCAAT box 0.90 2513-2523 2518 (−) 0.826 0.904 gcaaCCACtga
V$CDXF/CDX2.01 Cdx-2 mammalian caudal 0.84 2524-2542 2533 (+) 1.000 0.883 tttaaatTTTAtgctcaaa
related intestinal transcr.
factor
V$MYT1/MYT1.02 MyT1 zinc finger transcriotion 0.88 2539-2551 2545 (+) 1.000 0.891 caaAAGTtgaagc
factor involved in primary
neurogenesis
V$ETSF/FLI.01 ETS family member FLI 0.81 2560-2576 2568 (+) 1.000 0.829 tgaaCCGGtaattctac
V$MYT1/MYT1.01 MyT1 zinc finger transcription 0.75 2569-2581 2575 (−) 1.000 0.757 acaAAGTagaatt
factor involved in primary
neurogenesis
V$TBPF/ATATA.01 Avian C-type LTR TATA box 0.81 2576-2592 2584 (−) 0.750 0.816 aagtattTAATacaaag
V$SATB/SATB1.01 Special AT-rich sequence- 0.93 2578-2594 2586 (−) 1.000 0.939 acaagtattTAATacaa
binding protein 1,
predominantly expressed in
thymocytes, binds to matrix
attachment regions (MARS)
V$NKXH/NKX31.01 prostate-specific 0.84 2584-2596 2590 (−) 1.000 0.865 taacAAGTattta
homeodomain protein NKX3.1
V$PARF/DBP.01 Albumin D-box binding 0.84 2589-2603 2596 (+) 1.000 0.882 acttgTTATgcatcg
protein
V$PAX5/PAX5.02 B-cell-specific activating 0.75 2591-2619 2605 (−) 1.000 0.758 aacttgatttgttgAGCGatgcataacaa
protein
V$ECAT/NFY.03 nuclear factor Y (Y-box 0.80 2604-2618 2611 (+) 0.750 0.809 ctcaaCAAAtcaagt
binding factor)
V$GFI1/GFI1.01 Growth factor independence 1 0.97 2608-2622 2615 (+) 1.000 0.976 acaAATCaagtttta
zinc finger protein acts as
transcriptional repressor
V$HNF6/HNF6.01 Liver enriched Cut — 0.82 2608-2622 2615 (+) 1.000 0.830 acaaaTCAAgtttta
Homeodomain transcription
factor HNF6 (ONECUT)
V$MYT1/MYT1.01 MyT1 zinc finger transcription 0.75 2610-2622 2616 (−) 0.750 0.756 taaAACTtgattt
factor involved in primary
neurogenesis
V$PAX8/PAX8.01 PAX 2/5/8 binding site 0.88 2610-2622 2616 (+) 1.000 0.907 aaaTCAAgtttta
V$TTFF/TTF1.01 Thyroid transcription factor-1 0.92 2609-2623 2616 (+) 1.000 0.936 caaatCAAGttttaa
(TTF1) binding site
V$MYT1/MYT1.02 MyT1 zinc finger transcription 0.88 2612-2624 2618 (+) 1.000 0.887 atcAAGTtttaac
factor involved in primary
neurogenesis
V$CDXF/CDX2.01 Cdx-2 mammalian caudal 0.84 2612-2630 2621 (+) 1.000 0.883 atcaagtTTTAacacacca
related intestinal transcr.
factor
V$SORY/HMGIY.01 HMGI(Y) high-mobility-group 0.92 2649-2665 2657 (−) 1.000 0.925 ttaaaaAATTtaagata
protein I (Y), architectural
transcription factor organizing
the framework of a nuclear
protein-DNA transcriptional
complex
V$HOXF/EN1.01 Homeobox protein engrailed 0.77 2657-2673 2665 (+) 1.000 0.780 atttTTTAaatgggcat
(en-1)
V$OCT1/OCT1.06 octamer-binding factor 1 0.80 2662-2676 2669 (−) 0.750 0.818 tttatgccCATTtaa
V$BCL6/BCL6.01 POZ/zinc finger protein, 0.76 2683-2699 2691 (+) 1.000 0.796 ctaTTCCtacagaagtc
transcriptional repressor,
translocations observed in
diffuse large cell lymphoma
V$OCTP/OCT1P.01 octamer-binding factor 1, 0.86 2715-2727 2721 (+) 1.000 0.860 ctgaaaATGCatt
POU-specific domain
V$TEAF/TEF1.01 TEF-1 related muscle factor 0.84 2722-2734 2728 (+) 1.000 0.898 tgCATTcctgatt
V$GFI1/GFI1.01 Growth factor independence 1 0.97 2723-2737 2730 (−) 1.000 0.981 ataAATCaggaatgc
zinc finger protein acts as
transcriptional repressor
V$HOXT/ Homeobox protein MEIS1 0.79 2729-2741 2735 (+) 1.000 0.929 cTGATttatgtaa
MEIS1_HOXA9.01 binding site
V$HOXF/HOXA9.01 Member of the vertebrate 0.87 2728-2744 2736 (+) 1.000 0.964 cctGATTtatgtaaata
HOX - cluster of homeobox
factors
V$PARF/DBP.01 Albumin D-box binding 0.84 2729-2743 2736 (+) 1.000 0.861 ctgatTTATgtaaat
protein
V$VBPF/VBP.01 PAR-type chicken vitellogenin 0.86 2732-2742 2737 (−) 1.000 0.929 tTTACataaat
promoter-binding protein
V$CREB/E4BP4.01 E4BP4, bZIP domain, 0.80 2728-2748 2738 (+) 1.000 0.943 cctgatttatGTAAatatatg
transcriptional repressor
V$OCT1/OCT1.01 octamer-binding factor 1 0.77 2733-2747 2740 (+) 1.000 0.895 ttTATGtaaatatat
V$FKHD/XFD1.01 Xenopus fork head domain 0.90 2733-2749 2741 (+) 1.000 0.940 tttatgTAAAtatatgt
factor 1
V$SRFF/SRF.01 serum response factor 0.66 2736-2754 2745 (+) 1.000 0.691 atgtaaaTATAtgtatata
V$OCTP/OCT1P.01 octamer-binding factor 1, 0.86 2746-2758 2752 (+) 0.849 0.883 atgtatATACata
POU-speciflc domain
V$CLOX/CDPCR3.01 cut-like homeodomain protein 0.75 2748-2764 2756 (+) 0.888 0.755 gtatatacatatATAGc
V$TBPF/TATA.01 cellular and viral TATA box 0.90 2749-2765 2757 (−) 0.891 0.903 ggctaTATAtgtatata
elements
V$SRFF/SRF.01 serum response factor 0.66 2750-2768 2759 (+) 1.000 0.709 atatacaTATAtagcctta
V$TBPF/ATATA.01 Avian C-type LTR TATA box 0.81 2759-2775 2767 (−) 1.000 0.816 ttgttttTAAGgctata
V$TBPF/TATA.02 Mammalian C-type LTR TATA 0.89 2762-2778 2770 (+) 1.000 0.899 agcctTAAAaacaaaga
box
V$CABL/CABL.01 Multifunctional c-Abl src type 0.97 2769-2779 2774 (+) 1.000 0.973 aaAACAaagat
tyrosine kinase
V$LEFF/LEF1.01 TCF/LEF-1, involved in the 0.86 2766-2782 2774 (+) 1.000 0.863 ttaaaaaCAAAgattgt
Wnt signal transduction
pathway
V$OCT1/OCT1.06 octamer-binding factor 1 0.80 2775-2789 2782 (+) 1.000 0.811 aagattgtAATTttt
V$MEF2/MMEF2.01 myocyte enhancer factor 0.90 2776-2798 2787 (−) 1.000 0.900 acaatttaTAAAaattacaatct
V$OCT1/OCT1.06 octamer-binding factor 1 0.80 2780-2794 2787 (−) 1.000 0.844 tttataaaAATTaca
V$TBPF/TATA.01 cellular and viral TATA box 0.90 2779-2795 2787 (−) 1.000 0.956 atttaTAAAaattacaa
elements
V$CART/CART1.01 Cart-1 (cartilage 0.84 2780-2796 2788 (+) 1.000 0.875 tgTAATttttataaatt
homeoprotein 1)
V$FKHD/XFD2.01 Xenopus fork head domain 0.89 2780-2796 2788 (−) 1.000 0.903 aatttaTAAAaattaca
factor 2
V$MEF2/MEF2.05 MEF2 0.96 2778-2800 2789 (−) 1.000 0.973 tcacaatttaTAAAaattacaat
V$BRNF/BRN3.01 POU transcription factor Bm-3 0.78 2785-2801 2793 (−) 0.750 0.798 atcACAAtttataaaaa
V$TBPF/TATA.01 cellular and viral TATA box 0.90 2786-2802 2794 (+) 1.000 0.927 ttttaTAAAttgtgatt
elements
V$GFI1/GFI1.01 Growth factor independence 1 0.97 2791-2805 2798 (−) 1.000 0.997 aaaAATCacaattta
zinc finger protein acts as
transcriptional repressor
V$HOXT/ Homeobox protein MEIS1 0.79 2797-2809 2803 (+) 1.000 0.806 gTGATttttaaaa
MEIS1_HOXA9.01 binding site
V$MEF2/MMEF2.01 myocyte enhancer factor 0.90 2792-2814 2803 (−) 1.000 0.923 tattttttTAAAaatcacaattt
V$MEF2/MEF2.05 MEF2 0.96 2795-2817 2806 (+) 1.000 0.990 ttgtgattttTAAAaaaataaac
V$MEF2/MMEF2.01 myocyte enhancer factor 0.90 2797-2819 2808 (+) 1.000 0.905 gtgattttTAAAaaaataaacct
V$HNF1/HNF1.01 hepatic nuclear factor 1 0.78 2802-2818 2810 (−) 0.755 0.796 gGTTTatttttttaaaa
V$MEF2/MEF2.01 myogenic enhancer factor 2 0.74 2799-2821 2810 (+) 0.750 0.775 gatttttaAAAAaataaacctgc
V$HOXF/HOX1-3.01 Hox-1.3, vertebrate 0.83 2814-2830 2822 (+) 1.000 0.848 aaacctgcATTAtcttc
homeobox protein
V$PARF/DBP.01 Albumin D-box binding 0.84 2816-2830 2823 (−) 0.884 0.851 gaagaTAATgcaggt
protein
V$PDX1/ISL1.01 Pancreatic and intestinal lim- 0.82 2814-2834 2824 (−) 1.000 0.853 tgctgaagaTAATgcaggttt
homeodomain factor
V$GATA/GATA1.02 GATA-binding factor 1 0.99 2819-2831 2825 (−) 1.000 0.993 tgaaGATAatgca
V$HEAT/HSF1.01 heat shock factor 1 0.93 2845-2855 2850 (+) 0.867 0.951 TGAAtgttcct
V$MYT1/MYT1.02 MyT1 zinc finger transcription 0.88 2853-2865 2859 (+) 1.000 0.893 cctAAGTtttgta
factor involved in primary
neurogenesis
V$BCL6/BCL6.02 POZ/zinc finger protein, 0.77 2857-2873 2865 (+) 1.000 0.772 agttttgTAGAacttga
transcriptional repressor,
translocations observed in
diffuse large cell lymphoma
V$TTFF/TTF1.01 Thyroid transcription factor-1 0.92 2863-2877 2870 (−) 1.000 0.927 cgtgtCAAGttctac
(TTF1) binding site
V$EBOX/USF.02 upstream stimulating factor 0.94 2868-2884 2876 (−) 1.000 0.997 tctgccaCGTGtcaagt
V$HOXF/PTX1.01 Pituitary Homeobox 1 (Ptx1) 0.79 2892-2908 2900 (+) 1.000 0.795 aggattTTAGtctacac
V$MYOD/LMO2COM.01 complex of Lmo2 bound to 0.98 2901-2915 2908 (−) 1.000 0.981 gatgCAGGtgtagac
Tal-1, E2A proteins, and
GATA-1, half-site 1
V$REBV/EBVR.01 Epstein-Barr virus 0.81 2904-2924 2914 (−) 1.000 0.832 ctgtcctcagatgcaGGTGta
transcription factor R
V$ETSF/PU1.01 Pu.1 (Pu120) Ets-like 0.86 2932-2948 2940 (+) 1.000 0.873 ctaacaGGAAaggagac
transcription factor identified
in lymphoid B-cells
V$MITF/MIT.01 MIT (microphthalmia 0.81 2943-2961 2952 (+) 1.000 0.829 ggagacaCATGtgtggtag
transcription factor) and TFE3
V$HAML/AML1.01 runt-factor AML-1 1.00 2950-2964 2957 (+) 1.000 1.000 catgtgTGGTagttc
V$NFKB/CREL.01 c-Rel 0.91 2954-2968 2961 (+) 1.000 0.919 tgtggtagTTCCcag
V$IKRS/IK3.01 Ikaros 3, potential regulator 0.84 2958-2970 2964 (−) 1.000 0.841 aactgGGAActac
of lymphocyte differentiation
V$RBPF/RBPJK.01 Mammalian transcriptional 0.84 2957-2971 2964 (−) 1.000 0.842 aaacTGGGaactacc
repressor RBP-Jkappa/CBF1
V$E2FF/E2F.01 E2F, involved in cell cycle 0.74 2966-2980 2973 (−) 0.750 0.784 ttcacgtCAAAactg
regulation, interacts with Rb
p107 protein
V$E4FF/E4F.01 GLI-Krueppel-related 0.82 2968-2980 2974 (−) 1.000 0.830 ttcAcGTcaaaac
transcription factor, regulator
of adenovirus E4 promoter
V$CREB/ATF6.02 Activating transcription factor 0.85 2966-2986 2976 (+) 1.000 0.985 cagttttGACGtgaaaagtcc
6, member of b-zip family,
induced by ER stress
V$EBOX/ARNT.01 AhR nuclear translocator 0.89 2968-2984 2976 (+) 1.000 0.891 gttttgaCGTGaaaagt
homodimers
V$E4FF/E4F.01 GLI-Krueppel-related 0.82 2971-2983 2977 (+) 1.000 0.909 ttgACGTgaaaag
transcription factor, regulator
of adenovirus E4 promoter
V$EBOR/XBP1.01 X-box-binding protein 1 0.86 2970-2984 2977 (+) 1.000 0.890 tttgACGTgaaaagt
V$E2FF/E2F.01 E2F, involved in cell cycle 0.74 2971-2985 2978 (+) 1.000 0.837 ttgacgtGAAAagtc
regulation, interacts with Rb
p107 protein
V$STAT/STAT.01 signal transducers and 0.87 2989-3007 2998 (+) 1.000 0.937 cattcttactGGAAacctc
activators of transcription
V$BCL6/BCL6.02 POZ/zinc finger protein, 0.77 2991-3007 2999 (+) 0.800 0.805 ttcttacTGGAaacctc
transcriptional repressor,
translocations observed in
diffuse large cell lymphoma
V$XSEC/STAF.01 Se-Cys tRNA gene 0.77 3003-3025 3014 (+) 0.782 0.791 acctCCCTgaatccatgccaagc
transcription activating factor
V$NF1F/NF1.01 Nuclear factor 1 0.94 3007-3025 3016 (−) 1.000 0.964 gctTGGCatggattcaggg
V$OCT1/OCT1.02 octamer-binding factor 1 0.82 3014-3028 3021 (+) 1.000 0.820 tccATGCcaagcact
V$RCAT/ Mammalian C-type LTR 0.75 3019-3043 3031 (+) 1.000 0.787 gCCAAgcactacccatcaccttgac
CLTR_CAAT.01 CCAAT box
V$SF1F/SF1.01 SF1 steroidogenic factor 1 0.95 3033-3045 3039 (−) 1.000 0.954 cagtCAAGgtgat
V$OCT1/OCT1.01 octamer-binding factor 1 0.77 3038-3052 3045 (−) 1.000 0.800 ctTATGccagtcaag
V$PARF/DBP.01 Albumin D-box binding 0.84 3042-3056 3049 (−) 1.000 0.862 agtgcTTATgccagt
protein
V$ETSF/ETS1.01 c-Ets-1 binding site 0.92 3057-3073 3065 (−) 1.000 0.920 atcaaAGGAaatgagtg
V$LEFF/LEF1.01 TCF/LEF-1, involved in the 0.86 3062-3078 3070 (−) 1.000 0.969 ggggcatCAAAggaaat
Wnt signal transduction
pathway
V$MAZF/MAZ.01 Myc associated zinc finger 0.90 3072-3084 3078 (−) 1.000 0.912 gaggGAGGggcat
protein (MAZ)
V$SP1F/GC.01 GC box elements 0.88 3071-3085 3078 (−) 0.876 0.920 tgagGGAGgggcatc
V$TBPF/TATA.01 cellular and viral TATA box 0.90 3091-3107 3099 (+) 1.000 0.973 tattaTAAAagcacagt
elements
V$SEF1/SEF1.01 SEF1 binding site 0.69 3099-3117 3108 (−) 1.000 0.700 gaaagagacgaCTGTgctt
