# Patent

## Title
Generation of potent dominant negative transcriptional inhibitors

## Abstract

The present invention provides methods and compositions for regulating gene expression using transcription factors linked to proteins that localize to the transcriptional machinery.

## Background
CROSS-REFERENCES TO RELATED APPLICATIONS
The present application claims the benefit of U.S. Ser. No. 60/817,927, filed Jun. 30, 2006, herein incorporated by reference in its entirety.


STATEMENT AS TO RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
This invention was made with government support under Grant Nos. R01 AI29135 and R41CA 103407, awarded by the National Institutes of Health. The government has certain rights in this invention.


BACKGROUND OF THE INVENTION
The regulation of gene expression by transcription factors is a fundamental aspect of the physiology of all cells, whether prokaryotic or eukaryotic. In eukaryotic organisms, for instance, a variety of transcription factors govern cell growth, differentiation, and death. The appropriate spatial and temporal expression of specific transcription factors governs development. As examples, transcription factors such as Myc and E2F control progression through the cell cycle; homeodomain, paired box, and forkhead transcription factors, among others, are involved in embryonic development; p53 is involved with tumor suppression and cell death; steroid hormone receptors, such as sex hormone, glucocorticoid, mineralocorticoid, and thyroid hormone receptors have pleiotrophic effects on various aspects of physiology.
The aberrant expression of transcription factors can lead to abnormal development and various disease states. The inappropriate expression of proto-oncogenes such as c-Myc through chromosomal translocation can lead to cancers such as Burkitt's lymphoma. The formation of a PML-RARa fusion protein has been shown to be responsible for acute promyelocytic leukemia. Loss of p53 expression results in increased susceptibility to various cancers. The inappropriate expression or loss of expression of heart specific transcription factors such as Tbx1, Tbx5, NRx2.5, Gata4, Sal4, and Eya4 have been shown to result in congenital heart defects.
Improved methods for regulating gene expression by modulating transcription factor function would result in more optimal treatment of many diseases.
One disease which might be approached by modulating transcription factor function is acquired immune deficiency syndrome (AIDS). Human immunodeficiency virus (HIV) has been identified as the etiological agent responsible for AIDS, a fatal disease characterized by destruction of the immune system and the inability to fight off life threatening opportunistic infections. Recent statistics indicate that as many as 33 million people worldwide are infected with the virus. In addition to the large number of individuals already infected, the virus continues to spread. Estimates from 1998 point to close to 6 million new infections in that year alone. In the same year there were approximately 2.5 million deaths associated with HIV and AIDS.
HIV is a member of the class of viruses known as retroviruses. The retroviral genome is composed of RNA, which is converted to DNA by reverse transcription. This retroviral DNA is then stably integrated into a host cell's chromosome and, employing the replication machinery of the host cells, produces new retroviral particles and advances the infection to other cells. HIV appears to have a particular affinity for the human T-4 lymphocyte cell, which plays a vital role in the body's immune system. HIV infection of these white blood cells depletes this white cell population. Eventually, the immune system is rendered inoperative and ineffective against various opportunistic diseases such as, among others, pneumocystic carini pneumonia, Kaposi's sarcoma, and cancer of the lymph system.
There are currently a number of antiviral drugs available to combat the infection. These drugs can be divided into four classes based on the viral protein they target and their mode of action. In particular, one class of such antiviral drugs are competitive inhibitors of the aspartyl protease expressed by HIV. Other agents are nucleoside reverse transcriptase inhibitors that behave as substrate mimics to halt viral cDNA synthesis. A class of non-nucleoside reverse transcriptase inhibitors inhibit the synthesis of viral cDNA via a non-competitive (or uncompetitive) mechanism. Another class are drugs that block viral fusion. Used alone, these drugs show effectiveness in reducing viral replication. However, the effects are only temporary as the virus readily develops resistance to all known agents.
As indicated above, a number of critical points in the HIV life cycle have been identified as possible targets for antiviral drugs including (1) the initial attachment of the virion to the T-4 lymphocyte or macrophage site; (2) the transcription of viral RNA to viral DNA (reverse transcriptase, RT); and (3) the processing of gag-pol protein by HIV protease. An additional, potentially attractive therapeutic target is transcription of the HIV genome. Transcription of the HIV genome is essential for replication of the virus after integration of viral DNA into a host cell chromosome. However, attempts to target HIV transcription have been hampered, in part, by the fact that transcription of the integrated HIV genome utilizes the host cell transcriptional machinery as well as viral transcription factors. Thus, therapies that attempt to target the transcription of the HIV genome may also interfere with transcription of normal host cell genes. Attempts have been made to target specifically HIV transcription by the generation of dominant negative forms of Tat, a virally encoded transcription factor. However, these dominant forms have been shown to have poor activity at inhibiting HIV transcription and viral replication.
Effective new methods to target underexploited aspects of the HIV lifecycle, such as transcription of the HIV genome would be desirable.
BRIEF SUMMARY OF THE INVENTION
The present application demonstrates that potent dominant negative regulators of transcription can be generated by linking a transcription factor to a protein that localizes to the transcriptional machinery.
In one embodiment, a method of regulating transcription of a gene is provided in which a nucleic acid construct is expressed in a cell in an amount sufficient for modulation of transcription, where the construct contains a first nucleic acid sequence encoding a transcription factor protein or a fragment thereof linked to a second nucleic acid sequence encoding a protein or a fragment thereof that localizes to the transcriptional machinery. In various aspects, the transcription factor protein can be viral transcription factors, nuclear proto-oncogene or oncogene proteins, nuclear tumor suppressor proteins, heart specific transcription factors, and immune system transcription factors. In some further aspects, the viral transcription factors can be HIV-Tat, HPV-E2, HPV-E7, BPV-E2, Adenovirus IVa2, HSV-1 ICP4, EBNA-LP, EBNA-2, EBNA-3A, EBNA-3B, EBNA-3C, BZLF-1, CMV-IE-1, CMV-IE2, HHSV-8 K bZIP, HBV Hbx, Poxvirus Vaccinia, VETF, HCV NS5A, T-Ag, Adenovirus E1A, Herpesvirus VP16, HTLV Tax, Hepadnavirus X protein, or Baculovirus AcNPV IE-1. In some further aspects, the nuclear proto-oncogene or oncogene proteins can be Abl, Myc, Myb, Rel, Jun, Fos, Spl, Apl, NF-κB, STAT 3 or 5, β-catenin, Notch, GLI, or PML-RARα. In some further aspects, heart specific transcription factors can be Nkx 2, 3, 4, or 5, TBX5, GATA 4, 5, or 6, or MEF2. In some further aspects, the immune cell specific transcription factor can be Ikaros, PU.1, PAX-5, Oct-2, or BOB.1/OBF.1.
In various embodiments, the transcription factor can be a dominant negative transcription factor, or fragment thereof. In further embodiments, the transcription factor can be either a transcriptional activator or repressor. In yet further embodiments, the transcription factor can be an activation domain (AD) fragment of the transcription factor. In yet further embodiments, the transcription factor can be Tat or an activation domain fragment or other fragment of Tat.
In some embodiments, the protein or a fragment thereof that localizes to the transcriptional machinery is a protein with nuclear localization, a component of the transcriptional machinery, or a protein that functions in co-transcriptional processing of RNA. In some aspects, the protein that functions in co-transcriptional processing of RNA is a capping factor, a splicing factor, a polyadenylation factor, an RNA export factor, or a translation factor. In some aspects, the splicing factor is an RS domain containing protein. In yet other aspects, the splicing factor is SF1, U2AF65, or 9G8, and the polyadenylation factor is CstF1.
In some embodiments, the modulation of transcription is inhibition of transcription by at least 25%, or at least 50%, or at least 75%, or at least 95%. In some aspects, the modulation of transcription is by inhibition of transcriptional initiation, or elongation, or termination. In some embodiments, the modulation of transcription is activation of transcription.
In some embodiments, the cell is a T-cell infected with an immunodeficiency virus that can be HIV, FIV, SIV, or BIV. In yet further embodiments, the cell is a cancer cell, heart cell, or immune system cell. In some aspects, the cancer cell is a carcinoma, sarcoma, adenocarcinoma, lymphoma, leukemia, or solid tumors of the kidney, breast, lung, bladder, colon, ovarian, prostate, pancreas, stomach, brain, head and neck, skin, uterine, testicular, glioma, esophagus, or liver. In some aspects, the immune system cell can be a B-cell, T-cell, macrophage, or dendritic cell.
Also included as embodiments are vectors and cells containing the nucleic acids of the embodiments above, as well as, the proteins encoded by these nucleic acids. In further aspects, a composition comprising the nucleic acid construct or protein of the above embodiments and a physiologically acceptable carrier is provided.
In yet further embodiments, a method of regulating transcription of a gene is provided by expressing a nucleic acid construct in a cell in an amount sufficient for modulation of transcription, in which the construct contains a first nucleic acid sequence encoding a transcription factor protein or a fragment thereof linked to a second nucleic acid sequence encoding a splicing factor or a fragment thereof.
In still further embodiments, a method of inhibiting replication of an immunodeficiency virus by expressing a nucleic acid construct in a cell in an amount sufficient for modulation of viral transcription, in which the construct contains a first nucleic acid sequence encoding a transcription factor protein or a fragment thereof linked to a second nucleic acid sequence encoding a protein or a fragment thereof that localizes to the transcriptional machinery.
In another embodiment, provided is a method of inhibiting replication of an immunodeficiency virus by expressing in a cell a nucleic acid construct in an amount sufficient for modulation of viral transcription, in which the construct contains a first nucleic acid sequence encoding a Tat protein or a fragment thereof linked to a second nucleic acid sequence encoding a protein or a fragment thereof that localizes to the transcriptional machinery.
In another embodiment, provided is a method of inhibiting replication of an immunodeficiency virus by expressing in a cell a nucleic acid construct in an amount sufficient for modulation of viral transcription, in which the construct contains a first nucleic acid sequence encoding a transcription factor protein or a fragment thereof linked to a second nucleic acid sequence encoding a splicing factor or a fragment thereof.
In another embodiment, provided is a method of treating a subject infected with an immunodeficiency virus by administering a nucleic acid construct in an amount sufficient for inhibition of viral transcription, in which the construct contains a first nucleic acid sequence encoding a transcription factor or a fragment thereof linked to a second nucleic acid sequence encoding a protein or a fragment thereof that localizes to the transcriptional machinery. In some aspects, the treating is with a protein of the embodiments above.
In another embodiment, provided is a method of inhibiting transcription of a HIV genome in a cell by expressing in the cell a nucleic acid construct in an amount sufficient for inhibition of the transcription of the HIV genome, in which the construct contains a first nucleic acid sequence encoding a Tat protein or a fragment thereof linked to a second nucleic acid sequence encoding a U2AF65 protein or a fragment thereof.
In another embodiment, provided is a method of treating a subject with cancer by expressing in the subject a nucleic acid construct in an amount sufficient for modulation of transcription, in which the construct contains a first nucleic acid sequence encoding a transcription factor protein or a fragment thereof linked to a second nucleic acid sequence encoding a protein or a fragment thereof that localizes to the transcriptional machinery. In some aspects, the treating is with a protein of the embodiments above.
In another embodiment, provided is a method of treating or preventing a disease in a subject by expressing in the subject a nucleic acid construct in an amount sufficient for modulation of transcription, in which the construct contains a first nucleic acid sequence encoding a transcription factor protein or a fragment thereof linked to a second nucleic acid sequence encoding a protein or a fragment thereof that localizes to the transcriptional machinery, where the disease is viral infection, cancer, heart disease, and inflammation.
In another embodiment, provided is a method of validating a target by expressing a nucleic acid construct in a cell in an amount sufficient for modulation of transcription of the gene for the target, in which the construct contains a first nucleic acid sequence encoding a transcription factor protein or a fragment thereof linked to a second nucleic acid sequence encoding a protein or a fragment thereof that localizes to the transcriptional machinery, where altered expression of the gene for the target provides target confirmation.



DESCRIPTION OF THE DRAWINGS
FIG. 1 shows a potent dominant negative Tat inhibitor identified in a reporter assay. a, Left, Schematic of a dual reporter fluorescence assay in which T-BIVRBD (HIV TatAD with the BIV TatRBD) is used to activate an HIV LTR-DsRed reporter engineered with BIV TAR RNA in place of HIV TAR. The T-SF1 fusion protein is used to activate an HIV LTR-GFP reporter engineered with a BPS RNA site. Right, HeLa cells were co-transfected with both reporters and T-SF1 or T-BIVRBD expressors as indicated and sorted by flow cytometry. Expression of GFP is shown in green and DsRed in red. Numbers in each quadrant represent fold activation, calculated as the number of cells in the quadrant multiplied by their average fluorescence, relative to the same values calculated for the reporters alone. b, Dose response curves of T-SF1 activation on an LTR-HTAR-FFL reporter and T-SF1-mediated inhibition of T-BIVRBD activity on a LTR-BTAR-RL reporter. c, Potent inhibition by T-U2AF65 is independent of the RNA-protein interaction. Left, dose response curves showing inhibition of T-BIVRBD-mediated activation of a BIV TAR reporter by TatAD and T-U2AF65. Right, dose response curves showing inhibition of T-Rev-mediated activation of a RREIIB reporter by TatAD and T-U2AF65. The arrows indicate stoichiometric DNA concentrations of inhibitor and activator (5 ng). d, Promoter specificity of T-U2AF65. HeLa cells were transiently transfected with reporter, activator, and several concentrations of T-U2AF65 plasmids at the ratios indicated. For the heat shock response, endogenous HSF1 was activated 24 hr post-transfection cells with 50 μM AsNO2 for 12 hr. p53 activity was measured on SAOS2 cells. Activities of all activators were normalized to a cotransfected CMV-RL reporter control.
FIG. 2 shows contributions of subcellular localization and protein domains to dominant negative activity. a, HeLa cells were transiently co-transfected with an LTR-RREIIB-FFL reporter plasmid, T-Rev activator, and various inhibitors at 1:0.25 (grey bar) or 1:1 (black bar) ratios of activator to inhibitor. Activation levels are plotted relative to T-Rev without inhibitor, and confocal images of each GFP-tagged inhibitor are shown below the plot, including 3× magnification images (of boxed cells above) to highlight the subcellular compartments. T-NLS contains the 8 amino acid NLS of SV40 T-Ag (PPKKKRKV) (SEQ ID NO 1). b, Relative activities of T-U2AF65 RS domain and Tat AD variants, as determined in panel a, with corresponding confocal images. T-U2AF65ΔRS tagged with HA contains a deletion of the first 90 amino acids of U2AF65 and T-RS contains only residues 2-73 of U2AF65. K41A denotes a Tat AD mutation that abolishes interactions with cyclin T112. Confocal images of each HA-tagged inhibitor are shown below the plot, including 3× magnification images (of boxed cells above) to highlight the subcellular compartments.
FIG. 3 shows recruitment of the dominant negative to the HIV promoter via RNAP II blocks transcription elongation. a, T-U2AF65 interacts with RNAP II and P-TEFb. GFP-tagged T-U2AF65, T(K41A)-U2AF65 and T-NLS proteins were immunoprecipitated from cell extracts and analyzed by Western blot using the indicated antibodies. b, T-U2AF65 colocalizes with RNAP II and SC3515. Following HeLa cell transfection, GFP-tagged T-U2AF65 was visualized by confocal microscopy along with immunostained RNAP II and SC35. c, T-U2AF65 blocks transcription elongation. Cells were transfected with Tat or T-U2AF65 as indicated, and RNase protection was performed with a promoter proximal (Pp) probe directed to the LTR and a promoter distal (Pd) probe directed to the FFL ORF to quantify transcription rates in these regions of the LTR-HTAR-FFL reporter. d, Recruitment of RNAP II and T-U2AF65 to the HIV promoter. Left, activation and inhibition levels of a HeLa LTR-RREIIB-FFL reporter cell line used for ChIP assays, with the ratio of inhibitor to activation indicated. Right, ChIP assays from cells transfected with the HA- or GFP-tagged proteins indicated (panels 2-5) or untransfected cells (panel 1), using antibodies directed against HA, GFP, or RNAP II and monitoring the Pd and Pd regions. Mock lanes used normal rabbit IgG for the IP as a specificity control, and input refers to PCR reactions from isolated chromatin samples prior to the IP. e, Promoter-specific recruitment of T-U2AF65. ChIP assays were carried out in HeLa LTR-RRE-IIB-FFL cells transfected with T-U2AF65 or a T-NLS control using primers for HIV, gapdh, hsp70, p21/CIP, HLA-DRA and cad promoters. Known transcription factors that activate each promoter are indicated in parentheses. The percent of input DNA is shown for each individual ChIP experiment, and the amount of DNA used in the GFP lane is twice that for RNAP II.
FIG. 4 shows expression of the Tat dominant negative blocks HIV replication and generates a latency-like state. Sup T1 cells stably expressing the Tat domains or fusion proteins indicated were infected with either HIV Tat-TAR-dependent (a) or BIV Tat-TAR-dependent (b) viruses (18) at an m.o.i. of 1 and the kinetics of p24 antigen expression were monitored by ELISA. Viruses emerging from the inhibitor-expressing cell lines were harvested at day 30 (arrows) and used to re-infect the same cell lines from which they were derived, and identical replication rates were observed.
FIG. 5. Tat RBD is dispensable for dominant negative activity. a, Dose response curves showing inhibition of BIV Tat-TAR-mediated activation by TatAD, Tat, T-U2AF65 and T-HIVRBD-U2AF65. The arrow indicates the position of stoichiometric DNA concentrations (5 ng) of inhibitor and activator. b, Dose response curves showing inhibition of HIV Tat-TAR-mediated activation by TatAD, T-BIVRBD, T-U2AF65 and T-BIVRBD-U2AF65.
FIG. 6 shows relative expression levels of Tat activator and dominant negative. HeLa cells were co-transfected with HA-tagged versions of the T-Rev activator and/or the T-U2AF65 inhibitor along with a GFP-expresor to normalize for transfection efficiency. Nuclear extracts were probed for expression levels with an anti-HA antibody, an anti-GFP antibody, and an anti-C23 nucleolin antibody to provide a protein loading control.
FIG. 7 shows inhibition activities of other T-fusions. HeLa cells were co-transfected with an HIV LTR-RREIIB-FFL reporter plasmid along with the T-Rev activator in the absence or presence of the N-terminal T-fusions at sub-stoichiometric 1:0.25 (black bars) or stoichiometric 1:1 (gray bars) activator: inhibitor ratios. The data shown is normalized to activation by T-Rev alone. Nuclear DAPI staining and indirect immunofluorescence confocal images of the activator and each Tat-fusion protein are shown above, using an anti-Tat antibody and Alexa-488 or Alexa-546 coupled anti-mouse antibodies.
FIG. 8 shows subnuclear localization of U2AF65, T-U2AF65, and variants. HeLa cells were transfected with pEGFP-N3 plasmids expressing GFP fused to: U2AF65, T-U2AF65 (active dominant negative), T(K41A)-U2AF65 (inactive dominant negative), RS (U2AF65 RS domain only), T-RS (active dominant negative), T(K41A)-RS (inactive dominant negative), U2AF65ΔRS, and T-U2AF65ΔRS.
FIG. 9 shows promoter-specificity of the dominant negative. a, Characterization of the SupT1 cell lines by luciferase reporter assays. The indicated SupT1 cell lines were co-transfected with an appropriate activator and reporter pairs as shown. b, Total RNA was extracted from SupT1-TatAD and SupT1-T-U2AF65 stable cell populations and relative mRNA levels of the nine genes shown were quantitated; β-actin (actin), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), eukaryotic translation elongation factor 1 gamma (EEF1G), heterogeneous nuclear ribonucleoprotein A 1 (hnRNPA1), TATA box binding protein (TBP), hypoxanthine phosphoribosyltransferase 1 (HPRT1), HLA-DQA 1 major histocompatibility complex, class II, (MHCII), Interleukin 8 (IL-8), and androgen receptor (AR). Like HIV, the IL-8, androgen receptor, and HLA-DQA1 promoters require PTEF-b.
FIG. 10 shows re-infection of dominant negative-expressing cells with slowly-replicating viruses shows the same growth kinetics as the initial infection. SupT1 cells expressing TatAD and T-U2AF65 were re-infected with viral stocks harvested from day 30 of the first set of infections (see arrows in FIGS. 4a and 4b). a, Re-infection using the HIV Tat-TAR-dependent virus. b, Re-infection using the BIV Tat-TAR-dependent virus.



DETAILED DESCRIPTION OF THE INVENTION
Introduction
The gene product of a dominant negative mutation interferes with the function of a normal, wild-type gene product within the same cell. This usually occurs if the gene product of the dominant negative mutation can still interact with the same elements as the wild-type product, but blocks some aspect of the wild-type protein's function. As an example, in the case of multi-subunit protein complexes, an inactive dominant negative protein can bind to wild-type components of the complex rendering the resulting complex less active or inactive. Genetic engineering has allowed the construction of dominant negative forms of many different types of proteins. In the case of transcription factors, one approach has been to generate transcription factors that lack a gene activation domain but which retain a DNA binding domain. When expressed in cells, such dominant negative proteins are able to bind to their cognate DNA recognition sites thus preventing the binding of a wild type transcription factor and leading to reduced expression of a target gene. However, typically, for dominant negative inhibition to occur, a great excess of dominant negative protein must be expressed in order to effectively out compete the wild-type protein.
A dominant negative approach has previously been used in an attempt to inhibit transcription of the HIV genome and thus viral replication. When a truncated form of Tat, lacking the basic domain, was tested in transient co-transfection experiments, it was found that an 8-30 fold molar excess of the dominant negative Tat over wild-type Tat was required to inhibit the expression of a reporter gene under the control of the HIV-LTR.
The inventors have devised a new method of generating potent dominant negative transcriptional inhibitors for pharmaceutical treatment of diseases, gene therapy, target validation, disease diagnosis, and mechanistic studies of transcription, among other applications. As discussed above, previously described dominant negative transcription factors typically act by competing with other interacting factors or by creating defective oligomers, thus requiring a large excess of inhibitor while providing only a modest amount of inhibition. The inventors have discovered that linking a protein which localizes to the transcriptional machinery to a transcription factor can effectively target and generate high local concentrations of a dominant negative protein, thereby efficiently out-competing wild-type protein when expressed at stoichiometric amounts. In particular, the inventors have made the unexpected finding that fusion of the Tat protein or a fragment thereof, such as the Tat activation domain (Tat AD), to a protein that localizes to the transcriptional machinery, results in a potent inhibitor of transcription of the HIV genome. In particular, when Tat or Tat AD is fused to the splicing factors, SF1 or U2AF65, a potent dominant negative effect is observed. While one embodiment of this invention as described below in the Examples relates to the inhibition of HIV transcription and viral replication, it will be clear to the skilled artisan that the methods of the present invention can be used to generate dominant negative forms of other transcription factors and other classes of proteins.
Dominant Negative Tat
Immediately after HIV infects a cell, the viral RNA is copied into DNA, and the proviral genome is transported to the nucleus where it is integrated into the host genome. Once integrated into the host chromosome, the HIV proviral genome is subject to regulation by a variety of cellular transcription factors, as well as, by virally encoded factors. Among these virally encoded factors, the trans-activator protein (Tat) provides the primary control of HIV transcription.
Transcription of the HIV genome begins at the viral LTR when the host cell RNA polymerase complex binds to the HIV promoter. The HIV LTR, however, is a poor promoter in the absence of Tat. In the absence of Tat, only non-processive (basal) transcription of the HIV genome is observed. However, upon recruitment of Tat to the transcriptional complex at the promoter, transcription of the HIV genome is greatly stimulated. Recruitment of Tat to the HIV promoter is mediated at least in part by the binding of Tat to a short RNA sequence that forms a stem-loop, termed the transactivation-responsive region (TAR), which lies just downstream of the initiation site for transcription. Transcription of TAR by the basal transcriptional machinery to form the TAR RNA stem loop allows Tat to join the complex and stimulate transcription. Upon binding of Tat, it is believed that other cellular factors are recruited to the transcriptional complex that convert the complex into a form that is competent for processive transcript elongation.
In one embodiment of this invention, the inventors have made a fusion of the Tat protein or a fragment thereof, such as the Tat activation domain (Tat AD), to proteins that localize to the transcriptional machinery. When Tat or Tat AD is fused to splicing factors, such as, SF1 or U2AF65, a potent dominant negative effect is observed. Without limiting themselves to any particular mechanism of action, and as explained below in greater detail, the inventors have found that the fused splicing factor proteins act as tethering domains, directing the Tat fusion protein to RNA polymerase at the HIV-1 promoter thus blocking the activity of incoming wild-type Tat proteins. This results in a high local concentration of the inhibiting fusion protein at the site of action.
DEFINITIONS
As used herein, the following terms have the meanings ascribed to them unless specified otherwise.
A “dominant negative” gene product or protein is one that interferes with the function of another gene product or protein. The other gene product affected can be the same or different from the dominant negative protein. Dominant negative gene products can be of many forms, including truncations, full length proteins with point mutations or fragments thereof, or fusions of full length wild type or mutant proteins or fragments thereof with other proteins. The level of inhibition observed can be very low. For example, it may require a large excess of the dominant negative protein compared to the functional protein or proteins involved in a process in order to see an effect. It may be difficult to see effects under normal biological assay conditions.
A “transcription factor” is a protein that regulates transcription. Transcription factors may bind directly to DNA or RNA or may interact with the transcriptional machinery via protein-protein interactions with no direct nucleic acid contact to modulate transcription. Transcription factors in general are reviewed in Barnes and Adcock, Clin. Exp. Allergy 25 Suppl. 2: 46-9 (1995), Roeder, Methods Enzymol. 273: 165-71 (1996), and Brivanlou and Darnell, Science 1 Feb. 2002: 813-818 (2002), among other sources.
A “promoter” is defined as an array of nucleic acid control sequences that direct transcription. As used herein, a promoter typically includes necessary nucleic acid sequences near the start site of transcription, such as, in the case of certain RNA polymerase II type promoters, a TATA element, enhancer, CCAAT box, SP-1 site, etc. As used herein, a promoter also optionally includes distal enhancer or repressor elements, which can be located as much as several thousand base pairs from the start site of transcription. The promoters often have an element that is responsive to transactivation by a DNA-binding moiety such as a polypeptide, e.g., a nuclear receptor, Gal4, the lac repressor and the like.
A “target site” is the nucleic acid sequence recognized by a transcription factor protein. A single target site typically has about four to about ten or more base pairs. The target site is in any position that allows regulation of gene expression, e.g., adjacent to, up- or downstream of the transcription initiation site; proximal to an enhancer or other transcriptional regulation element such as a repressor (e.g., SP-1 binding sites, hypoxia response elements, nuclear receptor recognition elements, p53 binding sites, etc.), RNA polymerase pause sites; and intron/exon boundaries.
“Linking” or “fusing” as used in this application refers to entities that are directly linked, or linked via an amino acid linker, the size and composition of which can vary, or linked via a chemical linker.
The term “transcriptional machinery” generally refers to the complex of cellular components responsible for making RNA from a DNA template and related co-transcriptional RNA processing. The complex responsible for transcription in a cell is referred to as RNA polymerase. During transcription, a variety of factors join the RNA polymerase complex to effect various aspects of transcription and co-transcriptional RNA processing as described below. In eukaryotic cells, three forms of RNA polymerase exist, termed RNA polymerases I, II, and III. RNA polymerase I synthesizes a pre-rRNA 45S, which matures into 28 S, 18S and 5, 8 S rRNAs which form the major RNA portions of the ribosome. RNA polymerase II synthesizes precursors of mRNAs and most snRNA. Because of the large variety of cellular genes are transcribed by thus polymerase, RNAP II is subject to the highest level of control, requiring a wide range of transcription factors depending on the promoter. RNA polymerase III is responsible for the synthesis of tRNAs, rRNA 5S and other small RNAs found in the nucleus and cytosol. Additionally, other RNA polymerase types are found in mitochondria and chloroplasts.
A 550 kDa complex of 12 subunits, RNAP II is the most intensively studied type of RNA polymerase. A wide range of transcription factors are required for it to bind to its promoters and to begin transcription. In the process of transcription, there are three main stages: (1) initiation, which requires construction of the RNA polymerase complex on the gene's promoter; (2) elongation, during which the RNA transcript is made from the DNA template; (3) and termination, the step at which the formation of the RNA transcript is completed and disassembly of the RNA polymerase complex occurs.
The components of the transcriptional machinery that may be targeted by this invention comprise any factor that is brought into the RNA polymerase complex and can be exemplified by the order in which the TAFs (TBP Associated Factors) attach to form a polymerase complex on a promoter. TBP (TATA Binding Protein) and an attached complex of TAFs, collectively known as TFIID (Transcription Factor for polymerase II D), bind at the TATA box, although not all promoters have the TATA box. TFIIA (three subunits) binds TFIID and DNA, stabilizing the first interactions. TFIIB binds between TFIID and the location of Pol II binding in the near future. TFIIB binds partially sequence specifically, with some preference for BRE. TFIIF and Pol II (two subunits, RAP30 and RAP74, showing some similarity to bacterial sigma factors) enter the complex together. TFIIF helps to speed up the polymerization process. TFIIE enters the complex, and helps to open and close the PolII's ‘Jaw’ like structure, which enables movement down the DNA strand. TFIIE and TFIIH enter concomitantly. Finally TFIIH binds. TFIIH is a large protein complex that contains among others the CDK7/cyclin H kinase complex and a DNA helicase. TFIIH has three functions: it binds specifically to the template strand to ensure that the correct strand of DNA is transcribed and melts or unwinds the DNA (ATP dependently) to separate the two strands using its Helicase activity. It has a kinase activity that phosphorylates the C-terminal domain (CTD) of Pol II at the amino acid serine. This switches the RNA polymerase to start producing RNA, which marks the end of initiation and the start of elongation. Finally it is essential for Nucleotide Excision Repair (NER) of damaged DNA. TFIIH and TFIIE strongly interact with one another. TFIIE affects TFIIH's catalytic activity. Without TFIIE, TFIIH will not unwind the promoter. Mediator then encases all the transcription factors and the Pol II. Mediator interacts with enhancers, areas very far away (upstream or downstream) that help regulate transcription.
A “protein that localizes to the transcriptional machinery” is one that is capable of associating or interacting with the transcriptional machinery as described above or a component thereof. The association or interaction may be non-covalent or covalent and may be reversible or non-reversible. Examples of proteins that localize to the transcriptional machinery include nuclear localized proteins, RNA processing proteins, components of the transcriptional machinery, and proteins involved in co-transcriptional processes. Among the co-transcriptional processes that are subjects of the invention are capping, splicing, polyadenylation, RNA export, translation.
An RS domain containing protein (also referred to in the literature as an SR protein) is a protein with a domain that contains multiple arginine and serine di-peptides (single-letter code RS) and/or serine and arginine di-peptides (single-letter code SR). RS domains are found in a number of cellular proteins, particularly those involved with pre-mRNA splicing and RNA processing events.
A “transcriptional activator” and a “transcriptional repressor” refer to proteins or effector domains of proteins that have the ability to modulate transcription, by binding directly to DNA or RNA or by interacting with the transcriptional machinery via protein-protein interactions with no direct nucleic acid contact. Such proteins include, e.g., transcription factors and co-factors (e.g., KRAB, MAD, ERD, SID, nuclear factor kappa B subunit p65, early growth response factor 1, and nuclear hormone receptors, VP16, VP64), endonucleases, integrases, recombinases, methyltransferases, histone acetyltransferases, histone deacetylases etc. Activators and repressors include co-activators and co-repressors (see, e.g., Utley et al., Nature 394:498-502 (1998)).
The terms “modulating transcription” “inhibiting transcription” and “activating transcription” of a gene refer to the ability of a dominant negative to activate or inhibit transcription of a gene. Activation includes prevention of transcriptional inhibition (i.e., prevention of repression of gene expression) and inhibition includes prevention of transcriptional activation (i.e., prevention of gene activation).
Modulation can be assayed by determining any parameter that is indirectly or directly affected by the expression of the target gene. Such parameters include, e.g., changes in RNA or protein levels, changes in protein activity, changes in product levels, changes in downstream gene expression, changes in reporter gene transcription (luciferase, CAT, 3-galactosidase, β-glucuronidase, GFP (see, e.g., Mistili & Spector, Nature Biotechnology 15:961-964 (1997)); changes in signal transduction, phosphorylation and dephosphorylation, receptor-ligand interactions, second messenger concentrations (e.g., cGMP, cAMP, IP3, and Ca2+), cell growth, and neovascularization. These assays can be in vitro, in vivo, and ex vivo. Such functional effects can be measured by any means known to those skilled in the art, e.g., measurement of RNA or protein levels, measurement of RNA stability, identification of downstream or reporter gene expression, e.g., via chemiluminescence, fluorescence, colorimetric reactions, antibody binding, inducible markers, ligand binding assays; changes in intracellular second messengers such as cGMP and inositol triphosphate (IP3); changes in intracellular calcium levels; cytokine release, and the like.
To determine the level of gene expression modulation by a dominant negative construct, cells contacted with nucleic acids encoding dominant negative or dominant negative proteins are compared to control cells which have not received this treatment. Control samples are assigned a relative gene expression activity value of 100%. Modulation/inhibition of gene expression is achieved when the gene expression activity value relative to the control is about 80%, preferably 50% (i.e., 0.5× the activity of the control), more preferably 25%, more preferably 5-0%. Modulation/activation of gene expression is achieved when the gene expression activity value relative to the control is 110%, more preferably 150% (i.e., 1.5× the activity of the control), more preferably 200-500%, more preferably 1000-2000% or more.
The term “heterologous” is a relative term, which when used with reference to portions of a nucleic acid indicates that the nucleic acid comprises two or more subsequences that are not found in the same relationship to each other in nature. For instance, a nucleic acid that is recombinantly produced typically has two or more sequences from unrelated genes synthetically arranged to make a new functional nucleic acid, e.g., a promoter from one source and a coding region from another source. The two nucleic acids are thus heterologous to each other in this context. When added to a cell, the recombinant nucleic acids would also be heterologous to the endogenous genes of the cell. Thus, in a chromosome, a heterologous nucleic acid would include an non-native (non-naturally occurring) nucleic acid that has integrated into the chromosome, or a non-native (non-naturally occurring) extrachromosomal nucleic acid. In contrast, a naturally translocated piece of chromosome would not be considered heterologous in the context of this patent application, as it comprises an endogenous nucleic acid sequence that is native to the mutated cell.
Similarly, a heterologous protein indicates that the protein comprises two or more subsequences that are not found in the same relationship to each other in nature (e.g., a “fusion protein,” where the two subsequences are encoded by a single nucleic acid sequence). See, e.g., Ausubel, supra, for an introduction to recombinant techniques.
The term “recombinant” when used with reference, e.g., to a cell, or nucleic acid, protein, or vector, indicates that the cell, nucleic acid, protein or vector, has been modified by the introduction of a heterologous nucleic acid or protein or the alteration of a native nucleic acid or protein, or that the cell is derived from a cell so modified. Thus, for example, recombinant cells express genes that are not found within the native (naturally occurring) form of the cell or express a second copy of a native gene that is otherwise normally or abnormally expressed, under expressed or not expressed at all.
An “expression vector” is a nucleic acid construct, generated recombinantly or synthetically, with a series of specified nucleic acid elements that permit transcription of a particular nucleic acid in a host cell, and optionally integration or replication of the expression vector in a host cell. The expression vector can be part of a plasmid, virus, or nucleic acid fragment, of viral or non-viral origin. Typically, the expression vector includes an “expression cassette,” which comprises a nucleic acid to be transcribed operably linked to a promoter. The term expression vector also encompasses naked DNA operably linked to a promoter.
By “host cell” is meant a cell that contains an expression vector or nucleic acid encoding a dominant negative protein of the invention. The host cell typically supports the replication or expression of the expression vector. Host cells may be prokaryotic cells such as E. coli, or eukaryotic cells such as yeast, fungal, protozoal, higher plant, insect, or amphibian cells, or mammalian cells such as CHO, HeLa, 293, COS-1, and the like, e.g., cultured cells (in vitro), explants and primary cultures (in vitro and ex vivo), and cells in vivo.
“Nucleic acid” refers to deoxyribonucleotides or ribonucleotides and polymers thereof in either single- or double-stranded form. The term encompasses nucleic acids containing known nucleotide analogs or modified backbone residues or linkages, which are synthetic, naturally occurring, and non-naturally occurring, which have similar binding properties as the reference nucleic acid, and which are metabolized in a manner similar to the reference nucleotides. Examples of such analogs include, without limitation, phosphorothioates, phosphoramidates, methyl phosphonates, chiral-methyl phosphonates, 2-O-methyl ribonucleotides, peptide-nucleic acids (PNAs).
Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (e.g., degenerate codon substitutions) and complementary sequences, as well as the sequence explicitly indicated. Specifically, degenerate codon substitutions may be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues (Batzer et al., Nucleic Acid Res. 19:5081 (1991); Ohtsuka et al., J. Biol. Chem. 260:2605-2608 (1985); Rossolini et al., Mol. Cell. Probes 8:91-98 (1994)). The term nucleic acid is used interchangeably with gene, cDNA, mRNA, oligonucleotide, and polynucleotide.
The terms “polypeptide,” “peptide” and “protein” are used interchangeably herein to refer to a polymer of amino acid residues. The terms also apply to amino acid polymers in which one or more amino acid residues is an artificial chemical mimetic of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers and non-naturally occurring amino acid polymer.
The term “amino acid” refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function in a manner similar to the naturally occurring amino acids. Naturally occurring amino acids are those encoded by the genetic code, as well as those amino acids that are later modified, e.g., hydroxyproline, γ-carboxyglutamate, and O-phosphoserine. Amino acid analogs refers to compounds that have the same basic chemical structure as a naturally occurring amino acid, i.e., an α carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group, e.g., homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium. Such analogs have modified R groups (e.g., norleucine) or modified peptide backbones, but retain the same basic chemical structure as a naturally occurring amino acid. Amino acid mimetics refers to chemical compounds that have a structure that is different from the general chemical structure of an amino acid, but that functions in a manner similar to a naturally occurring amino acid.
Amino acids may be referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. Nucleotides, likewise, may be referred to by their commonly accepted single-letter codes.
“Conservatively modified variants” applies to both amino acid and nucleic acid sequences. With respect to particular nucleic acid sequences, conservatively modified variants refers to those nucleic acids which encode identical or essentially identical amino acid sequences, or where the nucleic acid does not encode an amino acid sequence, to essentially identical sequences. Because of the degeneracy of the genetic code, a large number of functionally identical nucleic acids encode any given protein. For instance, the codons GCA, GCC, GCG and GCU all encode the amino acid alanine. Thus, at every position where an alanine is specified by a codon, the codon can be altered to any of the corresponding codons described without altering the encoded polypeptide. Such nucleic acid variations are “silent variations,” which are one species of conservatively modified variations. Every nucleic acid sequence herein which encodes a polypeptide also describes every possible silent variation of the nucleic acid. One of skill will recognize that each codon in a nucleic acid (except AUG, which is ordinarily the only codon for methionine, and TGG, which is ordinarily the only codon for tryptophan) can be modified to yield a functionally identical molecule. Accordingly, each silent variation of a nucleic acid which encodes a polypeptide is implicit in each described sequence.
As to amino acid sequences, one of skill will recognize that individual substitutions, deletions or additions to a nucleic acid, peptide, polypeptide, or protein sequence which alters, adds or deletes a single amino acid or a small percentage of amino acids in the encoded sequence is a “conservatively modified variant” where the alteration results in the substitution of an amino acid with a chemically similar amino acid. Conservative substitution tables providing functionally similar amino acids are well known in the art. Such conservatively modified variants are in addition to and do not exclude polymorphic variants, interspecies homologs, and alleles of the invention.
The following eight groups each contain amino acids that are conservative substitutions for one another:
1) Alanine (A), Glycine (G);
2) Aspartic acid (D), Glutamic acid (E);
3) Asparagine (N), Glutamine (Q);
4) Arginine (R), Lysine (K);
5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V);
6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W);
7) Serine (S), Threonine (T); and
8) Cysteine (C), Methionine (M)
(see, e.g., Creighton, Proteins (1984)).
The term “substantially identical” indicates that two or more nucleotide sequences share a majority of their sequence. Generally, this will be at least about 90% of their sequence and preferably about 95% of their sequence. Another indication that sequences are substantially identical is if they hybridize to the same nucleotide sequence under stringent conditions (see, e.g., Sambrook and Russell, eds, Molecular Cloning: A Laboratory Manual, 3rd Ed, vols. 1-3, Cold Spring Harbor Laboratory Press, 2001; and Current Protocols in Molecular Biology, Ausubel, ed. John Wiley & Sons, Inc. New York, 1997). Stringent conditions are sequence-dependent and will be different in different circumstances. Generally, stringent conditions are selected to be about 5° C. (or less) lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. The Tm of a DNA duplex is defined as the temperature at which 50% of the nucleotides are paired and corresponds to the midpoint of the spectroscopic hyperchromic absorbance shift during DNA melting. The Tm indicates the transition from double helical to random coil.
Typically, stringent conditions will be those in which the salt concentration is about 0.2×SSC at pH 7 and the temperature is at least about 60° C. For example, a nucleic acid of the invention or fragment thereof can be identified in standard filter hybridizations using the nucleic acids disclosed here under stringent conditions, which for purposes of this disclosure, include at least one wash (usually 2) in 0.2×SSC at a temperature of at least about 60° C., usually about 65° C., sometimes 70° C. for 20 minutes, or equivalent conditions. For PCR, an annealing temperature of about 5° C. below Tm, is typical for low stringency amplification, although annealing temperatures may vary between about 32° C. and 72° C., e.g., 40° C., 42° C., 45° C., 52° C., 55° C., 57° C., or 62° C., depending on primer length and nucleotide composition or high stringency PCR amplification, a temperature at, or slightly (up to 5° C.) above, primer Tm is typical, although high stringency annealing temperatures can range from about 50° C. to about 72° C., and are often 72° C., depending on the primer and buffer conditions (Ahsen et al., Clin Chem. 47:1956-61, 2001). Typical cycle conditions for both high and low stringency amplifications include a denaturation phase of 90° C.-95° C. for 30 sec-2 min., an annealing phase lasting 30 sec.-10 min., and an extension phase of about 72° C. for 1-15 min.
The terms “identical” or percent “identity,” in the context of two or more nucleic acids, refer to two or more sequences or subsequences that are the same or have a specified percentage of nucleotides that are the same (i.e., at least 70% identity, preferably at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity, over a specified region, when compared and aligned for maximum correspondence over a comparison window, or designated region as measured using a BLAST or BLAST 2.0 sequence comparison algorithms with default parameters described below, or by manual alignment and visual inspection. Such sequences are then said to be “substantially identical.” This definition also refers to the complement of a test sequence. Preferably, the identity exists over a region that is at least about 15, 20 or 25 nucleotides in length, or more preferably over a region that is 50-100 nucleotides in length.
For sequence comparison, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. Default program parameters can be used, or alternative parameters can be designated. The sequence comparison algorithm then calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters.
A “comparison window”, as used herein, includes reference to a segment of any one of the number of contiguous positions selected from the group consisting of from 15 to 600, usually about 20 to about 200, more usually about 50 to about 150 in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned. Methods of alignment of sequences for comparison are well-known in the art. Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Nat'l. Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by manual alignment and visual inspection (see, e.g., Current Protocols in Molecular Biology (Ausubel et al., eds. 1995 supplement)).
A preferred example of algorithm that is suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al., Nuc. Acids Res. 25:3389-3402 (1977) and Altschul et al., J. Mol. Biol. 215:403-410 (1990), respectively. BLAST and BLAST 2.0 are used, with the default parameters described herein, to determine percent sequence identity for the nucleic acids described herein. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information. This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al., supra). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always <0). Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a word length (W) of 11, an expectation (E) of 10, M=5, N=−4 and a comparison of both strands.
The BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul, Proc. Nat'l. Acad. Sci. USA 90:5873-5787 (1993)). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide sequences would occur by chance. For example, a nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.2, more preferably less than about 0.01, and most preferably less than about 0.001.
“Administering” an expression vector, nucleic acid, protein, or a delivery vehicle to a cell comprises transducing, transfecting, electroporating, translocating, fusing, phagocytosing, shooting or ballistic methods, etc., i.e., any means by which a protein or nucleic acid can be transported across a cell membrane and preferably into the nucleus of a cell.
A “delivery vehicle” refers to a compound, e.g., a liposome, toxin, or a membrane translocation polypeptide, which is used to administer dominant negative proteins. Delivery vehicles can also be used to administer nucleic acids encoding dominant negative proteins of the invention, e.g., a lipid:nucleic acid complex, an expression vector, a virus, and the like.
Design of Dominant Negative Proteins
The dominant negative proteins of the invention comprise any of a number of possible fusions of a transcription factor or other protein, or fragment thereof, with a protein that is capable of localization to the transcriptional machinery, such as nuclear localized proteins, RNA processing proteins, components of the transcriptional machinery, and proteins involved in co-transcriptional processes. Among the co-transcriptional processes that are subjects of the invention are capping, splicing, polyadenylation, RNA export, translation. The transcription factor can be derived from any of a number of species including, and not limited to, viruses, HIV, bacteria, yeast, Drosophila, C. elegans, Xenopus, mouse, monkey, and human. For human applications, a human TF is generally preferred. One of skill in the art will recognize that a wide variety of transcription factor proteins known in the art may be used in this invention. See Goodrich et al., Cell 84:825-30 (1996), Barnes & Adcock, Clin. Exp. Allergy 25 Suppl. 2:46-9 (1995), and Roeder, Methods Enzymol. 273:165-71 (1996) for general reviews of transcription factors. Databases dedicated to transcription factors are known (see, e.g., Science 269:630 (1995)). Nuclear hormone receptor transcription factors are described in, for example, Rosen et al., J. Med. Chem. 38:4855-74 (1995). The C/EBP family of transcription factors are reviewed in Wedel et al., Immunobiology 193:171-85 (1995). Coactivators and co-repressors that mediate transcription regulation by nuclear hormone receptors are reviewed in, for example, Meier, Eur. J. Endocrinol. 134(2):158-9 (1996); Kaiser et al., Trends Biochem. Sci. 21:342-5 (1996); and Utley et al., Nature 394:498-502 (1998)). GATA transcription factors, which are involved in regulation of hematopoiesis, are described in, for example, Simon, Nat. Genet. 11:9-11 (1995); Weiss et al., Exp. Hematol. 23:99-107. TATA box binding protein (TBP) and its associated TAF polypeptides (which include TAF30, TAF55, TAF80, TAF 110, TAF 150, and TAF250) are described in Goodrich & Tjian, Curr. Opin. Cell Biol. 6:403-9 (1994) and Hurley, Curr. Opin. Struct. Biol. 6:69-75 (1996). The STAT family of transcription factors are reviewed in, for example, Barahmand-Pour et al., Curr. Top. Microbiol. Immunol. 211:121-8 (1996). Transcription factors involved in disease are reviewed in Aso et al., J. Clin. Invest. 97:1561-9 (1996).
As further examples, the transcription factor may be chosen from any of a number of different classes of known transcription factors such as those that contain homeodomains, POU domains, Helix-Loop-Helix (HLH), Zinc Fingers, Leucine Zippers, or Winged Helix, to name but a few of the structural motifs found in transcription factors. Currently, there are about 2000 known transcription factors. See, e.g., Brivanlou and Darnell, Science, 295: 813-818 (2002). Among some of the better known transcription factors include: c-Myc and Max, c-Fos and c-Jun, CREB, c-ErbA, c-Ets, GATA c-Myb, MyoD KF-kB, RAR, and SRF, to name a few.
Among the classes of transcription factors that find use in this invention are viral transcription factors, nuclear proto-oncogene or oncogene proteins, nuclear tumor suppressor proteins, heart specific transcription factors, and immune cell transcription factors. The viral transcription factors useful in the practice of this invention include: HIV-Tat, HPV-E2, HPV-E7, BPV-E2, Adenovirus IVa2, HSV-1 ICP4, EBNA-LP, EBNA-2, EBNA-3A, EBNA-3B, EBNA-3C, BZLF-1, CMV-IE-1, CMV-IE2, HHSV-8 K bZIP, HBV Hbx, Poxvirus Vaccinia, VETF, HCV NS5A, T-Ag, Adenovirus EIA, Herpesvirus VP16, HTLV Tax, Hepadnavirus X protein, and Baculovirus AcNPV IE-1, among others. The nuclear proto-oncogene or oncogene proteins and nuclear tumor suppressor proteins transcription factors useful in the practice of this invention include: Abl, Myc, Myb, Rel, Jun, Fos, Sp I, Apl, NF-κB, STAT 3 or 5, β-catenin, Notch, GLI, PML-RARα and p53, among others. The heart specific transcription factors useful in the practice of this invention include: Nkx 2, 3, 4, or 5, TBX5, GATA 4, 5, or 6, and MEF2, among others. The immune cell specific transcription factors useful in the practice of this invention include: Ikaros, PU.1, PAX-5, Oct-2, and BOB.1/OBF.1, among others. A non limiting list of transcription factors that may be used in the practice of this invention is provided in Table 3. The transcription factors useful in the practice of this invention can be human as well as derived from yeast or higher eukaryotes such as viruses, HIV, Drosophila, C. elegans, Xenopus, or mouse, among other species.
In the practice of this invention, the transcription factor can be either a transcriptional activator or repressor, examples of which are well known in the art. Non-limiting examples of transcriptional activators and repressors are provided in Table 3.
Proteins that localize to the transcriptional machinery include: components of the transcriptional machinery, nuclear localized proteins, RNA processing proteins, components of the transcriptional machinery, and proteins involved in co-transcriptional processes and RNA processing.
Among the components of the transcriptional machinery that may be used in the practice of this invention are TAFs, CDK7, cyclin H, DNA helicase, unwinding enzymes, transcription factors, among others.
A wide range of proteins have been shown to localize to the nucleus and may be used in the practice of this invention. A non-limiting list of such proteins is provided in Table 1.
Among the co-transcriptional processes and RNA processing activities that are subjects of the invention are capping, splicing, polyadenylation, RNA export, and translation. Accordingly, proteins involved in capping, splicing, polyadenylation, RNA export, and translation may be used in the practice of this invention. Splicing factors represent one particular class of proteins involved in co-transcriptional processing of RNA and are suitable for the practice of this invention. As many as 300 factors are known to comprise the spliceosome. The protein components of spliceosomes are disclosed in Rappsilber, J., Ryder, U., Lamond, A. I., and Mann, M. (2002) Genome Res 12(8), 1231-1245 and Zhou, Z., Licklider, L. J., Gygi, S. P., and Reed, R. (2002) Nature 419(6903), 182-185, among other sources. Many splicing factors useful for the practice of this invention are compiled in Table 2. Particular examples of splicing factors useful in the practice of this invention include SF1, U2AF65, and 9G8.
The RS domain is a structural and functional feature characteristic of many nuclear proteins, particularly splicing factors. A large number of RS domain proteins are known in the art, and many have been identified through a genome-wide survey of RS domain proteins from various species. See Boucher et al., RNA 7:1693-1701 (2001). Among the classes of known RS domain containing proteins that may be used in the practice of the invention are those listed in the table below.
In one embodiment of the invention, HIV Tat protein, or a fragment thereof, can used as the transcription factor in a dominant negative fusion protein as described herein. The human Tat protein is an 86 amino acid protein that is required efficient viral gene expression. The Tat sequence has been subdivided into several distinct regions based on structure and function: a N-terminal activation region (amino acids 1-19), a cysteine-rich domain (amino acids 20-31), a core region (amino acids 32-47), a basic region (amino acids 48-57), and a glutamine-rich region (amino acids 60-76). See Karn, J. (ref). In one particular embodiment, a full length Tat is linked to the splicing factors SF1 or U2AF65. In another embodiment, the Tat activation domain (Tat AD) is linked to the splicing factors SF1 or U2AF65.
Generation of Nucleic Acids Encoding Dominant Negative Proteins.
Dominant negative polypeptides and nucleic acids of the invention can be made using routine techniques in the field of recombinant genetics. Basic texts disclosing the general methods of use in this invention include Sambrook et al., Molecular Cloning, A Laboratory Manual (2nd ed. 1989); Kriegler, Gene Transfer and Expression: A Laboratory Manual (1990); and Current Protocols in Molecular Biology (Ausubel et al., eds., 1994)). In addition, essentially any nucleic acid can be custom ordered from any of a variety of commercial sources. Similarly, peptides and antibodies can be custom ordered from any of a variety of commercial sources.
Expression Vectors for Nucleic Acids Encoding Dominant Negative Proteins
A nucleic acid encoding a dominant negative protein is typically cloned into intermediate vectors for transformation into prokaryotic or eukaryotic cells for replication and/or expression. Intermediate vectors are typically prokaryote vectors, e.g., plasmids, or shuttle vectors, or insect vectors, for storage or manipulation of the nucleic acid encoding dominant negative proteins or production of protein. The nucleic acid encoding a dominant negative protein is also typically cloned into an expression vector, for administration to a plant cell, animal cell, preferably a mammalian cell or a human cell, fungal cell, bacterial cell, or protozoal cell.
To obtain expression of a cloned gene or nucleic acid, a nucleic acid encoding a dominant negative protein is typically subcloned into an expression vector that contains a promoter to direct transcription. Suitable bacterial and eukaryotic promoters are well known in the art and described, e.g., in Sambrook et al., Molecular Cloning, A Laboratory Manual (2nd ed. 1989); Kriegler, Gene Transfer and Expression: A Laboratory Manual (1990); and Current Protocols in Molecular Biology (Ausubel et al., eds., 1994). Bacterial expression systems for expressing a dominant negative protein are available in, e.g., E. coli, Bacillus sp., and Salmonella (Palva et al., Gene 22:229-235 (1983)). Kits for such expression systems are commercially available. Eukaryotic expression systems for mammalian cells, yeast, and insect cells are well known in the art and are also commercially available.
The promoter used to direct expression of a nucleic acid encoding a dominant negative protein depends on the particular application. For example, a strong constitutive promoter is typically used for expression and purification of a dominant negative protein. In contrast, when a dominant negative protein is administered in vivo for gene regulation, either a constitutive or an inducible promoter is used, depending on the particular use of the dominant negative protein. In addition, a preferred promoter for administration of a dominant negative protein can be a weak promoter, such as HSV TK or a promoter having similar activity. The promoter typically can also include elements that are responsive to transactivation, e.g., hypoxia response elements, Gal4 response elements, lac repressor response element, and small molecule control systems such as tet-regulated systems and the RU-486 system (see, e.g., Gossen & Bujard, PNAS 89:5547 (1992); Oligino et al., Gene Ther. 5:491-496 (1998); Wang et al., Gene Ther. 4:432-441 (1997); Neering et al., Blood 88:1147-1155 (1996); and Rendahl et al., Nat. Biotechnol. 16:757-761 (1998)).
In addition to the promoter, the expression vector typically contains a transcription unit or expression cassette that contains all the additional elements required for the expression of the nucleic acid in host cells, either prokaryotic or eukaryotic. A typical expression cassette thus contains a promoter operably linked, e.g., to the nucleic acid sequence encoding the dominant negative protein, and signals required, e.g., for efficient polyadenylation of the transcript, transcriptional termination, ribosome binding sites, or translation termination. Additional elements of the cassette may include, e.g., enhancers, and heterologous spliced intronic signals.
The particular expression vector used to transport the genetic information into the cell is selected with regard to the intended use of the dominant negative protein, e.g., expression in plants, animals, bacteria, fungus, protozoa etc. (see expression vectors described below). Standard bacterial expression vectors include plasmids such as pBR322 based plasmids, pSKF, pET23D, and commercially available fusion expression systems such as GST and LacZ. A preferred fusion protein is the maltose binding protein, “MBP.” Such fusion proteins are used for purification of the dominant negative protein. Epitope tags can also be added to recombinant proteins to provide convenient methods of isolation, for monitoring expression, and for monitoring cellular and subcellular localization, e.g., c-myc or FLAG.
Expression vectors containing regulatory elements from eukaryotic viruses are often used in eukaryotic expression vectors, e.g., SV40 vectors, papilloma virus vectors, and vectors derived from Epstein-Barr virus. Other exemplary eukaryotic vectors include pMSG, pAV009/A+, pMTO10/A+, pMAMneo-5, baculovirus pDSVE, and any other vector allowing expression of proteins under the direction of the SV40 early promoter, SV40 late promoter, metallothionein promoter, murine mammary tumor virus promoter, Rous sarcoma virus promoter, polyhedrin promoter, or other promoters shown effective for expression in eukaryotic cells.
Some expression systems have markers for selection of stably transfected cell lines such as thymidine kinase, hygromycin B phosphotransferase, and dihydrofolate reductase. High yield expression systems are also suitable, such as using a baculovirus vector in insect cells, with a dominant negative protein encoding sequence under the direction of the polyhedrin promoter or other strong baculovirus promoters.
The elements that are typically included in expression vectors also include a replicon that functions in E. coli, a gene encoding antibiotic resistance to permit selection of bacteria that harbor recombinant plasmids, and unique restriction sites in nonessential regions of the plasmid to allow insertion of recombinant sequences.
Standard transfection methods are used to produce bacterial, mammalian, yeast or insect cell lines that express large quantities of protein, which are then purified using standard techniques (see, e.g., Colley et al., J. Biol. Chem. 264:17619-17622 (1989); Guide to Protein Purification, in Methods in Enzymology, vol. 182 (Deutscher, ed., 1990)). Transformation of eukaryotic and prokaryotic cells are performed according to standard techniques (see, e.g., Morrison, J. Bact. 132:349-351 (1977); Clark-Curtiss & Curtiss, Methods in Enzymology 101:347-362 (Wu et al., eds, 1983).
Any of the well known procedures for introducing foreign nucleotide sequences into host cells may be used. These include the use of calcium phosphate transfection, polybrene, protoplast fusion, electroporation, liposomes, microinjection, naked DNA, plasmid vectors, viral vectors, both episomal and integrative, and any of the other well known methods for introducing cloned genomic DNA, cDNA, synthetic DNA or other foreign genetic material into a host cell (see, e.g., Sambrook et al., supra). It is only necessary that the particular genetic engineering procedure used be capable of successfully introducing at least one gene into the host cell capable of expressing the protein of choice.
Assays for Determining Regulation of Gene Expression by Dominant Negative Proteins
A variety of assays can be used to determine the level of gene expression regulation by dominant negative proteins. The activity of a particular dominant negative protein can be assessed using a variety of in vitro and in vivo assays, by measuring, e.g., protein or mRNA levels, product levels, enzyme activity, tumor growth; transcriptional activation or repression of a reporter gene such as a fluorescent protein (e.g., GFP); second messenger levels (e.g., cGMP, cAMP, IP3, DAG, Ca2+); cytokine and hormone production levels; and neovascularization, using, e.g., immunoassays (e.g., ELISA and immunohistochemical assays with antibodies), hybridization assays (e.g., RNase protection, northerns, in situ hybridization, oligonucleotide array studies), colorimetric assays, amplification assays, enzyme activity assays, tumor growth assays, phenotypic assays, and the like.
Dominant negative proteins are typically first tested for activity in vitro using cultured cells, e.g., 293 cells, CHO cells, VERO cells, BHK cells, HeLa cells, COS cells, and the like. Preferably, human cells are used. The dominant negative protein is often first tested using a transient expression system with a reporter gene, and then regulation of the target endogenous gene is tested in cells and in animals, both in vivo and ex vivo. The dominant negative protein can be recombinantly expressed in a cell, recombinantly expressed in cells transplanted into an animal, or recombinantly expressed in a transgenic animal, as well as administered as a protein to an animal or cell using delivery vehicles described below. The cells can be immobilized, be in solution, be injected into an animal, or be naturally occurring in a transgenic or non-transgenic animal.
Modulation of gene expression is tested using one of the in vitro or in vivo assays described herein. Samples or assays are treated with a dominant negative protein and compared to control samples without the test compound, to examine the extent of modulation.
The effects of the dominant negative proteins can be measured by examining any of the parameters described above. Any suitable gene expression, phenotypic, or physiological change can be used to assess the influence of a dominant negative protein. When the functional consequences are determined using intact cells or animals, one can also measure a variety of effects such as tumor growth, neovascularization, hormone release, transcriptional changes to both known and uncharacterized genetic markers (e.g., northern blots or oligonucleotide array studies), changes in cell metabolism such as cell growth or pH changes, and changes in intracellular second messengers such as cGMP.
Assays for dominant negative protein regulation of endogenous gene expression can be performed in vitro. In one preferred in vitro assay format, dominant negative protein regulation of endogenous gene expression in cultured cells is measured by examining protein production using an ELISA assay (see Examples VI and VII). The test sample is compared to control cells treated with an empty vector or an unrelated dominant negative protein that is targeted to another gene.
In another embodiment, dominant negative protein regulation of endogenous gene expression is determined in vitro by measuring the level of target gene mRNA expression. The level of gene expression is measured using amplification, e.g., using PCR, LCR, or hybridization assays, e.g., northern hybridization, RNase protection, dot blotting. RNase protection is used in one embodiment (see Example VIII and FIG. 10). The level of protein or mRNA is detected using directly or indirectly labeled detection agents, e.g., fluorescently or radioactively labeled nucleic acids, radioactively or enzymatically labeled antibodies, and the like, as described herein.
Alternatively, a reporter gene system can be devised using the target gene promoter operably linked to a reporter gene such as luciferase, green fluorescent protein, CAT, or β-gal. The reporter construct is typically co-transfected into a cultured cell. After treatment with the dominant negative protein of choice, the amount of reporter gene transcription, translation, or activity is measured according to standard techniques known to those of skill in the art.
Another example of an assay format useful for monitoring dominant negative protein regulation of endogenous gene expression is performed in vivo. This assay is particularly useful for examining dominant negative proteins that inhibit expression of tumor promoting genes, genes involved in tumor support, such as neovascularization (e.g., VEGF), or that activate tumor suppressor genes such as p53. In this assay, cultured tumor cells expressing the dominant negative protein of choice are injected subcutaneously into an immune compromised mouse such as an athymic mouse, an irradiated mouse, or a SCID mouse. After a suitable length of time, preferably 4-8 weeks, tumor growth is measured, e.g., by volume or by its two largest dimensions, and compared to the control. Tumors that have statistically significant reduction (using, e.g., Student's T test) are said to have inhibited growth. Alternatively, the extent of tumor neovascularization can also be measured. Immunoassays using endothelial cell specific antibodies are used to stain for vascularization of the tumor and the number of vessels in the tumor. Tumors that have a statistically significant reduction in the number of vessels (using, e.g., Student's T test) are said to have inhibited neovascularization.
Transgenic and non-transgenic animals are also used as a preferred embodiment for examining regulation of endogenous gene expression in vivo. Transgenic animals typically express the dominant negative protein of choice. Alternatively, animals that transiently express the dominant negative protein of choice, onto which the dominant negative protein has been administered in a delivery vehicle, can be used. Regulation of endogenous gene expression is tested using any one of the assays described herein.
Nucleic Acids Encoding Dominant Negative Proteins and Gene Therapy
Conventional viral and non-viral based gene transfer methods can be used to introduce nucleic acids encoding engineered dominant negative proteins in mammalian cells or target tissues. Such methods can be used to administer nucleic acids encoding dominant negative proteins to cells in vitro. Preferably, the nucleic acids encoding dominant negative proteins are administered for in vivo or ex vivo gene therapy uses. Non-viral vector delivery systems include DNA plasmids, naked nucleic acid, and nucleic acid complexed with a delivery vehicle such as a liposome. Viral vector delivery systems include DNA and RNA viruses, which have either episomal or integrated genomes after delivery to the cell. For a review of gene therapy procedures, see Anderson, Science 256:808-813 (1992); Nabel & Feigner, TIBTECH 11:211-217 (1993); Mitani & Caskey, TIBTECH 11:162-166 (1993); Dillon, TIBTECH 11:167-175 (1993); Miller, Nature 357:455-460 (1992); Van Brunt, Biotechnology 6(10):1149-1154 (1988); Vigne, Restorative Neurology and Neuroscience 8:35-36 (1995); Kremer & Perricaudet, British Medical Bulletin 51(1):31-44 (1995); Haddada et al., in Current Topics in Microbiology and Immunology Doerfler and Böhm (eds) (1995); and Yu et al., Gene Therapy 1:13-26 (1994).
Methods of non-viral delivery of nucleic acids encoding engineered dominant negative proteins include lipofection, microinjection, ballistics, virosomes, liposomes, immunoliposomes, polycation or lipid:nucleic acid conjugates, naked DNA, artificial virions, and agent-enhanced uptake of DNA. Lipofection is described in e.g., U.S. Pat. No. 5,049,386, U.S. Pat. No. 4,946,787; and U.S. Pat. No. 4,897,355) and lipofection reagents are sold commercially (e.g., TransfectamTM and LipofectinTM). Cationic and neutral lipids that are suitable for efficient receptor-recognition lipofection of polynucleotides include those of Feigner, WO 91/17424, WO 91/16024. Delivery can be to cells (ex vivo administration) or target tissues (in vivo administration).
The preparation of lipid:nucleic acid complexes, including targeted liposomes such as immunolipid complexes, is well known to one of skill in the art (see, e.g., Crystal, Science 270:404-410 (1995); Blaese et al., Cancer Gene Ther. 2:291-297 (1995); Behr et al., Bioconjugate Chem. 5:382-389 (1994); Remy et al., Bioconjugate Chem. 5:647-654 (1994); Gao et al., Gene Therapy 2:710-722 (1995); Ahmad et al., Cancer Res. 52:4817-4820 (1992); U.S. Pat. Nos. 4,186,183, 4,217,344, 4,235,871, 4,261,975, 4,485,054, 4,501,728, 4,774,085, 4,837,028, and 4,946,787).
The use of RNA or DNA viral based systems for the delivery of nucleic acids encoding engineered dominant negative protein take advantage of highly evolved processes for targeting a virus to specific cells in the body and trafficking the viral payload to the nucleus. Viral vectors can be administered directly to patients (in vivo) or they can be used to treat cells in vitro and the modified cells are administered to patients (ex vivo). Conventional viral based systems for the delivery of dominant negative proteins could include retroviral, lentivirus, adenoviral, adeno-associated and herpes simplex virus vectors for gene transfer. Viral vectors are currently the most efficient and versatile method of gene transfer in target cells and tissues. Integration in the host genome is possible with the retrovirus, lentivirus, and adeno-associated virus gene transfer methods, often resulting in long term expression of the inserted transgene. Additionally, high transduction efficiencies have been observed in many different cell types and target tissues.
The tropism of a retrovirus can be altered by incorporating foreign envelope proteins, expanding the potential target population of target cells. Lentiviral vectors are retroviral vector that are able to transduce or infect non-dividing cells and typically produce high viral titers. Selection of a retroviral gene transfer system would therefore depend on the target tissue. Retroviral vectors are comprised of cis-acting long terminal repeats with packaging capacity for up to 6-10 kb of foreign sequence. The minimum cis-acting LTRs are sufficient for replication and packaging of the vectors, which are then used to integrate the therapeutic gene into the target cell to provide permanent transgene expression. Widely used retroviral vectors include those based upon murine leukemia virus (MuLV), gibbon ape leukemia virus (GaLV), Simian Immuno deficiency virus (SIV), human immuno deficiency virus (HIV), and combinations thereof (see, e.g., Buchscher et al., J. Virol. 66:2731-2739 (1992); Johann et al., J. Virol. 66:1635-1640 (1992); Sommerfelt et al., Virol. 176:58-59 (1990); Wilson et al., J. Virol. 63:2374-2378 (1989); Miller et al., J. Virol. 65:2220-2224 (1991); PCT/US94/05700).
In applications where transient expression of the dominant negative protein is preferred, adenoviral based systems are typically used. Adenoviral based vectors are capable of very high transduction efficiency in many cell types and do not require cell division. With such vectors, high titer and levels of expression have been obtained. This vector can be produced in large quantities in a relatively simple system. Adeno-associated virus (“AAV”) vectors are also used to transduce cells with target nucleic acids, e.g., in the in vitro production of nucleic acids and peptides, and for in vivo and ex vivo gene therapy procedures (see, e.g., West et al., Virology 160:38-47 (1987); U.S. Pat. No. 4,797,368; WO 93/24641; Kotin, Human Gene Therapy 5:793-801 (1994); Muzyczka, J. Clin. Invest. 94:1351 (1994). Construction of recombinant AAV vectors are described in a number of publications, including U.S. Pat. No. 5,173,414; Tratschin et al., Mol. Cell. Biol. 5:3251-3260 (1985); Tratschin, et al., Mol. Cell. Biol. 4:2072-2081 (1984); Hermonat & Muzyczka, PNAS 81:6466-6470 (1984); and Samulski et al., J. Virol. 63:03822-3828 (1989).
In particular, at least six viral vector approaches are currently available for gene transfer in clinical trials, with retroviral vectors by far the most frequently used system. All of these viral vectors utilize approaches that involve complementation of defective vectors by genes inserted into helper cell lines to generate the transducing agent.
pLASN and MFG-S are examples are retroviral vectors that have been used in clinical trials (Dunbar et al., Blood 85:3048-305 (1995); Kohn et al., Nat. Med. 1:1017-102 (1995); Malech et al., PNAS 94:22 12133-12138 (1997)). PA317/pLASN was the first therapeutic vector used in a gene therapy trial. (Blaese et al., Science 270:475-480 (1995)). Transduction efficiencies of 50% or greater have been observed for MFG-S packaged vectors. (Ellem et al., Immunol Immunother. 44(1):10-20 (1997); Dranoff et al., Hum. Gene Ther. 1:111-2 (1997).
Recombinant adeno-associated virus vectors (rAAV) are a promising alternative gene delivery systems based on the defective and nonpathogenic parvovirus adeno-associated type 2 virus. All vectors are derived from a plasmid that retains only the AAV 145 by inverted terminal repeats flanking the transgene expression cassette. Efficient gene transfer and stable transgene delivery due to integration into the genomes of the transduced cell are key features for this vector system. (Wagner et al., Lancet 351:9117 1702-3 (1998), Kearns et al., Gene Ther. 9:748-55 (1996)).
Replication-deficient recombinant adenoviral vectors (Ad) are predominantly used for colon cancer gene therapy, because they can be produced at high titer and they readily infect a number of different cell types: Most adenovirus vectors are engineered such that a transgene replaces the Ad E1a, E1b, and E3 genes; subsequently the replication defector vector is propagated in human 293 cells that supply deleted gene function in trans. Ad vectors can transduce multiply types of tissues in vivo, including nondividing, differentiated cells such as those found in the liver, kidney and muscle system tissues. Conventional Ad vectors have a large carrying capacity. An example of the use of an Ad vector in a clinical trial involved polynucleotide therapy for antitumor immunization with intramuscular injection (Sterman et al., Hum. Gene Ther. 7:1083-9 (1998)). Additional examples of the use of adenovirus vectors for gene transfer in clinical trials include Rosenecker et al., Infection 24:1 5-10 (1996); Sterman et al., Hum. Gene Ther. 9:7 1083-1089 (1998); Welsh et al., Hum. Gene Ther. 2:205-18 (1995); Alvarez et al., Hum. Gene Ther. 5:597-613 (1997); Topf et al., Gene Ther. 5:507-513 (1998); Sterman et al., Hum. Gene Ther. 7:1083-1089 (1998).
Packaging cells are used to form virus particles that are capable of infecting a host cell: Such cells include 293 cells, which package adenovirus, and ψ2 cells or PA317 cells, which package retrovirus. Viral vectors used in gene therapy are usually generated by producer cell line that packages a nucleic acid vector into a viral particle. The vectors typically contain the minimal viral sequences required for packaging and subsequent integration into a host, other viral sequences being replaced by an expression cassette for the protein to be expressed. The missing viral functions are supplied in trans by the packaging cell line. For example, AAV vectors used in gene therapy typically only possess ITR sequences from the AAV genome which are required for packaging and integration into the host genome. Viral DNA is packaged in a cell line, which contains a helper plasmid encoding the other AAV genes, namely rep and cap, but lacking ITR sequences. The cell line is also infected with adenovirus as a helper. The helper virus promotes replication of the AAV vector and expression of AAV genes from the helper plasmid. The helper plasmid is not packaged in significant amounts due to a lack of ITR sequences. Contamination with adenovirus can be reduced by, e.g., heat treatment to which adenovirus is more sensitive than AAV.
In many gene therapy applications, it is desirable that the gene therapy vector be delivered with a high degree of specificity to a particular tissue type. A viral vector is typically modified to have specificity for a given cell type by expressing a ligand as a fusion protein with a viral coat protein on the viruses outer surface. The ligand is chosen to have affinity for a receptor known to be present on the cell type of interest. For example, Han et al., PNAS 92:9747-9751 (1995), reported that Moloney murine leukemia virus can be modified to express human heregulin fused to gp70, and the recombinant virus infects certain human breast cancer cells expressing human epidermal growth factor receptor. This principle can be extended to other pairs of virus expressing a ligand fusion protein and target cell expressing a receptor. For example, filamentous phage can be engineered to display antibody fragments (e.g., FAB or Fv) having specific binding affinity for virtually any chosen cellular receptor. Although the above description applies primarily to viral vectors, the same principles can be applied to nonviral vectors. Such vectors can be engineered to contain specific uptake sequences thought to favor uptake by specific target cells.
Gene therapy vectors can be delivered in vivo by administration to an individual patient, typically by systemic administration (e.g., intravenous, intraperitoneal, intramuscular, subdermal, or intracranial infusion) or topical application, as described below. Alternatively, vectors can be delivered to cells ex vivo, such as cells explanted from an individual patient (e.g., lymphocytes, bone marrow aspirates, tissue biopsy) or universal donor hematopoietic stem cells, followed by reimplantation of the cells into a patient, usually after selection for cells which have incorporated the vector.
Ex vivo cell transfection for diagnostics, research, or for gene therapy (e.g., via re-infusion of the transfected cells into the host organism) is well known to those of skill in the art. In a preferred embodiment, cells are isolated from the subject organism, transfected with a dominant negative protein nucleic acid (gene or cDNA), and re-infused back into the subject organism (e.g., patient). Various cell types suitable for ex vivo transfection are well known to those of skill in the art (see, e.g., Freshney et al., Culture of Animal Cells, A Manual of Basic Technique (3rd ed. 1994)) and the references cited therein for a discussion of how to isolate and culture cells from patients).
In one embodiment, stem cells are used in ex vivo procedures for cell transfection and gene therapy. The advantage to using stem cells is that they can be differentiated into other cell types in vitro, or can be introduced into a mammal (such as the donor of the cells) where they will engraft in the bone marrow. Methods for differentiating CD34+ cells in vitro into clinically important immune cell types using cytokines such a GM-CSF, IFN-γ and TNF-α are known (see Inaba et al., J. Exp. Med. 176:1693-1702 (1992)).
Stem cells are isolated for transduction and differentiation using known methods. For example, stem cells are isolated from bone marrow cells by panning the bone marrow cells with antibodies which bind unwanted cells, such as CD4+ and CD8+ (T cells), CD45+(panB cells), GR-1 (granulocytes), and Tad (differentiated antigen presenting cells) (see Inaba et al., J. Exp. Med. 176:1693-1702 (1992)).
Vectors (e.g., retroviruses, adenoviruses, liposomes, etc.) containing therapeutic dominant negative protein nucleic acids can be also administered directly to the organism for transduction of cells in vivo. Alternatively, naked DNA can be administered. Administration is by any of the routes normally used for introducing a molecule into ultimate contact with blood or tissue cells. Suitable methods of administering such nucleic acids are available and well known to those of skill in the art, and, although more than one route can be used to administer a particular composition, a particular route can often provide a more immediate and more effective reaction than another route.
Pharmaceutically acceptable carriers are determined in part by the particular composition being administered, as well as by the particular method used to administer the composition. Accordingly, there is a wide variety of suitable formulations of pharmaceutical compositions of the present invention, as described below (see, e.g., Remington's Pharmaceutical Sciences, 17th ed., 1989).
Delivery Vehicles for Dominant Negative Proteins
An important factor in the administration of polypeptide compounds, such as the dominant negative proteins of the present invention, is ensuring that the polypeptide has the ability to traverse the plasma membrane of a cell, or the membrane of an intra-cellular compartment such as the nucleus. Cellular membranes are composed of lipid-protein bilayers that are freely permeable to small, nonionic lipophilic compounds and are inherently impermeable to polar compounds, macromolecules, and therapeutic or diagnostic agents. However, proteins and other compounds such as liposomes have been described, which have the ability to translocate polypeptides such as dominant negative proteins across a cell membrane.
For example, “membrane translocation polypeptides” have amphiphilic or hydrophobic amino acid subsequences that have the ability to act as membrane-translocating carriers. In one embodiment, homeodomain proteins have the ability to translocate across cell membranes. The shortest internalizable peptide of a homeodomain protein, Antennapedia, was found to be the third helix of the protein, from amino acid position 43 to 58 (see, e.g., Prochiantz, Current Opinion in Neurobiology 6:629-634 (1996)). Another subsequence, the h (hydrophobic) domain of signal peptides, was found to have similar cell membrane translocation characteristics (see, e.g., Lin et al., J. Biol. Chem. 270:1 4255-14258 (1995)).
Examples of peptide sequences which can be linked to a dominant negative protein of the invention, for facilitating uptake of dominant negative protein into cells, include, but are not limited to: an 11 animo acid peptide of the tat protein of HIV; a 20 residue peptide sequence which corresponds to amino acids 84-103 of the p16 protein (see Fahraeus et al., Current Biology 6:84 (1996)); the third helix of the 60-amino acid long homeodomain of Antennapedia (Derossi et al., J. Biol. Chem. 269:10444 (1994)); the h region of a signal peptide such as the Kaposi fibroblast growth factor (K-FGF) h region (Lin et al., supra); or the VP22 translocation domain from HSV (Elliot & O'Hare, Cell 88:223-233 (1997)). Other suitable chemical moieties that provide enhanced cellular uptake may also be chemically linked to dominant negative proteins. For example, nuclear localization signals may be appended to enhance uptake into the nuclear compartment of cells.
Toxin molecules also have the ability to transport polypeptides across cell membranes. Often, such molecules are composed of at least two parts (called “binary toxins”): a translocation or binding domain or polypeptide and a separate toxin domain or polypeptide. Typically, the translocation domain or polypeptide binds to a cellular receptor, and then the toxin is transported into the cell. Several bacterial toxins, including Clostridium perfringens iota toxin, diphtheria toxin (DT), Pseudomonas exotoxin A (PE), pertussis toxin (PT), Bacillus anthracis toxin, and pertussis adenylate cyclase (CYA), have been used in attempts to deliver peptides to the cell cytosol as internal or amino-terminal fusions (Arora et al., J. Biol. Chem., 268:3334-3341 (1993); Perelle et al., Infect. Immun., 61:5147-5156 (1993); Stenmark et al., J. Cell Biol. 113:1025-1032 (1991); Donnelly et al., PNAS 90:3530-3534 (1993); Carbonetti et al., Abstr. Annu. Meet. Am. Soc. Microbiol. 95:295 (1995); Sebo et al., Infect. Immun. 63:3851-3857 (1995); Klimpel et al., PNAS U.S.A. 89:10277-10281 (1992); and Novak et al., J. Biol. Chem. 267:17186-17193 1992)).
Such subsequences can be used to translocate dominant negative proteins across a cell membrane. Dominant negative proteins can be conveniently fused to or derivatized with such sequences. Typically, the translocation sequence is provided as part of a fusion protein. Optionally, a linker can be used to link the dominant negative protein and the translocation sequence. Any suitable linker can be used, e.g., a peptide linker.
The dominant negative protein can also be introduced into an animal cell, preferably a mammalian cell, via a liposomes and liposome derivatives such as immunoliposomes. The term “liposome” refers to vesicles comprised of one or more concentrically ordered lipid bilayers, which encapsulate an aqueous phase. The aqueous phase typically contains the compound to be delivered to the cell, i.e., a dominant negative protein.
The liposome fuses with the plasma membrane, thereby releasing the drug into the cytosol. Alternatively, the liposome is phagocytosed or taken up by the cell in a transport vesicle. Once in the endosome or phagosome, the liposome either degrades or fuses with the membrane of the transport vesicle and releases its contents.
In current methods of drug delivery via liposomes, the liposome ultimately becomes permeable and releases the encapsulated compound (in this case, a dominant negative protein) at the target tissue or cell. For systemic or tissue specific delivery, this can be accomplished, for example, in a passive manner wherein the liposome bilayer degrades over time through the action of various agents in the body. Alternatively, active drug release involves using an agent to induce a permeability change in the liposome vesicle. Liposome membranes can be constructed so that they become destabilized when the environment becomes acidic near the liposome membrane (see, e.g., PNAS 84:7851 (1987); Biochemistry 28:908 (1989)). When liposomes are endocytosed by a target cell, for example, they become destabilized and release their contents. This destabilization is termed fusogenesis. Dioleoylphosphatidylethanolamine (DOPE) is the basis of many “fusogenic” systems.
Such liposomes typically comprise a dominant negative protein and a lipid component, e.g., a neutral and/or cationic lipid, optionally including a receptor-recognition molecule such as an antibody that binds to a predetermined cell surface receptor or ligand (e.g., an antigen). A variety of methods are available for preparing liposomes as described in, e.g., Szoka et al., Ann. Rev. Biophys. Bioeng. 9:467 (1980), U.S. Pat. Nos. 4,186,183, 4,217,344, 4,235,871, 4,261,975, 4,485,054, 4,501,728, 4,774,085, 4,837,028, 4,235,871, 4,261,975, 4,485,054, 4,501,728, 4,774,085, 4,837,028, 4,946,787, PCT Publication No. WO 91\17424, Deamer & Bangham, Biochim. Biophys. Acta 443:629-634 (1976); Fraley, et al., PNAS 76:3348-3352 (1979); Hope et al., Biochim. Biophys. Acta 812:55-65 (1985); Mayer et al., Biochim. Biophys. Acta 858:161-168 (1986); Williams et al., PNAS 85:242-246 (1988); Liposomes (Ostro (ed.), 1983, Chapter 1); Hope et al., Chem. Phys. Lip. 40:89 (1986); Gregoriadis, Liposome Technology (1984) and Lasic, Liposomes: from Physics to Applications (1993)). Suitable methods include, for example, sonication, extrusion, high pressure/homogenization, microfluidization, detergent dialysis, calcium-induced fusion of small liposome vesicles and ether-fusion methods, all of which are well known in the art.
In certain embodiments of the present invention, it is desirable to target the liposomes of the invention using targeting moieties that are specific to a particular cell type, tissue, and the like. Targeting of liposomes using a variety of targeting moieties (e.g., ligands, receptors, and monoclonal antibodies) has been previously described (see, e.g., U.S. Pat. Nos. 4,957,773 and 4,603,044).
Examples of targeting moieties include monoclonal antibodies specific to antigens associated with neoplasms, such as prostate cancer specific antigen and MAGE. Tumors can also be diagnosed by detecting gene products resulting from the activation or over-expression of oncogenes, such as ras or c-erbB2. In addition, many tumors express antigens normally expressed by fetal tissue, such as the alphafetoprotein (AFP) and carcinoembryonic antigen (CEA). Sites of viral infection can be diagnosed using various viral antigens such as hepatitis B core and surface antigens (HBVc, HBVs) hepatitis C antigens, Epstein-Barr virus antigens, human immunodeficiency type-1 virus (HIV1) and papilloma virus antigens. Inflammation can be detected using molecules specifically recognized by surface molecules which are expressed at sites of inflammation such as integrins (e.g., VCAM-1), selectin receptors (e.g., ELAM-1) and the like.
Standard methods for coupling targeting agents to liposomes can be used. These methods generally involve incorporation into liposomes lipid components, e.g., phosphatidylethanolamine, which can be activated for attachment of targeting agents, or derivatized lipophilic compounds, such as lipid derivatized bleomycin. Antibody targeted liposomes can be constructed using, for instance, liposomes which incorporate protein A (see Renneisen et al., J. Biol. Chem., 265:16337-16342 (1990) and Leonetti et al., PNAS 87:2448-2451 (1990).
Doses of Dominant Negative Proteins
For therapeutic applications of dominant negative proteins, the dose administered to a patient, in the context of the present invention should be sufficient to effect a beneficial therapeutic response in the patient over time. In addition, particular dosage regimens can be useful for determining phenotypic changes in an experimental setting, e.g., in functional genomics studies, and in cell or animal models. The dose will be determined by the condition of the patient, as well as the body weight or surface area of the patient to be treated. The size of the dose also will be determined by the existence, nature, and extent of any adverse side-effects that accompany the administration of a particular compound or vector in a particular patient.
The appropriate dose of an expression vector encoding a dominant negative protein can also be calculated by taking into account the average rate of dominant negative protein expression from the promoter and the average rate of dominant negative protein degradation in the cell. Preferably, a weak promoter such as a wild-type or mutant HSV TK is used.
In determining the effective amount of a dominant negative protein to be administered in the treatment or prophylaxis of disease, the physician evaluates circulating plasma levels of the dominant negative protein or nucleic acid encoding the dominant negative protein, potential dominant negative protein toxicities, progression of the disease, and the production of anti-dominant negative protein antibodies. Administration can be accomplished via single or divided doses.
Pharmaceutical Compositions and Administration
Dominant negative proteins and expression vectors encoding dominant negative proteins can be administered directly to the patient for modulation of gene expression and for therapeutic or prophylactic applications, for example, cancer, ischemia, diabetic retinopathy, macular degeneration, rheumatoid arthritis, psoriasis, HIV infection, sickle cell anemia, Alzheimer's disease, muscular dystrophy, neurodegenerative diseases, vascular disease, cystic fibrosis, stroke, and the like. Examples of microorganisms that can be inhibited by dominant negative protein gene therapy include pathogenic bacteria, e.g., chlamydia, rickettsial bacteria, mycobacteria, staphylococci, streptococci, pneumococci, meningococci and conococci, klebsiella, proteus, serratia, pseudomonas, legionella, diphtheria, salmonella, bacilli, cholera, tetanus, botulism, anthrax, plague, leptospirosis, and Lyme disease bacteria; infectious fungus, e.g., Aspergillus, Candida species; protozoa such as sporozoa (e.g., Plasmodia), rhizopods (e.g., Entamoeba) and flagellates (Trypanosoma, Leishmania, Trichomonas, Giardia, etc.); viral diseases, e.g., hepatitis (A, B, or C), herpes virus (e.g., VZV, HSV-1, HSV-6, HSV-II, CMV, and EBV), HIV, Ebola, adenovirus, influenza virus, flaviviruses, echovirus, rhinovirus, coxsackie virus, coronavirus, respiratory syncytial virus, mumps virus, rotavirus, measles virus, rubella virus, parvovirus, vaccinia virus, HTLV virus, dengue virus, papillomavirus, poliovirus, rabies virus, and arboviral encephalitis virus, etc.
Administration of therapeutically effective amounts is by any of the routes normally used for introducing dominant negative protein into ultimate contact with the tissue to be treated. The dominant negative proteins are administered in any suitable manner, preferably with pharmaceutically acceptable carriers. Suitable methods of administering such modulators are available and well known to those of skill in the art, and, although more than one route can be used to administer a particular composition, a particular route can often provide a more immediate and more effective reaction than another route.
Pharmaceutically acceptable carriers are determined in part by the particular composition being administered, as well as by the particular method used to administer the composition. Accordingly, there is a wide variety of suitable formulations of pharmaceutical compositions of the present invention (see, e.g., Remington's Pharmaceutical Sciences, 17th ed. 1985)).
The dominant negative proteins, alone or in combination with other suitable components, can be made into aerosol formulations (i.e., they can be “nebulized”) to be administered via inhalation. Aerosol formulations can be placed into pressurized acceptable propellants, such as dichlorodifluoromethane, propane, nitrogen, and the like.
Formulations suitable for parenteral administration, such as, for example, by intravenous, intramuscular, intradermal, and subcutaneous routes, include aqueous and non-aqueous, isotonic sterile injection solutions, which can contain antioxidants, buffers, bacteriostats, and solutes that render the formulation isotonic with the blood of the intended recipient, and aqueous and non-aqueous sterile suspensions that can include suspending agents, solubilizers, thickening agents, stabilizers, and preservatives. In the practice of this invention, compositions can be administered, for example, by intravenous infusion, orally, topically, intraperitoneally, intravesically or intrathecally. The formulations of compounds can be presented in unit-dose or multi-dose sealed containers, such as ampules and vials. Injection solutions and suspensions can be prepared from sterile powders, granules, and tablets of the kind previously described.
Functional Genomics Assays
Dominant negative proteins also have use for assays to determine the phenotypic consequences and function of gene expression. The recent advances in analytical techniques, coupled with focussed mass sequencing efforts have created the opportunity to identify and characterize many more molecular targets than were previously available. This new information about genes and their functions will speed along basic biological understanding and present many new targets for therapeutic intervention. In some cases analytical tools have not kept pace with the generation of new data. An example is provided by recent advances in the measurement of global differential gene expression. These methods, typified by gene expression microarrays, differential cDNA cloning frequencies, subtractive hybridization and differential display methods, can very rapidly identify genes that are up or down-regulated in different tissues or in response to specific stimuli. Increasingly, such methods are being used to explore biological processes such as, transformation, tumor progression, the inflammatory response, neurological disorders etc. One can now very easily generate long lists of differentially expressed genes that correlate with a given physiological phenomenon, but demonstrating a causative relationship between an individual differentially expressed gene and the phenomenon is difficult. Until now, simple methods for assigning function to differentially expressed genes have not kept pace with the ability to monitor differential gene expression.
Using conventional molecular approaches, over expression of a candidate gene can be accomplished by cloning a full-length cDNA, subcloning it into a mammalian expression vector and transfecting the recombinant vector into an appropriate host cell. This approach is straightforward but labor intensive, particularly when the initial candidate gene is represented by a simple expressed sequence tag (EST). Under expression of a candidate gene by “conventional” methods is yet more problematic. Antisense methods and methods that rely on targeted ribozymes are unreliable, succeeding for only a small fraction of the targets selected. Gene knockout by homologous recombination works fairly well in recombinogenic stem cells but very inefficiently in somatically derived cell lines. In either case large clones of syngeneic genomic DNA (on the order of 10 kb) should be isolated for recombination to work efficiently.
The dominant negative protein technology can be used to rapidly analyze differential gene expression studies. Engineered dominant negative proteins can be readily used to up or down-regulate any endogenous target gene. This makes the dominant negative protein technology ideal for analysis of long lists of poorly characterized differentially expressed genes.
This specific example of using engineered dominant negative proteins to add functional information to genomic data is merely illustrative. Any experimental situation that could benefit from the specific up or down-regulation of a gene or genes could benefit from the reliability and ease of use of engineered dominant negative proteins.
Additionally, greater experimental control can be imparted by dominant negative proteins than can be achieved by more conventional methods. This is because the production and/or function of an engineered dominant negative protein can be placed under small molecule control. Examples of this approach are provided by the Tet-On system, the ecdysone-regulated system and a system incorporating a chimeric factor including a mutant progesterone receptor. These systems are all capable of indirectly imparting small molecule control on any endogenous gene of interest or any transgene by placing the function and/or expression of a dominant negative protein under small molecule control.
Transgenic Mice
A further application of the dominant negative protein technology is manipulating gene expression in transgenic animals. Conventional down-regulation of gene expression in transgenic animals is plagued by technical difficulties. Gene knockout by homologous recombination is the method most commonly applied currently. This method requires a relatively long genomic clone of the gene to be knocked out (ca. 10 kb). Typically, a selectable marker is inserted into an exon of the gene of interest to effect the gene disruption, and a second counter-selectable marker provided outside of the region of homology to select homologous versus non-homologous recombinants. This construct is transfected into embryonic stem cells and recombinants selected in culture. Recombinant stem cells are combined with very early stage embryos generating chimeric animals. If the chimerism extends to the germline homozygous knockout animals can be isolated by back-crossing. When the technology is successfully applied, knockout animals can be generated in approximately one year. Unfortunately two common issues often prevent the successful application of the knockout technology; embryonic lethality and developmental compensation. Embryonic lethality results when the gene to be knocked out plays an essential role in development. This can manifest itself as a lack of chimerism, lack of germline transmission or the inability to generate homozygous back crosses. Genes can play significantly different physiological roles during development versus in adult animals. Therefore, embryonic lethality is not considered a rationale for dismissing a gene target as a useful target for therapeutic intervention in adults. Embryonic lethality most often simply means that the gene of interest can not be easily studied in mouse models, using conventional methods.
Developmental compensation is the substitution of a related gene product for the gene product being knocked out. Genes often exist in extensive families. Selection or induction during the course of development can in some cases trigger the substitution of one family member for another mutant member. This type of functional substitution may not be possible in the adult animal. A typical result of developmental compensation would be the lack of a phenotype in a knockout mouse when the ablation of that gene's function in an adult would otherwise cause a physiological change. This is a kind of false negative result that often confounds the interpretation of conventional knockout mouse models.
A few new methods have been developed to avoid embryonic lethality. These methods are typified by an approach using the cre recombinase and lox DNA recognition elements. The recognition elements are inserted into a gene of interest using homologous recombination (as described above) and the expression of the recombinase induced in adult mice post-development. This causes the deletion of a portion of the target gene and avoids developmental complications. The method is labor intensive and suffers form chimerism due to non-uniform induction of the recombinase.
The use of engineered dominant negative proteins to manipulate gene expression can be restricted to adult animals using the small molecule regulated systems described in the previous section. Expression and/or function of a dominant negative protein can be switched off during development and switched on at will in the adult animals. This approach relies on the expression of the dominant negative protein only; homologous recombination is not required. Because the dominant negative proteins are trans dominant, there is no concern about germline transmission or homozygosity. These issues dramatically affect the time and labor required to go from a poorly characterized gene candidate (a cDNA or EST clone) to a mouse model. This ability can be used to rapidly identify and/or validate gene targets for therapeutic intervention, generate novel model systems and permit the analysis of complex physiological phenomena (development, hematopoiesis, transformation, neural function etc.). Chimeric targeted mice can be derived according to Hogan et al., Manipulating the Mouse Embryo: A Laboratory Manual, (1988); Teratocarcinomas and Embryonic Stem Cells: A Practical Approach, Robertson, ed., (1987); and Capecchi et al., Science 244:1288 (1989).
All publications and patent applications cited in this specification are herein incorporated by reference as if each individual publication or patent application were specifically and individually indicated to be incorporated by reference.
Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be readily apparent to one of ordinary skill in the art in light of the teachings of this invention that certain changes and modifications may be made thereto without departing from the spirit or scope of the appended claims.
EXAMPLES
The following examples are provided by way of illustration only and not by way of limitation. Those of skill in the art will readily recognize a variety of noncritical parameters that could be changed or modified to yield essentially similar results.
Example 1
Dominant Negative Inhibition of Transcription by Linking Tat to a Protein that Localizes to the Transcriptional Machinery
The Tat-hybrid assay, in which Tat fused to a heterologous RNA-binding domain (RBD) elicits activation of an HIV-1 LTR reporter plasmid containing a cognate RNA-binding site, has been useful for studying RNA-protein interactions in living cells6. However, as with other types of fusion protein assays, dominant negative proteins can be generated unintentionally that score as false negatives. We discovered a novel class of highly potent dominant negatives, exemplified by Tat fusions to splicing factors, whose potency appears to be dictated by cotranscriptional recruitment to the HIV promoter.
We devised a dual-fluorescence Tat-hybrid assay to monitor RNA-binding specificity using two pairs of orthogonal reporters and Tat fusions, herein referred to as T-fusions. To calibrate the assay, T-BIVRBD, a fusion between the HIV Tat activation domain (AD) and the RBD of bovine immunodeficiency virus (BIV) Tat, was used to activate a BIV TAR (BTAR)-DsRed reporter, while T-SF1, a Tat fusion to human splicing factor SF1, was used to activate a branch point sequence (BPS)-GFP reporter (FIG. 1a). When transfected on their own, both T-BIVRBD and T-SF1 strongly activated only their cognate RNA reporters. Strikingly, however, activation via the T-BIVRBD-BTAR interaction was strongly inhibited when both T-fusions were co-transfected (3-fold activation) whereas activation via the T-SF1-BPS interaction was unafected (170-fold).
Using a more quantitative luciferase reporter, we found that inhibition was remarkably potent, with a stoichiometric amount of T-SF1 plasmid DNA (5 ng) sufficient to almost completely block activation mediated by the BIV Tat-BTAR interaction (FIG. 1b). The dose response of inhibition by T-SF1 mirrors activation of a BPS reporter (FIG. 1b), demonstrating that T-SF1 functions as an activator through its cognate RNA-binding site. We confirmed that the high potency observed in the transfection experiments accurately reflected relative protein stoichiometries by Western blot analysis of HA-tagged Tat activator and dominant negative proteins (FIG. 6). It is clear that the high potency results from the fusion, as SF1 alone does not inhibit Tat activation (data not shown) and it is known that the Tat AD without an RBD is a very weak dominant negative4,5. Given that several splicing factors, including SF1 and U2AF65, interact with CTD-associated factors or directly with RNAP II7, we hypothesized that the SF1 moiety targets the T-fusion to RNAP II. We propose a model in which this recruitment step increases the local concentration of the non-activating T-fusion at the HIV promoter thereby out-competing the wild-type Tat activator (see below).
If the targeting hypothesis is correct, then T-fusions to other RNAP II-localized splicing factors might show a similar phenotype. Indeed, T-U2AF65 is an even more potent inhibitor (FIG. 1c, left panel). U2AF65 fusions to either full-length Tat or the Tat AD are equally potent (FIG. 5), showing that the Tat RBD is dispensable for the dominant negative function. T-U2AF65 also is a potent inhibitor of Tat activation when mediated by the Rev-RRE IIB RNA interaction (FIG. 1c, right panel), further demonstrating that the inhibitor functions independently of the RNA-protein interaction. The Tat AD alone is a poor inhibitor (FIG. 1c), again showing the requirement of the targeting moiety. Besides splicing factors, other proteins interact with RNAP II before, during, or after pre-initiation complex (PIC) formation, including other RNA-processing proteins that are co-transcriptionally recruited to the CTD2. T-fusions to some, but not all, of these factors inhibited Tat-mediated activation to different extents, but none was as potent as T-U2AF65 (FIG. 7).
The specificity of inhibition for the HIV promoter was assessed by measuring effects of T-U2AF65 on other reporter-activator combinations. No inhibition was observed in any case, including activation by the P-TEFb-dependent MHC class II transactivator (CIITA) and heat-shock factor 1 (HSF1), as well as p53 and GAL4-VP16, and constitutive expression from the cytomegalovirus (CMV) promoter (FIG. 1d). Furthermore, no inhibition of cellular promoters was observed in stable cell lines expressing T-U2AF65 (FIG. 9).
Example 2
Effect of Localization of the Dominant Negative Protein on Inhibition of Transcription
To begin examining the effect of localization on inhibitor activity, we first asked whether nuclear localization alone might account for some of its potency, particularly because a variety of T-fusions showed activity, albeit not as strong as T-U2AF65 (FIG. 7). We generated T-fusions to GFP with or without a nuclear localization signal (NLS) and observed very weak dominant negative activity for the AD fusion alone (T-GFP) and only slightly enhanced inhibition for T-NLS-GFP (FIG. 2a). This result is consistent with the mild dominant negative phenotype observed for a Tat 1-53 truncation mutant that deletes part of the RNA-binding domain but still retains an NLS5. In contrast, T-U2AF65-GFP is a highly potent inhibitor (FIG. 2a), indicating that nuclear localization is not the major factor contributing to potency. T-GFP is distributed in the cytoplasm and nucleus, like unfused GFP, whereas T-NLS-GFP is greater than 95% nuclear and absent from the nucleolus, as expected (FIG. 2a). T-U2AF65-GFP shows a striking subnuclear pattern of “speckle-associated patches” (FIG. 2a). Related patterns are seen with RS-domain containing proteins8,9, which include U2AF65, prompting us to examine the domains of T-U2AF65 important for inhibition.
The RS domains of U2AF65 and other splicing factors help recruit these proteins to regions of active splicing within the nucleus8,9 and also are believed to interact with RNAP II during transcription complex asembly9. The presence of RNAP II and splicing and mRNA-export factors suggests an active role for the “speckle-associated patches” in mRNA processing, although they are otherwise considered mainly as storage sites for factors involved in mRNA metabolism10,11. To test the possible involvement of RS domains in dominant negative inhibition, we generated a T-fusion lacking the RS domain (T-U2AF65ΔRS, which contains U2AF65 residues 91-475) and a second with the RS domain alone (T-RS, which contains U2AF65 residues 2-73). Of these, only T-RS remained a potent inhibitor (FIG. 2b). T-RS shows a speckle pattern even more striking than full-length T-U2AF65, with T-RS concentrated in only about 10-30 speckles. To confirm that the Tat AD also is important for inhibition, we generated T-U2AF65 and T-RS mutants with a Lys41-to-Ala substitution in the AD that disrupts interactions with transcriptional co-activators, particularly P-TEFb12. Both are inactive as inhibitors despite having the same localization patterns as the non-mutant versions (FIGS. 2b and 8). U2AF65 RS-domain fusions to other transcriptional ADs, including VP16 and E1A, do not inhibit Tat-mediated activation (D'Orso and Frankel, unpublished observations), further demonstrating the specificity of inhibition and the requirement for the Tat AD. Thus, both an RS domain and a functional Tat AD are necessary and sufficient to generate the potent dominant negative phenotype. We envisage a model in which the U2AF65 RS-domain targets the T-fusion to subnuclear compartments (speckles) where transcription complexes are assembling, thereby facilitating the interaction of the Tat AD with one or more factors of the transcriptional machinery assembling at the HIV promoter.
Example 3
Recruitment of the Dominant Negative Protein to the Transcriptional Machinery
To examine the recruitment of T-U2AF65 to the transcriptional machinery, we first analyzed possible interactions with RNAP II by co-immunoprecipitation using antibodies against the Ser5-phosphorylated CTD (Ser5P-CTD), known as RNAP IIa. T-U2AF65-GFP, as well as the K41A Tat AD mutant, are complexed with RNAP IIa in a RNA-independent manner (FIG. 3a). Strikingly, no interaction is seen with T-NLS-GFP lacking the U2AF65 moiety despite the reported interaction of Tat with RNAP II in vitro13. Identical results were obtained using antibodies that recognize RNAPII with unphosphorylated CTD (data not shown). Thus, it appears that the U2AF65 RS moiety localizes the inhibitor to transcription complexes more efficiently than the Tat AD, consistent with the observations that U2AF65 interacts with RNAP II7 and that fusing an RS domain to a cytoplasmic reporter protein results in nuclear localization and interaction with RNAP II9,14. The interaction with RNAP II was confirmed by immunofluorescence, in which T-U2AF65-GFP was seen to co-localize with both unphosphorylated and Ser5P-CTD forms of polymerase (FIG. 3b). Partial co-localization ( ̃18%) was observed with SC35, a marker of speckle-associated patches15. Consistent with the hypothesis that the RS domain drives the interaction with RNAP II, T-RS-GFP showed the same co-localization as the full-length U2AF65 T-fusion (data not shown). In addition to interacting with RNAP II, T-U2AF65-GFP also is complexed to P-TEFb (FIG. 3a), as is the Tat AD fusion without the U2AF65 moiety. The Tat AD K41A mutation, known to abrogate the Tat-cyclin T1 interaction12, eliminates the interaction of T-U2AF65-GFP with P-TEFb, supporting the hypothesis that inhibitor potency results from bivalent interactions involving both the Tat AD and RS domain.
Example 4
Targeting of the Dominant Negative Protein to the HIV Promoter
A primary function of Tat is to enhance transcription elongation3 but it also participates in pre-initiation complex assembly3,16. RNase protection experiments using promoter proximal (Pp) and distal (Pd) probes indicate that the T-U2AF65 dominant negative primarily inhibits elongation (FIG. 3c). Tat transfected into HeLa cells substantially enhances transcription in the Pd but not Pp region of a luciferase reporter (compare lanes 1 and 2), as previously reported 3, whereas a stoichiometric amount of co-transfected T-U2AF65 reduces transcription in the Pd region to basal levels but does not effect Pp transcription (lane 3). Inhibition is dose responsive (data not shown) and requires the U2AF65 moiety as the Tat AD alone shows little inhibition (lane 4). We next used chromatin immunoprecipitation (ChIP) assays to examine recruitment of RNAP II, Tat, and T-U2AF65 to the HIV promoter and to test the hypothesis that the inhibitor is efficiently localized to the promoter. To assess complex assembly in an integrated chromatin context, we generated a stable HeLa cell line carrying an LTR-RREIIB-FFL reporter, which was strongly activated by T-Rev (215-fold) and inhibited by T-U2AF65 in a dose-responsive manner (FIG. 3d). In the absence of T-Rev, RNAP II is detected in the Pp but not Pd region (panel 1), implying a block to elongation, while RNAP II is seen in both regions following T-Rev transfection (panel 2), as previously reported16,17. The level of RNAP II detected in the Pp region increases  ̃5-fold in the presence of Tat, consistent with the proposed role of Tat in transcription complex assembly16. The T-Rev-HA activator was also detected in the Pp region (panel 2) but, notably, the T-U2AF65-GFP inhibitor showed even higher occupancy (panel 3); consistent with the observation that U2AF65 can be detected in the Pp region in the absence of Tat17. To more directly evaluate competition between the activator and inhibitor, we co-transfected both plasmids and observed strong occupancy of T-U2AF65-GFP in the Pp region whereas no T-Rev-HA could be detected (panel 4). Furthermore, the Tat AD alone, without the U2AF65 moiety, was not detectable at the promoter (panel 5, T-NLS-GFP). Thus, the ChIP experiments support the hypothesis that the T-U2AF65 inhibitor is recruited to the HIV promoter through an interaction with RNAP II, efficiently pre-loading the inhibitor into transcription complexes and blocking entry of the Tat activator.
The specificity of dominant negative inhibition for the HIV promoter is clear (FIG. 1d), but the co-localization data (FIG. 3b) suggest that a substantial amount of RNAP II interacts with the inhibitor, prompting us to test whether T-U2AF65 is recruited to other promoters. Of five cellular promoters analyzed by ChIP, including the P-TEFb-dependent MHC class II and hsp70 promoters, only hsp70 showed any detectable T-U2AF65-GFP, unlike the high occupancy observed at the HIV promoter (FIG. 3e). These data indicate that the efficiency of T-U2AF65 recruitment involves interactions other than to RNAP II, likely including interactions with PTEFb and other factors in the transcription machinery.
Example 5
Use of the Tat Dominant Negative to Inhibit HIV Replication
The high potency of the Tat dominant negatives and the requirement of Tat for viral replication suggested that they might be effective HIV inhibitors. To analyze this we generated SupT1 lymphocyte cell lines stably expressing T-U2AF65, T-HIVRBD-U2AF65, or T-BIVRBD-U2AF65 dominant negatives or the non-fusion controls, TatAD, Tat, T-BIVRBD, or U2AF65, and monitored HIV replication rates using viruses dependent on either the HIV or BIV Tat-TAR interactions18. We observed striking specificity of the dominant negatives in which replication was inhibited only in viruses driven by a non-cognate RNA-protein interaction. Expression of T-U2AF65, which contains no TAR RNA-binding domain, markedly suppressed replication of both viruses compared to the TatAD or U2AF65 controls, with no p24 antigen detectable until 18-20 days after infection (FIGS. 4a and 4b). Expression of T-HIVRBD-U2AF65 or T-BIVRBD-U2AF65 inhibited replication of the non-cognate virus to a similar extent as T-U2AF65 and showed only a slight inhibitory effect on the cognate virus (FIGS. 4a and 4b). Interestingly, expression of the Tat or T-BIVRBD activators actually accelerated replication of the cognate, but not non-cognate viruses, suggesting that Tat levels in these viruses are limiting and/or Tat may benefit viral adaptability. In the inhibitor cell lines, virus that emerged after 18-20 days displayed slow replication kinetics and reached a low plateau of p24 expression that remained constant for at least 110 days (FIGS. 4a and 4b) without producing cytophatic effects. Viral stocks harveted from these cell lines after 30 days displayed identical growth kinetics as the original stock upon re-infection (FIG. 10). Sequencing of integrated viral DNA showed no mutations in the LTR or Tat, indicating that the viruses do not acquire resistance mutations during this time period but rather grow poorly under these conditions of dominant negative inhibitor expression.
Example 6
Tat RBD is Dispensable for Dominant Negative Activity
To assess whether the RBD of Tat contributes to the dominant negative activity, we generated U2AF65 fusions to full-length Tat or TatAD and measured their effects using an LTR-BTAR-RL reporter and Tat-BIVRBD activator. Indeed, both T-HIVRBD-U2AF65 and T-U2AF65 inhibited activation more than 10-fold at sub-stoichiometric plasmid DNA levels relative to the activator (FIG. 5a). TatAD without tethered U2AF65, showed little inhibition. Similarly, full-length Tat is a weak dominant negative inhibitor of BIV Tat-TAR-mediated activation, consistent with a previous report [1]. In a converse experiment, activation of an LTR-HTAR-FFL reporter by Tat-HIVRBD is potently inhibited by T-U2AF65 and T-BIVRBD-U2AF65 but not by un-fused TatAD or T-BIVRBD (FIG. 5b). Additional control experiments showed that T-HIVRBD-U2AF65 and T-BIVRBD-U2AF65 fusion proteins activated expression of their cognate reporters to about 50% of the un-fused protein levels and that expression of non-Tat fused U2AF65 did not inhibit activation (data not shown).
Example 7
Relative Expression Levels of Tat Activator and Dominant Negative
Immunofluorescence experiments showed that the T-Rev activator and T-U2AF65 dominant negative were expressed similarly and localized to the nucleus (FIG. 2a). We analyzed protein levels more quantitatively by Western blot using HA-tagged proteins and confirmed that stoichiometric plasmid levels express similar amounts of protein (FIG. 6). Thus, the high potency of T-U2AF65 is striking given that the best reported dominant negative Tat inhibitors require more than 5-fold higher inhibitor levels to reduce activation by less than 10-fold [2-4].
Example 8
Inhibition Activities of Other T-Fusions
The potent inhibition observed with T-SF1 and T-U2AF65 prompted us to evaluate whether fusions to other transcription or RNA processing factors might also act as dominant negatives. While T-SF1 was slightly less potent than T-U2AF65, a fusion to the SR-protein 9G8 (T-9G8) was nearly as potent as T-U2AF65 (FIG. 7). Fusions to the CstF1 polyadenylation factor known to be recruited to the CTD [5,6] and to an hnRNP A1 fusion containing RRM RBDs also showed some modest inhibition (about 4 fold). In contrast, fusions to the DNA-binding transcription factors Spl or RelA showed relatively little inhibition (about 2 fold), consistent with a previous report showing little inhibitory effect by fusing Tat to other DNA-binding factors[7]. T-TAF8 also showed no inhibition, consistent with the proposal that Tat-activation is exerted through a TFIID-containing TBP complex but independent of TBP-associated factors (TAFs) [8]. All T-fusions were nuclear and expressed at similar levels as judged by indirect immunofluorescence (FIG. 7), except that T-RelA showed more prominent perinuclear localization in the absence of TNF-α activation. Thus, T-fusions to splicing factors containing RS domains (T-U2AF65 and T-9G8) are the most potent inhibitors.
Example 9
Possible Contribution of Subnuclear Localization to Dominant Negative Activity
Deleting the RS domain of T-U2AF65 eliminates dominant negative activity (see T-U2AF65ΔRS in FIG. 2b) and its subcellular localization is strikingly different (FIG. 2b). While T-U2AF65 shows speckle-associated patches typical of splicing factors, U2AF65ΔRS is spread throughout the nucleoplasm. To evaluate whether the Tat or U2AF65 moieties were responsible for these localization patterns, we first compared localization of T-U2AF65-GFP, U2FA65-GFP, and the inactive T(K41A)-U2AF65-GFP variant (FIG. 8). All three are localized similarly in speckles (Spk), implying that U2AF65 drives the localization of the dominant negative and that localization is necessary but not sufficient for inhibition.
An even more striking subnuclear localization pattern is seen for T-RS-GFP bearing only the U2AF65 RS-domain in which only a few (10-30) bright clusters are observed (FIG. 8). Again, the Tat AD K41A mutation does not alter its localization. Interestingly, an RS-GFP fusion lacking the Tat AD is no longer localized to speckles but rather to nucleoli (FIG. 8), suggesting that both the AD and RS domains of T-RS contribute to its speckle localization in this shorter context. Deletion of the RS-domain in both U2AF65 and T-U2AF65 also eliminates localization to speckles and shows a nuclear pattern with nucleolar exclusion (FIG. 8), further highlighting the importance of the RS domain for speckle localization.
Example 10
Dominant Negative Expression Levels and Functional Activity in Stable Supt1 Populations
To assess expression levels of the Tat activators (Tat, TatAD and T-BIVRBD) and dominant negative inhibitors (T-U2AF65, T-HIVRBD-U2AF65, and T-BIVRBD-U2AF65) in the stable SupT1 populations used for the viral replication assays, we first determined mRNA steady-state levels for each protein by quantitative real-time RT-PCR, using two sets of primers that amplify Tat or U2AF65 portions of the mRNAs. While the RNA expression levels varied widely between samples, all were clearly detectable, with the SupT1-Tat population expressing the highest levels (normalized expression level of 370 units), followed by T-BIVRBD (120 units), TatAD (100 units), TatAD-U2AF65 and T-BIVRBD-U2AF65 (35 units), and Tat-U2AF65 (7 units). We next characterized expression in a more functional assay in vivo by transfecting each stable cell population with an activatable GFP reporter, depending on the Tat protein expressed, and monitored activity by flow cytometry (data not shown). All stable SupT1 populations expressing the full-length Tat moiety activated an LTR-HTAR-GFP reporter, varying from 9-20 fold, while cell lines expressing TatAD did not activate. Stable cell populations expressing T-BIVRBD activated an LTR-BTAR-GFP reporter about 7-9 fold but not an LTR-HTAR-GFP reporter. The TatAD-U2AF65-expressing population weakly activated an LTR-BPS-GFP reporter, through its polypyrimidine tract (PPT) binding site [9]. This weak activity likely reflected the generally lower activation observed with the U2AF65-PPT interaction [9] and, probably, the low transfection efficiency of the SupT1 cells. Thus, expression of each Tat or Tat-fusion protein could be confirmed by RT-PCR and functional assays, but expression levels generally appeared low, as expected for a stable cell population transduced by a retrovirus but not clonally selected [10]. Weak expression was further confirmed by Western blot and immunofluorescence analysis using an anti-Tat antibody where expression was virtually undetectable (data not shown).
We also estimated the activities of the integrated dominant negatives in the SupT1 cell lines using functional assays. Cells were co-transfected with a fixed amount of the LTR-HTAR-FFL or LTR-BTAR-FFL reporter and varying concentrations of the corresponding Tat activator and levels of inhibition were measured. For example, SupT1 cells expressing T-U2AF65 and T-BIVRBD-U2AF65 were co-transfected with the LTR-HTAR-FFL reporter and HIV Tat, and no significant activation was observed at low levels (0.1-1 ng) of transfected activator (FIG. 9a). Significant activation was observed with higher (5-20 ng) plasmid amounts, further confirming that the cell lines do not express very large amount of protein and consequently do not block Tat activity completely. It seems probable that more highly expressing dominant negative cell lines can be identified through cloning that would result in even more effective viral inhibition than observed (FIG. 4).
Example 11
Lack of Dominant Negative Activity on Cellular Promoters
Transcriptional squelching has been described for many dominant negative transcription factors, such as yeast Gal4, and herpes simplex virus VP16, where common components of the transcriptional apparatus become “titrated of” of promoters[11,12]. Typically, these dominant negatives are rather promiscuous because the target co-activators do not need to be bound to the specific promoter. For HIV Tat, for example, it has been shown that Tat over-expression leads to decreased transcription from an MHC class II promoter, because both Tat and the class II transactivator (CIITA) require P-TEFb to function [13]. Because the Tat dominant negatives described here apparently operate via co-transcriptional recruitment to the HIV promoter, we suspected that they might display promoter specificity, unlike the more traditional dominant negatives. Reporter experiments show that T-U2AF65 has specificity for the HIV promoter versus other P-TEFb-regulated promoters (FIG. 1). To further analyze promoter specificity, we compared the relative expression levels of nine endogenous transcripts in the SupT1-TatAD (non-inhibitor)- and SupT1-T-U2AF65 (inhibitor)-expressing stable cell lines using quantitative RT-PCR and observed no significant differences in RNA levels from any of these promoters (FIG. 9b). The tested genes encode housekeeping proteins (actin, GAPDH, HPRT1), regulatory factors (TBP, hnRNPA1, EEF1G), and include an MHC class II (HLA-DQA1) and two other P-TEFb regulated genes (IL-8 and AR)[14]. Thus, whereas expression of T-U2AF65 effectively blocks Tat activation and HIV replication, it shows no significant effect on cellular promoters.
Example 12
Virus Emerging from the Dominant-Negative-Induced Latency-Like State Behaves as the Original Stock
We observed that virus eventually emerged after 18-20 days in the inhibitor-containing cell lines but with low replication kinetics and reaching a low steady-state plateau of p24 expression (FIG. 4). No mutations were found in these emergent viruses in the LTR or Tat coding region (data not shown), suggesting the cellular expression of the dominant negative inhibitor continuously suppressed replication. To test this, we harvested viruses that emerged after 30 days and performed a re-infection experiment to compare the kinetics of the original and emergent viruses. Indeed, identical growth kinetics were observed when the initial or new viral stocks were used to infect the SupT1-T-U2AF65 inhibitor cell line, reaching the same chronic p24-expressing plateau, whereas rapid growth was observed for both stocks in the SupT1-TatAD control cells (FIG. 10). As expected, inhibitor-expressing cells infected at a high m.o.i. (10 versus 1) showed a cytopathic effect, although again slower replication kinetics was observed than in the control cells (data not shown). Thus, even with low inhibitor expression and a high m.o.i. some protective effect still is seen, highlighting the efficacy of the inhibitor and the balance between activator and inhibitor observed upon transfection of the SupT1 cell lines (FIG. 9a).
Conclusions
The potent Tat dominant negative inhibitors described in this work represent a new mechanistic class in which we hypothesize that a transcription factor AD is efficiently recruited to its promoter via a tethering signal, in this case an RS domain, among other specific contacts with the transcriptional apparatus. Unlike other dominant negatives, these Tat inhibitors function at stoichiometric or even sub-stoichiometric levels and do not require the considerable over-expression typically required for squelching or other simple competition mechanisms1,19. We speculate that their specificity and potency is imposed by localization, first at the sub-cellular and sub-nuclear levels and second by efficient recruitment to the promoter. Ptashne and Gann proposed the concept of “regulated localization”, where specificity typically is imposed by simple binding interactions between a locator, the transcriptional machinery, and the DNA20. We propose that combining localization functions within a single polypeptide can substantially enhance activity. In the case of the T-U2AF65 inhibitor, it appears that the Tat AD provides the dominant negative function, in part through interactions with P-TEFb at the HIV promoter, while the RS domain, provides additional localization and timing functions utilizing co-transcriptional mechanisms that RNA-processing factors, including SR proteins, use to load into transcription complexes10,11. This hypothesis is supported by the observations that RS-domain-containing proteins localize to sub-nuclear speckles, which are thought to anchor splicing factors to the nuclear matrix and facilitate assembly with RNAP II,21 and that Tat and P-TEFb co-localize to nuclear speckles22. It remains to be determined if other transcription factors, including those that do not function at the elongation step, can be efficiently localized and assembled into transcription complexes in a similar manner, and if other types of targeting domains may be used.
HIV replication is substantially inhibited by low-level expression of the dominant negative in stable cell lines (FIG. 4), even without optimizing and selecting for lines with high activity (FIG. 9). It is interesting that these cells establish a chronic infection without cytopathic effects, reminiscent of other cellular environments that may resemble latent stages of HIV infection23. The balance of Tat clearly affects viral replication rates24 and also can drive phenotypic diversity25, and here we show that expression of the dominant negative provides another means to alter the Tat balance. Other dominant negative HIV proteins have been used to suppress HIV replication, including the nuclear export-deficient Rev M10 mutant26, but resistance mutations have been found27 and relatively high expression levels are required for inhibition despite the oligomeric nature of Rev27,28. It will be interesting to examine mechanisms by which resistance to the Tat dominant negative might arise and to evaluate its therapeutic potential.
Methods and Materials
Transcriptional Activation and Inhibition Reporter Assays
HeLa cells were transfected with GFP or firefly luciferase (FFL) reporter plasmids (typically 25 ng), appropriate amounts of Tat activator and inhibitor plasmids, and 5 ng of a CMV-Renilla luciferase (RL) plasmid using the Polyfect lipid transfection reagent (Qiagen) in a 48-well format. Reporter activity was measured 48 hr post-transfection using a Becton-Dickinson FACS Calibur (FIG. 1a) or Dual-Glo luciferase assay (Promega). All LTR reporter plasmids used contained an internal ribosome entry site (IRES) upstream of the FFL gene to ensure efficient translation irrespective of the 5′UTR sequence used, and RL activity was used to normalize for transfection efficiencies. For experiments presented in FIG. 2, cells were transfected with 10 ng of activator and 2.5 or 10 ng of Tat-fusion plasmids. All activation assays were performed in triplicate, and error bars'represent the SD of the mean.
Microsopy
HeLa or stably-integrated HeLa LTR-RREIIB-FFL cells were grown to 50% confluence on glass cover slips, transfected with 100 ng of plasmid DNAs, fixed in 4% paraformaldehyde in 1× PBS buffer (pH 7.6) 24 hr post-transfection, rinsed twice with PBS, and permeabilized with PBS-Triton 0.5% for 10 min at 4° C. Nonspecific antibody sites were blocked in 1× PBS, 3% goat serum, and 4% BSA for 1 hr at room temperature, cells were incubated with primary antibodies for 1 hr at room temperature, washed three times with PBS, incubated with appropriate Alexa 488- or Alexa 546-coupled secondary antibodies (Molecular Probes) for 1 hr at room temperature, and washed three times with PBS. Cells were mounted on DAPI-containing Vecta-shield slides (Vector Labs). Light microscopy was done using an LSM510 confocal microscope (Zeiss) and images were processed using LSM (Zeiss) software.
Co-Immunoprecipitation
To examine association of dominant negative inhibitors with RNAP II, HeLa cells were transiently transfected with T-U2AF65-GFP, T(K41A)-U2AF65-GFP, or T-NLS-GFP, and nuclear extracts were prepared with RIPA buffer. Half of the extract was used directly for the immunoprecipitation and the remaining half was treated with 1 μg of RNAse A, which was sufficient to quantitatively digest the RNA from 106 HeLa cells. RNAP II was immunoprecipitated using agarose-conjugated to 8WG16 and H14 antibodies overnight at 4° C. with mild shaking. Similarly, GFP-tagged proteins were immunoprecipitated using agarose-conjugated GFP-antibodies. After centrifuging and washing the beads immunocomplexes were dissociated by boiling for 10 min in 2× gel loading buffer, samples were separated by 10% SDSPAGE, transferred to PVDF, and analyzed by Western blot.
RNase Protection Assay
HeLa cells were transfected with the pLTR-HTAR-FFL reporter alone or with activator and inhibitor-expressing plasmids, total RNA was extracted using TRIzol (Invitrogen), and 15 μg of each sample was hybridized with proximal and distal probes corresponding to HIV promoter and luciferase ORF regions, respectively. The antisense probes were synthesized using a T3/T7 MaxiScript kit (Ambion) from plasmid templates linearized at a KpnI site, hybridization was performed with approximately 10,000 cpm of 32P-CTP-labeled probe (in 80% formamide, 40 mM PIPES, 400 mM NaCl, 1 mM EDTA) incubated at 42° C. overnight, RNase digestion was performed for 1.5 hr at 30° C. (in 10 mM Tris pH 8.0, 300 mM NaCl, 5 mM EDTA, 11 units/ml of RNase A, 11 units/ml RNase T1), samples were treated with proteinase K, extracted with phenol/chloroform, and RNA duplexes were precipitated with ethanol and glycogen carrier. RNAs were separated on a 6% polyacrylamide/8 M urea gel and visualized and quantified using a Typhoon phosphorimager (Molecular Dynamics). Experiments were performed in duplicate, with errors bars representing the SD of the mean.
Selection of a HeLA LTR-RREIIB-FFL Reporter Cell Line and ChIP Assays
HeLa cells were transfected in 6-well plates with a pcDNA3.1-derived plasmid (Invitrogen) bearing the LTR-RREIIB-FFL using Polyfect reagent (Qiagen). Clones were selected over more than four weeks in D-MEM-10% FBS supplemented with 750 μg/ml of G418 (Gibco). Twenty clones were analyzed for activation by pSV-T-Rev-HA by luciferase assays and a single highly active clone was chosen for ChIP analyses. ChIP assays were performed as described29 with minor modifications. HeLa LTR-RREIIB-FFL reporter cells were transfected with various expressor plasmids (5 μg each) using 30 μl of Lipofectamine 2000 (Invitrogen) per 25 cm culture dish, incubated for 36 hr, and washed in PBS. Chromatin was cross-linked with 1% formaldehyde for 15 min at RT and the reaction stopped by adding glycine to 125 mM. Cells were washed with PBS and harvested in RIPA buffer, and samples were sonicated to generate DNA fragments <500 bp. For immuno-precipitations, 1 mg of protein extract was pre-cleared for 2 hr with 40 μl of a 50% slurry of 50:50 protein A/G-agarose and -then incubated with protein A/G-agarose and the appropriate antibodies overnight at 4° C. preblocked with 1 mg/ml and 0.3 mg/ml of salmon sperm DNA. Immunocomplexes were recovered using anti-rabbit IgG/protein A/G-agarose beads (Santa Cruz), beads were washed twice with RIPA buffer, four times with ChIP wash buffer (100 mM Tris-HCl, pH 8.5, 500 mM LiCL, 1% v/v Nonidet P-40, 1% w/v deoxycholic acid), twice with RIPA buffer, and twice with 1× TE buffer. Immunocomplexes were eluted in 1% SDS for 10 min at 65° C. and cross-linking was reversed by adjusting to 200 mM NaCl and incubating for 5 hr at 65° C. A fraction of purified DNA was used for PCR amplification, with 25-32 cycles performed in the exponential range depending on the particular primers and antibodies. To ensure linearity, control PCR reactions were performed for one cycle using twice and half the amount of sample. PCR products (100-250 bp) were quantified by incorporation of SyBr Green and fluorescence detection (MJ Research) and by visualization on 2% agarose gels stained with ethidium bromide, using PCR products from known input DNAs as standards and IQMac 1.2 for analysis. Primer sequences are provided in Supplementary Information.
Dominant Negative-Expressing SupT1 Cells and Viral Replication Kinetics.
Plasmids expressing TatAD, Tat, T-BIVRBD, T-U2AF65, T-HIVRBD-U2AF65, T-BIVRBD-U2AF65, and U2AF65 were constructed in a pBMN retroviral vector (kindly provided by G. Nolan), using an SV40 promoter to express the Tat or Tat-fusion proteins. Plasmids were transfected into ONX packaging cells using the Polyfect reagent, and the retrovirus-containing supernatant recovered after 48 hr was used to transduce human CD4+ SupT1 cells. Populations of stable integrants were selected by growing cells in 2 mg/ml G418 (Invitrogen) for at least 4 weeks. Relative expression levels for each protein were assessed by real-time RT-PCR, transcriptional activation of transfected reporter plasmids and Western bloting (Supplementary Information). Each stable SupT1 population was infected with an HIV Tat-TAR-dependent (R7HTat/HTAR) or BIV Tat-TAR-dependent (R7 HBTat/BTAR) virus18 at an m.o.i of 1. Supernatant samples were harvested at different intervals following infection and the amount of viral replication was monitored by p24 antigen expression using ELISA (Immuno Diagnostics, Inc.) over a period of 110 days. Each experiment was performed in duplicate and mean values of p24 were calculated.
RNA Isolation and Expression Levels by Quantitative Real-Time RT-PCR
Total RNA was isolated from cells using the Trizol reagent according to manufacturer instructions (Invitrogen). Randomly primed cDNA was prepared from 1 μg of total RNA using MMULV reverse transcriptase (New England Biolabs). One twentieth of the resultant cDNA was amplified in 35 μl reactions containing 1.25 units of Taq DNA polymerase (ABI), 1.5 mM MgCl2, 300 nM of each primer, 0.5 mM dNTP mix, and 0.2× SYBR green I dye (Molecular Probes) in 1× Taq polymerase buffer. Real-time PCR was performed in an Opticon 2 DNA Engine (MJ Research) and analyzed using the Ct method (Applied Biosystems Prism 7700).
Expression Analysis by Western Blot
To more quantitatively assess relative inhibitor and activator expression levels, HeLa cells were co-transfected with 300 ng of pEGFPN3 (Clontech) and either 1.35 μg of pSV2-T-Rev-HA, 1.35 μg pSV2-T-U2AF65-HA, or both plasmids in 6-well plates. Nuclear extracts were prepared using NE-PER reagents (Pierce), samples were separated on a 12.5% SDS-PAGE gel, transferred to nitrocellulose, and probed with anti-HA, anti-GFP, or anti-nucleolin antibodies.
Functional Analysis of Protein Expression and Activity in SupT1 Cell Lines
Stable SupT1 G418-resistant cell populations (3×106 cells) were transfected by electroporation (Bio-Rad, 250V, 0.975 μF) with LTR-HTAR-GFP or LTR-BPS-BTAR-GFP reporters to assess the activities of integrated plasmids expressing Tat or T-fusion proteins. After 48 hours, cells were analyzed by flow cytometry and GFP activity was quantitated using Celquest software (Becton Dickinson). Populations expressing Tat and derivatives were transfected with LTR-HTAR-GFP, populations expressing T-BIVRBD and derivatives were transfected with LTR-BPS-BTAR-GFP, and populations expressing U2AF65 fusions were transfected with LTR-BPS-BTAR-GFP, which contains a BPS and PPT that binds U2AF65 cooperatively with SF1 [9]. For luciferase assays, we used the LTR-HTAR-FFL or LTR-BTAR-FFL reporters and CMV-RL as an internal control for data normalization.
Genomic DNA Extraction from SupT1-Infected Cells and Viral Genome Sequencing
SupT1-T-U2AF65, SupT1-T-BIVRBD-U2AF65, and SupT1-T-HIVRBD-U2AF65 infected populations (about 1×106 cells) were harvested 25 days post-infection and genomic DNA was extracted using Flexigene according to manufacturer instructions (Qiagen). DNA was amplified by PCR using Turbo Pfu (Stratagene), with primer pair specific to regions of the HIV LTR promoter and surrounding Tat coding sequence. PCR-amplified DNA was gel purified (Qiagen) and cloned into a TOPO vector (Invitrogen). Eight clones from each cell population were sequenced, and sequences were compared to the original viral isolate, HXB2, using the NCBI BLAST algorithm.
SUPPLEMENTARY REFERENCES


    1. Carol, R. et al., J Virol, 66:2000-7 (1992).
    2. Gren, M. et al., Cell, 58:215-23 (1989).
    3. Pearson, L. et al., Proc Natl Acad Sci USA, 87:5079-83 (1990).
    4. Caputo, A. et al., Gene Ther, 3:235-45 (1996).
    5. McCracken, S. et al., Nature, 385:357-61 (1997).
    6. Fong, N. & Bentley, D. L., Gene Dev, 15:1783-95 (2001).
    7. Fraisier, C. et al., Gene Ther 5:946-54 (1998).
    8. Raha, T. et al., PLoS Biol, 3:e44 (2005).
    9. Peled-Zehavi et al., Mol Cell Biol, 21:5232-41 (2001).
    10. Hamm, T. E. et al., J Virol, 73:5741-7 (1999).
    11. Hope, I. A. & Struhl, K., Cell, 46:885-94 (1986).
    12. Friedman, A. et al., Nature, 335:452-4 (1988).
    13. Kanazawa, S. et al., Immunity, 12:61-70 (2000).
    14. Luecke, H. F. & Yamamoto, K. R., Gene Dev, 19:1116-27 (2005).









TABLE 1





Nuclear localized proteins


Last updated: 2006 Feb. 26


nucleus















Accession: GO:0005634


Ontology: cellular_component


Synonyms: None


Definition:


A membrane-bounded organelle of eukaryotic cells in which chromosomes 


are housed and replicated. In most cells, the nucleus contains all of the 


cell's chromosomes except the organellar chromosomes, and is the site of


RNA synthesis and processing. In some species, or in specialized cell 


types, RNA metabolism or DNA replication may be absent.


Comment: None


Term Lineage


Graphical View


all: all (<167657)


GO:0005575: cellular_component (<105038)


GO:0005623: cell (<75863)


GO:0005622: intracellular (<61387)


GO:0043229: intracellular organelle (<55495)


GO:0043231: intracellular membrane-bound organelle (<51579)


GO:0005634: nucleus (<10723)


GO:0005634: nucleus (<10723)


GO:0043226: organelle (<55511)


GO:0043229: intracellular organelle (<55495)


GO:0043231: intracellular membrane-bound organelle (<51579)


GO:0005634: nucleus (<10723)


GO:0043227: membrane-bound organelle (<51596)


GO:0043231: intracellular membrane-bound organelle (<51579)


GO:0005634: nucleus (<10723)


External References


InterPro (333)


MIPS_funcat (1)


Pfam (221)


PRINTS (94)


ProDom (25)


PROSITE (99)


SMART (46)


SP_KW (1)


TIGR_role (1)


All Gene Product Associations


(1790 results)


Get ALL associations here:


Direct Associations All Associations All Associations With Terms


Filter Associations


Datasource


AllFlyBaseSGDMGIgenedb_spombeUniProtTAIRdictyBaseWorm-


baseEnsemblRGDTIGR_CMRTIGRFAMSTIGR_Ath1TIGR_Tba1-


Gramenegenedb_tsetsegenedb_tbruceigenedb_pfalciparumgenedb_lmajor-


ZFIN


Evidence Code


All Curator ApprovedICIMPIGIIPIISSIDAIEPTASNAS


Species


All A. japonica A. niger A. platyrhynchos A. thaliana A. trivirgatus 


B. anthracis str. Am B. coronavirus B. indicus B. mori B. taurus 


C. aethiops C. albicans C. briggsae C. burnetii RSA 493 C. carpio 


C. elegans C. familiaris C. griseus C. jacchus C. jejuni RM1221 


C. porcellus C. torquatus atys D. discoideum D. erecta D. ethenogenes 195


D. mauritiana D. melanogaster D. pseudoobscura D. rerio D. sechellia 


D. simulans D. sp. D. virilis D. yakuba E. caballus F. catus G. gallus 


G. gorilla G. gorilla gorilla G. sulfurreducens PCH. lar H. sapiens 


L. major L. monocytogenes str M. auratus M. capsulatus str. B 


M. fascicularis M. fuscata fuscata M. monax M. mulatta


M. musculus M. musculus castaneu M. musculus domestic M. musculus 


molossin M. musculus musculus M. natalensis M. nemestrina M. parviflora 


M. unguiculatus O. aries O. cuniculus O. kitabensis O. longistaminata


O. mykiss O. nivara O. officinalis O. sativa O. sativa (indica cu O. sativa 


(japonica O. vulgaris P. anubis P. falciparum P. monodon P. pygmaeus 


P. sativum P. syringae pv. toma P. syringae pv. toma P. troglodytes 


Panicum R. norvegicus R. sp. S. cerevisiae S. coronavirus S. oedipus 


S. oneidensis S. oneidensis MR-1 S. pombe S. pomeroyi DSS-3 


S. sciureus S. scrofa S. sp. PCC 6803 T. brucei T. brucei TREU927 


T. cambridgei T. vulpecula V. arvensis V. cholerae O1 biova V. odorata 


X. laevis X. tropicalis


























Symbol


Evi-
Refer-



Qualifier
Sequence/GOst
Information
Source
dence
ence








2A5D HUMAN
Splice Isoform Delta-1 of
UniProt
TAS

PMID: 8703017




Serine/threonine protein








phosphatase 2A, 56 kDa








regulatory subunit, delta








isoform, protein from








Homo sapiens







2A5G HUMAN
Splice Isoform Gamma-3
UniProt
IDA

PMID: 8703017




of Serine/threonine








Protein phosphatase 2A,








56 kDa regulatory








subunit, gamma isoform,








protein from Homo sapiens







2AAA HUMAN
Serine/threonine protein
UniProt
NAS

PMID: 11007961




phosphatase 2A, 65 kDa








regulatory subunit A,








alpha isoform, protein








from Homo sapiens







2AAB HUMAN
Serine/threonine protein
UniProt
ISS

UniProt: P30154




phosphatase 2A, 65 kDa








regulatory subunit A, beta








isoform, protein from








Homo sapiens







2ACC HUMAN
Protein phosphatase 2,
UniProt
TAS

PMID: 10629059




regulatory subunit B′′,








isoform 1, protein from








Homo sapiens







4ET HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 10856257




Eukaryotic translation








initiation factor 4E








transporter, protein from








Homo sapiens







AATF HUMAN
Protein AATF, protein
UniProt
IDA

PMID: 12429849




from Homo sapiens







AB2BP HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 10833507




Amyloid beta A4 protein-








binding family A member








2-binding protein, protein








from Homo sapiens







ABCCD HUMAN
Splice Isoform 1 of
UniProt
NAS

UniProt: Q9NSE7




Putative ATP-binding








cassette transporter C13,








protein from Homo sapiens







ABL1 HUMAN
Splice Isoform IA of
UniProt
NAS

PMID: 8242749




Proto-oncogene tyrosine-








protein kinase ABL1,








protein from Homo sapiens







ACINU HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 10490026




Apoptotic chromatin








condensation inducer in








the nucleus, protein from








Homo sapiens







ACL6B HUMAN
Actin-like protein 6B,
UniProt
IDA

PMID: 10380635




protein from Homo sapiens







ACTN4 HUMAN
Alpha-actinin 4, protein
UniProt
TAS

PMID: 9508771




from Homo sapiens







ADA10 HUMAN
ADAM 10 precursor,
UniProt
ISS

UniProt: O14672




protein from Homo sapiens







ADA2 HUMAN
Transcriptional adapter 2-
UniProt
TAS

PMID: 8552087




like, protein from Homo








sapiens







AF9 HUMAN
Protein AF-9, protein
UniProt
TAS

PMID: 8506309




from Homo sapiens







AFF3 HUMAN
AF4/FMR2 family member 
UniProt
TAS

PMID: 8555498




3, protein from Homo sapiens







AHNK HUMAN
Neuroblast differentiation-
UniProt
NAS

PMID: 1608957




associated protein AHNAK, 








protein from Homo sapiens







AHR HUMAN
Aryl hydrocarbon receptor
UniProt
IDA

PMID: 10395741




precursor, protein from








Homo sapiens







AIF1 HUMAN
Allograft inflammatory
UniProt
TAS

PMID: 9614071




factor 1, protein from








Homo sapiens







AIPL1 HUMAN
Aryl-hydrocarbon-
UniProt
IDA

PMID: 12374762




interacting protein-like 1,








protein from Homo sapiens







AIRE HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 9398840




Autoimmune regulator,








protein from Homo sapiens







AKAP8 HUMAN
A-kinase anchor protein 8, 
UniProt
TAS

PMID: 9473338




protein from Homo sapiens







AKIP HUMAN
Aurora kinase A-interacting 
UniProt
IDA

PMID: 12244051




protein, protein from Homo








sapiens







AKP8L HUMAN
A-kinase anchor protein-
UniProt
TAS

PMID: 10761695




like protein 8, protein








from Homo sapiens







ALP HUMAN
N-acetyltransferase-like
UniProt
NAS

PMID: 11214970




protein, protein from








Homo sapiens







ALX4 HUMAN
Homeobox protein
UniProt
NAS

PMID: 11137991




aristaless-like 4, protein








from Homo sapiens







AN32A HUMAN
Acidic leucine-rich
UniProt
IDA

PMID: 11555662




nuclear phosphoprotein 32








family member A, protein








from Homo sapiens







AN32E HUMAN
Acidic leucine-rich
UniProt
ISS

UniProt: Q9BTT0




nuclear phosphoprotein 32








family member E, protein








from Homo sapiens







ANDR HUMAN
Androgen receptor,
UniProt
IDA

PMID: 15572661




protein from Homo sapiens







ANKR2 HUMAN
Splice Isoform 1 of Ankyrin 
UniProt
ISS

PMID: 1204005




repeat domain protein 2, 








protein from Homo sapiens







ANM1 HUMAN
Splice Isoform 1 of Protein 
UniProt
IDA

PMID: 10749851




arginine N-methyltransferase 








1, protein from Homo sapiens







ANM2 HUMAN
Protein arginine N-
UniProt
TAS

PMID: 9545638




methyltransferase 2,








protein from Homo sapiens







AP2A HUMAN
OTTHUMP00000016011,
UniProt
TAS

PMID: 8321221




protein from Homo sapiens







APBB1 HUMAN
Splice Isoform 1 of
UniProt
ISS

UniProt: O00213




Amyloid beta A4 precursor 








protein-binding family B 








member 1, protein from Homo








sapiens










ISS

UniProt: Q96A93



APBB2 HUMAN
Splice Isoform 1 of
UniProt
ISS

UniProt: Q92870




Amyloid beta A4 precursor 








protein-binding family B 








member 2, protein from 








Homo sapiens







APBP2 HUMAN
Amyloid protein-binding
UniProt
NAS

PMID: 11742091




protein 2, protein from








Homo sapiens







APC HUMAN
Splice Isoform Long of
UniProt
IDA

PMID: 12072559




Adenomatous polyposis








coli protein, protein from








Homo sapiens







APEG1 HUMAN
Hypothetical protein
UniProt
TAS

PMID: 8663449




FLJ46856, protein from








Homo sapiens







APEX1 HUMAN
DNA-(apurinic or
UniProt
IDA

PMID: 9119221




apyrimidinic site) lyase,








protein from Homo sapiens







APLP2 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 7702756




Amyloid-like protein 2








precursor, protein from








Homo sapiens







ARD1H HUMAN
N-terminal acetyltransferase 
UniProt
IDA

PMID: 15496142




complex ARD1 subunit 








homolog, protein from Homo








sapiens







ARI1A HUMAN
Splice Isoform 1 of AT-
UniProt
NAS

UniProt: O14497




rich interactive domain-








containing protein 1A,








protein from Homo sapiens







ARI2 HUMAN
Ariadne-2 protein homolog, 
UniProt
TAS

PMID: 10422847




protein from Homo sapiens







ARI3A HUMAN
AT-rich interactive
UniProt
NAS

UniProt: Q99856




domain-containing protein








3A, protein from Homo








sapiens







ARI4A HUMAN
Splice Isoform I of AT-
UniProt
TAS

PMID: 8414517




rich interactive domain-








containing protein 4A,








protein from Homo sapiens










IDA

PMID: 11283269



ARI5B HUMAN
Splice Isoform 1 of AT-
UniProt
IC

PMID: 15640446




rich interactive domain-








containing protein 5B,








protein from Homo sapiens







ARL4A HUMAN
ADP-ribosylation factor-
UniProt
TAS

PMID: 10462049




like protein 4A, protein








from Homo sapiens







ARL4C HUMAN
ADP ribosylation factor-
UniProt
TAS

PMID: 10462049




like protein 7, protein








from Homo sapiens







ARNT2 HUMAN
Aryl hydrocarbon receptor
UniProt
IDA

PMID: 12239177




nuclear translocator 2,








protein from Homo sapiens







ARNT HUMAN
Splice Isoform Long of
UniProt
TAS

PMID: 1317062




Aryl hydrocarbon receptor








nuclear translocator,








protein from Homo sapiens







ASCL2 HUMAN
Achaete-scute homolog 2, 
UniProt
NAS

PMID: 8751384




protein from Homo sapiens







ASH2L HUMAN
Splice Isoform 1 of Set1/
UniProt
IDA

PMID: 15199122




Asb2 histone 








methyltransferase








complex subunit ASH2,








protein from Homo sapiens







ASPP1 HUMAN
Apoptosis stimulating of
UniProt
IDA

PMID: 11684014




p53 protein 1, protein








from Homo sapiens







ATBF1 HUMAN
Splice Isoform A of
UniProt
TAS

PMID: 1719379




Alpha-fetoprotein








enhancer binding protein,








protein from Homo sapiens







ATE1 HUMAN
Splice Isoform ATE1-1 of
UniProt
IDA

PMID: 9858543




Arginyl-tRNA--protein








transferase 1, protein








from Homo sapiens







ATF4 HUMAN
Cyclic AMP-dependent
UniProt
ISS

UniProt: P18848




transcription factor ATF-4, 








protein from Homo sapiens







ATF6B HUMAN
Splice Isoform 1 of Cyclic
UniProt
TAS

PMID: 8586413




AMP-dependent tran-








scription factor ATF-6 beta, 








protein from Homo sapiens







ATN1 HUMAN
Atropbin-1, protein from
UniProt
TAS

PMID: 10814707




Homo sapiens







ATRX HUMAN
Splice Isoform 4 of
UniProt
TAS

PMID: 7874112




Transcriptional regulator








ATRX, protein from








Homo sapiens







ATX1 HUMAN
Ataxin-1, protein from
UniProt
TAS

PMID: 7647801




Homo sapiens







ATX2 HUMAN
AtAxin 2, protein from
UniProt
TAS

PMID: 10973246




Homo sapiens







ATX7 HUMAN
Splice Isoform a of Ataxin-
UniProt
TAS

PMID: 10441328




7, protein from Homo sapiens







AURKC HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 10066797




Serine/threonine-protein








kinase 13, protein from








Homo sapiens







AXN1 HUMAN
Axin 1, protein from
UniProt
IDA

PMID: 12072559




Homo sapiens







AXN2 HUMAN
Axin-2, protein from
UniProt
IDA

PMID: 12072559




Homo sapiens







BAP1 HUMAN
Ubiquitin carboxyl-
UniProt
TAS

PMID: 9528852




terminal hydrolase BAP1,








protein from Homo sapiens







BARD1 HUMAN
BRCA1-associated RING
UniProt
IMP

PMID: 15632137




domain protein 1, protein








from Homo sapiens










IDA

PMID: 15265711



BAZ1B HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 11124022




Bromodomain adjacent to








zinc finger domain protein








1B, protein from Homo








sapiens







BC11A HUMAN
Splice Isoform 1 of B-cell
UniProt
NAS

UniProt: Q9H165




lymphoma/leukemia 11A,








protein from Homo sapiens







BCL6 HUMAN
B-cell lymphoma 6 protein, 
UniProt
IDA

PMID: 10898795




protein from Homo sapiens







BCLF1 HUMAN
Splice Isoform 1 of Bcl-2-
UniProt
NAS

UniProt: Q9NYF8




associated transcription








factor 1, protein from








Homo sapiens







BCOR HUMAN
Splice Isoform 1 of BCoR
UniProt
IDA

PMID: 10898795




protein, protein from








Homo sapiens







BHLH2 HUMAN
Class B basic helix-loop-
UniProt
NAS

PMID: 9240428




helix protein 2, protein








from Homo sapiens







BHLH3 HUMAN
Class B basic helix-loop-
UniProt
NAS

UniProt: Q9C0J9




helix protein 3, protein








from Homo sapiens







BI1 HUMAN
Bax inhibitor-1, protein
UniProt
TAS

PMID: 8530040




from Homo sapiens







BINCA HUMAN
Splice Isoform 1 of Bcl10-
UniProt
NAS

PMID: 15637807




interacting CARD protein, 








protein from Homo sapiens







BLMH HUMAN
Bleomycin hydrolase,
UniProt
TAS

PMID: 8639621




protein from Homo sapiens







BNC1 HUMAN
Zinc finger protein
UniProt
TAS

PMID: 8034748




basonuclin-1, protein








from Homo sapiens







BNIPL HUMAN
Splice Isoform 1 of Bcl-
UniProt
IDA

PMID: 11741952




2/adenovirus E1B 19 kDa-








interacting protein 2-like








protein, protein from








Homo sapiens







BRCA1 HUMAN
Breast cancer type 1
UniProt
TAS

PMID: 10918303




susceptibility protein,








protein from Homo sapiens







BRCA2 HUMAN
Breast cancer type 2
UniProt
IDA

PMID: 9560268




susceptibility protein,








protein from Homo sapiens







BRD1 HUMAN
Bromodomain-containing
UniProt
TAS

PMID: 10602503




protein 1, protein from








Homo sapiens







BRD3 HUMAN
Splice Isoform 1 of
UniProt
NAS

UniProt: Q15059




Bromodomain-containing








protein 3, protein from








Homo sapiens







BRD8 HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 8611617




Bromodomain-containing








protein 8, protein from








Homo sapiens







BRPF1 HUMAN
Peregrin, protein from
UniProt
TAS

PMID: 7906940




Homo sapiens







BRSK1 HUMAN
Splice Isoform 1 of BR
UniProt
IDA

PMID: 15150265




serine/threonine-protein








kinase 1, protein from








Homo sapiens







BSN HUMAN
Bassoon protein, protein
UniProt
TAS

PMID: 9806829




from Homo sapiens







BT3L2 HUMAN
Transcription factor BTF3
UniProt
NAS

UniProt: Q13891




homolog 2, protein from








Homo sapiens







BT3L3 HUMAN
Transcription factor BTF3
UniProt
NAS

UniProt: Q13892




homolog 3, protein from








Homo sapiens







BTAF1 HUMAN
TATA-binding-protein-
UniProt
NAS

UniProt: O14981




associated factor 172,








protein from Homo sapiens







BTG1 HUMAN
BTG1 protein, protein
UniProt
IMP

PMID: 11420681




from Homo sapiens










IEP

PMID: 9820826



CABIN HUMAN
Calcineurin-binding protein 
UniProt
NAS

UniProt: Q9Y6J0




Cabin 1, protein








from Homo sapiens







CAF1B HUMAN
Chromatin assembly factor 
UniProt
NAS

PMID: 9614144




1 subunit B, protein from 








Homo sapiens







CARM1 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 15221992




Histone-arginine








methyltransferase CARM1, 








protein from Homo sapiens







CASC5 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 10980622




Cancer susceptibility








candidate gene 5 protein,








protein from Homo sapiens







CASL HUMAN
Enhancer of filamentation
UniProt
TAS

PMID: 8668148




1, protein from Homo








sapiens







CBP HUMAN
CREB-binding protein,
UniProt
TAS

PMID: 7913207




protein from Homo sapiens







CBX2 HUMAN
Splice Isoform 1 of
UniProt
NAS

UniProt: Q14781




Chromobox protein homolog 








2, protein from Homo sapiens







CBX3 HUMAN
Chromobox protein homolog 
UniProt
TAS

PMID: 8663349




3, protein from Homo sapiens







CBX4 HUMAN
Chromobox homolog 4,
UniProt
TAS

PMID: 9315667




protein from Homo sapiens







CC14A HUMAN
Splice Isoform 1 of Dual
UniProt
TAS

PMID: 9367992




specificity protein








phosphatase CDC14A,








protein from Homo sapiens







CC14B HUMAN
Splice Isoform 2 of Dual
UniProt
IDA

PMID: 9367992




specificity protein








phosphatase CDC14B,








protein from Homo sapiens







CC45L HUMAN
CDC45-related protein,
UniProt
TAS

PMID: 9660782




protein from Homo sapiens







CCNE1 HUMAN
Splice Isoform E1L of
UniProt
NAS

UniProt: P24864




G1/S-specific cyclin-E1,








protein from Homo sapiens







CCNH HUMAN
Cyclin-H, protein from
UniProt
TAS

PMID: 7936635




Homo sapiens







CCP1 HUMAN
Calcipressin 1 large isoform, 
UniProt
TAS

PMID: 8595418




protein from Homo sapiens







CD2A1 HUMAN
Splice Isoform 1 of Cyclin-
UniProt
NR

UniProt: P42771




dependent kinase inhibitor 








2A, isoforms 1/2/3, 








protein from Homo sapiens







CD2L1 HUMAN
Splice Isoform SV9 of
UniProt
IEP

PMID: 8195233




PITSLRE








serine/threonine-protein








kinase CDC2L1, protein








from Homo sapiens







CD2L2 HUMAN
Splice Isoform SV6 of
UniProt
IEP

PMID: 8195233




PITSLRE








serine/threonine-protein








kinase CDC2L2, protein








from Homo sapiens







CD2L7 HUMAN
Cell division cycle 2-related 
UniProt
IDA

PMID: 11683387




protein kinase 7, protein 








from Homo sapiens







CDC2 HUMAN
Hypothetical protein
UniProt
TAS

PMID: 10767298




DKFZp686L20222,








protein from Homo sapiens







CDC6 HUMAN
Cell division control protein 
UniProt
TAS

PMID: 9566895




6 homolog, protein from 








Homo sapiens







CDC7 HUMAN
Cell division cycle 7-
UniProt
TAS

PMID: 9250678




related protein kinase,








protein from Homo sapiens







CDCA5 HUMAN
Sororin, protein from
UniProt
ISS

UniProt: Q96FF9




Homo sapiens







CDK1 HUMAN
Cyclin-dependent kinase
UniProt
TAS

PMID: 9506968




2-associated protein 1,








protein from Homo sapiens







CDK2 HUMAN
Cell division protein kinase 
UniProt
TAS

PMID: 10767298




2, protein from Homo sapiens







CDK5 HUMAN
Cell division protein kinase 
UniProt
ISS

UNIPROT: Q00535




5, protein from Homo sapiens







CDK7 HUMAN
Cell division protein kinase 
UniProt
TAS

PMID: 7936635




7, protein from Homo sapiens







CDK9 HUMAN
Splice Isoform 1 of Cell
UniProt
TAS

PMID: 8170997




division protein kinase 9,








protein from Homo sapiens







CDN1A HUMAN
Cyclin-dependent kinase
UniProt
TAS

PMID: 9660939




inhibitor 1, protein from








Homo sapiens







CDN1B HUMAN
Cyclin-dependent kinase
UniProt
IDA

PMID: 12093740




inhibitor 1B, protein from








Homo sapiens







CDN2C HUMAN
Cyclin-dependent kinase 6
UniProt
NR

UniProt: P42773




inhibitor, protein from








Homo sapiens







CDN2D HUMAN
Cyclin-dependent kinase 4
UniProt
TAS

PMID: 8741839




inhibitor D, protein from








Homo sapiens







CDR2 HUMAN
Cerebellar degeneration-
UniProt
NAS

UniProt: Q13977




related protein 2, protein








from Homo sapiens







CDT1 HUMAN
DNA replication factor Cdt1, 
UniProt
IDA

PMID: 11125146




protein from Homo sapiens







CEBPA HUMAN
CCAAT/enhancer binding
UniProt
NAS

PMID: 7575576




protein alpha, protein








from Homo sapiens







CEBPB HUMAN
CCAAT/enhancer binding
UniProt
TAS

PMID: 10821850




protein beta, protein from








Homo sapiens







CEBPG HUMAN
CCAAT/enhancer binding
UniProt
ISS

PMID: 7501458




protein gamma, protein








from Homo sapiens







CEBPZ HUMAN
CCAAT/enhancer binding
UniProt
TAS

PMID: 2247079




protein zeta, protein from








Homo sapiens







CENA1 HUMAN
Centaurin-alpha 1,
UniProt
IDA

PMID: 10448098




protein from Homo sapiens










IDA

PMID: 10333475



CENG1 HUMAN
Centaurin-gamma 1,
UniProt
ISS

PMID: 11136977




protein from Homo sapiens







CENPA HUMAN
Centromere protein A,
UniProt
TAS

PMID: 7962047




protein from Homo sapiens







CENPE HUMAN
Centromere protein E,
UniProt
IMP

PMID: 9763420




protein from Homo sapiens







CEZ1 HUMAN
Zinc finger protein CeZanne, 
UniProt
IDA

PMID: 11463333




protein from Homo sapiens







CHD6 HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 12592387




Chromodomain-helicase-








DNA-binding protein 6,








protein from Homo sapiens







CHD8 HUMAN
Chromodomain-helicase-
UniProt
NAS

UniProt: Q9HCK8




DNA-binding protein 8,








protein from Homo sapiens







CHK2 HUMAN
Splice Isoform 1 of
UniProt
NAS

UniProt: O96017




Serine/threonine-protein








kinase Chk2, protein








from Homo sapiens







CITE2 HUMAN
Splice Isoform 2 of
UniProt
NAS

PMID: 10552932




Cbp/p300-interacting








transactivator 2, protein








from Homo sapiens







CIZ1 HUMAN
Splice Isoform 1 of Cip1-
UniProt
TAS

PMID: 10529385




interacting zinc finger








protein, protein from








Homo sapiens







CK001 HUMAN
Protein C11orf1, protein
UniProt
NAS

PMID: 10873569




from Homo sapiens







CLAT HUMAN
Splice Isoform M of
UniProt
TAS

PMID: 10861222




Choline O-acetyltransferase, 








protein from Homo sapiens







CLIC2 HUMAN
Chloride intracellular
UniProt
TAS

PMID: 16130169




channel protein 2, protein








from Homo sapiens







CLIC3 HUMAN
Chloride intracellular
UniProt
IDA

PMID: 9880541




channel protein 3, protein








from Homo sapiens







CN004 HUMAN
Protein C14orf4, protein
UniProt
NAS

PMID: 11095982




from Homo sapiens







CND1 HUMAN
Condensin complex subunit 
UniProt
NAS

PMID: 10958694




1, protein from Homo sapiens







CND3 HUMAN
Condensin complex subunit 
UniProt
NAS

PMID: 10910072




3, protein from Homo sapiens







CNOT2 HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 10637334




CCR4-NOT transcription








complex subunit 2,








protein from Homo sapiens







CNOT7 HUMAN
CCR4-NOT transcription
UniProt
IEP

PMID: 9820826




complex subunit 7,








protein from Homo sapiens







CNOT8 HUMAN
CCR4-NOT transcription
UniProt
NAS

PMID: 10036195




complex subunit 8,








protein from Homo sapiens







COF1 HUMAN
Cofilin, non-muscle isoform, 
UniProt
TAS

PMID: 16130169




protein from Homo sapiens







COT2 HUMAN
COUP transcription factor
UniProt
TAS

PMID: 1899293




2, protein from Homo sapiens







CREB1 HUMAN
Splice Isoform CREB-A
UniProt
TAS

PMID: 10909971




of cAMP response element 








binding protein,








protein from Homo sapiens







CREB3 HUMAN
Splice Isoform 1 of Cyclic
UniProt
NAS

PMID: 9271389




AMP-responsive element








binding protein 3, protein








from Homo sapiens







CREB5 HUMAN
Splice Isoform 1 of cAMP
UniProt
IC

PMID: 8378084




response element-binding








protein 5, protein from








Homo sapiens







CREM HUMAN
CAMP responsive element 
UniProt
NAS

UniProt: Q16114




modulator,








protein from Homo sapiens







CRK HUMAN
Splice Isoform Crk-II of
UniProt
TAS

PMID: 10748058




Proto-oncogene C-crk,








protein from Homo sapiens







CRNL1 HUMAN
Crn, crooked neck-like 1,
UniProt
NAS

UniProt: Q9BZI9




protein from Homo sapiens







CRSP2 HUMAN
CRSP complex subunit 2,
UniProt
IDA

PMID: 10235267




protein from Homo sapiens







CRSP6 HUMAN
CRSP complex subunit 6,
UniProt
IDA

PMID: 10235267




protein from Homo sapiens







CRYAB HUMAN
Alpha crystallin B chain,
UniProt
NR

UniProt: P02511




protein from Homo sapiens







CSDC2 HUMAN
Cold shock domain protein 
UniProt
NAS

UniProt: Q9Y534




C2, protein from 








Homo sapiens







CSE1 HUMAN
Splice Isoform 1 of Importin-
UniProt
TAS

PMID: 9323134




alpha re-exporter, 








protein from Homo sapiens







CSR2B HUMAN
Splice Isoform 1 of
UniProt
IPI

PMID: 10924333




Cysteine-rich protein 2








binding protein, protein








from Homo sapiens







CSRP2 HUMAN
Cysteine and glycine-rich
UniProt
NAS

PMID: 96215313




protein 2, protein from








Homo sapiens







CSTF1 HUMAN
Cleavage stimulation
UniProt
TAS

PMID: 1358884




factor, 50 kDa subunit,








protein from Homo sapiens







CSTF2 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 1741396




Cleavage stimulation








factor, 64 kDa subunit,








protein from Homo sapiens







CSTF3 HUMAN
Cleavage stimulation
UniProt
TAS

PMID: 7984242




factor, 77 kDa subunit,








protein from Homo sapiens







CTCF HUMAN
Transcriptional repressor
UniProt
IDA

PMID: 9407128




CTCF, protein from








Homo sapiens







CTDS1 HUMAN
Carboxy-terminal domain
UniProt
TAS

PMID: 10967134




RNA polymerase II








polypeptide A small








phosphatase 1, protein








from Homo sapiens







CTNB1 HUMAN
Splice Isoform 1 of Beta-
UniProt
TAS

PMID: 9065401




catenin, protein from








Homo sapiens







CTND1 HUMAN
Splice Isoform 1ABC of
UniProt
NAS

PMID: 98317528




Catenin delta-1, protein








from Homo sapiens







CUGB1 HUMAN
Splice Isoform 2 of CUG
UniProt
NAS

PMID: 10893231




triplet repeat RNA-








binding protein 1, protein








from Homo sapiens







CUTL2 HUMAN
Homeobox protein cut-like 
UniProt
NAS

UniProt: O14529




2, protein from Homo sapiens







CX4NB HUMAN
Neighbor of COX4,
UniProt
TAS

PMID: 10337626




protein from Homo sapiens







CXCC1 HUMAN
CpG binding protein,
UniProt
IDA

PMID: 10688657




protein from Homo sapiens







DAPK3 HUMAN
Death-associated protein
UniProt
ISS

UniProt: O43293




kinase 3, protein from








Homo sapiens







DAXX HUMAN
Splice Isoform 1 of Death
UniProt
IDA

PMID: 15572661




domain-associated protein








6, protein from Homo sapiens







DCTN4 HUMAN
Dynactin subunit 4,
UniProt
TAS

PMID: 10671518




protein from Homo sapiens







DDX17 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 8871553




Probable ATP-dependent








RNA helicase DDX17,








protein from Homo sapiens







DDX39 HUMAN
ATP-dependent RNA
UniProt
ISS

PMID: 15047853




helicase DDX39, protein








from Homo sapiens







DDX3X HUMAN
ATP-dependent RNA
UniProt
IDA

PMID: 10329544




helicase DDX3X, protein








from Homo sapiens







DDX54 HUMAN
ATP-dependent RNA
UniProt
ISS

UniProt: Q9BRZ1




helicase DDX54, protein








from Homo sapiens







DDX5 HUMAN
Probable ATP-dependent
UniProt
NAS

PMID: 2451786




RNA helicase DDX5,








protein from Homo sapiens







DEAF1 HUMAN
Splice Isoform 1 of Deformed 
UniProt
TAS

PMID: 9773984




epidermal autoregulatory 








factor 1 homolog, protein 








from Homo sapiens







DEK HUMAN
Protein DEK, protein
UniProt
TAS

PMID: 9050861




from Homo sapiens







DFFA HUMAN
Splice Isoform DFF45 of
UniProt
IDA

PMID: 15572351




DNA fragmentation factor








alpha subunit, protein








from Homo sapiens







DFFB HUMAN
Splice Isoform Alpha of
UniProt
IDA

PMID: 15572351




DNA fragmentation factor








40 kDa subunit, protein








from Homo sapiens







DGC14 HUMAN
DGCR14 protein, protein
UniProt
ISS

PMID: 8703114




from Homo sapiens







DGCR8 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 15574589




DGCR8 protein, protein








from Homo sapiens







DGKI HUMAN
Diacylglycerol kinase, iota, 
UniProt
TAS

PMID: 9830018




protein from Homo sapiens







DGKZ HUMAN
Splice Isoform Long of
UniProt
TAS

PMID: 9716136




Diacylglycerol kinase, zeta, 








protein from Homo sapiens







DHRS2 HUMAN
Dehydrogenase/reductase,
UniProt
TAS

PMID: 7556196




protein from Homo sapiens







DHX15 HUMAN
Putative pre-mRNA splicing 
UniProt
TAS

PMID: 9388478




factor ATP-dependent 








RNA helicase DHX15, 








protein from Homo sapiens







DHX16 HUMAN
Putative pre-mRNA splicing 
UniProt
TAS

PMID: 9547260




factor ATP-dependent 








RNA helicase DHX16, 








protein from Homo sapiens







DHX9 HUMAN
DEAH (Asp-Glu-Ala-His)
UniProt
TAS

PMID: 9111062




box polypeptide 9 isoform 1, 








protein from Homo sapiens







DLG7 HUMAN
Splice Isoform 2 of Discs
UniProt
IDA

PMID: 12527899




large homolog 7, protein








from Homo sapiens







DLX1 HUMAN
Homeobox protein DLX-
UniProt
NAS

UniProt: P56177




1, protein from Homo sapiens







DMAP1 HUMAN
DNA methyltransferase 1-
UniProt
NAS

PMID: 10888872




associated protein 1,








protein from Homo sapiens







DNJC1 HUMAN
DnaJ homolog subfamily
UniProt
ISS

UniProt: Q96KC8




C member 1, protein








from Homo sapiens







DNL1 HUMAN
DNA ligase I, protein
UniProt
TAS

PMID: 8696349




from Homo sapiens







DNL3 HUMAN
Ligase III, DNA, ATP-
UniProt
TAS

PMID: 7565692




dependent, isoform alpha,








protein from Homo sapiens







DNL4 HUMAN
DNA ligase IV, protein
UniProt
TAS

PMID: 8798671




from Homo sapiens







DNM3A HUMAN
DNA, protein from Homo
UniProt
ISS

PMID: 12138111




sapiens







DNM3B HUMAN
Splice Isoform 1 of DNA,
UniProt
TAS

PMID: 10433969




protein from Homo sapiens







DNM3L HUMAN
DNA (cytosine-5)-
UniProt
NAS

PMID: 12202768




methyltransferase 3-like,








protein from Homo sapiens







DNMT1 HUMAN
Splice Isoform 1 of DNA,
UniProt
TAS

PMID: 8940105




protein from Homo sapiens







DP13A HUMAN
DCC-interacting protein
UniProt
IDA

PMID: 15016378




13 alpha, protein from








Homo sapiens







DP13B HUMAN
DCC-interacting protein
UniProt
IDA

PMID: 15016378




13 beta, protein from








Homo sapiens







DPF3 HUMAN
Zinc-finger protein DPF3, 
UniProt
NAS

UniProt: Q92784




protein from Homo sapiens







DPOA2 HUMAN
DNA polymerase alpha
UniProt
NAS

UniProt: Q14181




subunit B, protein from








Homo sapiens







DPOD2 HUMAN
DNA polymerase delta
UniProt
TAS

PMID: 8530069




subunit 2, protein from








Homo sapiens







DPOD4 HUMAN
DNA polymerase delta
UniProt
TAS

PMID: 10751307




subunit 4, protein from








Homo sapiens







DPOE3 HUMAN
DNA polymerase epsilon
UniProt
TAS

PMID: 10801849




subunit 3, protein from








Homo sapiens







DPOE4 HUMAN
DNA polymerase epsilon
UniProt
TAS

PMID: 10801849




subunit 4, protein from








Homo sapiens







DPOLA HUMAN
DNA polymerase alpha
UniProt
NAS

UniProt: P09884




catalytic subunit, protein








from Homo sapiens







DPOLL HUMAN
DNA polymerase lambda, 
UniProt
NAS

PMID: 10982892




protein from Homo sapiens







DRBP1 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 12220514




Developmentally regulated 








RNA-binding protein 1, 








protein from Homo sapiens







DRR1 HUMAN
DRR1 protein, protein
UniProt
IDA

PMID: 10564580




from Homo sapiens







DSRAD HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 7565688




Double-stranded RNA-








specific adenosine








deaminase, protein from








Homo sapiens







DTBP1 HUMAN
Splice Isoform 1 of
UniProt
ISS

UniProt: Q96EV8




Dystrobrevin-binding








protein 1, protein from








Homo sapiens







DUS10 HUMAN
Dual specificity protein
UniProt
TAS

PMID: 10391943




phosphatase 10, protein








from Homo sapiens







DUS11 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 9685386




RNA/RNP complex-1








intereracting phosphatase,








protein from Homo sapiens







DUS16 HUMAN
Dual specificity protein
UniProt
TAS

PMID: 11489891




phosphatase 16, protein








from Homo sapiens







DUS21 HUMAN
Dual specificity protein
UniProt
IDA

PMID: 12408986




phosphatase 21, protein








from Homo sapiens







DUS2 HUMAN
Dual specificity protein
UniProt
TAS

PMID: 8107850




phosphatase 2, protein








from Homo sapiens







DUS4 HUMAN
Dual specificity protein
UniProt
TAS

PMID: 7535768




phosphatase 4, protein








from Homo sapiens







DUS9 HUMAN
Dual specificity protein
UniProt
TAS

PMID: 9030581




phosphatase 9, protein








from Homo sapiens







DUT HUMAN
Splice Isoform DUT-M of
UniProt
TAS

PMID: 8631816




Deoxyuridine 5′-triphosphate








nucleotidohydrolase,








mitochondrial precursor,








protein from Homo sapiens







DYR1A HUMAN
Splice Isoform Long of
UniProt
IDA

PMID: 9748265




Dual specificity tyrosine-








phosphorylation regulated








kinase 1A, protein from








Homo sapiens







DYR1B HUMAN
Splice Isoform 1 of Dual
UniProt
TAS

PMID: 9918863




specificity tyrosine-








phosphorylation regulated








kinase 1B, protein from








Homo sapiens







DZIP1 HUMAN
Splice Isoform 1 of Zinc
UniProt
IDA

PMID: 15081113




finger protein DZIP1,








protein from Homo sapiens







ECM29 HUMAN
PREDICTED: KIAA0368
UniProt
IDA

PMID: 15496406




protein, protein from








Homo sapiens







EDD1 HUMAN
Ubiquitin--protein ligase
UniProt
IDA

PMID: 12011095




EDD1, protein from








Homo sapiens







EDF1 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 10567391




Endothelial differentiation-








related factor 1, protein 








from Homo sapiens







EGF HUMAN
Pro-epidermal growth
UniProt
NR

UniProt: P01133




factor precursor, protein








from Homo sapiens







EGFR HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 12828935




Epidermal growth factor








receptor precursor, 








protein from Homo sapiens







EGLN2 HUMAN
Egl nine homolog 2,
UniProt
IDA

PMID: 11850811




protein from Homo sapiens







EHD2 HUMAN
Similar to EH-domain
UniProt
TAS

PMID: 10673336




containing protein 2,








protein from Homo sapiens







EHD3 HUMAN
EH-domain containing
UniProt
TAS

PMID: 10673336




protein 3, protein from








Homo sapiens







EHD4 HUMAN
EH-domain containing
UniProt
TAS

PMID: 10673336




protein 4, protein from








Homo sapiens







EHMT1 HUMAN
Splice Isoform 2 of
UniProt
IC

PMID: 12004135




Histone-lysine N-








methyltransferase, H3








lysine-9 specific 5,








protein from Homo sapiens







ELF1 HUMAN
ETS-related transcription
UniProt
NAS

UniProt: P32519




factor Elf-1, protein from








Homo sapiens







ELF2 HUMAN
Splice Isoform 1 of ETS-
UniProt
IC

PMID: 14970218




related transcription factor








Elf-2, protein from Homo








sapiens







ELL3 HUMAN
RNA polymerase II
UniProt
IDA

PMID: 10882741




elongation factor ELL3,








protein from Homo sapiens







EMX1 HUMAN
Homeobox protein EMX1, 
UniProt
NAS

UniProt: Q04741




protein from Homo sapiens







EMX2 HUMAN
Homeobox protein EMX2, 
UniProt
NAS

UniProt: Q04743




protein from Homo sapiens







ENC1 HUMAN
Ectoderm-neural cortex 1
UniProt
TAS

PMID: 9566959




protein, protein from








Homo sapiens







ENL HUMAN
ENL protein, protein
UniProt
TAS

PMID: 8080983




from Homo sapiens







EP300 HUMAN
E1A-associated protein p300, 
UniProt
IDA

PMID: 9194565




protein from Homo sapiens







EPC1 HUMAN
Splice Isoform 1 of Enhancer 
UniProt
IDA

PMID: 10976108




of polycomb homolog 1, 








protein from Homo sapiens







ERCC2 HUMAN
TFIIH basal transcription
UniProt
NAS

UniProt: P18074




factor complex helicase








subunit, protein from








Homo sapiens







ERCC3 HUMAN
TFIIH basal transcription
UniProt
TAS

PMID: 8663148




factor complex helicase








XPB subunit, protein








from Homo sapiens







ERG HUMAN
Splice Isoform ERG-2 of
UniProt
TAS

PMID: 8502479




Transcriptional regulator 








ERG, protein from Homo








sapiens







ERR1 HUMAN
Steroid hormone receptor
UniProt
TAS

PMID: 9286700




ERR1, protein from








Homo sapiens







ERR3 HUMAN
Splice Isoform 1 of Estrogen-
UniProt
ISS

UniProt: P62508




related receptor gamma, 








protein from Homo sapiens







ESR2 HUMAN
Splice Isoform 1 of Estrogen 
UniProt
TAS

PMID: 11181953




receptor beta,








protein from Homo sapiens







ETV3 HUMAN
Splice Isoform 1 of ETS
UniProt
NAS

UniProt: P41162




translocation variant 3,








protein from Homo sapiens







ETV4 HUMAN
ETS translocation variant
UniProt
NAS

UniProt: P43268




4, protein from Homo sapiens







ETV7 HUMAN
Splice Isoform B of
UniProt
TAS

PMID: 10828014




Transcription factor ETV7, 








protein from Homo sapiens







EVI1 HUMAN
Splice Isoform 1 of
UniProt
NAS

UniProt: Q03112




Ecotropic virus integration 








1 site protein,








protein from Homo sapiens







EVX2 HUMAN
Homeobox even-skipped
UniProt
NAS

UniProt: Q03828




homolog protein 2,








protein from Homo sapiens







EXOS2 HUMAN
Exosome complex
UniProt
TAS

PMID: 8600032




exonuclease RRP4,








protein from Homo sapiens







FA50A HUMAN
Protein FAM50A, protein
UniProt
TAS

PMID: 9339379




from Homo sapiens







FAF1 HUMAN
Splice Isoform Long of
UniProt
IDA

PMID: 15596450




FAS-associated factor 1,








protein from Homo sapiens







FALZ HUMAN
Fetal Alzheimer antigen,
UniProt
IDA

PMID: 10727212




protein from Homo sapiens







FANCA HUMAN
Splice Isoform 1 of Fanconi 
UniProt
TAS

PMID: 9398857




anemia group A protein, 








protein from Homo sapiens







FANCC HUMAN
Fanconi anemia group C
UniProt
TAS

PMID: 9398857




protein, protein from








Homo sapiens







FANCE HUMAN
Fanconi anemia group E
UniProt
NAS

PMID: 11001585




protein, protein from








Homo sapiens







FANCJ HUMAN
Splice Isoform 1 of Fanconi 
UniProt
NAS

PMID: 11301010




anemia group J protein, 








protein from Homo sapiens







FGF10 HUMAN
Fibroblast growth factor 10 
UniProt
IDA

PMID: 11923311




precursor, protein








from Homo sapiens







FHL2 HUMAN
FHL2 isoform 5, protein
UniProt
TAS

PMID: 9150430




from Homo sapiens







FHOD1 HUMAN
FH1/FH2 domain-
UniProt
TAS

PMID: 10352228




containing protein, protein 








from Homo sapiens







FIBP HUMAN
Splice Isoform Short of
UniProt
TAS

PMID: 9806903




Acidic fibroblast growth








factor intracellular








binding protein, protein








from Homo sapiens







FIZ1 HUMAN
Flt3-interacting zinc
UniProt
ISS

UniProt: Q96SL8




finger protein 1, protein








from Homo sapiens







FMR1 HUMAN
Splice Isoform 6 of Fragile 
UniProt
TAS

PMID: 8515814




X mental retardation 1 








protein, protein from Homo








sapiens







FOS HUMAN
Proto-oncogene protein c-
UniProt
TAS

PMID: 9443941




fos, protein from Homo








sapiens







FOSL1 HUMAN
Fos-related antigen 1,
UniProt
TAS

PMID: 10918580




protein from Homo sapiens







FOSL2 HUMAN
Fos-related antigen 2,
UniProt
TAS

PMID: 8954781




protein from Homo sapiens







FOXC1 HUMAN
Forkhead box protein C1,
UniProt
NAS

UniProt: Q9BYM1




protein from Homo sapiens







FOXD3 HUMAN
Forkhead box protein D3,
UniProt
ISS

UniProt: Q9UJU5




protein from Homo sapiens







FOXD4 HUMAN
Forkhead box protein D4,
UniProt
NAS

UniProt: O43638




protein from Homo sapiens







FOXE3 HUMAN
Forkhead box protein E3,
UniProt
NAS

UniProt: Q13461




protein from Homo sapiens







FOXF1 HUMAN
Forkhead box protein F1,
UniProt
TAS

PMID: 9722567




protein from Homo sapiens







FOXF2 HUMAN
Forkhead box protein F2,
UniProt
TAS

PMID: 9722567




protein from Homo sapiens







FOXGC HUMAN
Forkhead box protein G1C, 
UniProt
NAS

UniProt: Q14488




protein from Homo sapiens







FOXI1 HUMAN
Forkhead box I1 isoForm a, 
UniProt
NAS

UniProt: Q12951




protein from Homo sapiens







FOXJ1 HUMAN
Forkhead box protein J1,
UniProt
TAS

PMID: 9073514




protein from Homo sapiens







FOXK2 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 1909027




Forkhead box protein K2,








protein from Homo sapiens







FOXL1 HUMAN
Forkhead box protein L1,
UniProt
NAS

UniProt: Q12952




protein from Homo sapiens







FOXL2 HUMAN
FOXL2, protein from
UniProt
NAS

UniProt: P58012




Homo sapiens







FOXN1 HUMAN
Forkhead box protein N1,
UniProt
TAS

PMID: 10767081




protein from Homo sapiens







FOXO3 HUMAN
Forkhead box protein O3A, 
UniProt
TAS

PMID: 10102273




protein from Homo sapiens







FOXO4 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 9010221




Putative fork head domain








transcription factor AFX1, 








protein from Homo sapiens







FOXP3 HUMAN
Splice Isoform 1 of
UniProt
NAS

UniProt: Q9BZS1




Forkhead box protein P3,








protein from Homo sapiens







FREA HUMAN
Forkhead-related
UniProt
NAS

UniProt: O43638




transcription factor 10,








protein from Homo sapiens







FRK HUMAN
Tyrosine-protein kinase FRK, 
UniProt
TAS

PMID: 7696183




protein from Homo sapiens







FUBP3 HUMAN
Splice Isoform 2 of Far
UniProt
NAS

PMID: 8940189




upstream element-binding








protein 3, protein from








Homo sapiens







FUS HUMAN
Fus-like protein, protein
UniProt
TAS

PMID: 8510758




from Homo sapiens







FUSIP HUMAN
Splice Isoform 1 of FUS-
UniProt
ISS

UniProt: Q96P17




interacting serine-








arginine-rich protein 1,








protein from Homo sapiens










IC

PMID: 9774382



FXL10 HUMAN
Splice Isoform 1 of F-
UniProt
NAS

PMID: 10799292




box/LRR-repeat protein 10, 








protein from Homo sapiens







FXR2 HUMAN
Fragile X mental retardation 
UniProt
TAS

PMID: 10888599




syndrome-related protein 2, 








protein from Homo sapiens







FYB HUMAN
Splice Isoform FYB-120
UniProt
TAS

PMID: 9207119




of FYN-binding protein,








protein from Homo sapiens







G10 HUMAN
G10 protein homolog,
UniProt
TAS

PMID: 7841202




protein from Homo sapiens







G3BP HUMAN
Ras-GTPase-activating
UniProt
TAS

PMID: 9889278




protein binding protein 1,








protein from Homo sapiens







GA45A HUMAN
Growth arrest and DNA-
UniProt
TAS

PMID: 7798274




damage-inducible protein








GADD45 alpha, protein








from Homo sapiens







GABP2 HUMAN
Splice Isoform 1 of GA
UniProt
TAS

PMID: 9016666




binding protein beta chain, 








protein from Homo sapiens







GABPA HUMAN
GA binding protein alpha
UniProt
TAS

PMID: 9016666




chain, protein from Homo








sapiens







GATA1 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 2300555




Erythroid transcription








factor, protein from








Homo sapiens







GATA2 HUMAN
Endothelial transcription
UniProt
TAS

PMID: 1370462




factor GATA-2, protein








from Homo sapiens







GATA4 HUMAN
Transcription factor GATA-4, 
UniProt
NAS

PMID: 12845333




protein from Homo sapiens







GCFC HUMAN
Splice Isoform A of GC-
UniProt
NAS

UniProt: Q9Y5B6




rich sequence DNA-binding 








factor homolog, 








protein from Homo sapiens







GCM1 HUMAN
Chorion-specific transcription 
UniProt
TAS

PMID: 8962155




factor GCMa, protein 








from Homo sapiens







GCM2 HUMAN
Chorion-specific transcription 
UniProt
TAS

PMID: 9928992




factor GCMb, protein 








from Homo sapiens







GCR HUMAN
Splice Isoform Alpha of
UniProt
TAS

PMID: 9873044




Glucocorticoid receptor,








protein from Homo sapiens







GLI3 HUMAN
Zinc finger protein GLI3,
UniProt
TAS

PMID: 10077605




protein from Homo sapiens







GLI4 HUMAN
Zinc finger protein GLI4,
UniProt
NAS

UniProt: P10075




protein from Homo sapiens







GLIS1 HUMAN
Zinc finger protein GLIS1, 
UniProt
ISS

UniProt: Q8NBF1




protein from Homo sapiens







GLIS3 HUMAN
Zinc finger protein GLIS3, 
UniProt
ISS

UniProt: Q8NEA6




protein from Homo sapiens







GLRX2 HUMAN
Splice Isoform 1 of
UniProt
IEP

PMID: 11297543




Glutaredoxin-2,








mitochondrial precursor,








protein from Homo sapiens







GMEB1 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 10386584




Glucocorticoid modulatory 








element-binding protein 1, 








protein from Homo sapiens







GMEB2 HUMAN
Glucocorticoid modulatory 
UniProt
TAS

PMID: 10523663




element-binding protein 2, 








protein from Homo sapiens







GNEFR HUMAN
Splice Isoform 2 of
UniProt
IDA

PMID: 10571079




Guanine nucleotide exchange 








factor-related protein, 








protein from Homo sapiens







GNL3 HUMAN
Splice Isoform 1 of
UniProt
ISS

UniProt: Q9BVP2




Guanine nucleotide








binding protein-like 3,








protein from Homo sapiens







GO45 HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 9129147




Golgin 45, protein from








Homo sapiens







GRAA HUMAN
Granzyme A precursor,
UniProt
TAS

PMID: 11909973




protein from Homo sapiens







GRAB HUMAN
Endogenous granzyme B,
UniProt
TAS

PMID: 11909973




protein from Homo sapiens







GRLF1 HUMAN
Glucocorticoid receptor DNA 
UniProt
IC

PMID: 1894621




bindinG factor 1 isoform b, 








protein from Homo sapiens







GRP78 HUMAN
78 kDa glucose-regulated
UniProt
IDA

PMID: 12665508




protein precursor, protein








from Homo sapiens







GSC HUMAN
Homeobox protein goosecoid, 
UniProt
NAS

UniProt: P56915




protein from Homo sapiens







GT2D1 HUMAN
Splice Isoform 1 of General 
UniProt
NAS

PMID: 11438732




transcription factor II-I repeat 








domain-containing protein 1,








protein from Homo sapiens







H2AFX HUMAN
Histone H2A.x, protein
UniProt
IDA

PMID: 15604234




from Homo sapiens










IDA

PMID: 11331621



HAIR HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 9445480




Hairless protein, protein








from Homo sapiens







HASP HUMAN
Splice Isoform 1 of
UniProt
IEP

PMID: 11228240




Serine/threonine-protein








kinase Haspin, protein








from Homo sapiens







HAT1 HUMAN
Histone acetyltransferase
UniProt
TAS

PMID: 9427644




type B catalytic subunit,








protein from Homo sapiens







HBXAP HUMAN
Remodeling and spacing
UniProt
IDA

PMID: 12972596




factoR 1, protein from








Homo sapiens










IDA

PMID: 11788598



HCC1 HUMAN
Nuclear protein Hcc-1,
UniProt
NAS

PMID: 11356193




protein from Homo sapiens







HCFC1 HUMAN
Splice Isoform 1 of Host
UniProt
IDA

PMID: 7876203




cell factor, protein from








Homo sapiens







HCFC2 HUMAN
Host cell factor 2, protein
UniProt
IDA

PMID: 10196288




from Homo sapiens







HDA10 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 11861901




Histone deacetylase 10,








protein from Homo sapiens







HDA11 HUMAN
Histone deacetylase 11,
UniProt
IDA

PMID: 11948178




protein from Homo sapiens







HDAC1 HUMAN
Histone deacetylase 1,
UniProt
TAS

PMID: 12711221




protein from Homo sapiens







HDAC2 HUMAN
Histone deacetylase 2,
UniProt
TAS

PMID: 12711221




protein from Homo sapiens







HDAC3 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 12711221




Histone deacetylase 3,








protein from Homo sapiens







HDAC4 HUMAN
Histone deacetylase 4,
UniProt
NAS

UniProt: P56524




protein from Homo sapiens







HDAC5 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 12711221




Histone deacetylase 5,








protein from Homo sapiens







HDAC6 HUMAN
Histone deacetylase 6,
UniProt
NAS

UNIPROT: Q9UBN7




protein from Homo sapiens







HDAC7 HUMAN
Histone deacetylase,
UniProt
TAS

PMID: 12711221




protein from Homo sapiens







HDAC9 HUMAN
Splice Isoform 1 of
UniProt
NAS

UniProt: Q9UKV0




Histone deacetylase 9,








protein from Homo sapiens







HDGR3 HUMAN
Hepatoma-derived growth
UniProt
IDA

PMID: 10581169




factor-related protein 3,








protein from Homo sapiens







HD HUMAN
Huntingtin, protein from
UniProt
TAS

PMID: 9778247




Homo sapiens







HELI HUMAN
Splice Isoform 1 of Zinc
UniProt
NAS

UniProt: Q9UKS7




finger protein Helios,








protein from Homo sapiens







HIC1 HUMAN
Splice Isoform 2 of Hyper-
UniProt
NAS

UniProt: Q14526




methylated in cancer 1 protein, 








protein from Homo sapiens







HIC2 HUMAN
Splice Isoform 1 of Hyper-
UniProt
IEP

PMID: 11554746




methylated in cancer 2 protein, 








protein from Homo sapiens







HIF1A HUMAN
Hypoxia-inducible factor
UniProt
IDA

PMID: 15261140




1 alpha, protein from








Homo sapiens







HINT1 HUMAN
Histidine triad nucleotide-
UniProt
TAS

PMID: 9770345




binding protein 1, protein








from Homo sapiens







HIPK2 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 12220523




Homeodomain-interacting








protein kinase 2, protein








from Homo sapiens







HIPK3 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 11034606




Homeodomain-interacting








protein kinase 3, protein








from Homo sapiens







HIRA HUMAN
Splice Isoform Long of
UniProt
TAS

PMID: 9710638




HIRA protein, protein








from Homo sapiens







HIRP3 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 9710638




HIRA-interacting protein








3, protein from Homo sapiens







HKR1 HUMAN
Krueppel-related zinc
UniProt
NAS

UniProt: P10072




finger protein 1, protein








from Homo sapiens







HKR2 HUMAN
Krueppel-related zinc
UniProt
NAS

UniProt: P10073




finger protein 2, protein








from Homo sapiens







HLF HUMAN
Hepatic leukemia factor,
UniProt
TAS

PMID: 1386162




protein from Homo sapiens







HLXB9 HUMAN
Homeobox protein HB9,
UniProt
NAS

UniProt: P50219




protein from Homo sapiens










NAS

UniProt: Q9Y648



HM20B HUMAN
SWI/SNF-related matrix-
UniProt
NAS

UniProt: Q9P0W2




associated actin-dependent 








regulator of chromatin 








subfamily E








member 1-related, protein








from Homo sapiens







HM2L1 HUMAN
High mobility group
UniProt
NAS

UniProt: Q9UGU5




protein 2-like 1, protein








from Homo sapiens







HMG17 HUMAN
Nonhistone chromosomal
UniProt
NAS

UniProt: P05204




protein HMG-17, protein








from Homo sapiens







HMG1 HUMAN
High mobility group
UniProt
TAS

PMID: 16130169




protein 1, protein from








Homo sapiens







HMGN3 HUMAN
High mobility group
UniProt
NAS

UniProt: Q15651




nucleosome binding








domain 3, protein from








Homo sapiens







HNF1B HUMAN
Splice Isoform A of
UniProt
TAS

PMID: 1677179




Hepatocyte nuclear factor








1-beta, protein from








Homo sapiens







HNF3G HUMAN
Hepatocyte nuclear factor
UniProt
TAS

PMID: 7739897




3-gamma, protein from








Homo sapiens







HNF4A HUMAN
Hepatocyte nuclear factor
UniProt
TAS

PMID: 9048927




4 alpHa isoform b,








protein from Homo sapiens







HNF6 HUMAN
Hepatocyte nuclear factor
UniProt
NAS

UniProt: Q9UBC0




6, protein from Homo sapiens







HNRPD HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 1433497




Heterogeneous nuclear








ribonucleoprotein D0,








protein from Homo sapiens







HNRPQ HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 9847309




Heterogeneous nuclear








ribonucleoprotein Q,








protein from Homo sapiens







HRX HUMAN
Splice Isoform 1 of Zinc
UniProt
IDA

PMID: 11313484




finger protein HRX,








protein from Homo sapiens







HS74L HUMAN
Heat shock 70 kDa
UniProt
ISS

UniProt: O95757




protein 4L, protein from








Homo sapiens







HSBP1 HUMAN
Heat shock factor binding
UniProt
TAS

PMID: 9649501




protein 1, protein from








Homo sapiens







HSP71 HUMAN
Heat shock 70 kDa
UniProt
TAS

PMID: 10205060




protein 1, protein from








Homo sapiens







HTRA2 HUMAN
Splice Isoform 1 of Serine
UniProt
TAS

PMID: 10971580




protease HTRA2,








mitochondrial precursor,








protein from Homo sapiens







HUWE1 HUMAN
Splice Isoform 1 of
UniProt
ISS

UniProt: Q7Z6Z7




HECT, UBA and WWE








domain containing protein








1, protein from Homo sapiens







HXA5 HUMAN
Homeobox protein Hox-A5, 
UniProt
NAS

UniProt: P20719




protein from Homo sapiens







HXB1 HUMAN
Homeobox protein Hox-B1, 
UniProt
NAS

UniProt: P14653




protein from Homo sapiens







HXB4 HUMAN
Homeobox protein Hox-B4, 
UniProt
NAS

UniProt: P17483




protein from Homo sapiens







HXB6 HUMAN
Splice Isoform 1 of
UniProt
NAS

UniProt: P17509




Homeobox protein Hox-B6, 








protein from Homo sapiens







HXB7 HUMAN
Homeobox protein Hox-B7, 
UniProt
NAS

PMID: 1678287




protein from Homo sapiens







HXB8 HUMAN
Homeobox protein Hox-B8, 
UniProt
NAS

UniProt: P17481




protein from Homo sapiens







HXB9 HUMAN
Homeobox protein Hox-B9, 
UniProt
NAS

UniProt: P17482




protein from Homo sapiens







HXC13 HUMAN
Homeobox protein Hox-C13, 
UniProt
NAS

UniProt: P31276




protein from Homo sapiens







HXC4 HUMAN
Homeobox protein Hox-C4, 
UniProt
NAS

UniProt: P09017




protein from Homo sapiens







HXC8 HUMAN
Homeobox protein Hox-C8, 
UniProt
NAS

UniProt: P31273




protein from Homo sapiens







HXD11 HUMAN
Homeobox protein Hox-D11, 
UniProt
NAS

UniProt: P31277




protein from Homo sapiens







HXD4 HUMAN
Homeobox protein Hox-D4, 
UniProt
NAS

UniProt: P09016




protein from Homo sapiens







HXD8 HUMAN
Homeobox protein Hox-D8, 
UniProt
NAS

PMID: 2568311




protein from Homo sapiens







IASPP HUMAN
Splice Isoform 1 of RelA-
UniProt
TAS

PMID: 10336463




associated inhibitor,








protein from Homo sapiens







IF16 HUMAN
Splice Isoform 2 of
UniProt
IDA

PMID: 7536752




Gamma-interferon-








inducible protein Ifi-16,








protein from Homo sapiens







IF6 HUMAN
Eukaryotic translation
UniProt
TAS

PMID: 9374518




initiation factor 6, protein








from Homo sapiens







IKBA HUMAN
NF-kappaB inhibitor alpha, 
UniProt
IDA

PMID: 7679069




protein from Homo sapiens







ILF2 HUMAN
Interleukin enhancer-
UniProt
IDA

PMID: 7519613




binding factor 2, protein








from Homo sapiens







ILF3 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 11739746




Interleukin enhancer-binding 








factor 3, protein








from Homo sapiens










NAS

PMID: 10400669



IMA2 HUMAN
Importin alpha-2 subunit,
UniProt
TAS

PMID: 9020106




protein from Homo sapiens







IMB3 HUMAN
Importin beta-3, protein
UniProt
TAS

PMID: 9114010




from Homo sapiens







IMUP HUMAN
Similar to Immortalization-
UniProt
TAS

PMID: 11080599




upregulated protein,








protein from Homo sapiens







IN35 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 8288566




Interferon-induced 35 kDa








protein, protein from








Homo sapiens







ING1 HUMAN
Splice Isoform 1 of Inhibitor 
UniProt
NAS

PMID: 10866301




of growth protein 1, 








protein from Homo sapiens







ING2 HUMAN
Inhibitor of growth protein 2, 
UniProt
IEP

PMID: 15243141




protein from Homo sapiens







ING4 HUMAN
Splice Isoform 1 of Inhibitor 
UniProt
IDA

PMID: 15029197




of growth protein 4, 








protein from Homo sapiens







IP6K1 HUMAN
Inositol hexaphosphate kinase 
UniProt
TAS

PMID: 11502751




1, protein from Homo sapiens







IP6K2 HUMAN
Splice Isoform 1 of Inositol 
UniProt
ISS

UniProt: Q9UHH9




hexakisphosphate kinase 








2, protein from Homo sapiens







IP6K3 HUMAN
Inositol hexaphosphate
UniProt
IDA

PMID: 11502751




kinase 3, protein from








Homo sapiens










ISS

UniProt: Q96PC2



IRF4 HUMAN
Splice Isoform 1 of Interferon 
UniProt
IC

PMID: 12374808




regulatory factor 4, 








protein from Homo sapiens







IRF7 HUMAN
Splice Isoform A of
UniProt
ISS

UniProt: Q92985




Interferon regulatory factor 








7, protein from Homo sapiens







IRS1 HUMAN
Insulin receptor substrate
UniProt
ISS

UniProt: P35568




1, protein from Homo sapiens







IRTF HUMAN
Transcriptional regulator
UniProt
TAS

PMID: 1630447




ISGF3 gamma subunit,








protein from Homo sapiens







ITF2 HUMAN
Splice Isoform SEF2-1B
UniProt
TAS

PMID: 1681116




of Transcription factor 4,








protein from Homo sapiens







JAD1A HUMAN
Jumonji/ARID domain-
UniProt
TAS

PMID: 8414517




containing protein 1A,








protein from Homo sapiens







JERKL HUMAN
Jerky homolog-like,
UniProt
TAS

PMID: 9240447




protein from Homo sapiens







KCY HUMAN
UMP-CMP kinase,
UniProt
TAS

PMID: 10462544




protein from Homo sapiens







KIF22 HUMAN
Kinesin-like protein KIF22, 
UniProt
TAS

PMID: 8599929




protein from Homo sapiens







KLF10 HUMAN
Transforming growth
UniProt
TAS

PMID: 9748269




factor-beta-inducible early








growth response protein 1, 








protein from Homo sapiens







KLF11 HUMAN
Transforming growth
UniProt
TAS

PMID: 9748269




factor-beta-inducible early








growth response protein








2, protein from Homo sapiens







KLF2 HUMAN
Kruppel-like factor 2,
UniProt
NAS

UniProt: Q9Y5W3




protein from Homo sapiens







KLF4 HUMAN
Kruppel-like factor 4,
UniProt
ISS

PMID: 9422764




protein from Homo sapiens







KLF6 HUMAN
Splice Isoform 1 of Core
UniProt
TAS

PMID: 9689109




promoter element-binding








protein, protein from








Homo sapiens







KNTC1 HUMAN
Kinetochore-associated
UniProt
NAS

PMID: 11146660




protein 1, protein from








Homo sapiens







KPCI HUMAN
Protein kinase C, iota type, 
UniProt
ISS

UniProt: P41743




protein from Homo sapiens







KR18 HUMAN
Zinc finger protein Kr18,
UniProt
NAS

UniProt: Q9HCG1




protein from Homo sapiens







KS6A2 HUMAN
Ribosomal protein S6
UniProt
TAS

PMID: 7623830




kinase alpha 2, protein








from Homo sapiens







KS6A4 HUMAN
Ribosomal protein S6
UniProt
IEP

PMID: 9792677




kinase alpha 4, protein








from Homo sapiens










ISS

UniProt: O75585






IDA

PMID: 11035004



KS6A5 HUMAN
Ribosomal protein S6
UniProt
IEP

PMID: 9687510




kinase alpha 5, protein








from Homo sapiens







KU70 HUMAN
ATP-dependent DNA
UniProt
TAS

PMID: 10508516




helicase II, 70 kDa








subunit, protein from








Homo sapiens







KU86 HUMAN
ATP-dependent DNA
UniProt
TAS

PMID: 7957065




helicase II 80 kDa








subunit, protein from








Homo sapiens







LANC2 HUMAN
LanC-like protein 2,
UniProt
IDA

PMID: 12566319




protein from Homo sapiens







LAP2 HUMAN
Splice Isoform 1 of LAP2
UniProt
ISS

PMID: 11375975




protein, protein from








Homo sapiens










IDA

PMID: 11375975



LATS2 HUMAN
Serine/threonine-protein
UniProt
NAS

PMID: 10673337




kinase LATS2, protein








from Homo sapiens







LDOC1 HUMAN
Protein LDOC1, protein
UniProt
TAS

PMID: 10403563




from Homo sapiens







LEG3 HUMAN
LGALS3 protein, protein
UniProt
IDA

PMID: 14961764




from Homo sapiens







LHX3 HUMAN
Splice Isoform A of
UniProt
TAS

PMID: 10598593




LIM/homeobox protein Lhx3, 








protein from Homo sapiens







LIMK2 HUMAN
Splice Isoform LIMK2a
UniProt
TAS

PMID: 8954941




of LIM domain kinase 2,








protein from Homo sapiens







LMBL2 HUMAN
Splice Isoform 1 of
UniProt
NAS

UniProt: Q969R5




Lethal(3)malignant brain








tumor-like 2 protein,








protein from Homo sapiens







LMBL3 HUMAN
Splice Isoform 1 of
UniProt
NAS

UniProt: Q96JM7




Lethal(3)malignant brain








tumor-like 3 protein,








protein from Homo sapiens







LMO7 HUMAN
Splice Isoform 3 of LIM
UniProt
TAS

PMID: 9826547




domain only protein 7,








protein from Homo sapiens







LMX1B HUMAN
Splice Isoform Short of
UniProt
NAS

UniProt: O60663




LIM homeobox








transcription factor 1 beta, 








protein from Homo sapiens










IDA

PMID: 10767331



LPIN1 HUMAN
Lipin-1, protein from
UniProt
ISS

PMID: 11138012




Homo sapiens







LPPRC HUMAN
130 kDa leucine-rich protein, 
UniProt
IDA

PMID: 12832482




protein from Homo sapiens










ISS

UniProt: P42704



LSM1 HUMAN
U6 snRNA-associated
UniProt
TAS

PMID: 10369684




Sm-like protein LSm1,








protein from Homo sapiens







LSM2 HUMAN
U6 snRNA-associated
UniProt
NAS

UniProt: Q9Y333




Sm-like protein LSm2,








protein from Homo sapiens







LSM3 HUMAN
U6 snRNA-associated
UniProt
TAS

PMID: 10369684




Sm-like protein LSm3,








protein from Homo sapiens







LSM5 HUMAN
U6 snRNA-associated
UniProt
TAS

PMID: 10369684




Sm-like protein LSm5,








protein from Homo sapiens







LSM7 HUMAN
U6 snRNA-associated
UniProt
NAS

UNIPROT: Q9UK45




Sm-like protein LSm7,








protein from Homo sapiens







LSM8 HUMAN
U6 snRNA-associated
UniProt
NAS

UniProt: O95777




Sm-like protein LSm8,








protein from Homo sapiens







LZTS1 HUMAN
Leucine zipper, putative
UniProt
NAS

UniProt: Q9Y5V7




tumor suppressor 1,








protein from Homo sapiens










NAS

UniProt: Q9Y5W2






NAS

UniProt: Q9Y5W1






NAS

UniProt: Q9Y5W0






NAS

UniProt: Q9Y5V8



MAD HUMAN
MAD protein, protein
UniProt
TAS

PMID: 8425218




from Homo sapiens







MAFB HUMAN
Transcription factor MafB, 
UniProt
TAS

PMID: 8001130




protein from Homo sapiens







MAGC2 HUMAN
Melanoma-associated
UniProt
IDA

PMID: 12920247




antigen C2, protein from








Homo sapiens







MAGE1 HUMAN
Melanoma-associated
UniProt
ISS

PMID: 14623885




antigen E1, protein from








Homo sapiens







MAML1 HUMAN
Mastermind-like protein
UniProt
IDA

PMID: 11101851




1, protein from Homo sapiens







MAML2 HUMAN
MasterMind-like 2,
UniProt
IDA

PMID: 12370315




protein from Homo sapiens







MAML3 HUMAN
MasterMind-like 3,
UniProt
IDA

PMID: 12370315




protein from Homo sapiens







MAPK2 HUMAN
Splice Isoform 1 of MAP
UniProt
TAS

PMID: 8280084




kinase-activated protein








kinase 2, protein from








Homo sapiens







MAPK3 HUMAN
MAP kinase-activated
UniProt
TAS

PMID: 10781029




protein kinase 3, protein








from Homo sapiens







MBB1A HUMAN
Splice Isoform 1 of Myb-
UniProt
ISS

UniProt: Q9BQG0




binding protein 1A,








protein from Homo sapiens







MBD1 HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 10454587




Methyl-CpG-binding








domain protein 1, protein








from Homo sapiens







MBD2 HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 10441743




Methyl-CpG-binding








domain protein 2, protein








from Homo sapiens







MBD4 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 9774669




Methyl-CpG-binding








domain protein 4, protein








from Homo sapiens







MBNL HUMAN
Splice Isoform EXP35 of
UniProt
IDA

PMID: 10970838




Muscleblind-like protein,








protein from Homo sapiens







MCA3 HUMAN
Eukaryotic translation
UniProt
ISS

UniProt: O43324




elongation factor 1 epsilon-1, 








protein from Homo sapiens







MCE1 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 9473487




mRNA capping enzyme,








protein from Homo sapiens







MCM2 HUMAN
DNA replication licensing
UniProt
TAS

PMID: 8175912




factor MCM2, protein








from Homo sapiens







MCM3A HUMAN
80 kda MCM3-associated
UniProt
TAS

PMID: 9712829




protein, protein from








Homo sapiens







MCM4 HUMAN
DNA replication licensing
UniProt
NAS

PMID: 8265339




factor MCM4, protein








from Homo sapiens







MCM5 HUMAN
DNA replication licensing
UniProt
TAS

PMID: 8751386




factor MCM5, protein








from Homo sapiens







MCM6 HUMAN
DNA replication licensing
UniProt
NAS

PMID: 9286856




factor MCM6, protein








from Homo sapiens







MD2BP HUMAN
MAD2L1 binding protein, 
UniProt
IDA

PMID: 10942595




protein from Homo sapiens







MDC1 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 15604234




Mediator of DNA damage








checkpoint protein 1,








protein from Homo sapiens







MDM4 HUMAN
Mdm4 protein, protein
UniProt
NAS

PMID: 9226370




from Homo sapiens







MDN1 HUMAN
Midasin, protein from
UniProt
NAS

PMID: 12102729




Homo sapiens







MECP2 HUMAN
Methyl-CpG-binding protein 
UniProt
TAS

PMID: 10773092




2, protein from Homo sapiens







MECT1 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 14506290




Mucoepidermoid








carcinoma translocated








protein 1, protein from








Homo sapiens







MED12 HUMAN
Mediator of RNA polymerase 
UniProt
IDA

PMID: 10235267




II transcription subunit 12,








protein from Homo sapiens







MED4 HUMAN
Mediator complex subunit
UniProt
IDA

PMID: 10235267




4, protein from Homo sapiens







MED6 HUMAN
RNA polymerase
UniProt
TAS

PMID: 10024883




transcriptional regulation








mediator, subunit 6 homolog, 








protein from Homo sapiens







MEF2A HUMAN
Splice Isoform MEF2 of
UniProt
TAS

PMID: 1516833




Myocyte-specific








enhancer factor 2A,








protein from Homo sapiens







MEF2B HUMAN
Myocyte-specific
UniProt
TAS

PMID: 1516833




enhancer factor 2B,








protein from Homo sapiens







MEFV HUMAN
Splice Isoform 1 of Pyrin,
UniProt
IDA

PMID: 11115844




protein from Homo sapiens







MEN1 HUMAN
Splice Isoform 1 of Menin, 
UniProt
IDA

PMID: 15199122




protein from Homo sapiens







MERL HUMAN
Splice Isoform 1 of Merlin, 
UniProt
IDA

PMID: 10401006




protein from Homo sapiens







MGMT HUMAN
Methylated-DNA--
UniProt
TAS

PMID: 2188979




protein-cysteine








methyltransferase, protein








from Homo sapiens







MGN HUMAN
Mago nashi protein homolog, 
UniProt
NAS

UniProt: P61326




protein from Homo sapiens







MITF HUMAN
Splice Isoform A2 of
UniProt
NAS

PMID: 9647758




Microphthalmia-








associated transcription








factor, protein from








Homo sapiens










NAS

PMID: 10578055



MK14 HUMAN
Mitogen-activated protein
UniProt
ISS

UniProt: Q16539




kinase 14 isoforM 2,








protein from Homo sapiens







MKL2 HUMAN
Splice Isoform 1 of
UniProt
IC

PMID: 14565952




MKL/myocardin-like








protein 2, protein from








Homo sapiens







MLH3 HUMAN
Splice Isoform 1 of DNA
UniProt
TAS

PMID: 10615123




mismatch repair protein








Mlh3, protein from Homo








sapiens







MLL2 HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 9247308




Myeloid/lymphoid or








mixed-lineage leukemia








protein 2, protein from








Homo sapiens







MLL4 HUMAN
Splice Isoform 1 of
UniProt
NAS

UniProt: Q9UMN6




Myeloid/lymphoid or








mixed-lineage leukemia








protein 4, protein from








Homo sapiens







MLX HUMAN
Splice Isoform Gamma of
UniProt
IDA

PMID: 10918583




MAx-like protein X,








protein from Homo sapiens







MLZE HUMAN
Melanoma-derived
UniProt
NAS

PMID: 11223543




leucine zipper-containing








extranuclear factor,








protein from Homo sapiens







MO4L1 HUMAN
Similar to Testis
UniProt
NAS

UniProt: Q9UBU8




expressed gene 189,








protein from Homo sapiens







MO4L2 HUMAN
Mortality factor 4-like
UniProt
NAS

UniProt: Q15014




protein 2, protein from








Homo sapiens







MOL1A HUMAN
Mps one binder kinase
UniProt
IDA

PMID: 15067004




activator-like 1A, protein








from Homo sapiens







MOS1A HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 9731530




Molybdenum cofactor








biosynthesis protein 1 A,








protein from Homo sapiens







MPP8 HUMAN
M-phase phosphoprotein
UniProt
IDA

PMID: 8885239




8, protein from Homo sapiens







MRE11 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 10802669




Double-strand break








repair protein MRE11A,








protein from Homo sapiens







MS3L1 HUMAN
Splice Isoform 1 of Male-
UniProt
TAS

PMID: 10395802




specific lethal 3-like 1,








protein from Homo sapiens







MSH2 HUMAN
DNA mismatch repair
UniProt
NAS

PMID: 7923193




protein Msh2, protein








from Homo sapiens







MSH4 HUMAN
MutS protein homolog 4,
UniProt
TAS

PMID: 9299235




protein from Homo sapiens







MSMB HUMAN
Splice Isoform PSP94 of
UniProt
TAS

PMID: 7566962




Beta-microseminoprotein








precursor, protein from








Homo sapiens







MTA70 HUMAN
Splice Isoform 1 of N6-
UniProt
IDA

PMID: 9409616




adenosine-methyltransferase 








70 kDa subunit, 








protein from Homo sapiens







MTF1 HUMAN
Metal-regulatory
UniProt
TAS

PMID: 3208749




transcription factor 1,








protein from Homo sapiens







MTMR2 HUMAN
Myotubularin-related
UniProt
IDA

PMID: 12837694




protein 2, protein from








Homo sapiens







MUSC HUMAN
Musculin, protein from
UniProt
TAS

PMID: 9584154




Homo sapiens







MUTYH HUMAN
Splice Isoform Alpha-1 of
UniProt
TAS

PMID: 7823963




A/G-specific adenine








DNA glycosylase, protein








from Homo sapiens







MVP HUMAN
Major vault protein,
UniProt
TAS

PMID: 7585126




protein from Homo sapiens







MX2 HUMAN
Interferon-induced GTP-
UniProt
TAS

PMID: 8798556




binding protein Mx2,








protein from Homo sapiens







MXI1 HUMAN
Splice Isoform 1 of MAX
UniProt
TAS

PMID: 8425219




interacting protein 1,








protein from Homo sapiens







MYBA HUMAN
Myb-related protein A,
UniProt
NAS

PMID: 8058310




protein from Homo sapiens







MYC HUMAN
Myc proto-oncogene protein, 
UniProt
IDA

PMID: 15994933




protein from Homo sapiens







MYCBP HUMAN
C-Myc binding protein,
UniProt
TAS

PMID: 9797456




protein from Homo sapiens







MYCN HUMAN
N-myc proto-oncogene
UniProt
TAS

PMID: 3796607




protein, protein from








Homo sapiens







MYF6 HUMAN
Myogenic factor 6,
UniProt
TAS

PMID: 2311584




protein from Homo sapiens







MYOD1 HUMAN
Myoblast determination
UniProt
TAS

PMID: 3175662




protein 1, protein from








Homo sapiens







MYST2 HUMAN
Histone acetyltransferase
UniProt
TAS

PMID: 10438470




MYST2, protein from








Homo sapiens







MYT1 HUMAN
Myelin transcription factor 
UniProt
NAS

PMID: 1280325




1, protein from Homo sapiens







NAB1 HUMAN
Splice Isoform Long of
UniProt
NAS

PMID: 8668170




NGFI-A binding protein








1, protein from Homo sapiens







NARG1 HUMAN
Splice Isoform 1 of NMDA 
UniProt
IDA

PMID: 12145306




receptor regulated protein 1, 








protein from Homo sapiens










IDA

PMID: 12140756



NARGL HUMAN
Splice Isoform 1 of NMDA 
UniProt
ISS

UniProt: Q6N069




receptor regulated








1-like protein, protein








from Homo sapiens







NASP HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 1426632




Nuclear autoantigenic








sperm protein, protein








from Homo sapiens







NCBP2 HUMAN
Nuclear cap binding
UniProt
NAS

PMID: 7651522




protein subunit 2, protein








from Homo sapiens







NCOA1 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 9223431




Nuclear receptor coactivator 








1, protein from Homo sapiens







NCOA2 HUMAN
Nuclear receptor coactivator 
UniProt
NAS

UniProt: Q15596




2, protein from Homo sapiens







NCOA3 HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 97410321




Nuclear receptor coactivator 








3, protein from Homo sapiens










NAS

UniProt: Q9UPC9



NCOA4 HUMAN
Splice Isoform Alpha of
UniProt
TAS

PMID: 8643607




Nuclear receptor coactivator 








4, protein from Homo sapiens







NCOA6 HUMAN
Nuclear receptor coactivator 
UniProt
IDA

PMID: 11443112




6, protein from Homo sapiens










NAS

PMID: 10567404



NCOR2 HUMAN
Nuclear receptor co-repressor 
UniProt
TAS

PMID: 10097068




2, protein from Homo sapiens







NDKA HUMAN
Nucleoside diphosphate
UniProt
NAS

UniProt: P15531




kinase A, protein from








Homo sapiens










TAS

PMID: 16130169



NDKB HUMAN
Nucleoside diphosphate
UniProt
NAS

UniProt: P22392




kinase B, protein from








Homo sapiens







NEDD8 HUMAN
NEDD8 precursor,
UniProt
TAS

PMID: 9353319




protein from Homo sapiens







NEK1 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 15604234




Serine/threonine-protein








kinase Nek1, protein








from Homo sapiens







NEK3 HUMAN
Serine/threonine-protein
UniProt
NAS

PMID: 7522034




kinase Nek3, protein








from Homo sapiens







NELFE HUMAN
Splice Isoform 1 of Negative 
UniProt
NAS

PMID: 2119325




elongation factor E, 








protein from Homo sapiens







NFAC2 HUMAN
Splice Isoform C of
UniProt
TAS

PMID: 8668213




Nuclear factor of activated








T-cells, cytoplasmic 2,








protein from Homo sapiens







NFAT5 HUMAN
Splice Isoform C of Nuclear 
UniProt
TAS

PMID: 10051678




factor of activated T cells 








5, protein from Homo sapiens







NFE2 HUMAN
Transcription factor NF-
UniProt
TAS

PMID: 7774011




E2 45 kDa subunit,








protein from Homo sapiens







NFIA HUMAN
Nuclear factor 1 A-type,
UniProt
NAS

PMID: 7590749




protein from Homo sapiens







NFIB HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 7590749




Nuclear factor 1 B-type,








protein from Homo sapiens







NFKB2 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 15677444




Nuclear factor NF-kappa-








B p100 subunit, protein








from Homo sapiens







NFS1 HUMAN
Cysteine desulfurase,
UniProt
TAS

PMID: 9885568




mitochondrial precursor,








protein from Homo sapiens







NFYA HUMAN
Splice Isoform Long of
UniProt
IDA

PMID: 15243141




Nuclear transcription








factor Y subunit alpha,








protein from Homo sapiens







NFYB HUMAN
Nuclear transcription
UniProt
IEP

PMID: 15243141




factor Y subunit beta,








protein from Homo sapiens







NFYC HUMAN
Splice Isoform 3 of
UniProt
IEP

PMID: 15243141




Nuclear transcription








factor Y subunit gamma,








protein from Homo sapiens







NHRF2 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 9054412




Na(+)/H(+) exchange








regulatory cofactor NHE-RF2, 








protein from Homo sapiens







NKRF HUMAN
NF-kappa-B-repressing
UniProt
IDA

PMID: 10562553




factor, protein from








Homo sapiens







NKX31 HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 11137288




Homeobox protein Nkx-3.1, 








protein from Homo sapiens







NLK HUMAN
Serine/threonine kinase NLK, 
UniProt
ISS

UniProt: Q9UBE8




protein from Homo sapiens







NMES1 HUMAN
Normal mucosa of
UniProt
IDA

PMID: 12209954




esophagus-specific gene 1








protein, protein from








Homo sapiens







NMNA1 HUMAN
Nicotinamide
UniProt
IDA

PMID: 11248244




mononucleotide








adenylyltransferase 1,








protein from Homo sapiens







NNP1 HUMAN
NNP-1 protein, protein
UniProt
TAS

PMID: 9192856




from Homo sapiens







NOCT HUMAN
Nocturnin, protein from
UniProt
TAS

PMID: 10521507




Homo sapiens







NOG2 HUMAN
Nucleolar GTP-binding
UniProt
TAS

PMID: 8822211




protein 2, protein from








Homo sapiens







NONO HUMAN
Non-POU domain-
UniProt
TAS

PMID: 9360842




containing octamer-








binding protein, protein








from Homo sapiens







NOTC1 HUMAN
Neurogenic locus notch
UniProt
TAS

PMID: 10713164




homolog protein 1 precursor, 








protein from Homo sapiens







NOTC2 HUMAN
Neurogenic locus notch
UniProt
IDA

PMID: 1303260




homolog protein 2 precursor, 








protein from Homo sapiens







NOTC4 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 8681805




Neurogenic locus notch








homolog protein 4 precursor, 








protein from Homo sapiens







NP1L2 HUMAN
Nucleosome assembly
UniProt
TAS

PMID: 8789438




protein 1-like 2, protein








from Homo sapiens







NPM2 HUMAN
Nucleoplasmin-2, protein
UniProt
IEP

PMID: 12714744




from Homo sapiens







NPM HUMAN
Nucleophosmin, protein
UniProt
IDA

PMID: 12080348




from Homo sapiens










TAS

PMID: 16130169



NR1D1 HUMAN
Orphan nuclear receptor
UniProt
TAS

PMID: 8622974




NR1D1, protein from








Homo sapiens







NR1D2 HUMAN
Orphan nuclear receptor
UniProt
TAS

PMID: 7997240




NR1D2, protein from








Homo sapiens







NR1H2 HUMAN
Oxysterols receptor LXR-
UniProt
TAS

PMID: 7926814




beta, protein from Homo








sapiens







NR1H3 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 7744246




Oxysterols receptor LXR-








alpha, protein from Homo








sapiens







NR2E3 HUMAN
Splice Isoform Long of
UniProt
TAS

PMID: 10220376




Photoreceptor-specific








nuclear receptor, protein








from Homo sapiens







NR4A2 HUMAN
Orphan nuclear receptor
UniProt
TAS

PMID: 7877627




NR4A2, protein from








Homo sapiens







NR4A3 HUMAN
Nuclear receptor
UniProt
NAS

PMID: 8634690




subfamily 4, group A,








member 3 isoform b,








protein from Homo sapiens







NR5A2 HUMAN
Splice Isoform 2 of Orphan 
UniProt
TAS

PMID: 9786908




nuclear receptor NR5A2, 








protein from Homo sapiens







NRIF3 HUMAN
Splice Isoform 2 of
UniProt
TAS

PMID: 10490654




Nuclear receptor-








interacting factor 3,








protein from Homo sapiens







NRIP1 HUMAN
Nuclear receptor-
UniProt
IDA

PMID: 7641693




interacting protein 1,








protein from Homo sapiens










IDA

PMID: 12773562






IDA

PMID: 11266503



NRL HUMAN
Neural retina-specific
UniProt
TAS

PMID: 8939891




leucine zipper protein,








protein from Homo sapiens







NSBP1 HUMAN
Nucleosomal binding protein 
UniProt
NAS

PMID: 11161810




1, protein from Homo sapiens







NSG1 HUMAN
Neuron-specific protein
UniProt
TAS

PMID: 9013775




family member 1, protein








from Homo sapiens







NT5C HUMAN
Splice Isoform 1 of 5′(3′)-
UniProt
TAS

PMID: 10702291




deoxyribonucleotidase,








cytosolic type, protein








from Homo sapiens







NTHL1 HUMAN
Endonuclease III-like protein 
UniProt
IDA

PMID: 12531031




1, protein from Homo sapiens







NUMA1 HUMAN
Splice Isoform 1 of Nuclear 
UniProt
TAS

PMID: 1541636




mitotic apparatus protein 1, 








protein from Homo sapiens







NUPL2 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 10358091




Nucleoporin-like 2,








protein from Homo sapiens







NUPR1 HUMAN
Nuclear protein 1, protein
UniProt
IDA

PMID: 10092851




from Homo sapiens







NVL HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 9286697




Nuclear valosin-








containing protein-like,








protein from Homo sapiens







NXF2 HUMAN
Nuclear RNA export factor 
UniProt
ISS

UniProt: Q9GZY0




2, protein from Homo sapiens







NXF3 HUMAN
Nuclear RNA export factor 
UniProt
IDA

PMID: 11545741




3, protein from Homo sapiens







NXF5 HUMAN
Splice Isoform A of Nuclear 
UniProt
IDA

PMID: 11566096




RNA export factor 5, 








protein from Homo sapiens







O00290
Adenovirus E3-14.7K
UniProt
IDA

PMID: 11073942




interacting protein 1,








protein from Homo sapiens







O00366
Putative p150, protein
UniProt
ISS

UniProt: O00366




from Homo sapiens







O14777
Retinoblastoma-
UniProt
TAS

PMID: 9315664




associated protein HEC,








protein from Homo sapiens







O14789
Testis-specific BRDT protein, 
UniProt
TAS

PMID: 9367677




protein from Homo sapiens







O15125
Alternative spliced form
UniProt
IDA

PMID: 9230210




of p15 CDK inhibitor,








protein from Homo sapiens







O15150
Cerebrin-50, protein from
UniProt
TAS

PMID: 9373037




Homo sapiens







O15183
Trinucleotide repeat DNA
UniProt
TAS

PMID: 8626781




binding protein p20-CGGBP, 








protein from Homo sapiens







O15415
CAGH3, protein from
UniProt
TAS

PMID: 9225980




Homo sapiens







O43148
MRNA (Guanine-7-)
UniProt
TAS

PMID: 9705270




methyltransferase, 








protein from Homo sapiens







O43245
Protein p65, protein from
UniProt
NAS

PMID: 8706045




Homo sapiens







O43663
Protein regulating
UniProt
TAS

PMID: 9885575




cytokinesis 1, protein








from Homo sapiens







O43719
HIV TAT specific factor
UniProt
TAS

PMID: 10454543




1, protein from Homo sapiens







O43809
Pre-mRNA cleavage
UniProt
TAS

PMID: 9659921




factor I 25 kDa subunit,








protein from Homo sapiens







O43812
Homeobox protein DUX3, 
UniProt
TAS

PMID: 9736770




protein from Homo sapiens







O60519
Cre binding protein-like 2, 
UniProt
TAS

PMID: 9693048




protein from Homo sapiens







O60592
Arg/Abl-interacting
UniProt
TAS

PMID: 9211900




protein ArgBP2a, protein








from Homo sapiens







O60593
SORBS2 protein, protein
UniProt
NAS

PMID: 9211900




from Homo sapiens







O60671
Cell cycle checkpoint
UniProt
IC

PMID: 9660799




protein Hrad1, protein








from Homo sapiens







O60870
Kin17 protein, protein
UniProt
TAS

PMID: 1923796




from Homo sapiens







O75525
T-Star, protein from
UniProt
TAS

PMID: 10332027




Homo sapiens







O75530
Embryonic ectoderm
UniProt
NAS

PMID: 9584199




development protein








homolog, protein from








Homo sapiens







O75766
TRIP protein, protein
UniProt
TAS

PMID: 9705290




from Homo sapiens







O75799
Transcription repressor,
UniProt
NAS

PMID: 9705290




protein from Homo sapiens







O75805
HOXA-9A, protein from
UniProt
NAS

UniProt: O75805




Homo sapiens







O75806
HOXA-9B, protein from
UniProt
NAS

UniProt: O75806




Homo sapiens







O94992
HEXIM1 protein, protein
UniProt
IDA

PMID: 12581153




from Homo sapiens







O95082
EH-binding protein,
UniProt
TAS

PMID: 10644451




protein from Homo sapiens







O95133
SOX-29 protein, protein
UniProt
NAS

UniProt: O95133




from Homo sapiens







O95268
Origin recognition
UniProt
NAS

PMID: 9765232




complex subunit ORC5T,








protein from Homo sapiens







O95273
D-type cyclin-interacting
UniProt
IDA

PMID: 12437976




protein 1, protein from








Homo sapiens







O95391
Step II splicing factor SLU7, 
UniProt
NR

UNIPROT: O95391




protein from Homo sapiens







O95443
AT rich interactive domain 3B 
UniProt
NAS

PMID: 10446990




(BRIGHT-like) protein, 








protein from Homo sapiens







O95480
Hypothetical protein,
UniProt
NAS

UniProt: O95480




protein from Homo sapiens







O95926
Hypothetical protein
UniProt
NAS

PMID: 11118353




DKFZp564O2082,








protein from Homo sapiens







OGT1 HUMAN
Splice Isoform 2 of UDP-
UniProt
TAS

PMID: 9083067




N-acetylglucosamine--








peptide N-








acetylglucosaminyltransferase








110 kDa subunit,








protein from Homo sapiens







OI106 HUMAN
Splice Isoform 1 of 106 kDA
UniProt
ISS

UniProt: Q9UPV9




O-GlcNAc transferase-








interacting protein, 








protein from Homo sapiens







ORC1 HUMAN
Origin recognition
UniProt
TAS

PMID: 7502077




complex subunit 1,








protein from Homo sapiens







ORC2 HUMAN
Origin recognition
UniProt
TAS

PMID: 8808289




complex subunit 2,








protein from Homo sapiens







ORC4 HUMAN
Origin recognition
UniProt
TAS

PMID: 9353276




complex subunit 4,








protein from Homo sapiens







ORC5 HUMAN
Origin recognition
UniProt
TAS

PMID: 9765232




complex subunit 5,








protein from Homo sapiens







OTX1 HUMAN
Homeobox protein OTX1, 
UniProt
NAS

UniProt: P32242




protein from Homo sapiens







OTX2 HUMAN
Homeobox protein OTX2, 
UniProt
NAS

UniProt: P32243




protein from Homo sapiens







OVOL1 HUMAN
Putative transcription
UniProt
NAS

UniProt: O14753




factor Ovo-like 1, protein








from Homo sapiens







OZF HUMAN
Zinc finger protein OZF,
UniProt
TAS

PMID: 8665923




protein from Homo sapiens







P53 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 7720704




Cellular tumor antigen p53, 








protein from Homo sapiens







P66A HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 12183469




Transcriptional repressor








p66 alpha, protein from








Homo sapiens










ISS

UniProt: Q96F28



P73L HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 12446779




Tumor protein p73-like,








protein from Homo sapiens







P78365
Polyhomeotic 2 homolog,
UniProt
TAS

PMID: 9121482




protein from Homo sapiens







P80C HUMAN
Coilin, protein from
UniProt
TAS

PMID: 7971277




Homo sapiens







PA2G4 HUMAN
Proliferation-associated
UniProt
IDA

PMID: 15073182




protein 2G4, protein from








Homo sapiens







PAPOA HUMAN
Poly(A) Polymerase alPha, 
UniProt
TAS

PMID: 8302877




protein from Homo sapiens







PAR6A HUMAN
Splice Isoform 1 of
UniProt
ISS

UniProt: Q9NPB6




Partitioning defective 6








homolog alpha, protein








from Homo sapiens







PARK7 HUMAN
Protein DJ-1, protein
UniProt
IDA

PMID: 12446870




from Homo sapiens







PARN HUMAN
Poly(A)-specific
UniProt
TAS

PMID: 9736620




ribonuclease PARN,








protein from Homo sapiens







PARP1 HUMAN
Poly [ADP-ribose]
UniProt
TAS

PMID: 2513174




polymerase 1, protein








from Homo sapiens







PARP4 HUMAN
Poly [ADP-ribose]
UniProt
NAS

PMID: 10644454




polymerase 4, protein








from Homo sapiens







PARP9 HUMAN
Splice Isoform 1 of Poly
UniProt
TAS

PMID: 11110709




[ADP-ribose] polymerase








9, protein from Homo sapiens







PAWR HUMAN
PRKC apoptosis WT1
UniProt
NAS

UniProt: Q96IZ0




regulator protein, protein








from Homo sapiens







PAX8 HUMAN
Splice Isoform 1 of Paired
UniProt
NAS

UniProt: Q16339




box protein Pax-8,








protein from Homo sapiens







PAX9 HUMAN
Paired box protein Pax-9,
UniProt
NAS

UniProt: P55771




protein from Homo sapiens







PBX1 HUMAN
Splice Isoform PBX1a of
UniProt
ISS

UniProt: P40424




Pre-B-cell leukemia








transcription factor 1,








protein from Homo sapiens







PBX3 HUMAN
Splice Isoform PBX3a of
UniProt
ISS

UniProt: P40426




Pre-B-cell leukemia








transcription factor 3,








protein from Homo sapiens







PBX4 HUMAN
Pre-B-cell leukemia
UniProt
ISS

UniProt: Q9BYU1




transcriPtion factor 4,








protein from Homo sapiens







PCAF HUMAN
Histone acetyltransferase
UniProt
TAS

PMID: 10891508




PCAF, protein from








Homo sapiens







PCBP1 HUMAN
Poly(rC)-binding protein
UniProt
NAS

UNIPROT: Q15365




1, protein from Homo sapiens







PCBP2 HUMAN
Poly(rC)-binding protein
UniProt
NAS

UniProt: Q15366




2, protein from Homo sapiens







PDCD8 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 9989411




Programmed cell death








protein 8, mitochondrial








precursor, protein from








Homo sapiens







PDZK3 HUMAN
Splice Isoform 1 of PDZ
UniProt
ISS

PMID: 12671685




domain containing protein








3, protein from Homo sapiens







PEPP1 HUMAN
Paired-like homeobox
UniProt
IDA

PMID: 11980563




protein PEPP-1, protein








from Homo sapiens







PERM HUMAN
Splice Isoform H17 of
UniProt
TAS

PMID: 2829220




Myeloperoxidase precursor, 








protein from Homo sapiens







PFD5 HUMAN
Prefoldin subunit 5,
UniProt
TAS

PMID: 9792694




protein from Homo sapiens







PFTK1 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 9202329




Serine/threonine-protein








kinase PFTAIRE-1,








protein from Homo sapiens







PGEA1 HUMAN
Chibby protein, protein
UniProt
IDA

PMID: 12712206




from Homo sapiens







PGH1 HUMAN
Cyclooxygenase 1b3,
UniProt
ISS

UniProt: P23219




protein from Homo sapiens







PGH2 HUMAN
Prostaglandin G/H
UniProt
ISS

UniProt: P35354




synthase 2 precursor,








protein from Homo sapiens







PHB HUMAN
Prohibitin, protein from
UniProt
TAS

PMID: 16130169




Homo sapiens







PHC1 HUMAN
Polyhomeotic-like protein
UniProt
TAS

PMID: 9121482




1, protein from Homo sapiens







PHF12 HUMAN
Splice Isoform 2 of PHD
UniProt
IDA

PMID: 11390640




finger protein 12, protein








from Homo sapiens







PHF2 HUMAN
PHD finger protein 2,
UniProt
TAS

PMID: 10051327




protein from Homo sapiens







PIAS1 HUMAN
Protein inhibitor of
UniProt
TAS

PMID: 9724754




activated STAT protein 1,








protein from Homo sapiens







PIAS4 HUMAN
Protein inhibitor of
UniProt
IDA

PMID: 11248056




activated STAT protein 4,








protein from Homo sapiens










NAS

PMID: 9724754



PIN1 HUMAN
Peptidyl-prolyl cis-trans
UniProt
TAS

PMID: 8606777




isomerase NIMA-interacting 








1, protein from Homo sapiens







PIR HUMAN
Pirin, protein from Homo
UniProt
TAS

PMID: 9079676




sapiens







PKP1 HUMAN
Splice Isoform 2 of
UniProt
NAS

PMID: 9369526




Plakophilin-1, protein








from Homo sapiens







PKP2 HUMAN
Splice Isoform 2 of
UniProt
NAS

PMID: 8922383




Plakophilin-2, protein








from Homo sapiens







PLCB1 HUMAN
Splice Isoform A of 1-
UniProt
NAS

PMID: 10760467




phosphatidylinositol-4,5-








bisphosphate








phosphodiesterase beta 1,








protein from Homo sapiens







PML HUMAN
Splice Isoform PML-1 of
UniProt
IDA

PMID: 9294197




Probable transcription








factor PML, protein from








Homo sapiens







PMS1 HUMAN
PMS1 protein homolog 1,
UniProt
TAS

PMID: 8072530




protein from Homo sapiens







PMS2 HUMAN
Postmeiotic segregation
UniProt
TAS

PMID: 8072530




increased 2 nirs variant 2,








protein from Homo sapiens







PNKP HUMAN
Bifunctional polynucleotide
UniProt
IDA

PMID: 10446193




phosphatase/kinase,








protein from Homo sapiens







PNRC1 HUMAN
Proline-rich nuclear
UniProt
TAS

PMID: 7578250




receptor coactivator 1,








protein from Homo sapiens







PO2F1 HUMAN
Splice Isoform 1 of POU
UniProt
IDA

PMID: 11891224




domain, class 2,








transcription factor 1,








protein from Homo sapiens







PO5FL HUMAN
POU domain, class 5,
UniProt
TAS

UniProt: Q06416




transcription factor 1-like








protein 1, protein from








Homo sapiens







PO6F2 HUMAN
Splice Isoform 1 of POU
UniProt
IC

PMID: 8601806




domain, class 6,








transcription factor 2,








protein from Homo sapiens







POLS HUMAN
DNA polymerase sigma,
UniProt
IDA

PMID: 10066793




protein from Homo sapiens







POP7 HUMAN
Ribonuclease P protein
UniProt
TAS

PMID: 9630247




subunit p20, protein from








Homo sapiens







PP2AA HUMAN
Serine/threonine protein
UniProt
NAS

PMID: 11007961




phosphatase 2A, catalytic








subunit, alpha isoform,








protein from Homo sapiens







PP2CD HUMAN
Protein phosphatase 2C
UniProt
TAS

PMID: 9177166




isoform delta, protein








from Homo sapiens







PP2CE HUMAN
Splice Isoform 1 of
UniProt
ISS

UniProt: Q96MI6




Protein phosphatase 2C








isoform eta, protein from








Homo sapiens







PP2CG HUMAN
Protein phosphatase 2C
UniProt
TAS

PMID: 9271424




isoform gamma, protein








from Homo sapiens







PP4C HUMAN
Serine/threonine protein
UniProt
NAS

UniProt: P60510




phosphatase 4 catalytic








subunit, protein from








Homo sapiens







PPARA HUMAN
Peroxisome proliferator-
UniProt
TAS

PMID: 16271724




activated receptor alpha,








protein from Homo sapiens







PPARB HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 11551955




Peroxisome proliferator-








activated receptor delta,








protein from Homo sapiens







PPIE HUMAN
Splice Isoform A of
UniProt
IDA

PMID: 11313484




Peptidyl-prolyl cis-trans








isomerase E, protein from








Homo sapiens







PPIG HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 9153302




Peptidyl-prolyl cis-trans








isomerase G, protein








from Homo sapiens







PPIL2 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 8660300




Peptidyl-prolyl cis-trans








isomerase-like 2, protein








from Homo sapiens







PPP5 HUMAN
Serine/threonine protein
UniProt
TAS

PMID: 7925273




phosphatase 5, protein








from Homo sapiens







PPRB HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 10235267




Peroxisome proliferator-








activated receptor-binding








protein, protein from








Homo sapiens







PQBP1 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 10198427




Polyglutamine-binding








protein 1, protein from








Homo sapiens







PRD15 HUMAN
PR-domain zinc finger
UniProt
NAS

UniProt: P57071




protein 15, protein from








Homo sapiens







PRD16 HUMAN
Splice Isoform 1 of PR-
UniProt
IC

PMID: 11050005




domain zinc finger protein 16, 








protein from Homo sapiens







PRDM2 HUMAN
Splice Isoform 1 of PR-
UniProt
NAS

PMID: 7590293




domain zinc finger protein








2, protein from Homo sapiens










NAS

PMID: 7538672



PREB HUMAN
Prolactin regulatory
UniProt
TAS

PMID: 10194769




element-binding protein,








protein from Homo sapiens







PRGC1 HUMAN
Peroxisome proliferator-
UniProt
TAS

PMID: 12588810




activated receptor gamma








coactivator 1-alpha,








protein from Homo sapiens







PRP16 HUMAN
Pre-mRNA splicing factor
UniProt
NAS

PMID: 9524131




ATP-dependent RNA








helicase PRP16, protein








from Homo sapiens







PRS6A HUMAN
26S protease regulatory
UniProt
TAS

PMID: 2194290




subunit 6A, protein from








Homo sapiens







PSA1 HUMAN
Splice Isoform Short of
UniProt
TAS

PMID: 7681138




Proteasome subunit alpha








type 1, protein from








Homo sapiens







PSA3 HUMAN
Proteasome subunit alpha
UniProt
TAS

PMID: 16130169




type 3, protein from








Homo sapiens







PSB4 HUMAN
Proteasome subunit beta
UniProt
TAS

PMID: 16130169




type 4 precursor, protein








from Homo sapiens







PSF1 HUMAN
DNA replication complex
UniProt
IDA

PMID: 10942595




GINS protein PSF1,








protein from Homo sapiens







PTDSR HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 14729065




Protein PTDSR, protein








from Homo sapiens







PTHR1 HUMAN
Parathyroid
UniProt
TAS

PMID: 10709993




hormone/parathyroid








hormone-related peptide








receptor precursor,








protein from Homo sapiens







PTMA HUMAN
Prothymosin alpha,
UniProt
TAS

PMID: 10854063




protein from Homo sapiens







PTMS HUMAN
Parathymosin, protein
UniProt
TAS

PMID: 10854063




from Homo sapiens







PTTG1 HUMAN
Securin, protein from
UniProt
TAS

PMID: 9811450




Homo sapiens







PTTG HUMAN
Pituitary tumor-transforming 
UniProt
IDA

PMID: 10781616




gene 1 protein-interacting 








protein precursor, protein 








from Homo sapiens







PWP1 HUMAN
Periodic tryptophan
UniProt
TAS

PMID: 7828893




protein 1 homolog,








protein from Homo sapiens







Q02313
Kruppel-related zinc
UniProt
NAS

UniProt: Q02313




finger protein, protein








from Homo sapiens







Q03989
ARID5A protein, protein
UniProt
IC

PMID: 15640446




from Homo sapiens







Q12771
P37 AUF1, protein from
UniProt
NAS

PMID: 8246982




Homo sapiens







Q12869
R kappa B, protein from
UniProt
NR

UniProt: Q12869




Homo sapiens







Q13028
Homeo box protein,
UniProt
NAS

PMID: 7647458




protein from Homo sapiens







Q13051
Nuclear factor I, protein
UniProt
NAS

PMID: 8799200




from Homo sapiens







Q13127
REST protein, protein
UniProt
TAS

PMID: 7697725




from Homo sapiens







Q13137
NDP52, protein from
UniProt
TAS

PMID: 7540613




Homo sapiens







Q13395
TAR RNA loop binding
UniProt
TAS

PMID: 8846792




protein, protein from








Homo sapiens







Q13826
Autoantigen, protein
UniProt
IDA

PMID: 7520377




from Homo sapiens







Q13862
DNA-binding protein,
UniProt
TAS

PMID: 7887923




protein from Homo sapiens







Q13901
Hypothetical protein C1D, 
UniProt
TAS

PMID: 9469821




protein from Homo sapiens







Q14211
E4BP4 protein, protein
UniProt
TAS

PMID: 7565758




from Homo sapiens







Q14333
Facioscapulohumeral
UniProt
NAS

UniProt: Q14333




muscular dystrophy,








protein from Homo sapiens







Q14501
HCREM 1alpha protein,
UniProt
NAS

PMID: 8206879




protein from Homo sapiens







Q14503
HCREM 2beta-a protein,
UniProt
NAS

PMID: 8206879




protein from Homo sapiens







Q14548
HOX2.8 protein, protein
UniProt
IDA

PMID: 1871139




from Homo sapiens







Q14561
HPX-5 protein, protein
UniProt
NAS

PMID: 7518789




from Homo sapiens







Q14655
C-MYC promoter-binding
UniProt
NAS

UniProt: Q14655




protein IRLB, protein








from Homo sapiens







Q14820
ZFM1 protein, alternatively 
UniProt
NAS

PMID: 7912130




spliced product, protein from 








Homo sapiens







Q14869
MSSP-2 protein, protein
UniProt
NAS

PMID: 7838710




from Homo sapiens







Q14901
Myc protein, protein from
UniProt
NAS

PMID: 2834731




Homo sapiens







Q15156
PML-RAR protein,
UniProt
NAS

UniProt: Q15156




protein from Homo sapiens







Q15170
Pp21 protein, protein
UniProt
TAS

PMID: 7971997




from Homo sapiens







Q15270
HPX-153 protein, protein
UniProt
NAS

UniProt: Q15270




from Homo sapiens







Q15288
No distinctive protein
UniProt
NAS

PMID: 8543184




motifs; ORF, protein








from Homo sapiens







Q15299
RARB protein, protein
UniProt
IDA

PMID: 2177841




from Homo sapiens







Q15325
DNA-binding protein,
UniProt
TAS

PMID: 3174636




protein from Homo sapiens







Q15327
Nuclear protein, protein
UniProt
TAS

PMID: 7730328




from Homo sapiens







Q15361
Transcription factor,
UniProt
NAS

PMID: 7597036




protein from Homo sapiens







Q15376
Y-chromosome RNA
UniProt
NAS

PMID: 9598316




recognition motif protein,








protein from Homo sapiens







Q15381
Y-chromosome RNA
UniProt
TAS

PMID: 9598316




recognition motif protein,








protein from Homo sapiens







Q15435
Yeast sds22 homolog,
UniProt
TAS

PMID: 7498485




protein from Homo sapiens







Q15552
CACCC box-binding protein, 
UniProt
TAS

PMID: 8355710




protein from Homo sapiens







Q15574
Hypothetical protein TAF1B, 
UniProt
NAS

PMID: 7801123




protein from Homo sapiens







Q15736
Zinc finger protein 223,
UniProt
NAS

UniProt: Q9UMW0




protein from Homo sapiens







Q15936
Zinc-finger protein,
UniProt
NAS

UniProt: Q15936




protein from Homo sapiens







Q16247
Histone H1 transcription
UniProt
NAS

PMID: 7969168




factor large subunit 2A,








protein from Homo sapiens







Q16365
GATA-4 transcription factor, 
UniProt
NAS

PMID: 7791790




protein from Homo sapiens







Q16464
Chromosome 17q21
UniProt
NAS

UniProt: Q16464




mRNA clone 694:2.,








protein from Homo sapiens







Q16624
Long overlapping ORF,
UniProt
NAS

PMID: 3265124




protein from Homo sapiens







Q16630
HPBRII-4 mRNA,
UniProt
TAS

PMID: 9659921




protein from Homo sapiens







Q16670
Transcriptional regulator
UniProt
NAS

PMID: 1569959




SCAN domain containing








protein, protein from








Homo sapiens







Q5W1B6
OTTHUMP00000028668,
UniProt
ISS

UniProt: Q5W1B6




protein from Homo sapiens







Q6ZNA8
Hypothetical protein
UniProt
ISS

UniProt: Q6ZNA8




FLJ16262, protein from








Homo sapiens







Q7RTV3
ZNF367, protein from
UniProt
IDA

PMID: 15344908




Homo sapiens







Q86T11
Discs large homolog 7;
UniProt
ISS

UniProt: Q86T11




Drosophila Discs large-1








tumor suppressor-like;








hepatoma up-regulateD








protein, protein from








Homo sapiens







Q86TP4
TCFL5 protein, protein
UniProt
ISS

UniProt: Q86TP4




from Homo sapiens







Q86XB9
BRUNOL4 protein,
UniProt
ISS

UniProt: Q86XB9




protein from Homo sapiens







Q86XF5
DNA cytosine
UniProt
ISS

PMID: 12138111




methyltransferase 3 alpha,








isoform a, protein from








Homo sapiens







Q86XW5
P621, protein from Homo
UniProt
IDA

PMID: 12665582




sapiens







Q86YN6
Peroxisome proliferator-
UniProt
ISS

UniProt: Q86YN6




activated receptor gamma








coactivator 1beta-1a,








protein from Homo sapiens







Q8IWR7
CGI-121 L1 isoform,
UniProt
NAS

PMID: 12659830




protein from Homo sapiens







Q8IXI0
Early hematopoietic zinc
UniProt
IDA

PMID: 12393497




finger, protein from








Homo sapiens







Q8IZV0
DNA cytosine
UniProt
IDA

PMID: 12138111




methyltransferase 3 alpha








isoform b, protein from








Homo sapiens







Q8N717
KLF4 protein, protein
UniProt
ISS

UniProt: Q8N717




from Homo sapiens







Q8N9B5
Hypothetical protein
UniProt
ISS

UniProt: Q8N9B5




FLJ37870, protein from








Homo sapiens







Q8NFW5
Homeoprotein MBX-L,
UniProt
ISS

UniProt: Q8NFW5




protein from Homo sapiens







Q8NFW6
Homeoprotein MBX-S,
UniProt
ISS

UniProt: Q8NFW6




protein from Homo sapiens







Q8NHW3
V-maf musculoaponeurotic
UniProt
IDA

PMID: 12368292




fibrosarcoma oncogene








homolog A, protein from








Homo sapiens







Q8TAL0
PPARGC1B protein,
UniProt
ISS

UniProt: Q8TAL0




protein from Homo sapiens







Q8TD23
TRAF6-binding zinc
UniProt
IDA

PMID: 11751921




finger protein, protein








from Homo sapiens







Q8TDE4
PGC-1-related estrogen
UniProt
ISS

PMID: 10713165




receptor alpha coactivator








short isoform, protein








from Homo sapiens










IDA

PMID: 11854298



Q8TEY4
Adaptor protein FE65a2,
UniProt
ISS

UniProt: Q8TEY4




protein from Homo sapiens







Q8WX93
Myoneurin, protein from
UniProt
IDA

PMID: 11598191




Homo sapiens







Q8WYA4
Brain-muscle-ARNT-like
UniProt
IDA

PMID: 12055078




transcription factor 2a,








protein from Homo sapiens







Q92657
HP8 peptide, protein
UniProt
NAS

PMID: 8758458




from Homo sapiens







Q92728
RB1 protein, protein from
UniProt
NAS

PMID: 3413073




Homo sapiens







Q96BU1
S100P binding protein
UniProt
IDA

PMID: 15632002




Riken, isoform a, protein








from Homo sapiens







Q96BX9
Hypothetical protein
UniProt
IDA

PMID: 15843405




FLJ32915, protein from








Homo sapiens







Q96C70
Transcription factor
UniProt
IDA

PMID: 15994933




RAM2 splice variant c,








protein from Homo sapiens







Q96HR3
TRAP/Mediator complex
UniProt
IDA

PMID: 10235267




component TRAP25,








protein from Homo sapiens







Q96JL8
JADE1L protein, protein
UniProt
ISS

UniProt: Q96JL8




from Homo sapiens







Q96L96
Muscle alpha-kinase,
UniProt
ISS

UniProt: Q96L96




protein from Homo sapiens







Q96MH2
Hypothetical protein
UniProt
ISS

UniProt: Q96MH2




FLJ32384, protein from








Homo sapiens







Q96S66
Mid-1-related chloride
UniProt
ISS

PMID: 11279057




channel 1, protein from








Homo sapiens







Q96SQ1
Hypothetical protein
UniProt
IDA

PMID: 12169691




FLJ14714, protein from








Homo sapiens







Q99419
ICSAT transcription factor, 
UniProt
ISS

UniProt: Q99419




protein from Homo sapiens







Q99638
RAD9A protein, protein
UniProt
TAS

PMID: 8943031




from Homo sapiens







Q99718
ESE-1a, protein from
UniProt
NAS

PMID: 9234700




Homo sapiens







Q9BRV3
LOC55974 protein,
UniProt
IC

PMID: 8630032




protein from Homo sapiens







Q9BXX3
Breast cancer antigen NY-
UniProt
NAS

PMID: 11280766




BR-1, protein from Homo








sapiens







Q9BYE0
BHLH factor Hes7,
UniProt
NAS

PMID: 11260262




protein from Homo sapiens







Q9BYG9
Nucleophosmin/B23.2,
UniProt
ISS

UniProt: Q9BYG9




protein from Homo sapiens







Q9BYU3
MORF/CBP protein,
UniProt
NAS

PMID: 11157802




protein from Homo sapiens







Q9BZ95
Putative chromatin
UniProt
NAS

UniProt: Q9BZ95




modulator, protein from








Homo sapiens







Q9BZC1
Bruno-like 4, RNA
UniProt
ISS

UniProt: Q9BZC1




Binding protein; RNA-








Binding protein








BRUNOL-5; CUG-BP








and ETR-3 like factor 4,








protein from Homo sapiens







Q9BZC2
Trinucleotide repeat
UniProt
NAS

PMID: 11158314




containing 4, protein








from Homo sapiens







Q9BZS0
Kappa B and V(D)J
UniProt
NAS

UniProt: Q9BZS0




recombination signal








sequences binding protein, 








protein from Homo sapiens







Q9C056
NK6 transcription factor
UniProt
NAS

PMID: 11210186




related, locus 2, protein








from Homo sapiens







Q9H2G4
CTCL tumor antigen se20-4, 
UniProt
IDA

PMID: 11395479




protein from Homo sapiens







Q9H2M1
Estrogen receptor alpha,
UniProt
NAS

UniProt: Q9H2M1




protein from Homo sapiens







Q9H2M4
Cycle-like factor CLIF,
UniProt
NAS

PMID: 11018023




protein from Homo sapiens







Q9H2S9
Zinc finger transcription
UniProt
TAS

PMID: 10978333




factor Eos, protein from








Homo sapiens







Q9H315
ARTS protein, protein
UniProt
NAS

PMID: 11146656




from Homo sapiens







Q9H4E3
Probable ATP-dependent
UniProt
NAS

PMID: 11024137




RNA helicase DDX47,








protein from Homo sapiens







Q9H509
DJ875K15.1.1, protein
UniProt
ISS

UniProt: Q9H509




from Homo sapiens







Q9HB90
GTPase-interacting protein 2, 
UniProt
IDA

PMID: 11073942




protein from Homo sapiens







Q9HBE0
Beta protein 1 BP1,
UniProt
NAS

PMID: 11069021




protein from Homo sapiens







Q9HBU2
Lim-homeobox transcription 
UniProt
NAS

UniProt: Q9HBU2




factor LHX3, protein from








Homo sapiens







Q9HD85
Pre-B-cell leukemia
UniProt
NAS

PMID: 10825160




transcription factor








interacting protein 1,








protein from Homo sapiens







Q9NP66
High-mobility group 20A
UniProt
NAS

PMID: 10773667




variant, protein from








Homo sapiens







Q9NPE2
Mesenchymal stem cell
UniProt
NAS

PMID: 11118320




protein DSC92, protein








from Homo sapiens







Q9NQL2
OTTHUMP00000016853,
UniProt
IDA

PMID: 11073942




protein from Homo sapiens







Q9NQL9
Doublesex and mab-3
UniProt
NAS

UniProt: Q9NQL9




related transcription factor








3, protein from Homo sapiens







Q9NR48
Ash1, protein from Homo
UniProt
TAS

PMID: 10860993




sapiens







Q9NR55
Jun dimerization protein
UniProt
TAS

PMID: 10878360




p21SNFT, protein from








Homo sapiens







Q9NS72
K562 cell-derived
UniProt
NAS

PMID: 10873651




leucine-zipper-like protein








1, protein from Homo sapiens







Q9NX07
Hypothetical protein
UniProt
ISS

UniProt: Q9NX07




FLJ20503, protein from








Homo sapiens







Q9NYW8
RB-associated KRAB
UniProt
TAS

PMID: 10702291




repressor, protein from








Homo sapiens







Q9NZC4
Ets domain transcription
UniProt
ISS

UniProt: Q9NZC4




factor, protein from








Homo sapiens







Q9P016
THY28 protein, protein
UniProt
ISS

PMID: 14601557




from Homo sapiens







Q9P112
Chromosome 16 open
UniProt
NAS

PMID: 10570909




reading frame 5, protein








from Homo sapiens







Q9P1Z2
KIAA1536 protein,
UniProt
ISS

UniProt: Q9P1Z2




protein from Homo sapiens







Q9P2R9
SRp25 nuclear protein
UniProt
TAS

PMID: 10708573




isoform 2, protein from








Homo sapiens







Q9P2S7
Hypothetical protein
UniProt
NR

UniProt: Q9P2S7




FLJ11063, protein from








Homo sapiens







Q9UC05
22 Kruppel-related zinc
UniProt
NAS

UniProt: Q9UC05




finger protein, protein








from Homo sapiens







Q9UCY6
Nuclear receptor subfamily 
UniProt
NAS

PMID: 7479914




5, group A, member 1, 








protein from Homo sapiens







Q9UD04
GHDTA = GROWTH
UniProt
NAS

PMID: 7642589




hormone gene-derived








transcriptional








activator/hepatic nuclear








factor-1 alpha homolog,








protein from Homo sapiens







Q9UD29
Surfactant protein B-
UniProt
NAS

PMID: 7887923




binding protein, protein








from Homo sapiens







Q9UD78
LBP-1A transcription
UniProt
TAS

PMID: 8114710




factor protein, protein








from Homo sapiens







Q9UD83
ATF-A0 transcription
UniProt
NAS

PMID: 8288576




factor protein, protein








from Homo sapiens







Q9UEP1
Cell cycle checkpoint protein, 
UniProt
ISS

UniProt: Q9UEP1




protein from Homo sapiens







Q9UGK6
Putative secreted ligand,
UniProt
NR

UniProt: Q9UGK6




protein from Homo sapiens







Q9UGL1
RB-binding protein,
UniProt
TAS

PMID: 12657635




protein from Homo sapiens







Q9UH59
Bromodomain protein
UniProt
TAS

PMID: 10526152




CELTIX1, protein from








Homo sapiens







Q9UHK0
Nuclear fragile X mental
UniProt
TAS

PMID: 10556305




retardation protein








interacting protein 1,








protein from Homo sapiens







Q9ULW3
Basal transcriptional
UniProt
TAS

PMID: 10648625




activator hABT1, protein








from Homo sapiens







Q9UMC5
Zinc finger protein 2, isoform 
UniProt
NAS

UniProt: Q9UMC5




a, protein from Homo sapiens







Q9Y294
ASF1A protein, protein
UniProt
NAS

PMID: 10759893




from Homo sapiens







Q9Y2A1
P53TG1-B, protein from
UniProt
NAS

UniProt: Q9Y2A1




Homo sapiens







Q9Y2A2
P53TG1-C, protein from
UniProt
NAS

UniProt: Q9Y2A2




Homo sapiens







Q9Y2A3
P53TG1-D, protein from
UniProt
NAS

UniProt: Q9Y2A3




Homo sapiens







Q9Y2Y4
Testis zinc finger protein,
UniProt
TAS

PMID: 10572087




protein from Homo sapiens







Q9Y310
CGI-21 protein, protein
UniProt
NR

UniProt: Q9Y310




from Homo sapiens







Q9Y3C4
My019 protein, protein
UniProt
IDA

PMID: 12659830




from Homo sapiens







Q9Y451
Androgen-induced
UniProt
TAS

PMID: 10215036




prostate proliferative








shutoff associated protein, 








protein from Homo sapiens







Q9Y474
Zinc-finger motif-
UniProt
TAS

PMID: 9305772




enhancer binding-protein-








1, protein from Homo sapiens







Q9Y489
Centrosomal protein 1,
UniProt
TAS

PMID: 10359848




protein from Homo sapiens







Q9Y4I0
Zinc-finger helicase,
UniProt
NAS

PMID: 9688266




protein from Homo sapiens







Q9Y586
MAB21L2 protein,
UniProt
NR

UniProt: Q9Y586




protein from Homo sapiens







Q9Y655
Splice Isoform 1 of
UniProt
TAS

PMID: 2601707




Myelin expression factor 2, 








protein from Homo sapiens







Q9Y664
Actin-associated protein
UniProt
TAS

PMID: 1372044




2E4/kaptin, protein from








Homo sapiens







Q9Y675
SNRPN upstream reading
UniProt
NAS

PMID: 10318933




frame protein, protein








from Homo sapiens







Q9Y6B2
PTD014, protein from
UniProt
IDA

PMID: 11073990




Homo sapiens







Q9Y6D4
MORC1 protein, protein
UniProt
TAS

PMID: 10369865




from Homo sapiens







Q9Y6R2
HUEL, protein from
UniProt
IDA

PMID: 10409434




Homo sapiens







Q9Y6Z7
Collectin sub-family
UniProt
ISS

PMID: 12450124




member 10, protein from








Homo sapiens







R51A1 HUMAN
Splice Isoform 1 of RAD51-
UniProt
IC

PMID: 9396801




associated protein 1, protein 








from Homo sapiens







RA51B HUMAN
Splice Isoform 2 of DNA
UniProt
TAS

PMID: 9512535




repair protein RAD51








homolog 2, protein from








Homo sapiens







RA51C HUMAN
DNA repair protein RAD51 
UniProt
TAS

PMID: 9469824




homolog 3, 








protein from Homo sapiens







RA51D HUMAN
Splice Isoform 1 of DNA
UniProt
TAS

PMID: 9570954




repair protein RAD51








homolog 4, protein from








Homo sapiens







RAB3I HUMAN
Splice Isoform 2 of RAB3A-
UniProt
IDA

PMID: 12007189




interacting protein, 








protein from Homo sapiens







RAD18 HUMAN
Postreplication repair
UniProt
NAS

PMID: 10884424




protein RAD18, protein








from Homo sapiens







RAD51 HUMAN
Splice Isoform 1 of DNA
UniProt
ISS

UniProt: Q06609




repair protein RAD51








homolog 1, protein from








Homo sapiens










IDA

PMID: 12442171



RAD52 HUMAN
RAD52 homolog isoform
UniProt
TAS

PMID: 7774919




alpha, protein from Homo








sapiens







RAD54 HUMAN
DNA repair and
UniProt
TAS

PMID: 8805304




recombination protein








RAD54-like, protein








from Homo sapiens







RAE1L HUMAN
mRNA-associated protein
UniProt
TAS

PMID: 9370289




mrnp 41, protein from








Homo sapiens







RAG2 HUMAN
V(D)J recombination-
UniProt
NAS

UniProt: P55895




activating protein 2,








protein from Homo sapiens







RANB3 HUMAN
Splice Isoform 1 of Ran-
UniProt
TAS

PMID: 9637251




binding protein 3, protein








from Homo sapiens







RANB9 HUMAN
Splice Isoform 1 of Ran-
UniProt
IDA

PMID: 12220523




binding protein 9, protein








from Homo sapiens







RANG HUMAN
Ran-specific GTPase-
UniProt
TAS

PMID: 16130169




activating protein, protein








from Homo sapiens







RASF1 HUMAN
Splice Isoform D of Ras
UniProt
IEP

PMID: 14743218




association domain family 1, 








protein from Homo sapiens







RASF7 HUMAN
Splice Isoform 1 of Ras
UniProt
NAS

UniProt: Q02833




association domain protein 








7, protein from Homo sapiens







RB HUMAN
Retinoblastoma-
UniProt
TAS

PMID: 3657987




associated protein,








protein from Homo sapiens







RBBP4 HUMAN
Chromatin assembly
UniProt
TAS

PMID: 8350924




factor 1 subunit C,








protein from Homo sapiens







RBBP5 HUMAN
Retinoblastoma-binding
UniProt
IDA

PMID: 15199122




protein 5, protein from








Homo sapiens







RBBP8 HUMAN
RBBP8 protein, protein
UniProt
TAS

PMID: 10764811




from Homo sapiens







RBM10 HUMAN
RNA binding motif
UniProt
NAS

UniProt: P98175




protein 10, isoform 1,








protein from Homo sapiens







RBM5 HUMAN
RNA-binding protein 5,
UniProt
TAS

PMID: 10352938




protein from Homo sapiens







RBM6 HUMAN
RNA-binding protein 6,
UniProt
TAS

PMID: 10352938




protein from Homo sapiens







RBM8A HUMAN
Splice Isoform 1 of RNA-
UniProt
NAS

PMID: 11013075




binding protein 8A,








protein from Homo sapiens










NAS

PMID: 11030346



RBM9 HUMAN
Splice Isoform 1 of RNA-
UniProt
IDA

PMID: 11875103




binding protein 9, protein








from Homo sapiens







RBX2 HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 10082581




RING-box protein 2,








protein from Homo sapiens







RBY1A HUMAN
RNA-binding motif
UniProt
TAS

PMID: 9598316




protein, Y chromosome,








family 1 member A1,








protein from Homo sapiens







RCL HUMAN
c-Myc-responsive protein
UniProt
TAS

PMID: 9271375




Rcl, protein from Homo








sapiens







RD23B HUMAN
UV excision repair protein
UniProt
TAS

PMID: 8168482




RAD23 homolog B,








protein from Homo sapiens







RECQ1 HUMAN
ATP-dependent DNA
UniProt
TAS

PMID: 7961977




helicase Q1, protein from








Homo sapiens







RED1 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 8995285




Double-stranded RNA-








specific editase 1, protein








from Homo sapiens







REN3A HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 11163187




Regulator of nonsense








transcripts 3A, protein








from Homo sapiens







REN3B HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 11163187




Regulator of nonsense








transcripts 3B, protein








from Homo sapiens







RERE HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 10814707




Arginine-glutamic acid








dipeptide repeats protein,








protein from Homo sapiens







RERG HUMAN
Ras-related and estrogen-
UniProt
IDA

PMID: 11533059




regulated growth inhibitor, 








protein from Homo sapiens







REXO4 HUMAN
Splice Isoform 1 of RNA
UniProt
NAS

PMID: 10908561




exonuclease 4, protein








from Homo sapiens







RFX3 HUMAN
Splice Isoform 1 of
UniProt
IC

PMID: 12411430




Transcription factor RFX3, 








protein from Homo sapiens







RFX5 HUMAN
DNA-binding protein
UniProt
TAS

PMID: 9806546




RFX5, protein from








Homo sapiens







RHOB HUMAN
Rho-related GTP-binding
UniProt
ISS

UniProt: P62745




protein RhoB, protein








from Homo sapiens







RING1 HUMAN
Polycomb complex
UniProt
IDA

PMID: 9199346




protein RING1, protein








from Homo sapiens







RM19 HUMAN
39S ribosomal protein
UniProt
IDA

PMID: 10942595




L19, mitochondrial








precursor, protein from








Homo sapiens







RM40 HUMAN
39S ribosomal protein
UniProt
TAS

PMID: 9790763




L40, mitochondrial








precursor, protein from








Homo sapiens







RMP HUMAN
RNA polymerase II
UniProt
TAS

PMID: 9878255




subunit 5-mediating protein, 








protein from Homo sapiens







RNF14 HUMAN
RING finger protein 14,
UniProt
IDA

PMID: 11322894




protein from Homo sapiens







RNF4 HUMAN
RING finger protein 4,
UniProt
TAS

PMID: 9710597




protein from Homo sapiens







RNPS1 HUMAN
Splice Isoform 1 of RNA-
UniProt
TAS

PMID: 9580558




binding protein with








serine-rich domain 1,








protein from Homo sapiens







RP14 HUMAN
Ribonuclease P protein
UniProt
TAS

PMID: 10024167




subunit p14, protein from








Homo sapiens







RP30 HUMAN
Ribonuclease P protein
UniProt
TAS

PMID: 9630247




subunit p30, protein from








Homo sapiens







RPB1 HUMAN
DNA-directed RNA
UniProt
NAS

PMID: 7622068




polymerase II largest subunit, 








protein from Homo sapiens







RPB8 HUMAN
DNA-directed RNA
UniProt
TAS

UniProt: P52434




polymerases I, II, and III








17.1 kDa polypeptide,








protein from Homo sapiens







RPGF5 HUMAN
Splice Isoform 1 of Rap
UniProt
IDA

PMID: 10486569




guanine nucleotide








exchange factor 5, protein








from Homo sapiens







RPP38 HUMAN
Ribonuclease P protein
UniProt
TAS

PMID: 9630247




subunit p38, protein from








Homo sapiens







RPP40 HUMAN
Ribonuclease P protein
UniProt
TAS

PMID: 9630247




subunit p40, protein from








Homo sapiens







RRP5 HUMAN
RRP5 protein homolog,
UniProt
IDA

PMID: 14624448




protein from Homo sapiens







RSSA HUMAN
40S ribosomal protein SA, 
UniProt
TAS

PMID: 16130169




protein from Homo sapiens







RUNX1 HUMAN
Splice Isoform AML-1B
UniProt
NAS

UniProt: O60473




of Runt-related transcription 








factor 1,








protein from Homo sapiens







RUNX3 HUMAN
Splice Isoform 1 of Runt-
UniProt
NAS

UniProt: Q13761




related transcription factor 3, 








protein from Homo sapiens







RUVB1 HUMAN
RuvB-like 1, protein from
UniProt
IDA

PMID: 9843967




Homo sapiens







RUVB2 HUMAN
RuvB-like 2, protein from
UniProt
IDA

PMID: 10524211




Homo sapiens







S100P HUMAN
S-100P protein, protein
UniProt
IDA

PMID: 15632002




from Homo sapiens







S10AB HUMAN
Calgizzarin, protein from
UniProt
TAS

PMID: 10851017




Homo sapiens







S14L2 HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 11444841




SEC14-like protein 2,








protein from Homo sapiens







S2A4R HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 10825161




GLUT4 enhancer factor








DNA binding domain,








protein from Homo sapiens







SAFB1 HUMAN
Scaffold attachment factor
UniProt
TAS

PMID: 1324173




B, protein from Homo sapiens







SALL2 HUMAN
Sal-like protein 2, protein
UniProt
NAS

UniProt: Q9Y467




from Homo sapiens







SAM68 HUMAN
Splice Isoform 1 of KH
UniProt
IDA

PMID: 1374686




domain containing, RNA








binding, signal transduction 








associated protein 1, 








protein from Homo sapiens







SAS10 HUMAN
Something about silencing
UniProt
ISS

UniProt: Q9NQZ2




protein 10, protein from








Homo sapiens







SATB1 HUMAN
DNA-binding protein SATB1, 
UniProt
TAS

PMID: 1505028




protein from Homo sapiens







SCMH1 HUMAN
Splice Isoform 1 of
UniProt
IC

PMID: 10524249




Polycomb protein SCMH1, 








protein from Homo sapiens







SCND1 HUMAN
SCAN domain-containing
UniProt
ISS

UniProt: P57086




protein 1, protein from








Homo sapiens







SCRN1 HUMAN
Secernin-1, protein from
UniProt
IDA

PMID: 10942595




Homo sapiens







SCRT1 HUMAN
Transcriptional repressor
UniProt
NAS

UniProt: Q9BWW7




scratch 1, protein from








Homo sapiens







SDCB1 HUMAN
Syntenin-1, protein from
UniProt
NAS

PMID: 11179419




Homo sapiens







SELB HUMAN
Selenocysteine-specific
UniProt
NAS

UniProt: P57772




elongation factor, protein








from Homo sapiens







SENP1 HUMAN
Sentrin/SUMO-specific
UniProt
TAS

PMID: 10652325




protease 1, protein from








Homo sapiens







SENP7 HUMAN
Similar to SUMO-1-
UniProt
ISS

PMID: 10652325




specific protease, protein








from Homo sapiens







SEPT2 HUMAN
Septin-2, protein from
UniProt
IDA

PMID: 10942595




Homo sapiens







SEPT7 HUMAN
Septin-7, protein from
UniProt
IDA

PMID: 15485874




Homo sapiens







SESN1 HUMAN
Splice Isoform T1 of
UniProt
TAS

PMID: 9926927




Sestrin-1, protein from








Homo sapiens







SET7 HUMAN
Histone-lysine N-
UniProt
NAS

UniProt: Q8WTS6




methyltransferase, H3








lysine-4 specific SET7,








protein from Homo sapiens







SET HUMAN
Splice Isoform 1 of SET
UniProt
IDA

PMID: 11555662




protein, protein from








Homo sapiens







SFR11 HUMAN
Splicing factor
UniProt
TAS

PMID: 1896467




arginine/serine-rich 11,








protein from Homo sapiens







SFRS2 HUMAN
Splicing factor,
UniProt
IDA

PMID: 15652350




arginine/serine-rich 2,








protein from Homo sapiens







SFRS4 HUMAN
Splicing factor,
UniProt
TAS

PMID: 8321209




arginine/serine-rich 4,








protein from Homo sapiens







SFRS7 HUMAN
Splice Isoform 1 of Splicing 
UniProt
TAS

PMID: 8013463




factor, arginine/serine-rich 7,








protein from Homo sapiens







SH3L1 HUMAN
SH3 domain-binding glutamic 
UniProt
TAS

PMID: 16130169




acid-rich-like protein, 








protein from Homo sapiens







SIN3A HUMAN
Paired amphipathic helix
UniProt
ISS

UniProt: Q96ST3




protein Sin3a, protein








from Homo sapiens







SIP1 HUMAN
Zinc finger homeobox
UniProt
IC

PMID: 9853615




protein 1b, protein from








Homo sapiens







SIPA1 HUMAN
Signal-induced proliferation-
UniProt
IC

PMID: 9183624




associated protein 1, 








protein from Homo sapiens







SIRT6 HUMAN
Splice Isoform 1 of Mono-
UniProt
ISS

UniProt: Q8N6T7




ADP-ribosyltransferase 








sirtuin-6, 








protein from Homo sapiens







SKI HUMAN
Ski oncogene, protein
UniProt
NAS

UniProt: P12755




from Homo sapiens







SKIL HUMAN
Splice Isoform SNON of
UniProt
ISS

UniProt: P12757




Ski-like protein, protein








from Homo sapiens







SLUG HUMAN
Zinc finger protein SLUG, 
UniProt
TAS

PMID: 10866665




protein from Homo sapiens







SMAD1 HUMAN
Mothers against
UniProt
ISS

UniProt: Q15797




decapentaplegic homolog








1, protein from Homo sapiens










NAS

PMID: 9759503



SMAD2 HUMAN
Splice Isoform Long of
UniProt
ISS

UniProt: Q15796




Mothers against








decapentaplegic homolog








2, protein from Homo sapiens







SMAD4 HUMAN
Mothers against
UniProt
TAS

PMID: 10980615




decapentaplegic homolog








4, protein from Homo sapiens







SMAD5 HUMAN
Mothers against
UniProt
NAS

PMID: 9759503




decapentaplegic homolog








5, protein from Homo sapiens







SMC1A HUMAN
Structural maintenance of
UniProt
IDA

PMID: 11076961




chromosome 1-like 1 protein, 








protein from Homo sapiens







SMC2 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 9789013




Structural maintenance of








chromosome 2-like 1 protein, 








protein from Homo sapiens







SMC4 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 11850403




Structural maintenance of








chromosomes 4-like 1 protein, 








protein from Homo sapiens







SMCA1 HUMAN
SWI/SNF related, matrix
UniProt
TAS

PMID: 1408766




associated, actin dependent 








regulator of chromatin, 








subfamily a, member 1, 








protein from Homo sapiens







SMCA4 HUMAN
Possible global transcription 
UniProt
TAS

PMID: 8232556




activator SNF2L4, 








protein from Homo sapiens







SMCA5 HUMAN
SWI/SNF-related matrix
UniProt
IDA

PMID: 12972596




associated actin dependent








regulator of chromatin








subfamily A member 5,








protein from Homo sapiens







SMRA3 HUMAN
SWI/SNF-related matrix-
UniProt
TAS

PMID: 7876228




associated actin-dependent 








regulator of chromatin 








subfamily A member 3, 








protein from Homo sapiens







SMRD3 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 14701856




SWI/SNF-related matrix-








associated actin-dependent 








regulator of chromatin 








subfamily D member 3, 








protein from Homo sapiens







SMUF2 HUMAN
Smad ubiquitination
UniProt
NAS

PMID: 11163210




regulatory factor 2,








protein from Homo sapiens







SND1 HUMAN
Staphylococcal nuclease
UniProt
TAS

PMID: 7651391




domain-containing protein








1, protein from Homo sapiens







SNPC2 HUMAN
snRNA-activating protein
UniProt
TAS

PMID: 7715707




complex subunit 2,








protein from Homo sapiens







SNPC3 HUMAN
snRNA-activating protein
UniProt
TAS

PMID: 7715707




complex subunit 3,








protein from Homo sapiens







SNPC5 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 9732265




snRNA-activating protein








complex subunit 5,








protein from Homo sapiens







SOX15 HUMAN
SOX-15 protein, protein
UniProt
NAS

PMID: 8332506




from Homo sapiens







SOX1 HUMAN
SOX-1 protein, protein
UniProt
NAS

PMID: 9337405




from Homo sapiens







SOX21 HUMAN
Transcription factor SOX-21, 
UniProt
NAS

PMID: 1614875




protein from Homo sapiens







SOX2 HUMAN
Transcription factor SOX-2, 
UniProt
NAS

PMID: 7849401




protein from Homo sapiens







SOX6 HUMAN
HMG1/2 (high mobility
UniProt
NAS

PMID: 1614875




group) box family protein, 








protein from Homo sapiens







SOX9 HUMAN
Transcription factor SOX-9, 
UniProt
TAS

PMID: 10805756




protein from Homo sapiens







SP100 HUMAN
Splice Isoform Sp100-HMG 
UniProt
TAS

PMID: 2258622




of Nuclear autoantigen 








Sp-100,








protein from Homo sapiens







SP110 HUMAN
Splice Isoform 1 of Sp110
UniProt
TAS

PMID: 7693701




nuclear body protein,








protein from Homo sapiens







SP1 HUMAN
Transcription factor Sp1,
UniProt
NAS

UniProt: P08047




protein from Homo sapiens







SP3 HUMAN
Transcription factor Sp3,
UniProt
NAS

UniProt: Q02447




protein from Homo sapiens







SPAST HUMAN
Splice Isoform 1 of Spastin, 
UniProt
TAS

PMID: 10610178




protein from Homo sapiens







SPNXA HUMAN
Sperm protein associated
UniProt
TAS

PMID: 10906052




with the nucleus on the X








chromosome A, protein








from Homo sapiens







SPNXB HUMAN
Sperm protein associated
UniProt
TAS

PMID: 10906052




with the nucleus on the X








chromosome B/F, protein








from Homo sapiens







SPNXC HUMAN
Sperm protein associated
UniProt
TAS

PMID: 10626816




with the nucleus on the X








chromosome C, protein








from Homo sapiens







SPOP HUMAN
Speckle-type POZ protein, 
UniProt
TAS

PMID: 9414087




protein from Homo sapiens







SPT6H HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 8786132




Transcription elongation








factor SPT6, protein from








Homo sapiens







SRBS1 HUMAN
Splice Isoform 1 of Sorbin
UniProt
IDA

PMID: 11371513




and SH3 domain-








containing protein 1,








protein from Homo sapiens







SRF HUMAN
Serum response factor,
UniProt
TAS

PMID: 3203386




protein from Homo sapiens







SRPK1 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 11509566




Serine/threonine-protein








kinase SRPK1, protein








from Homo sapiens







SRPK2 HUMAN
Serine/threonine-protein
UniProt
IDA

PMID: 9472028




kinase SRPK2, protein








from Homo sapiens







SRY HUMAN
Sex-determining region Y
UniProt
NAS

PMID: 8265659




protein, protein from








Homo sapiens










NAS

PMID: 1425584



SSBP2 HUMAN
Single-stranded DNA-
UniProt
NAS

UniProt: P81877




binding protein 2, protein








from Homo sapiens







SSBP3 HUMAN
Splice Isoform 1 of
UniProt
ISS

UniProt: Q9BWW4




Single-stranded DNA-








binding protein 3, protein








from Homo sapiens







SSF1 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 15302935




Suppressor of SWI4 1








homolog, protein from








Homo sapiens







SSNA1 HUMAN
Sjogren's syndrome
UniProt
TAS

PMID: 9430706




nuclear autoantigen 1,








protein from Homo sapiens







SSX1 HUMAN
Protein SSX1, protein
UniProt
TAS

PMID: 10072425




from Homo sapiens







SSXT HUMAN
Splice Isoform 1 of SSXT
UniProt
TAS

PMID: 10072425




protein, protein from








Homo sapiens







ST17A HUMAN
Serine/threonine-protein
UniProt
IEP

PMID: 9786912




kinase 17A, protein from








Homo sapiens







ST17B HUMAN
Serine/threonine-protein
UniProt
IEP

PMID: 9786912




kinase 17B, protein from








Homo sapiens







ST65G HUMAN
Splice Isoform 1 of STAGA 
UniProt
NAS

PMID: 10987294




complex 65 gamma subunit, 








protein from Homo sapiens







STABP HUMAN
STAM-binding protein,
UniProt
TAS

PMID: 10383417




protein from Homo sapiens







STAG1 HUMAN
Cohesin subunit SA-1,
UniProt
TAS

PMID: 9305759




protein from Homo sapiens







STAG2 HUMAN
Cohesin subunit SA-2,
UniProt
TAS

PMID: 9305759




protein from Homo sapiens







STAG3 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 10698974




Cohesin subunit SA-3,








protein from Homo sapiens







STAT1 HUMAN
Splice Isoform Alpha of
UniProt
TAS

PMID: 10820245




Signal transducer and








activator of transcription








1-alpha/beta, protein








from Homo sapiens







STAT3 HUMAN
Splice Isoform 1 of Signal
UniProt
TAS

PMID: 7512451




transducer and activator of








transcription 3, protein








from Homo sapiens







STF1 HUMAN
Steroidogenic factor 1,
UniProt
IDA

PMID: 10567391




protein from Homo sapiens







STIP1 HUMAN
Stress-induced-
UniProt
TAS

PMID: 16130169




phosphoprotein 1, protein








from Homo sapiens







STK19 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 9812991




Serine/threonine-protein








kinase 19, protein from








Homo sapiens







STK38 HUMAN
Serine/threonine-protein
UniProt
IDA

PMID: 12493777




kinase 38, protein from








Homo sapiens







STK39 HUMAN
STE20/SPS1-related
UniProt
NAS

PMID: 10980603




proline-alanine-rich








protein kinase, protein








from Homo sapiens







STK6 HUMAN
Serine/threonine-protein
UniProt
TAS

PMID: 9153231




kinase 6, protein from








Homo sapiens







STRN3 HUMAN
Splice Isoform Alpha of
UniProt
IDA

PMID: 7910562




Striatin-3, protein from








Homo sapiens







SUFU HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 10559945




Suppressor of fused








homolog, protein from








Homo sapiens







SUH HUMAN
Splice Isoform APCR-2 of
UniProt
NAS

UniProt: Q06330




Recombining binding








protein suppressor of








hairless, protein from








Homo sapiens










IDA

PMID: 9874765



SUPT3 HUMAN
Splice Isoform 1 of
UniProt
IEP

PMID: 9726987




Transcription initiation








protein SPT3 homolog,








protein from Homo sapiens







SUV91 HUMAN
Histone-lysine N-
UniProt
TAS

PMID: 10949293




methyltransferase, H3








lysine-9 specific 1,








protein from Homo sapiens







SVIL HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 12711699




Supervillin, protein from








Homo sapiens







SYCP2 HUMAN
Synaptonemal complex
UniProt
NAS

PMID: 10341103




protein 2, protein from








Homo sapiens







TAD3L HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 9674425




Transcriptional adapter 3-like, 








protein from Homo sapiens







TADBP HUMAN
TAR DNA-binding protein 
UniProt
TAS

PMID: 7745706




43, protein from 








Homo sapiens







TAF1 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 7680771




Transcription initiation








factor TFIID subunit 1,








protein from Homo sapiens







TAF1L HUMAN
Transcription initiation
UniProt
ISS

PMID: 12217962




factor TFIID 210 kDa








subunit, protein from








Homo sapiens







TAF4B HUMAN
PREDICTED: TAF4b
UniProt
NAS

UniProt: Q92750




RNA polymerase II, TATA 








box binding protein 








(TBP)-associated factor, 








105 kDa, protein








from Homo sapiens







TB182 HUMAN
182 kDa tankyrase 1-
UniProt
NAS

PMID: 11854288




binding protein, protein








from Homo sapiens







TBX18 HUMAN
T-box transcription factor
UniProt
NAS

UniProt: O95935




TBX18, protein from








Homo sapiens







TBX21 HUMAN
T-box transcription factor
UniProt
NAS

UniProt: Q9UL17




TBX21, protein from








Homo sapiens







TBX22 HUMAN
T-box transcription factor
UniProt
NAS

UniProt: Q9Y458




TBX22, protein from








Homo sapiens







TBX4 HUMAN
T-box transcription factor
UniProt
NAS

UniProt: P57082




TBX4, protein from








Homo sapiens







TCF20 HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 10995766




Transcription factor 20,








protein from Homo sapiens







TCFL5 HUMAN
TranscripTion facTor-like
UniProt
IDA

PMID: 9763657




5 proTein, protein from








Homo sapiens







TCRG1 HUMAN
Transcription elongation
UniProt
TAS

PMID: 9315662




regulator 1, protein from








Homo sapiens







TEAD2 HUMAN
Transcriptional enhancer
UniProt
NAS

PMID: 8702974




factor TEF-4, protein








from Homo sapiens







TERA HUMAN
Transitional endoplasmic
UniProt
IDA

PMID: 10855792




reticulum ATPase,








protein from Homo sapiens










TAS

PMID: 16130169



TERF1 HUMAN
Splice Isoform TRF1 of
UniProt
NAS

PMID: 9739097




Telomeric repeat binding








factor 1, protein from








Homo sapiens










NAS

PMID: 7502076



TESK2 HUMAN
Splice Isoform 1 of Dual
UniProt
ISS

UniProt: Q96S53




specificity testis-specific








protein kinase 2, protein








from Homo sapiens







TF65 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 3140380




Transcription factor p65,








protein from Homo sapiens







TF7L1 HUMAN
Transcription factor 7-like
UniProt
NAS

PMID: 11085512




1, protein from Homo sapiens










NAS

PMID: 1741298



TF7L2 HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 10919662




Transcription factor 7-like








2, protein from Homo sapiens







TFE2 HUMAN
Splice Isoform E12 of
UniProt
NAS

PMID: 2493990




Transcription factor E2-alpha, 








protein from Homo sapiens







TFEB HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 2115126




Transcription factor EB,








protein from Homo sapiens







TGIF2 HUMAN
Homeobox protein TGIF2, 
UniProt
TAS

PMID: 11006116




protein from Homo sapiens







THB1 HUMAN
Thyroid hormone receptor
UniProt
TAS

PMID: 1618799




beta-1, protein from








Homo sapiens







THB2 HUMAN
Thyroid hormone receptor
UniProt
TAS

PMID: 1618799




beta-2, protein from








Homo sapiens







THOC1 HUMAN
THO complex subunit 1,
UniProt
TAS

PMID: 7525595




protein from Homo sapiens







TIAF1 HUMAN
TGFB1-induced anti-
UniProt
NAS

PMID: 9918798




apoptotic factor 1, protein








from Homo sapiens







TIF1A HUMAN
Splice Isoform Long of
UniProt
TAS

PMID: 9115274




Transcription intermediary 








factor 1-alpha, 








protein from Homo sapiens







TIF1G HUMAN
Splice Isoform Alpha of
UniProt
NAS

UniProt: Q9UPN9




Transcription intermediary 








factor 1-gamma, protein 








from Homo sapiens







TIM HUMAN
Splice Isoform 1 of
UniProt
IC

PMID: 9856465




Timeless homolog,








protein from Homo sapiens







TIP60 HUMAN
Splice Isoform 1 of Histone 
UniProt
TAS

PMID: 8607265




acetyltransferase HTATIP, 








protein from Homo sapiens







TITF1 HUMAN
Splice Isoform 1 of Thyroid 
UniProt
NAS

UniProt: P43699




transcription factor 1, 








protein from Homo sapiens







TLE1 HUMAN
Transducin-like enhancer
UniProt
TAS

PMID: 1303260




protein 1, protein from








Homo sapiens







TLE2 HUMAN
Transducin-like enhancer
UniProt
TAS

PMID: 1303260




protein 2, protein from








Homo sapiens







TLE3 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 1303260




Transducin-like enhancer








protein 3, protein from








Homo sapiens







TLE4 HUMAN
TLE4 protein, protein
UniProt
NAS

PMID: 1303260




from Homo sapiens







TLK1 HUMAN
Splice Isoform 1 of
UniProt
IEP

PMID: 10523312




Serine/threonine-protein








kinase tousled-like 1,








protein from Homo sapiens










TAS

PMID: 9427565



TLK2 HUMAN
Splice Isoform 1 of
UniProt
IEP

PMID: 9427565




Serine/threonine-protein








kinase tousled-like 2,








protein from Homo sapiens










NAS

PMID: 98087437



TNAP3 HUMAN
Tumor necrosis factor,
UniProt
IDA

PMID: 11463333




alpha-induced protein 3,








protein from Homo sapiens







TNPO1 HUMAN
Importin beta-2 subunit,
UniProt
TAS

PMID: 9144189




protein from Homo sapiens







TNPO2 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 9298975




Transportin-2, protein








from Homo sapiens







TOB2 HUMAN
Tob2 protein, protein
UniProt
TAS

PMID: 10602502




from Homo sapiens







TOP2A HUMAN
Splice Isoform 1 of DNA
UniProt
TAS

PMID: 6267071




topoisomerase 2-alpha,








protein from Homo sapiens







TOP3A HUMAN
Splice Isoform Long of DNA 
UniProt
TAS

PMID: 8622991




topoisomerase III alpha, 








protein from Homo sapiens







TOP3B HUMAN
Splice Isoform 1 of DNA
UniProt
TAS

PMID: 9786843




topoisomerase III beta-1,








protein from Homo sapiens







TOPB1 HUMAN
DNA topoisomerase II
UniProt
TAS

PMID: 9461304




binding protein 1, protein








from Homo sapiens







TPX2 HUMAN
Targeting protein for Xklp2, 
UniProt
TAS

PMID: 9207457




protein from Homo sapiens







TR100 HUMAN
Thyroid hormone receptor-
UniProt
IDA

PMID: 10235267




associated protein complex 








100 kDa component, 








protein from Homo sapiens







TR150 HUMAN
Thyroid hormone receptor-
UniProt
IDA

PMID: 10235267




associated protein complex 








150 kDa component, 








protein from Homo sapiens







TR240 HUMAN
Thyroid hormone receptor-
UniProt
IDA

PMID: 10235267




associated protein complex 








240 kDa component, 








protein from Homo sapiens







TR95 HUMAN
Splice Isoform 1 of Thyroid 
UniProt
NAS

PMID: 10198638




hormone receptor-associated








protein complex 95 kDa








component, protein from








Homo sapiens







TRA2A HUMAN
Splice Isoform Long of
UniProt
IDA

PMID: 9546399




Transformer-2 protein








homolog, protein from








Homo sapiens







TRA2B HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 9546399




Arginine/serine-rich








splicing factor 10, protein








from Homo sapiens







TRABD HUMAN
TRABID protein, protein
UniProt
IDA

PMID: 11463333




from Homo sapiens







TRAF4 HUMAN
Splice Isoform 1 of TNF
UniProt
TAS

PMID: 7592751




receptor-associated factor








4, protein from Homo sapiens







TRBP2 HUMAN
TAR RNA-binding protein 2, 
UniProt
TAS

PMID: 2011739




protein from Homo sapiens







TREF1 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 11349124




Transcriptional-regulating








factor 1, protein from








Homo sapiens







TRI22 HUMAN
Splice Isoform 1 of Tripartite 
UniProt
TAS

PMID: 7797467




motif protein 22, protein 








from Homo sapiens







TRI32 HUMAN
Tripartite motif protein 32, 
UniProt
TAS

PMID: 7778269




protein from Homo sapiens







TRIB3 HUMAN
Tribbles homolog 3,
UniProt
ISS

UniProt: Q96RU7




protein from Homo sapiens







TRIP4 HUMAN
Activating signal cointegrator 
UniProt
IDA

PMID: 10454579




1, protein from Homo sapiens







TRP13 HUMAN
Splice Isoform 1 of Thyroid 
UniProt
TAS

PMID: 7776974




receptor-interacting protein 








13, protein from Homo








sapiens







TRRAP HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 9708738




Transformation/transcription








domain-associated protein, 








protein from Homo sapiens







TRUA HUMAN
tRNA pseudouridine
UniProt
NAS

UniProt: Q9Y606




synthase A, protein from








Homo sapiens







TSN HUMAN
Translin, protein from
UniProt
TAS

PMID: 7663511




Homo sapiens







TUB HUMAN
Tubby protein homolog,
UniProt
TAS

PMID: 11000483




protein from Homo sapiens







TULP3 HUMAN
Tubby related protein 3,
UniProt
NAS

PMID: 11375483




protein from Homo sapiens







TWST2 HUMAN
Twist-related protein 2,
UniProt
IDA

PMID: 11062344




protein from Homo sapiens







TYDP1 HUMAN
Tyrosyl-DNA
UniProt
NAS

PMID: 10521354




phosphodiesterase 1,








protein from Homo sapiens







U2AFL HUMAN
U2 small nuclear
UniProt
NAS

UniProt: Q15695




ribonucleoprotein








auxiliary factor 35 kDa








subunit related-protein 1,








protein from Homo sapiens







U360 HUMAN
Hypothetical protein
UniProt
NAS

PMID: 10873569




DKFZp586N0222,








protein from Homo sapiens







UB2R1 HUMAN
Ubiquitin-conjugating
UniProt
NAS

PMID: 8248134




enzyme E2-32 kDa








complementing, protein








from Homo sapiens







UB2V1 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 9305758




Ubiquitin-conjugating








enzyme E2 variant 1,








protein from Homo sapiens







UB7I1 HUMAN
Splice Isoform 1 of E3
UniProt
NR

UniProt: Q9NWF9




ubiquitin ligase TRIAD3,








protein from Homo sapiens







UBIQ HUMAN
Ubiquitin, protein from
UniProt
IC

PMID: 14528304




Homo sapiens







UBP18 HUMAN
Ubl carboxyl-terminal
UniProt
TAS

PMID: 10777664




hydrolase 18, protein








from Homo sapiens







UBP4 HUMAN
Splice Isoform UNPEL of
UniProt
TAS

PMID: 8183569




Ubiquitin carboxyl-








terminal hydrolase 4,








protein from Homo sapiens







UBP7 HUMAN
Ubiquitin carboxyl-
UniProt
TAS

PMID: 9130697




terminal hydrolase 7,








protein from Homo sapiens







UBQL4 HUMAN
Ubiquilin-4, protein from
UniProt
IDA

PMID: 11001934




Homo sapiens







UGTAP HUMAN
Splice Isoform 1 of UGA
UniProt
ISS

UniProt: Q9HD40




suppressor tRNA-








associated protein,








protein from Homo sapiens







UHMK1 HUMAN
Splice Isoform 1 of
UniProt
ISS

UniProt: Q8TAS1




Serine/threonine-protein








kinase Kist, protein from








Homo sapiens







UK14 HUMAN
Ribonuclease UK114,
UniProt
TAS

PMID: 8530410




protein from Homo sapiens







ULE1A HUMAN
Ubiquitin-like 1-activating
UniProt
NAS

PMID: 10187858




enzyme E1A, protein








from Homo sapiens










ISS

UniProt: O95717






ISS

UniProt: Q9P020



UNG HUMAN
Splice Isoform 2 of
UniProt
NAS

PMID: 9016624




Uracil-DNA glycosylase,








protein from Homo sapiens







USF1 HUMAN
Upstream stimulatory factor 
UniProt
TAS

PMID: 2249772




1, protein from Homo sapiens







UTP11 HUMAN
Probable U3 small nucleolar 
UniProt
IDA

PMID: 12559088




RNA-associated protein 11, 








protein from Homo sapiens







VAV HUMAN
Vav proto-oncogene,
UniProt
NR

UniProt: P15498




protein from Homo sapiens







VCX1 HUMAN
Variable charge X-linked
UniProt
IDA

PMID: 12826317




protein 1, protein from








Homo sapiens







VCX3 HUMAN
Variable charge X-linked
UniProt
ISS

UniProt: Q9NNX9




protein 3, protein from








Homo sapiens







VCXC HUMAN
VCX-C protein, protein
UniProt
ISS

UniProt: Q9H321




from Homo sapiens







VGLL1 HUMAN
Transcription cofactor
UniProt
NAS

PMID: 10518497




vestigial-like protein 1,








protein from Homo sapiens







VHL HUMAN
Splice Isoform 1 of Von
UniProt
TAS

PMID: 7604013




Hippel-Lindau disease








tumor suppressor, protein








from Homo sapiens







WBP11 HUMAN
WW domain-binding
UniProt
TAS

PMID: 10593949




protein 11, protein from








Homo sapiens







WDFY1 HUMAN
WD repeat and FYVE
UniProt
IDA

PMID: 11739631




domain containing protein








1, protein from Homo sapiens







WDR33 HUMAN
WD-repeat protein 33,
UniProt
IDA

PMID: 11162572




protein from Homo sapiens







WDR3 HUMAN
WD-repeat protein 3,
UniProt
TAS

PMID: 10395803




protein from Homo sapiens







WDR50 HUMAN
WD-repeat protein 50,
UniProt
IDA

PMID: 15199122




protein from Homo sapiens







WEE1 HUMAN
Wee1-like protein kinase,
UniProt
TAS

PMID: 8348613




protein from Homo sapiens







WRB HUMAN
Tryptophan-rich protein,
UniProt
TAS

PMID: 9544840




protein from Homo sapiens







WRIP1 HUMAN
Splice Isoform 1 of ATPase 
UniProt
ISS

UniProt: Q96S55




WRNIP1, protein from Homo








sapiens







WRN HUMAN
Werner syndrome ATP-
UniProt
TAS

PMID: 9288107




dependent helicase,








protein from Homo sapiens







WT1 HUMAN
Wilms tumor 1 isoform D, 
UniProt
NAS

UniProt: Q16256




protein from Homo sapiens










NAS

UniProt: P19544



WTAP HUMAN
Splice Isoform 2 of Wilms' 
UniProt
IDA

PMID: 10942595




tumor 1-associating protein,








protein from Homo sapiens







WWTR1 HUMAN
WW domain containing
UniProt
NAS

PMID: 11118213




transcription regulator








protein 1, protein from








Homo sapiens







XAB2 HUMAN
XPA-binding protein 2,
UniProt
IC

PMID: 10944529




protein from Homo sapiens







XPA HUMAN
DNA-repair protein
UniProt
TAS

PMID: 1601884




complementing XP-A cells, 








protein from Homo sapiens







XPO7 HUMAN
Exportin-7, protein from
UniProt
IDA

PMID: 11071879




Homo sapiens







XRN2 HUMAN
5′-3′ exoribonuclease 2,
UniProt
ISS

UniProt: Q9H0D6




protein from Homo sapiens







YAF2 HUMAN
Splice Isoform 2 of YY1-
UniProt
IDA

PMID: 11593398




associated factor 2,








protein from Homo sapiens







YBOX1 HUMAN
Nuclease sensitive
UniProt
NAS

UniProt: P67809




element binding protein 1, 








protein from Homo sapiens







YBOX2 HUMAN
Y-box binding protein 2,
UniProt
TAS

PMID: 10100484




protein from Homo sapiens







YETS4 HUMAN
YEATS domain-
UniProt
TAS

PMID: 9302258




containing protein 4,








protein from Homo sapiens







YL1 HUMAN
Protein YL-1, protein
UniProt
TAS

PMID: 7702631




from Homo sapiens







YYY1 HUMAN
Hypothetical protein,
UniProt
TAS

PMID: 8121495




protein from Homo sapiens







ZBT16 HUMAN
Splice Isoform PLZFB of
UniProt
IDA

PMID: 9294197




Zinc finger and BTB domain-








containing protein 16, 








protein from Homo sapiens







ZBT38 HUMAN
Zinc finger and BTB domain-
UniProt
ISS

UniProt: Q8NAP3




containing protein 38, 








protein from Homo sapiens







ZBT7A HUMAN
Zinc finger and BTB domain-
UniProt
ISS

PMID: 15337766




containing protein 7A, 








protein from Homo sapiens







ZCSL2 HUMAN
Splice Isoform 1 of CSL-
UniProt
IDA

PMID: 14980502




type zinc finger-








containing protein 2,








protein from Homo sapiens







ZEP1 HUMAN
Zinc finger protein 40,
UniProt
TAS

PMID: 2106471




protein from Homo sapiens







ZEP2 HUMAN
Human immunodeficiency
UniProt
NAS

UniProt: P31629




virus type I enHancer








binding protein 2, protein








from Homo sapiens







ZF161 HUMAN
Zinc finger protein 161
UniProt
TAS

PMID: 9177479




homolog, protein from








Homo sapiens







ZFP37 HUMAN
Zinc finger protein 37
UniProt
NAS

UniProt: Q9Y6Q3




homolog, protein from








Homo sapiens







ZFP38 HUMAN
Hypothetical protein
UniProt
NAS

UniProt: Q9Y5A6




DKFZp686H10254,








protein from Homo sapiens







ZFP95 HUMAN
Zinc finger protein 95
UniProt
NAS

PMID: 10585779




homolog, protein from








Homo sapiens







ZFPL1 HUMAN
Splice Isoform 1 of Zinc
UniProt
NAS

PMID: 9653652




finger protein-like 1,








protein from Homo sapiens







ZHANG HUMAN
Host cell factor-binding
UniProt
IDA

PMID: 15705566




transcription factor Zhangfei, 








protein from Homo sapiens







ZHX1 HUMAN
Zinc fingers and
UniProt
IDA

PMID: 12237128




homeoboxes protein 1,








protein from Homo sapiens







ZHX2 HUMAN
Zinc fingers and
UniProt
IDA

PMID: 12741956




homeoboxes protein 2,








protein from Homo sapiens







ZHX3 HUMAN
Zinc fingers and
UniProt
IDA

PMID: 12659632




homeoboxes protein 3,








protein from Homo sapiens







ZIC1 HUMAN
Zinc finger protein ZIC 1,
UniProt
IDA

PMID: 8542595




protein from Homo sapiens







ZKSC1 HUMAN
Zinc finger with KRAB
UniProt
NAS

PMID: 7557990




and SCAN domain-








containing protein 1,








protein from Homo sapiens







ZMY11 HUMAN
Zinc finger MYND domain 
UniProt
TAS

PMID: 7621829




containing protein 11, 








protein from Homo sapiens







ZN117 HUMAN
Zinc finger protein 117,
UniProt
NAS

UniProt: Q03924




protein from Homo sapiens







ZN11A HUMAN
Zinc finger protein 11A,
UniProt
NAS

PMID: 8464732




protein from Homo sapiens







ZN11B HUMAN
Zinc finger protein 11B,
UniProt
NAS

UniProt: Q06732




protein from Homo sapiens







ZN123 HUMAN
Zinc finger protein 123,
UniProt
NAS

PMID: 1339395




protein from Homo sapiens







ZN125 HUMAN
Zinc finger protein 125,
UniProt
NAS

PMID: 1339395




protein from Homo sapiens







ZN126 HUMAN
Zinc finger protein 126,
UniProt
NAS

PMID: 1339395




protein from Homo sapiens







ZN131 HUMAN
Splice Isoform 1 of Zinc
UniProt
NAS

PMID: 7557990




finger protein 131,








protein from Homo sapiens







ZN134 HUMAN
Zinc finger protein 134,
UniProt
NAS

PMID: 7557990




protein from Homo sapiens







ZN135 HUMAN
Similar to Zinc finger
UniProt
NAS

PMID: 7557990




protein 135, protein from








Homo sapiens







ZN138 HUMAN
Zinc finger protein 138,
UniProt
NAS

PMID: 7557990




protein from Homo sapiens







ZN154 HUMAN
Zinc finger protein 154,
UniProt
NAS

PMID: 7557990




protein from Homo sapiens







ZN165 HUMAN
Zinc finger protein 165,
UniProt
NAS

UniProt: P49910




protein from Homo sapiens







ZN169 HUMAN
KRAB box family protein, 
UniProt
NAS

UniProt: Q14929




protein from Homo sapiens







ZN184 HUMAN
Zinc finger protein 184,
UniProt
NAS

UniProt: Q99676




protein from Homo sapiens







ZN195 HUMAN
Hypothetical protein
UniProt
NAS

UniProt: O14628




DKFZp666D035, protein








from Homo sapiens







ZN200 HUMAN
Zinc finger protein 200,
UniProt
NAS

UniProt: P98182




protein from Homo sapiens







ZN205 HUMAN
Zinc finger protein 205,
UniProt
NAS

UniProt: O95201




protein from Homo sapiens







ZN207 HUMAN
Splice Isoform 1 of Zinc
UniProt
NAS

PMID: 9799612




finger protein 207,








protein from Homo sapiens







ZN208 HUMAN
Zinc finger protein 208,
UniProt
NAS

UNIPROT: O43345




protein from Homo sapiens







ZN211 HUMAN
Zinc finger protein 211
UniProt
NAS

UniProt: Q13398




isoform 2, protein from








Homo sapiens







ZN212 HUMAN
Zinc finger protein 212,
UniProt
NAS

UniProt: Q9UDV6




protein from Homo sapiens







ZN214 HUMAN
Zinc finger protein 214,
UniProt
NAS

UniProt: Q9UL59




protein from Homo sapiens







ZN215 HUMAN
Zinc finger protein 215,
UniProt
NAS

UniProt: Q9UL58




protein from Homo sapiens







ZN219 HUMAN
Zinc finger protein 219,
UniProt
TAS

PMID: 10819330




protein from Homo sapiens







ZN236 HUMAN
Similar to Mszf28,
UniProt
NAS

UniProt: Q9UL36




protein from Homo sapiens







ZN253 HUMAN
Zinc finger protein 253,
UniProt
NAS

UniProt: O75346




protein from Homo sapiens







ZN257 HUMAN
Zinc finger protein 257,
UniProt
NAS

UniProt: Q9Y2Q1




protein from Homo sapiens







ZN265 HUMAN
Splice Isoform ZIS-1 of
UniProt
TAS

PMID: 9931435




Zinc finger protein 265,








protein from Homo sapiens







ZN268 HUMAN
Splice Isoform A of Zinc
UniProt
NAS

PMID: 11311945




finger protein 268,








protein from Homo sapiens







ZN277 HUMAN
Zinc finger protein 277,
UniProt
NAS

UniProt: Q9NRM2




protein from Homo sapiens







ZN278 HUMAN
Splice Isoform 1 of Zinc
UniProt
TAS

PMID: 10713105




finger protein 278,








protein from Homo sapiens







ZN282 HUMAN
Zinc finger protein 282,
UniProt
NAS

UniProt: Q9UDV7




protein from Homo sapiens







ZN297 HUMAN
Zinc finger protein 297,
UniProt
TAS

PMID: 9545376




protein from Homo sapiens







ZN331 HUMAN
Zinc finger protein 331,
UniProt
NAS

UniProt: Q9NQX6




protein from Homo sapiens







ZN33A HUMAN
Zinc finger protein 33A,
UniProt
NAS

UniProt: Q06730




protein from Homo sapiens







ZN33B HUMAN
Zinc finger protein 33B,
UniProt
NAS

UniProt: Q06731




protein from Homo sapiens







ZN346 HUMAN
Splice Isoform 1 of Zinc
UniProt
TAS

PMID: 10488071




finger protein 346,








protein from Homo sapiens







ZN37A HUMAN
Zinc finger protein 37A,
UniProt
NAS

PMID: 8464732




protein from Homo sapiens







ZN396 HUMAN
Splice Isoform 1 of Zinc
UniProt
IMP

UniProt: Q96N95




finger protein 396,








protein from Homo sapiens







ZN398 HUMAN
Splice Isoform 1 of Zinc
UniProt
NAS

PMID: 11779858




finger protein 398,








protein from Homo sapiens







ZN482 HUMAN
Zinc finger protein 482,
UniProt
TAS

PMID: 7958847




protein from Homo sapiens







ZNF19 HUMAN
Zinc finger protein 19,
UniProt
NAS

PMID: 7557990




protein from Homo sapiens







ZNF22 HUMAN
Zinc finger protein 22,
UniProt
ISS

UniProt: P17026




protein from Homo sapiens







ZNF24 HUMAN
Zinc finger protein 24,
UniProt
IC

PMID: 10585455




protein from Homo sapiens







ZNF38 HUMAN
KRAB box family protein, 
UniProt
IC

PMID: 2288909




protein from Homo sapiens










NAS

UniProt: Q9NNX8



ZNF41 HUMAN
Splice Isoform 1 of Zinc
UniProt
NAS

UniProt: P51814




finger protein 41, protein








from Homo sapiens







ZNF69 HUMAN
Zinc finger protein 69,
UniProt
NAS

UniProt: Q9UC07




protein from Homo sapiens







ZNF70 HUMAN
Zinc finger protein 70,
UniProt
NAS

UniProt: Q9UC06




protein from Homo sapiens







ZNF71 HUMAN
Endothelial zinc finger
UniProt
NAS

UniProt: Q9UC09




protein induced by tumor








necrosis factor alpha,








protein from Homo sapiens







ZNF73 HUMAN
Zinc finger protein 73,
UniProt
NAS

UniProt: O43830




protein from Homo sapiens







ZNF75 HUMAN
Hypothetical protein
UniProt
NAS

UniProt: P51815




DKFZp667L2223,








protein from Homo sapiens







ZNF79 HUMAN
Zinc finger protein 79,
UniProt
NAS

UniProt: Q15937




protein from Homo sapiens







ZNF80 HUMAN
Zinc finger protein 80,
UniProt
NAS

UniProt: P51504




protein from Homo sapiens







ZNF81 HUMAN
Zinc finger protein 81,
UniProt
NAS

UniProt: P51508




protein from Homo sapiens







ZNF83 HUMAN
Zinc finger protein 83,
UniProt
NAS

UniProt: P51522




protein from Homo sapiens







ZNF84 HUMAN
Zinc finger protein 84,
UniProt
NAS

UniProt: P51523




protein from Homo sapiens







ZNF85 HUMAN
Zinc finger protein 85,
UniProt
TAS

PMID: 9839802




protein from Homo sapiens







ZNF8 HUMAN
Zinc finger protein 8,
UniProt
NAS

UniProt: P17098




protein from Homo sapiens







ZNF90 HUMAN
Zinc finger protein 90,
UniProt
NAS

UniProt: Q03938




protein from Homo sapiens







ZNF91 HUMAN
Zinc finger protein 91,
UniProt
NAS

UniProt: Q05481




protein from Homo sapiens







ZNF92 HUMAN
Splice Isoform 1 of Zinc
UniProt
NAS

UniProt: Q03936




finger protein 92, protein








from Homo sapiens







ZNF93 HUMAN
Splice Isoform 1 of Zinc
UniProt
NAS

UniProt: P35789




finger protein 93, protein








from Homo sapiens







ZPR1 HUMAN
Zinc-finger protein ZPR1, 
UniProt
TAS

PMID: 8650580




protein from Homo sapiens







ZRF1 HUMAN
Zuotin-related factor 1,
UniProt
NAS

UniProt: Q99543




protein from Homo sapiens







ZW10 HUMAN
Centromere/kinetochore
UniProt
NAS

PMID: 11146660




protein zw10 homolog,








protein from Homo sapiens







ZWIA HUMAN
ZW10 interactor, antisense, 
UniProt
IDA

PMID: 8885239




protein from Homo sapiens







ZXDA HUMAN
Zinc finger X-linked
UniProt
NAS

UniProt: P98168




protein ZXDA, protein








from Homo sapiens







ZXDB HUMAN
Zinc finger X-linked
UniProt
NAS

UniProt: P98169




protein ZXDB, protein








from Homo sapiens







ACF HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 10781591




APOBEC1








complementation factor,








protein from Homo sapiens







HILS1 HUMAN
Spermatid-specific linker
UniProt
IDA

PMID: 12920187




histone H1-like protein,








protein from Homo sapiens







HNRH1 HUMAN
Heterogeneous nuclear
UniProt
TAS

PMID: 7499401




ribonucleoprotein H1,








protein from Homo sapiens







HNRH2 HUMAN
Heterogeneous nuclear
UniProt
TAS

PMID: 7499401




ribonucleoprotein H′,








protein from Homo sapiens







HNRH3 HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 10858537




Heterogeneous nuclear








ribonucleoprotein H3,








protein from Homo sapiens







HNRPC HUMAN
Full-length cDNA clone
UniProt
NR

UniProt: P07910




CS0DA009YK08 of








Neuroblastoma of Homo








sapiens, protein from








Homo sapiens







HNRPF HUMAN
Heterogeneous nuclear
UniProt
TAS

PMID: 7499401




ribonucleoprotein F,








protein from Homo sapiens







HNRPG HUMAN
Heterogeneous nuclear
UniProt
NAS

PMID: 7692398




ribonucleoprotein G,








protein from Homo sapiens







HNRPL HUMAN
Heterogeneous nuclear
UniProt
TAS

PMID: 2687284




ribonucleoprotein L








isoform a, protein from








Homo sapiens







HNRPR HUMAN
Heterogeneous nuclear
UniProt
TAS

PMID: 9421497




ribonucleoprotein R,








protein from Homo sapiens







HNRPU HUMAN
Splice Isoform Long of
UniProt
TAS

PMID: 7509195




Heterogenous nuclear








ribonucleoprotein U,








protein from Homo sapiens







HNRU2 HUMAN
Heterogeneous nuclear
UniProt
NAS

UniProt: P07029




ribonucleoprotein UP2,








protein from Homo sapiens







O14979
JKTBP2, protein from
UniProt
TAS

PMID: 9538234




Homo sapiens







O76022
E1B-55 kDa-associated
UniProt
TAS

PMID: 9733834




protein, protein from








Homo sapiens







PTBP1 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 1641332




Polypyrimidine tract-








binding protein 1, protein








from Homo sapiens







Q9UCE7
D(TTAGGG)N-binding
UniProt
TAS

PMID: 8321232




protein B37 = TYPE A-B








heterogeneous nuclear








ribonucleoprotein








homolog, protein from








Homo sapiens







RALY HUMAN
RNA binding protein,
UniProt
TAS

PMID: 9376072




protein from Homo sapiens







ROA0 HUMAN
Heterogeneous nuclear
UniProt
TAS

PMID: 7585247




ribonucleoprotein A0,








protein from Homo sapiens







ROA1 HUMAN
Heterogeneous nuclear
UniProt
TAS

PMID: 8521471




ribonucleoprotein A1 isoform 








b, protein from Homo sapiens







ROA2 HUMAN
Splice Isoform B1 of
UniProt
TAS

PMID: 7789969




Heterogeneous nuclear








ribonucleoproteins A2/B1, 








protein from Homo sapiens







O60934
Nibrin, protein from
UniProt
IDA

PMID: 9590181




Homo sapiens







Q63HR6
Hypothetical protein
UniProt
ISS

UniProt: Q63HR6




DKFZp686G19151,








protein from Homo sapiens







RAD50 HUMAN
Splice Isoform 1 of DNA
UniProt
TAS

PMID: 15279769




repair protein RAD50,








protein from Homo sapiens







BARX1 HUMAN
Homeobox protein BarH-like 
UniProt
NAS

UniProt: Q9HBU1




1, protein from Homo sapiens







GBX1 HUMAN
Homeobox protein GBX-1, 
UniProt
NAS

UniProt: Q14549




protein from Homo sapiens







HDAC8 HUMAN
Splice Isoform 3 of
UniProt
TAS

PMID: 10748112




Histone deacetylase 8,








protein from Homo sapiens







HMG2 HUMAN
High mobility group protein 
UniProt
TAS

PMID: 1551873




2, protein from Homo sapiens







HXD12 HUMAN
Homeo box D12, protein
UniProt
NAS

UniProt: P35452




from Homo sapiens







JUN HUMAN
Transcription factor AP-1, 
UniProt
TAS

PMID: 10918580




protein from Homo sapiens







PRRX2 HUMAN
Paired mesoderm
UniProt
NAS

UniProt: Q99811




homeobox protein 2,








protein from Homo sapiens







SMC3 HUMAN
Structural maintenance of
UniProt
NR

UniProt: Q9UQE7




chromosome 3, protein








from Homo sapiens







SMCE1 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 9435219




SWI/SNF-related matrix-








associated actin-dependent 








regulator of chromatin 








subfamily E member 1, 








protein from Homo sapiens







TE2IP HUMAN
Telomeric repeat binding
UniProt
TAS

PMID: 10850490




factor 2 interacting protein








1, protein from Homo sapiens







ZBED1 HUMAN
Zinc finger BED domain
UniProt
TAS

PMID: 9887332




containing protein 1,








protein from Homo sapiens







ZN238 HUMAN
Zinc finger protein 238,
UniProt
TAS

PMID: 9756912




protein from Homo sapiens







CHK1 HUMAN
Serine/threonine-protein
UniProt
TAS

PMID: 9382850




kinase Chk1, protein








from Homo sapiens







CHM1A HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 11559747




Charged multivesicular








body protein 1a, protein








from Homo sapiens







DMC1 HUMAN
Meiotic recombination
UniProt
TAS

PMID: 8602360




protein DMC1/LIM15








homolog, protein from








Homo sapiens







MCP33 HUMAN
Metaphase chromosomal
UniProt
IDA

PMID: 9543011




protein 1, protein from








Homo sapiens







MK67I HUMAN
MKI67 FHA domain-
UniProt
IDA

PMID: 11342549




interacting nucleolar








phosphoprotein, protein








from Homo sapiens







NOL6 HUMAN
Splice Isoform 1 of
UniProt
ISS

PMID: 11895476




Nucleolar protein 6,








protein from Homo sapiens







Q8WZ42
Titin, protein from Homo
UniProt
ISS

PMID: 9548712




sapiens










TAS

PMID: 10481174



RCC1 HUMAN
RCC1 protein, protein
UniProt
IDA

PMID: 15014043




from Homo sapiens







RGS12 HUMAN
Splice Isoform 1 of Regulator 
UniProt
TAS

PMID: 10869340




of G-protein signaling 12, 








protein from Homo sapiens







SMC1A HUMAN
Structural maintenance of
UniProt
TAS

PMID: 7757074




chromosome 1-like 1 protein, 








protein from Homo sapiens







SUV91 HUMAN
Histone-lysine N-
UniProt
TAS

PMID: 10202156




methyltransferase, H3








lysine-9 specific 1,








protein from Homo sapiens







TBG1 HUMAN
Tubulin gamma-1 chain,
UniProt
ISS

UNIPROT: P23258




protein from Homo sapiens







NO55 HUMAN
Nucleolar autoantigen No55, 
UniProt
TAS

PMID: 8862517




protein from Homo sapiens







Q6ZNA8
Hypothetical protein
UniProt
ISS

UniProt: Q6ZNA8




FLJ16262, protein from








Homo sapiens







RAD51 HUMAN
Splice Isoform 1 of DNA
UniProt
ISS

UniProt: Q06609




repair protein RAD51








homolog 1, protein from








Homo sapiens







STAG3 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 10698974




Cohesin subunit SA-3,








protein from Homo sapiens







SYCP2 HUMAN
Synaptonemal complex
UniProt
NAS

PMID: 10341103




protein 2, protein from








Homo sapiens










NAS

PMID: 9592139



Q6PIF2
PREDICTED: hypothetical 
UniProt
ISS

PMID: 15944401




protein XP_497609, 








protein from Homo sapiens







Q8N0S2
Conserved hypothetical
UniProt
ISS

PMID: 15944401




protein, protein from








Homo sapiens







SYCP1 HUMAN
Synaptonemal complex
UniProt
ISS

PMID: 15944401




protein 1, protein from








Homo sapiens







NPM2 HUMAN
Nucleoplasmin-2, protein
UniProt
IDA

PMID: 12714744




from Homo sapiens







Q8N7S8
Hypothetical protein
UniProt
ISS

UniProt: Q8N7S8




FLJ40400, protein from








Homo sapiens







Q96GH7
KLHDC3 protein, protein
UniProt
ISS

UniProt: Q96GH7




from Homo sapiens







RCC1 HUMAN
RCC1 protein, protein
UniProt
IDA

PMID: 15014043




from Homo sapiens







ATRX HUMAN
Splice Isoform 4 of
UniProt
TAS

PMID: 10570185




Transcriptional regulator








ATRX, protein from








Homo sapiens







CBX1 HUMAN
Chromobox protein homolog 
UniProt
TAS

PMID: 9169582




1, protein from Homo sapiens







CBX5 HUMAN
Chromobox protein homolog 
UniProt
TAS

PMID: 8663349




5, protein from Homo sapiens







Q9Y654
Heterochromatin-specific
UniProt
ISS

UniProt: Q9Y654




nonhistone protein,








protein from Homo sapiens







TB182 HUMAN
182 kDa tankyrase 1-
UniProt
NAS

PMID: 11854288




binding protein, protein








from Homo sapiens







H2AW HUMAN
Core histone macro-H2A.2, 
UniProt
IDA

PMID: 11331621




protein from Homo sapiens







H2AY HUMAN
H2A histone family,
UniProt
IDA

PMID: 11331621




member Y, isoform 3,








protein from Homo sapiens







Q96AP0
24432 protein, protein
UniProt
IDA

PMID: 15181449




from Homo sapiens







O95268
Origin recognition
UniProt
NAS

PMID: 9765232




complex subunit ORC5T,








protein from Homo sapiens







Q9NZH2
Replication initiator 1,
UniProt
TAS

PMID: 10606657




protein from Homo sapiens







MCM3 HUMAN
DNA replication licensing
UniProt
TAS

PMID: 1549468




factor MCM3, protein








from Homo sapiens







DPOD3 HUMAN
DNA polymerase delta
UniProt
NAS

PMID: 10219083




subunit 3, protein from








Homo sapiens







PCNA HUMAN
Proliferating cell nuclear
UniProt
TAS

PMID: 2565339




antigen, protein from








Homo sapiens







RFC3 HUMAN
Activator 1 38 kDa subunit, 
UniProt
TAS

PMID: 7774928




protein from Homo sapiens







RFC4 HUMAN
Activator 1 37 kDa subunit, 
UniProt
TAS

PMID: 7774928




protein from Homo sapiens







RFC5 HUMAN
Activator 1 36 kDa subunit, 
UniProt
NAS

PMID: 8999859




protein from Homo sapiens







RFA1 HUMAN
Replication protein A 70 kDa
UniProt
TAS

PMID: 8756712




DNA-binding subunit, 








protein from Homo sapiens







RFA2 HUMAN
Replication protein A 32 kDa
UniProt
TAS

PMID: 2406247




subunit, protein from








Homo sapiens







RFA3 HUMAN
Replication protein A 14 kDa
UniProt
TAS

PMID: 8454588




subunit, protein from








Homo sapiens







RFA4 HUMAN
Replication protein A 30 kDa
UniProt
TAS

PMID: 7760808




subunit, protein from








Homo sapiens







CHRC1 HUMAN
Chromatin accessibility
UniProt
NAS

PMID: 10880450




complex protein 1,








protein from Homo sapiens







Q9P288
TOK-1alpha, protein
UniProt
IDA

PMID: 10878006




from Homo sapiens







AKAP6 HUMAN
A-kinase anchor protein 6, 
UniProt
IDA

PMID: 10413680




protein from Homo sapiens







ANX11 HUMAN
Annexin A11, protein
UniProt
NAS

PMID: 12577318




from Homo sapiens







ATF6A HUMAN
Cyclic AMP-dependent
UniProt
TAS

PMID: 10866666




transcription factor ATF-6








alpha, protein from Homo








sapiens







CBX5 HUMAN
Chromobox protein homolog 
UniProt
TAS

PMID: 8663349




5, protein from Homo sapiens







CENPF HUMAN
CENP-F kinetochore protein, 
UniProt
IDA

PMID: 12154071




protein from Homo sapiens







CLIC1 HUMAN
Chloride intracellular
UniProt
IDA

PMID: 9139710




channel protein 1, protein








from Homo sapiens







EMD HUMAN
Emerin, protein from
UniProt
TAS

PMID: 8589715




Homo sapiens







GNAZ HUMAN
Guanine nucleotide-binding 
UniProt
TAS

PMID: 2117645




protein G(z), alpha subunit, 








protein from Homo sapiens







HAX1 HUMAN
HS1-associating protein X-1, 
UniProt
TAS

PMID: 9058808




protein from Homo sapiens







LAP2A HUMAN
Lamina-associated
UniProt
TAS

PMID: 8530026




polypeptide 2 isoform alpha, 








protein from Homo sapiens







LAP2B HUMAN
ThymopoieTin isoform beTa, 
UniProt
TAS

PMID: 8530026




protein from Homo sapiens







LIS1 HUMAN
Platelet-activating factor
UniProt
IDA

PMID: 11940666




acetylhydrolase IB alpha








subunit, protein from








Homo sapiens







LY10 HUMAN
Splice Isoform LYSp100-B of 
UniProt
TAS

PMID: 8695863




Nuclear body protein SP140, 








protein from Homo sapiens







MYOF HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 10607832




Myoferlin, protein from








Homo sapiens







PE2R3 HUMAN
Splice Isoform EP3A of
UniProt
TAS

PMID: 10336471




Prostaglandin E2 receptor,








EP3 subtype, protein








from Homo sapiens







PTGDS HUMAN
Prostaglandin-H2 D-
UniProt
ISS

UniProt: P41222




isomerase precursor,








protein from Homo sapiens







Q86UU5
Gametogenetin protein 1a, 
UniProt
ISS

UniProt: Q86UU5




protein from Homo sapiens







Q9UN92
Nurim, protein from
UniProt
TAS

PMID: 10402458




Homo sapiens







RTN4 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 11126360




Reticulon-4, protein from








Homo sapiens







S10A6 HUMAN
Calcyclin, protein from
UniProt
NAS

PMID: 12577318




Homo sapiens







SRBP1 HUMAN
Sterol regulatory element
UniProt
TAS

PMID: 8156598




binding transcription factor 








1, isoform a,








protein from Homo sapiens







SYNE1 HUMAN
Splice Isoform 1 of Nesprin-1, 
UniProt
IDA

PMID: 11792814




protein from Homo sapiens







TIP30 HUMAN
Conserved hypothetical
UniProt
IDA

PMID: 15282309




protein, protein from








Homo sapiens







TREX1 HUMAN
Splice Isoform 1 of Three
UniProt
ISS

UniProt: Q9Y4X2




prime repair exonuclease 1, 








protein from Homo sapiens










ISS

UniProt: Q8TEU2






NAS

PMID: 10391904



UN84B HUMAN
Sad1/unc-84-like protein 2, 
UniProt
TAS

PMID: 10375507




protein from Homo sapiens







LMNB2 HUMAN
Lamin B2, protein from
UniProt
NAS

UniProt: Q03252




Homo sapiens







Q9UHQ1
Nuclear prelamin A
UniProt
TAS

PMID: 10514485




recognition factor,








protein from Homo sapiens







LMNA HUMAN
Splice Isoform A of
UniProt
TAS

PMID: 10080180




Lamin A/C, protein from








Homo sapiens







LMNB1 HUMAN
Lamin B1, protein from
UniProt
TAS

PMID: 7557986




Homo sapiens







Q9BWC6
Nuclear prelamin A
UniProt
IDA

PMID: 10514485




recognition factor, isoform b, 








protein from Homo sapiens







RM19 HUMAN
39S ribosomal protein L19, 
UniProt
IDA

PMID: 10942595




mitochondrial precursor, 








protein from Homo sapiens







SCRN1 HUMAN
Secernin-1, protein from
UniProt
IDA

PMID: 10942595




Homo sapiens







TAGL2 HUMAN
Transgelin-2, protein
UniProt
IDA

PMID: 10942595




from Homo sapiens







WTAP HUMAN
Splice Isoform 2 of Wilms' 
UniProt
IDA

PMID: 10942595




tumor 1-associating protein,








protein from Homo sapiens







AT11B HUMAN
Probable phospholipid-
UniProt
NAS

PMID: 11790799




transporting ATPase IF,








protein from Homo sapiens







MATR3 HUMAN
Matrin-3, protein from
UniProt
TAS

PMID: 2033075




Homo sapiens







LBR HUMAN
Lamin-B receptor,
UniProt
TAS

PMID: 8157662




protein from Homo sapiens







MAN1 HUMAN
Inner nuclear membrane
UniProt
TAS

PMID: 10671519




protein Man1, protein








from Homo sapiens







PSN1 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 9298903




Presenilin-1, protein from








Homo sapiens







PSN2 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 9298903




Presenilin-2, protein from








Homo sapiens







DHCR7 HUMAN
7-dehydrocholesterol
UniProt
IDA

PMID: 9878250




reductase, protein from








Homo sapiens







GUC2D HUMAN
Retinal guanylyl cyclase 1
UniProt
TAS

PMID: 7777544




precursor, protein from








Homo sapiens







GUC2F HUMAN
Retinal guanylyl cyclase 2
UniProt
TAS

PMID: 7777544




precursor, protein from








Homo sapiens







Q6NUM9
All-trans-13,14-
UniProt
ISS

PMID: 15358783




dihydroretinol saturase,








protein from Homo sapiens







RAE1L HUMAN
mRNA-associated protein
UniProt
TAS

PMID: 9256445




mrnp 41, protein from








Homo sapiens






colocalizes_with
AAAS HUMAN
Aladin, protein from
UniProt
IDA

PMID: 12730363




Homo sapiens







DD19B HUMAN
Splice Isoform 1 of ATP-
UniProt
TAS

PMID: 10428971




dependent RNA helicase








DDX19B, protein from








Homo sapiens







RAE1L HUMAN
mRNA-associated protein
UniProt
TAS

PMID: 9256445




mrnp 41, protein from








Homo sapiens







IMA1 HUMAN
Importin alpha-1 subunit,
UniProt
TAS

PMID: 8052633




protein from Homo sapiens







IMA3 HUMAN
Importin alpha-3 subunit,
UniProt
TAS

PMID: 9154134




protein from Homo sapiens







IMB1 HUMAN
Importin beta-1 subunit,
UniProt
TAS

PMID: 7627554




protein from Homo sapiens







IMB3 HUMAN
Importin beta-3, protein
UniProt
TAS

PMID: 9271386




from Homo sapiens






colocalizes_with
IPO4 HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 11823430




Importin-4, protein from








Homo sapiens







IPO7 HUMAN
Importin-7, protein from
UniProt
TAS

PMID: 9214382




Homo sapiens







NU107 HUMAN
Nuclear pore complex
UniProt
IDA

PMID: 11564755




protein Nup107, protein








from Homo sapiens










IDA

PMID: 11684705



NU133 HUMAN
Nuclear pore complex
UniProt
IDA

PMID: 11684705




protein Nup133, protein








from Homo sapiens










IDA

PMID: 11564755



NU153 HUMAN
Nuclear pore complex
UniProt
TAS

PMID: 8110839




protein Nup153, protein








from Homo sapiens







NU160 HUMAN
NucleoporiN 160 kDa,
UniProt
IDA

PMID: 11564755




protein from Homo sapiens










IDA

PMID: 11684705



NU205 HUMAN
Nuclear pore complex
UniProt
NAS

PMID: 9348540




protein Nup205, protein








from Homo sapiens







NU214 HUMAN
Nuclear pore complex
UniProt
TAS

PMID: 8108440




protein Nup214, protein








from Homo sapiens







NUP50 HUMAN
Nucleoporin 50 kDa,
UniProt
TAS

PMID: 10449902




protein from Homo sapiens







NUP54 HUMAN
Nucleoporin 54 kDa variant, 
UniProt
TAS

PMID: 870784




protein from Homo sapiens







NUP62 HUMAN
Nuclear pore glycoprotein
UniProt
IDA

PMID: 1915414




p62, protein from Homo








sapiens







NUP88 HUMAN
Nuclear pore complex
UniProt
TAS

PMID: 9049309




protein Nup88, protein








from Homo sapiens







NUP98 HUMAN
Splice Isoform 1 of Nuclear 
UniProt
IDA

PMID: 9348540




pore complex protein 








Nup98-Nup96 precursor, 








protein from Homo sapiens










NAS

PMID: 10087256



NUPL HUMAN
Nucleoporin-like protein RIP, 
UniProt
TAS

PMID: 7637788




protein from Homo sapiens







NXT1 HUMAN
NTF2-related export protein 
UniProt
TAS

PMID: 10567585




1, protein from Homo sapiens







O75761
Ranbp3 protein, protein
UniProt
NAS

PMID: 9637251




from Homo sapiens







Q6GTM2
Nucleoporin 62 kDa,
UniProt
ISS

UniProt: Q6GTM2




protein from Homo sapiens







RAE1L HUMAN
mRNA-associated protein
UniProt
TAS

PMID: 9256445




mrnp 41, protein from








Homo sapiens







RAN HUMAN
GTP-binding nuclear
UniProt
NAS

PMID: 8421051




protein RAN, protein








from Homo sapiens







RBP17 HUMAN
Ran-binding protein 17,
UniProt
NAS

PMID: 11024021




protein from Homo sapiens







RBP23 HUMAN
Ran-binding protein 2-like
UniProt
NAS

PMID: 9480752




3, protein from Homo sapiens







RBP2 HUMAN
Ran-binding protein 2,
UniProt
TAS

PMID: 7603572




protein from Homo sapiens







RGP1 HUMAN
Ran GTPase-activating
UniProt
TAS

PMID: 8978815




protein 1, protein from








Homo sapiens







RNUT1 HUMAN
SNURPORTIN1, protein
UniProt
TAS

PMID: 9670026




from Homo sapiens







SENP2 HUMAN
Sentrin-specific protease 2, 
UniProt
IDA

PMID: 12192048




protein from Homo sapiens







TPR HUMAN
Translocated promoter
UniProt
TAS

PMID: 7798308




region, protein from








Homo sapiens







XPO7 HUMAN
Exportin-7, protein from
UniProt
IDA

PMID: 11024021




Homo sapiens







EXOS3 HUMAN
Exosome complex
UniProt
IDA

PMID: 11110791




exonuclease RRP40,








protein from Homo sapiens







EXOS9 HUMAN
Polymyositis/scleroderma
UniProt
NAS

PMID: 11879549




autoantigen 1, protein








from Homo sapiens







O60934
Nibrin, protein from
UniProt
IDA

PMID: 12447371




Homo sapiens







Q63HR6
Hypothetical protein
UniProt
ISS

UniProt: Q63HR6




DKFZp686G19151,








protein from Homo sapiens







Q9BWC6
Nuclear prelamin A
UniProt
IDA

PMID: 10514485




recognition factor, isoform b, 








protein from Homo sapiens







CENPF HUMAN
CENP-F kinetochore protein, 
UniProt
IDA

PMID: 7542657




protein from Homo sapiens







CHM1A HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 11559747




Charged multivesicular








body protein 1a, protein








from Homo sapiens







DNM3A HUMAN
DNA, protein from Homo
UniProt
ISS

PMID: 12138111




sapiens







ERCC8 HUMAN
Splice Isoform 1 of DNA
UniProt
IDA

PMID: 11782547




excision repair protein








ERCC-8, protein from








Homo sapiens







MYB HUMAN
Splice Isoform 1 of Myb
UniProt
NAS

PMID: 3014652




proto-oncogene protein,








protein from Homo sapiens







P53 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 11080164




Cellular tumor antigen p53, 








protein from Homo sapiens







PML HUMAN
Splice Isoform PML-1 of
UniProt
TAS

PMID: 9294197




Probable transcription








factor PML, protein from








Homo sapiens







Q86XF5
DNA cytosine
UniProt
ISS

PMID: 12138111




methyltransferase 3 alpha,








isoform a, protein from








Homo sapiens







Q8IZV0
DNA cytosine
UniProt
IDA

PMID: 12138111




methyltransferase 3 alpha








isoform b, protein from








Homo sapiens







SMC3 HUMAN
Structural maintenance of
UniProt
IDA

PMID: 11590136




chromosome 3, protein








from Homo sapiens







SMRCD HUMAN
SWI/SNF-related, matrix
UniProt
NAS

PMID: 11031099




associated, actin-dependent 








regulator of chromatin 








subfamily A containing 








DEAD/H box 1, 








protein from Homo sapiens







SPTN4 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 11294830




Spectrin beta chain, brain 3, 








protein from Homo sapiens







TEP1 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 7876352




Telomerase protein








component 1, protein








from Homo sapiens







ARSA1 HUMAN
Arsenical pump-driving
UniProt
TAS

PMID: 9736449




ATPase, protein from








Homo sapiens







EXOS9 HUMAN
Polymyositis/scleroderma
UniProt
TAS

PMID: 2007859




autoantigen 1, protein








from Homo sapiens







P53 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 12080348




Cellular tumor antigen p53, 








protein from Homo sapiens







DDX21 HUMAN
Splice Isoform 2 of
UniProt
TAS

PMID: 8614622




Nucleolar RNA helicase 2, 








protein from Homo sapiens







DDX54 HUMAN
ATP-dependent RNA
UniProt
ISS

UniProt: Q9BRZ1




helicase DDX54, protein








from Homo sapiens







DDX56 HUMAN
Probable ATP-dependent
UniProt
TAS

PMID: 10749921




RNA helicase DDX56,








protein from Homo sapiens







DEDD2 HUMAN
Splice Isoform 1 of DNA-
UniProt
IDA

PMID: 11741985




binding death effector








domain-containing protein 2, 








protein from Homo sapiens







DEDD HUMAN
Splice Isoform 1 of Death
UniProt
ISS

UniProt: O75618




effector domain-








containing protein,








protein from Homo sapiens







DKC1 HUMAN
H/ACA ribonucleoprotein
UniProt
TAS

PMID: 10556300




complex subunit 4,








protein from Homo sapiens







DNJB9 HUMAN
DnaJ homolog subfamily
UniProt
ISS

UniProt: Q9UBS3




B member 9, protein








from Homo sapiens







EXOS1 HUMAN
3′-5′ exoribonuclease
UniProt
IDA

PMID: 11812149




CSL4 homolog, protein








from Homo sapiens







EXOS4 HUMAN
Exosome complex
UniProt
NAS

PMID: 11110791




exonuclease RRP41,








protein from Homo sapiens







EXOS5 HUMAN
Exosome complex
UniProt
NAS

PMID: 11110791




exonuclease RRP46,








protein from Homo sapiens







EXOS9 HUMAN
Polymyositis/scleroderma
UniProt
TAS

PMID: 2007859




autoantigen 1, protein








from Homo sapiens







EXOSX HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 1383382




Exosome component 10,








protein from Homo sapiens







FXR1 HUMAN
Fragile X mental retardation 
UniProt
TAS

PMID: 10888599




syndrome-related protein 1, 








protein from Homo sapiens







GEMI4 HUMAN
Component of gems 4,
UniProt
TAS

PMID: 10725331




protein from Homo sapiens







GNL3 HUMAN
Splice Isoform 1 of Guanine 
UniProt
ISS

UniProt: Q9BVP2




nucleotide








binding protein-like 3,








protein from Homo sapiens







IF16 HUMAN
Splice Isoform 2 of Gamma-
UniProt
IDA

PMID: 14654789




interferon-inducible protein 








Ifi-16,








protein from Homo sapiens







ILF2 HUMAN
Interleukin enhancer-binding 
UniProt
IDA

PMID: 11790298




factor 2, protein








from Homo sapiens







IMP3 HUMAN
U3 small nucleolar
UniProt
IDA

PMID: 12655004




ribonucleoprotein protein








IMP3, protein from








Homo sapiens







IMP4 HUMAN
U3 small nucleolar
UniProt
IDA

PMID: 12655004




ribonucleoprotein protein








IMP4, protein from








Homo sapiens







KI67 HUMAN
Splice Isoform Long of
UniProt
NR

UniProt: P46013




Antigen KI-67, protein








from Homo sapiens







MBB1A HUMAN
Splice Isoform 1 of Myb-
UniProt
ISS

UniProt: Q9BQG0




binding protein 1A,








protein from Homo sapiens







MDM2 HUMAN
Splice Isoform Mdm2 of
UniProt
IDA

PMID: 10707090




Ubiquitin-protein ligase








E3 Mdm2, protein from








Homo sapiens







MK67I HUMAN
MKI67 FHA domain-
UniProt
IDA

PMID: 11342549




interacting nucleolar








phosphoprotein, protein








from Homo sapiens







MO4L2 HUMAN
Mortality factor 4-like
UniProt
IDA

PMID: 10942595




protein 2, protein from








Homo sapiens







NEK11 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 15161910




Serine/threonine-protein








kinase Nek11, protein








from Homo sapiens







NHPX HUMAN
NHP2-like protein 1,
UniProt
TAS

PMID: 10593953




protein from Homo sapiens







NO55 HUMAN
Nucleolar autoantigen No55, 
UniProt
TAS

PMID: 8862517




protein from Homo sapiens







NOL1 HUMAN
Proliferating-cell
UniProt
TAS

PMID: 1394192




nucleolar antigen p120,








protein from Homo sapiens







NOL3 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 10196175




Nucleolar protein 3,








protein from Homo sapiens







NOL4 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 9813152




Nucleolar protein 4,








protein from Homo sapiens







NOL6 HUMAN
Splice Isoform 1 of
UniProt
ISS

PMID: 11895476




Nucleolar protein 6,








protein from Homo sapiens







NOLC1 HUMAN
Nucleolar and coiled-body
UniProt
TAS

PMID: 7657714




phosphoprotein 1, protein








from Homo sapiens







NOP56 HUMAN
Nucleolar protein Nop56,
UniProt
TAS

PMID: 9372940




protein from Homo sapiens







NOP5 HUMAN
Nucleolar protein NOP5,
UniProt
TAS

PMID: 10925205




protein from Homo sapiens







NPA1P HUMAN
Nucleolar preribosomal-
UniProt
NAS

PMID: 12429849




associated protein 1,








protein from Homo sapiens







NPM HUMAN
Nucleophosmin, protein
UniProt
IDA

PMID: 12080348




from Homo sapiens







NUCL HUMAN
Nucleolin, protein from
UniProt
TAS

PMID: 2394707




Homo sapiens







O00366
Putative p150, protein
UniProt
ISS

UniProt: O00366




from Homo sapiens







OASL HUMAN
Splice Isoform p56 of 59 kDa
UniProt
TAS

PMID: 9826176




2′-5′-oligoadenylate








synthetase-like protein,








protein from Homo sapiens







P53 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 12080348




Cellular tumor antigen p53, 








protein from Homo sapiens







PNMA1 HUMAN
Paraneoplastic antigen Ma1, 
UniProt
TAS

PMID: 10050892




protein from Homo sapiens







PTBP1 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 1641332




Polypyrimdine tract-








binding protein 1, protein








from Homo sapiens







Q76D35
Nop132, protein from
UniProt
IDA

PMID: 14660641




Homo sapiens







Q8WYJ1
MDM2 protein, protein
UniProt
ISS

UniProt: Q8WYJ1




from Homo sapiens







Q8WYJ2
MDM2 protein, protein
UniProt
ISS

UniProt: Q8WYJ2




from Homo sapiens







Q96Q89
M-phase phosphoprotein 1, 
UniProt
IDA

PMID: 11470801




protein from Homo sapiens







Q9H2G4
CTCL tumor antigense 20-4, 
UniProt
IDA

PMID: 11395479




protein from Homo sapiens







Q9P1T7
HIC protein isoform p40,
UniProt
NAS

PMID: 10671520




protein from Homo sapiens







Q9UFR5
M-phase phosphoprotein 1, 
UniProt
ISS

UniProt: Q9UFR5




protein from Homo sapiens







RCL1 HUMAN
RNA 3′-terminal phosphate 
UniProt
NAS

UniProt: Q9Y2P8




cyclase-like protein, 








protein from Homo sapiens







DKC1 HUMAN
H/ACA ribonucleoprotein
UniProt
TAS

PMID: 10556300




complex subunit 4,








protein from Homo sapiens







IF16 HUMAN
Splice Isoform 2 of
UniProt
IDA

PMID: 14654789




Gamma-interferon-








inducible protein Ifi-16,








protein from Homo sapiens







RL35 HUMAN
60S ribosomal protein L35, 
UniProt
TAS

PMID: 2891103




protein from Homo sapiens







RL3 HUMAN
60S ribosomal protein L3, 
UniProt
TAS

PMID: 2891103




protein from Homo sapiens







RPF1 HUMAN
Ribosome production factor 
UniProt
IDA

PMID: 12429849




1, protein from Homo sapiens







RS7 HUMAN
40S ribosomal protein S7,
UniProt
IDA

PMID: 11823430




protein from Homo sapiens







S29A2 HUMAN
Solute carrier family 29
UniProt
TAS

PMID: 7639753




(Nucleoside transporters),








member 2, protein from








Homo sapiens







SRP68 HUMAN
Splice Isoform 1 of Signal
UniProt
TAS

PMID: 10618370




recognition particle 68 kDa








protein, protein from








Homo sapiens







SUH HUMAN
Splice Isoform APCR-2 of
UniProt
IDA

PMID: 9874765




Recombining binding








protein suppressor of hairless, 








protein from Homo sapiens







TCOF HUMAN
Treacle protein, protein
UniProt
IDA

PMID: 15249688




from Homo sapiens







UBF1 HUMAN
Splice Isoform UBF1 of
UniProt
TAS

PMID: 2330041




Nucleolar transcription factor 








1, protein from Homo sapiens







VCX1 HUMAN
Variable charge X-linked
UniProt
IEP

PMID: 12826317




protein 1, protein from








Homo sapiens







VCX3 HUMAN
Variable charge X-linked
UniProt
ISS

UniProt: Q9NNX9




protein 3, protein from








Homo sapiens







VCXC HUMAN
VCX-C protein, protein
UniProt
ISS

UniProt: Q9H321




from Homo sapiens







ZN239 HUMAN
Zinc finger protein 239,
UniProt
NR

UniProt: Q16600




protein from Homo sapiens







ZN274 HUMAN
Splice Isoform 1 of Zinc
UniProt
TAS

PMID: 10777669




finger protein 274,








protein from Homo sapiens







ZN330 HUMAN
Zinc finger protein 330,
UniProt
IDA

PMID: 10593942




protein from Homo sapiens







ZN346 HUMAN
Splice Isoform 1 of Zinc
UniProt
TAS

PMID: 10488071




finger protein 346,








protein from Homo sapiens







ZPR1 HUMAN
Zinc-finger protein ZPR1, 
UniProt
TAS

PMID: 9763455




protein from Homo sapiens







RPA1 HUMAN
DNA-directed RNA
UniProt
NAS

UniProt: O95602




polymerase I largest subunit, 








protein from Homo sapiens







RPA5 HUMAN
Splice Isoform 1 of DNA-
UniProt
TAS

PMID: 9540830




directed RNA polymerase








I 40 kDa polypeptide,








protein from Homo sapiens







SURF6 HUMAN
Surfeit locus protein 6,
UniProt
ISS

UniProt: O75683




protein from Homo sapiens







POP1 HUMAN
Ribonucleases P/MRP
UniProt
IDA

PMID: 8918471




protein subunit POP1,








protein from Homo sapiens







POP7 HUMAN
Ribonuclease P protein
UniProt
TAS

PMID: 9630247




subunit p20, protein from








Homo sapiens







RP30 HUMAN
Ribonuclease P protein
UniProt
TAS

PMID: 9630247




subunit p30, protein from








Homo sapiens







RPP38 HUMAN
Ribonuclease P protein
UniProt
TAS

PMID: 9630247




subunit p38, protein from








Homo sapiens







RPP40 HUMAN
Ribonuclease P protein
UniProt
TAS

PMID: 9630247




subunit p40, protein from








Homo sapiens







BAZ2A HUMAN
Hypothetical protein
UniProt
NAS

PMID: 10662543




DKFZp781B109, protein








from Homo sapiens







POP1 HUMAN
Ribonucleases P/MRP
UniProt
IDA

PMID: 8918471




protein subunit POP1,








protein from Homo sapiens







RP29 HUMAN
Ribonuclease P protein
UniProt
TAS

PMID: 10352175




subunit p29, protein from








Homo sapiens







O15446
Nucleolar fibrillar center
UniProt
TAS

PMID: 9426281




protein, protein from








Homo sapiens







MPP10 HUMAN
U3 small nucleolar
UniProt
NAS

PMID: 9450966




ribonucleoprotein protein








MPP10, protein from








Homo sapiens







NOLA2 HUMAN
H/ACA ribonucleoprotein
UniProt
ISS

UniProt: Q9NX24




complex subunit 2,








protein from Homo sapiens







NOLA3 HUMAN
H/ACA ribonucleoprotein
UniProt
TAS

PMID: 9843512




complex subunit 3,








protein from Homo sapiens







U3IP2 HUMAN
U3 small nucleolar RNA-
UniProt
TAS

PMID: 9418896




interacting protein 2,








protein from Homo sapiens







3MG HUMAN
Splice Isoform 1 of DNA-
UniProt
TAS

PMID: 10854423




3-methyladenine glycosylase, 








protein from Homo sapiens







ANX11 HUMAN
Annexin A11, protein
UniProt
NAS

PMID: 12577318




from Homo sapiens







ATF6A HUMAN
Cyclic AMP-dependent
UniProt
TAS

PMID: 10866666




transcription factor ATF-6








alpha, protein from Homo








sapiens







ATX3 HUMAN
Splice Isoform 1 of Machado-
UniProt
TAS

PMID: 9580663




Joseph disease protein 1, 








protein from Homo sapiens







CB80 HUMAN
80 kDa nuclear cap
UniProt
TAS

PMID: 7937105




binding protein, protein








from Homo sapiens







CBX1 HUMAN
Chromobox protein
UniProt
TAS

PMID: 9169582




homolog 1, protein from








Homo sapiens







CPSF3 HUMAN
Cleavage and polyadenylation
UniProt
TAS

PMID: 7969155




specificity factor, 73 kDa








subunit, protein from








Homo sapiens







DKC1 HUMAN
H/ACA ribonucleoprotein
UniProt
TAS

PMID: 10556300




complex subunit 4,








protein from Homo sapiens







DPOQ HUMAN
DNA polymerase theta,
UniProt
TAS

PMID: 10395804




protein from Homo sapiens







FMR1 HUMAN
Splice Isoform 6 of Fragile X 
UniProt
TAS

PMID: 10888599




mental retardation 1 protein,








protein from Homo sapiens







FUSIP HUMAN
Splice Isoform 1 of FUS-
UniProt
IDA

PMID: 11684676




interacting serine-








arginine-rich protein 1,








protein from Homo sapiens







GIT2 HUMAN
Splice Isoform 2 of ARF
UniProt
IDA

PMID: 10942595




GTPase-activating protein








GIT2, protein from Homo








sapiens







HNRPL HUMAN
Heterogeneous nuclear
UniProt
TAS

PMID: 2687284




ribonucleoprotein L isoform 








a, protein from Homo sapiens







HSP1 HUMAN
Sperm protamine P1,
UniProt
TAS

PMID: 2081589




protein from Homo sapiens







IF16 HUMAN
Splice Isoform 2 of
UniProt
IDA

PMID: 14654789




Gamma-interferon-








inducible protein Ifi-16,








protein from Homo sapiens







IMA2 HUMAN
Importin alpha-2 subunit,
UniProt
TAS

PMID: 7565597




protein from Homo sapiens







ISG20 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 9235947




Interferon-stimulated gene








20 kDa protein, protein








from Homo sapiens







LY10 HUMAN
Splice Isoform LYSp100-B of 
UniProt
TAS

PMID: 8695863




Nuclear body protein SP140, 








protein from Homo sapiens







MCRS1 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 9765390




Microspherule protein 1,








protein from Homo sapiens







MDM2 HUMAN
Splice Isoform Mdm2 of
UniProt
IDA

PMID: 10707090




Ubiquitin-protein ligase








E3 Mdm2, protein from








Homo sapiens







MK67I HUMAN
MKI67 FHA domain-
UniProt
IDA

PMID: 11342549




interacting nucleolar








phosphoprotein, protein








from Homo sapiens







MRE11 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 9651580




Double-strand break








repair protein MRE11A,








protein from Homo sapiens







NB6M HUMAN
Cell death-regulatory
UniProt
IDA

PMID: 10924506




protein GRIM19, protein








from Homo sapiens







NUP54 HUMAN
Nucleoporin 54 kDa variant, 
UniProt
TAS

PMID: 8707840




protein from Homo sapiens







NUP98 HUMAN
Splice Isoform 1 of Nuclear 
UniProt
TAS

PMID: 7736573




pore complex protein 








Nup98-Nup96 precursor, 








protein from Homo sapiens







OGG1 HUMAN
Splice Isoform 2A of N-
UniProt
TAS

PMID: 9223305




glycosylase/DNA lyase,








protein from Homo sapiens







P53 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 11080164




Cellular tumor antigen p53, 








protein from Homo sapiens










IDA

PMID: 12915590



PHB HUMAN
Prohibitin, protein from
UniProt
IDA

PMID: 12466959




Homo sapiens







PML HUMAN
Splice Isoform PML-1 of
UniProt
IDA

PMID: 12915590




Probable transcription








factor PML, protein from








Homo sapiens










TAS

PMID: 9294197



POLH HUMAN
Splice Isoform 1 of DNA
UniProt
TAS

PMID: 10385124




polymerase eta, protein








from Homo sapiens







POLI HUMAN
DNA polymerase iota,
UniProt
TAS

PMID: 10458907




protein from Homo sapiens







PPIG HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 9153302




Peptidyl-prolyl cis-trans








isomerase G, protein








from Homo sapiens







PRM2 HUMAN
Protamine-2, protein
UniProt
TAS

PMID: 2081589




from Homo sapiens







PTBP1 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 1641332




Polypyrimidine tract-








binding protein 1, protein








from Homo sapiens







Q8WYJ1
MDM2 protein, protein
UniProt
ISS

UniProt: Q8WYJ1




from Homo sapiens










IDA

PMID: 12915590



Q8WYJ2
MDM2 protein, protein
UniProt
ISS

UniProt: Q8WYJ2




from Homo sapiens







Q96Q89
M-phase phosphoprotein 1, 
UniProt
IDA

PMID: 11470801




protein from Homo sapiens







Q96SB3
Neurabin II protein,
UniProt
IMP

PMID: 11278317




protein from Homo sapiens







Q9UFR5
M-phase phosphoprotein 1, 
UniProt
ISS

UniProt: Q9UFR5




protein from Homo sapiens







Q9Y654
Heterochromatin-specific
UniProt
ISS

UniProt: Q9Y654




nonhistone protein,








protein from Homo sapiens







RECQ5 HUMAN
Splice Isoform Alpha of
UniProt
NAS

PMID: 10710432




ATP-dependent DNA








helicase Q5, protein from








Homo sapiens







RNPC2 HUMAN
Splice Isoform 2 of RNA-
UniProt
TAS

PMID: 8227358




binding region containing








protein 2, protein from








Homo sapiens







ROA1 HUMAN
Heterogeneous nuclear
UniProt
TAS

PMID: 8521471




ribonucleoprotein A1 isoform 








b, protein from Homo sapiens







RTC1 HUMAN
Splice Isoform 1 of RNA
UniProt
TAS

PMID: 9184239




3′-terminal phosphate cyclase, 








protein from Homo sapiens







SMCA2 HUMAN
Splice Isoform Long of
UniProt
TAS

PMID: 8670841




Possible global transcription 








activator SNF2L2, 








protein from Homo sapiens







SMCA4 HUMAN
Possible global transcription 
UniProt
TAS

PMID: 8208605




activator SNF2L4, 








protein from Homo sapiens







SMCA5 HUMAN
SWI/SNF-related matrix
UniProt
TAS

PMID: 9730600




associated actin dependent








regulator of chromatin








subfamily A member 5,








protein from Homo sapiens







SMRC1 HUMAN
SWI/SNF-related matrix-
UniProt
TAS

PMID: 8804307




associated actin-dependent 








regulator of chromatin 








subfamily C member 1, 








protein from Homo sapiens







SMRD2 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 8804307




SWI/SNF-related matrix-








associated actin-dependent 








regulator of chromatin 








subfamily D member 2, 








protein from Homo sapiens







SMRD3 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 8804307




SWI/SNF-related matrix-








associated actin-dependent 








regulator of chromatin 








subfamily D member 3, 








protein from Homo sapiens







SNF5 HUMAN
Splice Isoform A of
UniProt
TAS

PMID: 7801128




SWI/SNF related, matrix








associated, actin dependent 








regulator of chromatin 








subfamily B member 1, 








protein from Homo sapiens







SRR35 HUMAN
OTTHUMP00000016846,
UniProt
ISS

PMID: 11684676




protein from Homo sapiens







SYMPK HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 8769423




Symplekin, protein from








Homo sapiens







TDG HUMAN
G/T mismatch-specific
UniProt
TAS

PMID: 9489705




thymine DNA glycosylase, 








protein from Homo sapiens







TP53B HUMAN
Tumor suppressor p53-
UniProt
IDA

PMID: 9748285




binding protein 1, protein








from Homo sapiens







UNG2 HUMAN
Uracil-DNA glycosylase 2, 
UniProt
IDA

PMID: 12161446




protein from Homo sapiens







WDHD1 HUMAN
WD repeat and HMG-box
UniProt
TAS

PMID: 9175701




DNA binding protein 1,








protein from Homo sapiens







XPO1 HUMAN
Exportin-1, protein from
UniProt
TAS

PMID: 9368044




Homo sapiens







ZN638 HUMAN
Splice Isoform 1 of Zinc
UniProt
TAS

PMID: 8647861




finger protein 638,








protein from Homo sapiens







ESR1 HUMAN
Splice Isoform Long of
UniProt
NAS

PMID: 12351687




Estrogen receptor, protein








from Homo sapiens







Q9Y294
ASF1A protein, protein
UniProt
IDA

PMID: 10759893




from Homo sapiens







SMRD1 HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 9693044




SWI/SNF-related matrix-








associated actin-dependent 








regulator of chromatin 








subfamily D member 1, 








protein from Homo sapiens







CHRC1 HUMAN
Chromatin accessibility
UniProt
NAS

PMID: 10880450




complex protein 1,








protein from Homo sapiens







CAF1A HUMAN
Chromatin assembly
UniProt
TAS

PMID: 7600578




factor 1, subunit A,








protein from Homo sapiens







CAF1B HUMAN
Chromatin assembly
UniProt
TAS

PMID: 7600578




factor 1 subunit B,








protein from Homo sapiens







NP1L1 HUMAN
Nucleosome assembly
UniProt
TAS

PMID: 8297347




protein 1-like 1, protein








from Homo sapiens







NP1L2 HUMAN
Nucleosome assembly
UniProt
TAS

PMID: 8789438




protein 1-like 2, protein








from Homo sapiens







NP1L3 HUMAN
Nucleosome assembly
UniProt
TAS

PMID: 8976385




protein 1-like 3, protein








from Homo sapiens







NP1L4 HUMAN
Nucleosome assembly
UniProt
TAS

PMID: 9325046




protein 1-like 4, protein








from Homo sapiens







SIRT2 HUMAN
Splice Isoform 1 of NAD-
UniProt
NAS

PMID: 12697818




dependent deacetylase








sirtuin-2, protein from








Homo sapiens







HBXAP HUMAN
Remodeling and spacing
UniProt
IPI

PMID: 9836642




factoR 1, protein from








Homo sapiens







SMCA5 HUMAN
SWI/SNF-related matrix
UniProt
IPI

PMID: 9836642




associated actin dependent








regulator of chromatin








subfamily A member 5,








protein from Homo sapiens







ACL6B HUMAN
Actin-like protein 6B,
UniProt
ISS

UniProt: O94805




protein from Homo sapiens







ARI1A HUMAN
Splice Isoform 1 of AT-
UniProt
ISS

UniProt: O14497




rich interactive domain-








containing protein 1A,








protein from Homo sapiens










IDA

PMID: 9584200



ARI1B HUMAN
Splice Isoform 1 of AT-
UniProt
IDA

PMID: 11734557




rich interactive domain-








containing protein 1B,








protein from Homo sapiens







NCTR1 HUMAN
Splice Isoform 1 of Natural 
UniProt
ISS

UniProt: O76036




cytotoxicity triggering 








receptor 1 precursor, 








protein from Homo sapiens







SMRC1 HUMAN
SWI/SNF-related matrix-
UniProt
IDA

PMID: 10078207




associated actin-dependent 








regulator of chromatin 








subfamily C member 1, 








protein from Homo sapiens







SMRC2 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 10078207




SWI/SNF-related matrix-








associated actin-dependent 








regulator of chromatin 








subfamily C member 2, 








protein from Homo sapiens







SMRD3 HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 14701856




SWI/SNF-related matrix-








associated actin-dependent 








regulator of chromatin 








subfamily D member 3, 








protein from Homo sapiens







HCLS1 HUMAN
Hematopoietic lineage
UniProt
TAS

PMID: 2587259




cell-specific protein,








protein from Homo sapiens







MED21 HUMAN
Mediator of RNA polymerase 
UniProt
TAS

PMID: 8598913




II transcription subunit 21,








protein from Homo sapiens







PRGC1 HUMAN
Peroxisome proliferator-
UniProt
TAS

PMID: 12588810




activated receptor gamma








coactivator 1-alpha,








protein from Homo sapiens







Q15161
POLR2 protein, protein
UniProt
NAS

PMID: 3145407




from Homo sapiens







Q99590
SRrp129 protein, protein
UniProt
TAS

PMID: 9224939




from Homo sapiens







RMP HUMAN
RNA polymerase II
UniProt
TAS

PMID: 9819440




subunit 5-mediating protein, 








protein from Homo sapiens







RPB11 HUMAN
RPB11a protein, protein
UniProt
TAS

PMID: 8797801




from Homo sapiens







RPB1 HUMAN
DNA-directed RNA
UniProt
TAS

PMID: 2999107




polymerase II largest subunit, 








protein from Homo sapiens







RPB2 HUMAN
DNA-directed RNA
UniProt
TAS

PMID: 1518060




polymerase II 140 kDa








polypeptide, protein from








Homo sapiens







RPB3 HUMAN
DNA-directed RNA
UniProt
NR

UniProt: P19387




polymerase II 33 kDa








polypeptide, protein from








Homo sapiens







RPB4 HUMAN
DNA-directed RNA 
UniProt
IC

PMID: 9528765




polymerase II 16 kDa








polypeptide, protein from








Homo sapiens







RPB5 HUMAN
DNA-directed RNA
UniProt
TAS

PMID: 7828586




polymerase II 23 kDa








polypeptide, protein from








Homo sapiens







RPB9 HUMAN
DNA-directed RNA
UniProt
NR

UniProt: P36954




polymerase II 14.5 kDa








polypeptide, protein from








Homo sapiens







RPC10 HUMAN
DNA-directed RNA
UniProt
NR

UniProt: P53803




polymerases I, II, and III








7.0 kDa polypeptide,








protein from Homo sapiens







ZN148 HUMAN
Zinc finger protein 148,
UniProt
TAS

PMID: 8355710




protein from Homo sapiens







ZN281 HUMAN
Zinc finger protein 281,
UniProt
TAS

PMID: 10448078




protein from Homo sapiens







BCL6 HUMAN
B-cell lymphoma 6 protein, 
UniProt
NR

UniProt: P41182




protein from Homo sapiens







CDK8 HUMAN
Cell division protein kinase 8, 
UniProt
IDA

PMID: 14638676




protein from Homo sapiens







CRSP2 HUMAN
CRSP complex subunit 2,
UniProt
IDA

PMID: 10198638




protein from Homo sapiens







CRSP6 HUMAN
CRSP complex subunit 6,
UniProt
IDA

PMID: 10198638




protein from Homo sapiens







MED12 HUMAN
Mediator of RNA polymerase 
UniProt
IDA

PMID: 10198638




II transcription subunit 12,








protein from Homo sapiens







MED21 HUMAN
Mediator of RNA polymerase 
UniProt
IDA

PMID: 12037571




II transcription subunit 21,








protein from Homo sapiens







MED4 HUMAN
Mediator complex subunit 4, 
UniProt
IEP

PMID: 10882111




protein from Homo sapiens







MED6 HUMAN
RNA polymerase
UniProt
IDA

PMID: 14638676




transcriptional regulation








mediator, subunit 6 homolog,








protein from Homo sapiens










IDA

PMID: 12037571



MED8 HUMAN
Splice Isoform 1 of Mediator 
UniProt
IDA

PMID: 14638676




of RNA polymerase II








transcription subunit 8








homolog, protein from








Homo sapiens







PPRB HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 10198638




Peroxisome proliferator-








activated receptor-binding








protein, protein from








Homo sapiens







Q5XX09
Intersex-like protein,
UniProt
IDA

PMID: 14638676




protein from Homo sapiens







Q8TDE4
PGC-1-related estrogen
UniProt
IDA

PMID: 11854298




receptor alpha coactivator








short isoform, protein








from Homo sapiens







Q96HR3
TRAP/Mediator complex
UniProt
IDA

PMID: 10198638




component TRAP25,








protein from Homo sapiens







Q9BUE0
MED18 protein, protein
UniProt
IDA

PMID: 14638676




from Homo sapiens







Q9P086
Similar to HSPC296,
UniProt
IDA

PMID: 14638676




protein from Homo sapiens







RBM14 HUMAN
Splice Isoform 1 of RNA-
UniProt
NAS

PMID: 11443112




binding protein 14,








protein from Homo sapiens







SURF5 HUMAN
Splice Isoform Surf5A of
UniProt
IDA

PMID: 14638676




Surfeit locus protein 5,








protein from Homo sapiens







TR100 HUMAN
Thyroid hormone receptor-
UniProt
NAS

PMID: 9653119




associated protein 








complex 100 kDa component, 








protein from Homo sapiens







TR150 HUMAN
Thyroid hormone receptor-
UniProt
IDA

PMID: 10198638




associated protein complex 








150 kDa component, 








protein from Homo sapiens







TR240 HUMAN
Thyroid hormone
UniProt
IDA

PMID: 10198638




receptor-associated protein 








complex 240 kDa component,








protein from Homo sapiens







TR95 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 10198638




Thyroid hormone








receptor-associated protein 








complex 95 kDa component, 








protein from Homo sapiens







TRFP HUMAN
TRF-proximal protein
UniProt
NAS

PMID: 9933582




homolog, protein from








Homo sapiens







T2AG HUMAN
Transcription initiation
UniProt
NAS

PMID: 7958900




factor IIA gamma chain,








protein from Homo sapiens







TF2AA HUMAN
Transcription initiation
UniProt
NR

UniProt: P52655




factor IIA subunit 1,








protein from Homo sapiens






colocalizes_with
EDF1 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 12040021




Endothelial differentiation-








related factor 1, protein from








Homo sapiens







O43604
Cofactor of initiator function, 
UniProt
TAS

PMID: 9418870




protein from Homo sapiens







Q7Z7C8
OTTHUMP00000016392,
UniProt
IDA

PMID: 14580349




protein from Homo sapiens







Q9BQS9
TAF3 RNA polymerase II, 
UniProt
IDA

PMID: 11438666




TATA box binding protein, 








protein from Homo sapiens







RBP56 HUMAN
Splice Isoform Long of
UniProt
NR

UnitProt: Q92804




TATA-binding protein








associated factor 2N,








protein from Homo sapiens







TAF10 HUMAN
Transcription initiation
UniProt
IDA

PMID: 14580349




factor TFIID subunit 10,








protein from Homo sapiens







TAF11 HUMAN
Transcription initiation
UniProt
IDA

PMID: 14580349




factor TFIID subunit 11,








protein from Homo sapiens







TAF12 HUMAN
Transcription initiation
UniProt
IDA

PMID: 14580349




factor TFIID subunit 12,








protein from Homo sapiens







TAF13 HUMAN
Transcription initiation
UniProt
TAS

PMID: 7729427




factor TFIID subunit 13,








protein from Homo sapiens







TAF1 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 7680771




Transcription initiation








factor TFIID subunit 1,








protein from Homo sapiens







TAF1L HUMAN
Transcription initiation
UniProt
ISS

PMID: 12217962




factor TFIID 210 kDa subunit, 








protein from Homo sapiens







TAF4 HUMAN
Transcription initiation
UniProt
IDA

PMID: 14580349




factor TFIID subunit 4,








protein from Homo sapiens







TAF5 HUMAN
Splice Isoform Long of
UniProt
IDA

PMID: 14580349




Transcription initiation








factor TFIID subunit 5,








protein from Homo sapiens







TAF6 HUMAN
Transcription initiation
UniProt
IDA

PMID: 14580349




factor TFIID subunit 6,








protein from Homo sapiens







TAF7 HUMAN
Transcription initiation
UniProt
IDA

PMID: 14580349




factor TFIID subunit 7,








protein from Homo sapiens







TAF9 HUMAN
Transcription initiation
UniProt
IDA

PMID: 14580349




factor TFIID subunit 9,








protein from Homo sapiens







TBP HUMAN
TATA-box binding protein, 
UniProt
IDA

PMID: 14580349




protein from Homo sapiens







TAF6 HUMAN
Transcription initiation
UniProt
TAS

PMID: 7667268




factor TFIID subunit 6,








protein from Homo sapiens







T2FA HUMAN
Transcription initiation
UniProt
TAS

PMID: 1734283




factor IIF alpha subunit,








protein from Homo sapiens







ERCC2 HUMAN
TFIIH basal transcription
UniProt
TAS

PMID: 7663514




factor complex helicase








subunit, protein from








Homo sapiens







ERCC3 HUMAN
TFIIH basal transcription
UniProt
TAS

PMID: 7663514




factor complex helicase








XPB subunit, protein








from Homo sapiens







TF2H1 HUMAN
TFIIH basal transcription
UniProt
TAS

PMID: 9118947




factor complex p62 subunit, 








protein from Homo sapiens







TF2H2 HUMAN
TFIIH basal transcription
UniProt
NR

UniProt: Q13888




factor complex p44 subunit, 








protein from Homo sapiens







TF2H3 HUMAN
TFIIH basal transcription
UniProt
NAS

UniProt: Q13889




factor complex p34 subunit, 








protein from Homo sapiens







TF2H4 HUMAN
TFIIH basal transcription
UniProt
TAS

PMID: 9118947




factor complex p52 subunit, 








protein from Homo sapiens







RPC10 HUMAN
DNA-directed RNA
UniProt
NR

UniProt: P53803




polymerases I, II, and III








7.0 kDa polypeptide,








protein from Homo sapiens







RPC11 HUMAN
DNA-directed RNA
UniProt
TAS

PMID: 9869639




polymerases III 12.5 kDa








polypeptide, protein from








Homo sapiens







RPC1 HUMAN
DNA-directed RNA
UniProt
NAS

UniProt: O14802




polymerase III largest subunit, 








protein from Homo sapiens







RPC62 HUMAN
DNA-directed RNA
UniProt
TAS

PMID: 9171375




polymerase III 62 kDa








polypeptide, protein from








Homo sapiens







RPC6 HUMAN
DNA-directed RNA
UniProt
NAS

PMID: 10623476




polymerase III 39 kDa








polypeptide, protein from








Homo sapiens







RPC7 HUMAN
DNA-directed RNA
UniProt
TAS

PMID: 9171375




polymerase III 32 kDa








polypeptide, protein from








Homo sapiens







RPC8 HUMAN
Splice Isoform 1 of DNA-
UniProt
IDA

PMID: 12391170




directed RNA polymerase








III subunit 22.9 kDa








polypeptide, protein from








Homo sapiens







MEN1 HUMAN
Splice Isoform 1 of Menin, 
UniProt
IDA

PMID: 14992727




protein from Homo sapiens







NSD1 HUMAN
Splice Isoform 1 of
UniProt
ISS

UniProt: Q96L73




Histone-lysine N-








methyltransferase, H3








lysine-36 and H4 lysine-








20 specific, protein from








Homo sapiens







PCF11 HUMAN
Pre-mRNA cleavage
UniProt
NAS

PMID: 11060040




comPlex II Protein Pcf11,








protein from Homo sapiens







CPSF1 HUMAN
Cleavage and polyadenylation
UniProt
IDA

PMID: 7590244




specificity factor, 160 kDa








subunit, protein from








Homo sapiens







GEMI5 HUMAN
Gem-associated protein 5, 
UniProt
IDA

PMID: 11714716




protein from Homo sapiens







GEMI6 HUMAN
Gem-associated protein 6, 
UniProt
IDA

PMID: 11748230




protein from Homo sapiens







GEMI7 HUMAN
Gem-associated protein 7,
UniProt
IDA

PMID: 12065586




protein from Homo sapiens







HIPK2 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 14626429




Homeodomain-interacting








protein kinase 2, protein








from Homo sapiens







Q9Y474
Zinc-finger motif-enhancer 
UniProt
TAS

PMID: 9305772




binding-protein-1, 








protein from Homo sapiens







Q8WWY3
U4/U6 snRNP-associated
UniProt
IDA

PMID: 11867543




61 kDa protein, protein








from Homo sapiens







SMN HUMAN
Splice Isoform SMN of
UniProt
NAS

PMID: 9845364




Survival motor neuron








protein, protein from








Homo sapiens










NAS

PMID: 8670859



U2AF1 HUMAN
Splicing factor U2AF 35 kDa
UniProt
TAS

PMID: 1388271




subunit, protein from








Homo sapiens







Q8WWY3
U4/U6 snRNP-associated
UniProt
IDA

PMID: 11867543




61 kDa protein, protein








from Homo sapiens







ZBT16 HUMAN
Splice Isoform PLZFB of
UniProt
IDA

PMID: 8541544




Zinc finger and BTB domain-








containing protein 16, 








protein from Homo sapiens







ELF4 HUMAN
ETS-related transcription
UniProt
IDA

PMID: 14970218




factor Elf-4, protein from








Homo sapiens







HIPK3 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 11034606




Homeodomain-interacting








protein kinase 3, protein








from Homo sapiens







ISG20 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 9235947




Interferon-stimulated gene








20 kDa protein, protein








from Homo sapiens






colocalizes_with
PML HUMAN
Splice Isoform PML-1 of
UniProt
IDA

PMID: 10910364




Probable transcription








factor PML, protein from








Homo sapiens










TAS

PMID: 9294197


not
SFRS2 HUMAN
Splicing factor,
UniProt
IDA

PMID: 15652350




arginine/serine-rich 2,








protein from Homo sapiens







SP100 HUMAN
Splice Isoform Sp100-
UniProt
TAS

PMID: 9230084




HMG of Nuclear








autoantigen Sp-100,








protein from Homo sapiens







SPTN4 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 11294830




Spectrin beta chain, brain 3, 








protein from Homo sapiens







NXF2 HUMAN
Nuclear RNA export factor 2, 
UniProt
NAS

PMID: 11073998




protein from Homo sapiens







NXF3 HUMAN
Nuclear RNA export factor 3, 
UniProt
IDA

PMID: 11545741




protein from Homo sapiens







CDK9 HUMAN
Splice Isoform 1 of Cell
UniProt
TAS

PMID: 10866664




division protein kinase 9,








protein from Homo sapiens







ELL2 HUMAN
RNA polymerase II
UniProt
TAS

PMID: 9108030




elongation factor ELL2,








protein from Homo sapiens







ELL3 HUMAN
RNA polymerase II
UniProt
NAS

PMID: 10882741




elongation factor ELL3,








protein from Homo sapiens







TCEA2 HUMAN
Transcription elongation
UniProt
NAS

PMID: 8566795




factor A protein 2,








protein from Homo sapiens







CRSP3 HUMAN
Splice Isoform 1 of CRSP
UniProt
IDA

PMID: 9989412




complex subunit 3,








protein from Homo sapiens







CRSP6 HUMAN
CRSP complex subunit 6,
UniProt
IDA

PMID: 9989412




protein from Homo sapiens







CSP9 HUMAN
Cofactor required for Sp1
UniProt
IDA

PMID: 9989412




transcriptional activation








subunit 9, protein from








Homo sapiens







FOXE3 HUMAN
Forkhead box protein E3,
UniProt
IDA

PMID: 10652278




protein from Homo sapiens







FOXF1 HUMAN
Forkhead box protein F1,
UniProt
TAS

PMID: 9722567




protein from Homo sapiens







FOXF2 HUMAN
Forkhead box protein F2,
UniProt
TAS

PMID: 9722567




protein from Homo sapiens







HES6 HUMAN
Splice Isoform 1 of
UniProt
ISS

PMID: 10851137




Transcription cofactor HES-6, 








protein from Homo sapiens







KU70 HUMAN
ATP-dependent DNA
UniProt
IDA

PMID: 12145306




helicase II, 70 kDa subunit, 








protein from Homo sapiens







LMO4 HUMAN
LIM domain transcription
UniProt
ISS

UniProt: P61968




factor LMO4, protein








from Homo sapiens







NARG1 HUMAN
Splice Isoform 1 of NMDA 
UniProt
IDA

PMID: 12145306




receptor regulated protein 1, 








protein from Homo sapiens







NARGL HUMAN
Splice Isoform 1 of NMDA 
UniProt
ISS

UniProt: Q6N069




receptor regulated 1-like 








protein, protein








from Homo sapiens







NCOA6 HUMAN
Nuclear receptor coactivator 
UniProt
TAS

PMID: 11443112




6, protein from Homo sapiens







NKX2S HUMAN
Homeobox protein Nkx-2.5, 
UniProt
ISS

UniProt: P52952




protein from Homo sapiens







Q9UBQ3
Polyamine-modulated factor 
UniProt
TAS

PMID: 10419538




1, protein from Homo sapiens







Q9UKB0
High mobility group 
UniProt
TAS

PMID: 10428834




protein-R, protein from








Homo sapiens







Q9Y6Y0
Influenza vIrus NS1A
UniProt
TAS

PMID: 9696811




binding protein; NS1-








binding protein; likely








ortholog of mouse kelch








family protein Nd1,








protein from Homo sapiens







RBM14 HUMAN
Splice Isoform 1 of RNA-
UniProt
IPI

PMID: 11443112




binding protein 14,








protein from Homo sapiens







SMAD2 HUMAN
Splice Isoform Long of
UniProt
ISS

UniProt: Q15796




Mothers against








decapentaplegic homolog 2, 








protein from Homo sapiens







TCP4 HUMAN
Activated RNA polymerase 
UniProt
IDA

PMID: 8062391




II transcriptional coactivator








p15, protein from Homo








sapiens







TF65 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 12048232




Transcription factor p65,








protein from Homo sapiens







WBS14 HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 11230181




Williams-Beuren 








syndrome chromosome








region 14 protein, protein








from Homo sapiens







ING2 HUMAN
Inhibitor of growth protein 
UniProt
IDA

PMID: 15243141




2, protein from Homo sapiens







NFYA HUMAN
Splice Isoform Long of
UniProt
IDA

PMID: 15243141




Nuclear transcription








factor Y subunit alpha,








protein from Homo sapiens







NFYB HUMAN
Nuclear transcription
UniProt
IDA

PMID: 15243141




factor Y subunit beta,








protein from Homo sapiens







NFYC HUMAN
Splice Isoform 3 of
UniProt
IDA

PMID: 15243141




Nuclear transcription








factor Y subunit gamma,








protein from Homo sapiens







CNOT7 HUMAN
CCR4-NOT transcription
UniProt
NAS

PMID: 9820826




complex subumt 7,








protein from Homo sapiens







TRRAP HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 9885574




Transformation/transcription








domain-associated protein, 








protein from Homo sapiens







ACL6A HUMAN
Splice Isoform 1 of Actin-
UniProt
IDA

PMID: 10966108




like protein 6A, protein








from Homo sapiens







ACTB HUMAN
Actin, cytoplasmic 1,
UniProt
IDA

PMID: 10966108




protein from Homo sapiens







RUVB1 HUMAN
RuvB-like 1, protein from
UniProt
IDA

PMID: 10966108




Homo sapiens







RUVB2 HUMAN
RuvB-like 2, protein from
UniProt
IDA

PMID: 10966108




Homo sapiens







TIP60 HUMAN
Splice Isoform 1 of Histone 
UniProt
IDA

PMID: 10966108




acetyltransferase HTATIP, 








protein from Homo sapiens







TRRAP HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 10966108




Transformation/transcription








domain-associated protein,








protein from Homo sapiens







HDA10 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 11861901




Histone deacetylase 10,








protein from Homo sapiens







HDA11 HUMAN
Histone deacetylase 11,
UniProt
IDA

PMID: 11948178




protein from Homo sapiens







HDAC1 HUMAN
Histone deacetylase 1,
UniProt
TAS

PMID: 12711221




protein from Homo sapiens







HDAC2 HUMAN
Histone deacetylase 2,
UniProt
TAS

PMID: 12711221




protein from Homo sapiens







HDAC3 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 12711221




Histone deacetylase 3,








protein from Homo sapiens







HDAC4 HUMAN
Histone deacetylase 4,
UniProt
TAS

PMID: 12711221




protein from Homo sapiens







HDAC5 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 12711221




Histone deacetylase 5,








protein from Homo sapiens







HDAC6 HUMAN
Histone deacetylase 6,
UniProt
IDA

PMID: 11948178




protein from Homo sapiens







HDAC7 HUMAN
Histone deacetylase,
UniProt
TAS

PMID: 12711221




protein from Homo sapiens







HDAC8 HUMAN
Splice Isoform 3 of
UniProt
TAS

PMID: 12711221




Histone deacetylase 8,








protein from Homo sapiens







HDAC9 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 12711221




Histone deacetylase 9,








protein from Homo sapiens







MTA2 HUMAN
Metastasis-associated
UniProt
TAS

PMID: 10444591




protein MTA2, protein








from Homo sapiens







SAP18 HUMAN
Sin3 associated
UniProt
TAS

PMID: 9150135




polypeptide p18, protein








from Homo sapiens







SAP30 HUMAN
Histone deacetylase
UniProt
TAS

PMID: 9651585




complex subunit SAP30,








protein from Homo sapiens







TAF6L HUMAN
TAF6-like RNA
UniProt
TAS

PMID: 9674425




polymerase II p300/CBP-








associated factor-associated 








factor 65 kDa subunit 6L, 








protein from Homo sapiens






colocalizes_with
DP13A HUMAN
DCC-interacting protein
UniProt
IDA

PMID: 15016378




13 alpha, protein from








Homo sapiens






colocalizes_with
DP13B HUMAN
DCC-interacting protein
UniProt
IDA

PMID: 15016378




13 beta, protein from








Homo sapiens







P66A HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 12183469




Transcriptional repressor








p66 alpha, protein from








Homo sapiens










ISS

UniProt: Q96F28



SDS3 HUMAN
Sin3 histone deacetylase
UniProt
ISS

PMID: 11909966




corepressor complex








component SDS3, protein








from Homo sapiens







Q16219
Insulin activator factor,
UniProt
NAS

PMID: 7935390




protein from Homo sapiens







TF3B HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 20380946




Transcription factor IIIB








90 kDa subunit, protein








from Homo sapiens










NAS

PMID: 8943358



TF3C1 HUMAN
Splice Isoform 1 of
UniProt
NR

UniProt: Q12789




General transcription








factor 3C polypeptide 1,








protein from Homo sapiens







TF3C2 HUMAN
G-protein beta WD-40
UniProt
NR

UniProt: Q8WUA4




repeat containing protein,








protein from Homo sapiens







TF3C3 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 10373544




General transcription








factor 3C polypeptide 3,








protein from Homo sapiens







TF3C4 HUMAN
General transcription
UniProt
TAS

PMID: 10523658




factor 3C polypeptide 4,








protein from Homo sapiens







TF3C5 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 10373544




General transcription








factor 3C polypeptide 5,








protein from Homo sapiens







ARI4A HUMAN
Splice Isoform I of AT-
UniProt
IPI

PMID: 12724404




rich interactive domain-








containing protein 4A,








protein from Homo sapiens










IDA

PMID: 11283269



JAZF1 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 15302918




Juxtaposed with another








zinc finger protein 1,








protein from Homo sapiens







PHF12 HUMAN
Splice Isoform 2 of PHD
UniProt
IDA

PMID: 11390640




finger protein 12, protein








from Homo sapiens







Q9HAQ4
Zinc finger protein 350,
UniProt
IDA

PMID: 11090615




protein from Homo sapiens







RNF12 HUMAN
RING finger protein 12,
UniProt
NAS

PMID: 11013082




protein from Homo sapiens







SMCE1 HUMAN
Splice Isoform 1 of
UniProt
IPI

PMID: 12192000




SWI/SNF-related matrix-








associated actin-dependent 








regulator of chromatin 








subfamily E member 1, 








protein from Homo sapiens






colocalizes_with
SMRC2 HUMAN
Splice Isoform 1 of
UniProt
IPI

PMID: 12192000




SWI/SNF-related matrix-








associated actin-dependent 








regulator of chromatin 








subfamily C member 2, 








protein from Homo sapiens







ZBT16 HUMAN
Splice Isoform PLZFB of
UniProt
IDA

PMID: 12802276




Zinc finger and BTB








domain-containing protein 16, 








protein from Homo sapiens







DPOLZ HUMAN
DNA polymerase zeta
UniProt
NR

UNIPROT: O60673




catalytic subunit, protein








from Homo sapiens







ANC4 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 9469815




Anaphase promoting








complex subunit 4,








protein from Homo sapiens







ANC5 HUMAN
Splice Isoform 1 of Anaphase 
UniProt
TAS

PMID: 9469815




promoting complex subunit 5,








protein from Homo sapiens







APC10 HUMAN
Anaphase promoting
UniProt
NAS

PMID: 10318877




complex subunit 10,








protein from Homo sapiens







APC11 HUMAN
Splice Isoform 1 of Anaphase 
UniProt
IDA

PMID: 11739784




promoting 








complex subunit 11,








protein from Homo sapiens







APC7 HUMAN
Anaphase promoting
UniProt
NR

UniProt: Q9UJX3




complex subunit 7,








protein from Homo sapiens







BUB1B HUMAN
Mitotic checkpoint
UniProt
TAS

PMID: 10477750




serine/threonine-protein








kinase BUB1 beta,








protein from Homo sapiens







CDC23 HUMAN
Splice Isoform 1 of Cell
UniProt
IDA

PMID: 14657031




division cycle protein 23








homolog, protein from








Homo sapiens







CDC27 HUMAN
Protein CDC27Hs,
UniProt
NR

UniProt: P30260




protein from Homo sapiens







CUL7 HUMAN
Cullin-7, protein from
UniProt
NAS

PMID: 12481031




Homo sapiens







FZR HUMAN
Splice Isoform 1 of Fizzy-
UniProt
TAS

PMID: 9734353




related protein homolog,








protein from Homo sapiens







Q8NHZ8
CDC26 subunit of anaphase 
UniProt
IDA

PMID: 10922056




promoting complex, 








protein from Homo sapiens







BARD1 HUMAN
BRCA1-associated RING
UniProt
IDA

PMID: 15265711




domain protein 1, protein








from Homo sapiens







BRCA1 HUMAN
Breast cancer type 1
UniProt
IDA

PMID: 15265711




susceptibility protein,








protein from Homo sapiens







ERCC1 HUMAN
DNA excision repair
UniProt
IDA

PMID: 3290851




protein ERCC-1, protein








from Homo sapiens







ERCC4 HUMAN
Excision rEpair cross-
UniProt
IDA

PMID: 10644440




complEmEnting rodEntr








Epair dEficiEncy,








complEmEntation group 4, 








protein from Homo sapiens







ERCC8 HUMAN
Splice Isoform 1 of DNA
UniProt
IDA

PMID: 12732143




excision repair protein








ERCC-8, protein from








Homo sapiens







CSN2 HUMAN
Splice Isoform 1 of COP9
UniProt
IDA

PMID: 9535219




signalosome complex subunit 








2, protein from Homo sapiens







GEMI4 HUMAN
Component of gems 4,
UniProt
TAS

PMID: 10725331




protein from Homo sapiens







LSM6 HUMAN
U6 snRNA-associated
UniProt
TAS

PMID: 10523320




Sm-like protein LSm6,








protein from Homo sapiens







RSMB HUMAN
Splice Isoform SM-B′ of
UniProt
TAS

PMID: 2531083




Small nuclear








ribonucleoprotein








associated proteins B and B′, 








protein from Homo sapiens







RUXE HUMAN
Small nuclear
UniProt
NAS

PMID: 2974536




ribonucleoprotein E,








protein from Homo sapiens







RSMB HUMAN
Splice Isoform SM-B′ of
UniProt
TAS

PMID: 2531083




Small nuclear








ribonucleoprotein








associated proteins B and B′, 








protein from Homo sapiens







RUXE HUMAN
Small nuclear
UniProt
NAS

PMID: 2974536




ribonucleoprotein E,








protein from Homo sapiens







RUXG HUMAN
Small nuclear
UniProt
NAS

PMID: 7744013




ribonucleoprotein G,








protein from Homo sapiens







SF3A2 HUMAN
Splicing factor 3A subunit 2, 
UniProt
TAS

PMID: 8211113




protein from Homo sapiens







SF3B3 HUMAN
Splicing factor 3B subunit 3, 
UniProt
TAS

PMID: 10490618




protein from Homo sapiens







U3IP2 HUMAN
U3 small nucleolar RNA-
UniProt
TAS

PMID: 9418896




interacting protein 2,








protein from Homo sapiens







RU1C HUMAN
U1 small nuclear
UniProt
TAS

PMID: 2971157




ribonucleoprotein C,








protein from Homo sapiens







SNRPA HUMAN
U1 small nuclear
UniProt
NR

UniProt: P09012




ribonucleoprotein A,








protein from Homo sapiens







PHF5A HUMAN
PHD finger-like domain
UniProt
IDA

PMID: 12234937




protein 5A, protein from








Homo sapiens







RU2A HUMAN
U2 small nuclear
UniProt
TAS

PMID: 2928112




ribonucleoprotein A′,








protein from Homo sapiens







RU2B HUMAN
U2 small nuclear
UniProt
TAS

PMID: 2951739




ribonucleoprotein B′′,








protein from Homo sapiens







LSM4 HUMAN
U6 snRNA-associated
UniProt
TAS

PMID: 10369684




Sm-like protein LSm4,








protein from Homo sapiens







Q8WWY3
U4/U6 snRNP-associated
UniProt
IDA

PMID: 11867543




61 kDa protein, protein








from Homo sapiens







API5 HUMAN
Splice Isoform 1 of
UniProt
ISS

PMID: 11555636




Apoptosis inhibitor 5,








protein from Homo sapiens







BCAS2 HUMAN
Breast carcinoma
UniProt
IDA

PMID: 12169396




amplified sequence 2,








protein from Homo sapiens







DHX8 HUMAN
ATP-dependent RNA
UniProt
TAS

PMID: 7935475




helicase DHX8, protein








from Homo sapiens







GEMI2 HUMAN
Splice Isoform 1 of
UniProt
TAS

PMID: 9323129




Survival of motor neuron








protein-interacting protein








1, protein from Homo sapiens







PPIH HUMAN
Peptidyl-prolyl cis-trans
UniProt
TAS

PMID: 9570313




isomerase H, protein








from Homo sapiens







PRP17 HUMAN
Pre-mRNA splicing factor
UniProt
TAS

PMID: 9524131




PRP17, protein from








Homo sapiens







PRP18 HUMAN
Splice Isoform 1 of Pre-
UniProt
TAS

PMID: 9000057




mRNA splicing factor 18,








protein from Homo sapiens







PRP4 HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 9328476




U4/U6 small nuclear








ribonucleoprotein Prp4,








protein from Homo sapiens







PRPF3 HUMAN
Splice Isoform 1 of
UniProt
NAS

PMID: 9328476




U4/U6 small nuclear








ribonucleoprotein Prp3,








protein from Homo sapiens







PRPU HUMAN
U5 snRNP-associated 102 kDa
UniProt
NAS

PMID: 10788320




protein, protein from








Homo sapiens







Q9Y6Y0
Influenza vIrus NS1A
UniProt
TAS

PMID: 9696811




binding protein; NS1-








binding protein; likely








ortholog of mouse kelch








family protein Nd1,








protein from Homo sapiens







RSMB HUMAN
Splice Isoform SM-B′ of
UniProt
TAS

PMID: 2531083




Small nuclear








ribonucleoprotein








associated proteins B and B′, 








protein from Homo sapiens







RUXE HUMAN
Small nuclear
UniProt
NAS

PMID: 2974536




ribonucleoprotein E,








protein from Homo sapiens







RUXG HUMAN
Small nuclear
UniProt
TAS

PMID: 7744013




ribonucleoprotein G,








protein from Homo sapiens







SF3A2 HUMAN
Splicing factor 3A subunit 2, 
UniProt
TAS

PMID: 8211113




protein from Homo sapiens







SF3A3 HUMAN
Splicing factor 3A subunit 3, 
UniProt
TAS

PMID: 8022796




protein from Homo sapiens







SF3B1 HUMAN
Splicing factor 3B subunit 1, 
UniProt
NAS

PMID: 9585501




protein from Homo sapiens







SF3B2 HUMAN
Splicing factor 3B Subunit 2, 
UniProt
TAS

PMID: 8566756




protein from Homo sapiens







SF3B3 HUMAN
Splicing factor 3B subunit 3, 
UniProt
TAS

PMID: 10490618




protein from Homo sapiens







SF3B4 HUMAN
Splicing factor 3B subunit 4, 
UniProt
TAS

PMID: 7958871




protein from Homo sapiens







SNW1 HUMAN
Nuclear protein Skip,
UniProt
IDA

PMID: 15194481




protein from Homo sapiens







SPF30 HUMAN
Survival of motor neuron-
UniProt
TAS

PMID: 9731529




related splicing factor 30,








protein from Homo sapiens







TXN4A HUMAN
Thioredoxin-like protein 4A, 
UniProt
TAS

PMID: 10610776




protein from Homo sapiens







U520 HUMAN
U5 small nuclear
UniProt
IDA

PMID: 8670905




ribonucleoprotein 200 kDa








helicase, protein








from Homo sapiens







U5S1 HUMAN
116 kDa U5 small nuclear
UniProt
TAS

PMID: 9233818




ribonucleoprotein








component, protein from








Homo sapiens







DKC1 HUMAN
H/ACA ribonucleoprotein
UniProt
IDA

PMID: 12135483




complex subunit 4,








protein from Homo sapiens







TEBP HUMAN
Telomerase-binding
UniProt
IDA

PMID: 12135483




protein p23, protein from








Homo sapiens







TEP1 HUMAN
Splice Isoform 1 of
UniProt
IDA

PMID: 12135483




Telomerase protein 








component 1, protein








from Homo sapiens







TERT HUMAN
Telomerase reverse
UniProt
IDA

PMID: 12135483




transcriptase, protein








from Homo sapiens
















TABLE 2







Proteins With a Known Function in Splicing and RNA Processing









Acc. no.a
Name
Comments





snRNP core proteins




SWISS-PROT: Q15357a
Sm G



SWISS-PROT: Q15356
Sm F



SWISS-PROT: P08578
Sm E



SWISS-PROT: P13641
Sm D1



SWISS-PROT: P43330
Sm D2



SWISS-PROT: P43331
Sm D3



SWISS-PROT: P14678
Sm B/B′



U1 snRNP




SWISS-PROT: P09234
U1 snRNP C



SWISS-PROT: P09012
U1 snRNP A



SWISS-PROT: P08621
U1 snRNP 70 kDa



U2 snRNP




SWISS-PROT: Q15427
SAP 49



SWISS-PROT: Q12874
SAP 61



SWISS-PROT: Q15428
SAP 62



SWISS-PROT: Q15459
SAP 114



SWISS-PROT: Q15393
SAP 130



SWISS-PROT: Q13435
SAP 145



SWISS-PROT: 075533
SAP 155



SWISS-PROT: Q01081
U2AF 35 kDa



SWISS-PROT: P26368
U2AF 65 kDa



SWISS-PROT: P09661
U2 snRNP A′



SWISS-PROT: P08579
U2 snRNP B′′



US snRNP




ENSP00000263694,
U5 snRNP 40 kDa



Q96D17




ENSP00000261905,
U5 snRNP 100 kDa



Q9BUQ8




ENSP00000266079,
U5 snRNP 102 kDa



O94906




SWISS-PROT: Q15029
U5 snRNP 116 kDa



SWISS-PROT: 075643
U5 snRNP 200 kDa



ENSP00000254706,
U5 snRNP 220 kDa



Q6P2Q9




U6 snRNP




SWISS-PROT: Q9Y333
LSm2



SWISS-PROT: Q9Y4Z1
LSm3



SWISS-PROT: Q9Y4Z0
LSm4



SWISS-PROT: Q9Y4Y8
LSm6



SWISS-PROT: Q9UK45
LSm7



SWISS-PROT: O95777
LSm8



U4/U6 snRNP




ENSP00000259401
U4/U6 snRNP hPrp4



ENSP00000236015,
U4/U6 snRNP hPrp3



O4339S




ENSP00000291763
U4/U6 snRNP 61 kDa



U4/U6.U5 snRNP




SWISS-PROT: P55769
U4/U6.snRNP 15.5 kDa



ENSP00000263858
U4/U6.U5 snRNP 65 kDa



ENSP00000256313
SART-1 = U4/U6.U5




snRNP 110 kDa



SR proteins




SWISS-PROT: Q07955
SF2



SWISS-PROT: Q16629
9G8



SWISS-PROT: Q01130
SC35



SWISS-PROT: P23152
SRp20



SWISS-PROT: Q13242
SRp30C



SWISS-PROT: Q05519
SRp54



SWISS-PROT: Q13247
SRp55



TREMBL: Q8WXA9
Splicing factor, arginine/serine-




rich 12



ENSP00000255590
Ser/Arg-related nuclear matrix




protein



Other splicing factors




ENSP00000227503
SF1



ENSP00000235397
SPF27



ENSP00000239010
SPF30



ENSP00000263697
SPF31



TREMBL: O75939;
SPF45



Q96GY6




ENSP00000265414
CDC5-related protein



SWISS-PROT: Q13573
SKIP



TREMBL: Q9NZA0
PUF60



TREMBL: O43660
Pleiotropic regulator 1



ENSP00000253363
CC1.3



ENSP00000296702
CA150



SWISS-PROT: Q14562
DEAH-box protein 8



SWISS-PROT: O43143
DEAD/H-box-15



SWISS-PROT: O60231
DEAD/H-box-16



ENSP00000268482
hPRP16



SWISS-PROT: O60508
hPRP17



ENSP00000198939
ERPROT 213-21 (+N-



(+ENSP00000248044)
terminal




extension of ERPROT)



ENSP00000290341
IGE-II mRNA-binding protein 1



SWISS-PROT: P23246
PTB-associated splicing factor



ENSP00000266611
IK factor



ENSP00000257528
SLU7



ENSP00000216727
poly(A)-binding protein II



ENSP00000293531
KH-type splicing regulatory




protein



ENSP00000294623
far upstream element-binding




protein 1



ENSP00000227524
nuclear matrix protein NMP200



TREMBL: Q96HB0
HCNP protein



ENSP00000278799
crooked neck-like 1



SWISS-PROT: Q9Y3B4
pre-mRNA branch site




protein p14



ENSP00000292123
scaffold attachment factor B



ENSP00000261167
SH3 domain-binding protein




SNP70



hnRNP




ENSP00000257767
GRY-RBP



SWISS-PROT: Q13151
hnRNP A0



SWISS-PROT: P09651
hnRNP A1



SWISS-PROT: P22626
hnRNP A2/hnRNP B1



ENSP00000298069
hnRNP A3



ENSP00000261952
hnRNP AB, isoform a



SWISS-PROT: P07910
hnRNP C



SWISS-PROT: Q14103
hnRNP D



ENSP00000295469
hnRNP D-like



SWISS-PROT: P52597
hnRNP F



SWISS-PROT: P38159
hnRNP G



SWISS-PROT: P31943
hnRNP H



ENSP00000265866
hnRNP H3



SWISS-PROT: P26599
Polypyrimidine tract-binding




protein; hnRNP I



ENSP00000297818
hnRNP K



SWISS-PROT: P14866
hnRNP L



SWISS-PROT: P52272
hnRNP M



SWISS-PROT: O43390
hnRNP R



Q00839
hnRNP U



TREMBL: O76022
E1B-55kDa-associated protein 5



RNA processing




SWISS-PROT: P52298
CBP 20 kDa



SWISS-PROT: Q09161
CBP 80 kDa



SWISS-PROT: P17844
DEAD/H-box-5; RNA




helicase p68



SWISS-PROT: P35637
RNA-binding protein FUS



SWISS-PROT: Q01844
RNA-binding protein EWS



SWISS-PROT: Q12906
Interleukin enhancer-




binding factor 3



ENSP00000270794
TLS-associated serine-




arginine protein 2



RNA processing




ENSP00000269407
Aly



SWISS-PROT: Q9UBU9
Tap



ENSP00000261600
hHpr1



SWISS-PROT: Q08211
RNA helicase A



ENSP00000264073
ELAV-like protein 1 (Hu-




antigen R)



SWISS-PROT: P43243
matrin 3



SWISS-PROT: P55265
Double-stranded RNA-




specific adenosine




deaminase (DRADA)



ENSP00000300291
CPSF 25 kDa



ENSP00000292476
CPSF 30 kDa



ENSP00000266679
similar to CPSF 68 kDa



SWISS-PROT: Q9UKF6
CPSF 73 kDa



SWISS-PROT: Q9P2I0
CPSF 100 kDa



SWISS-PROT: Q10570
CPSF 160 kDa



ENSP00000227158
cleavage stimulation factor




subunit 3



SWISS-PROT: P05455
Lupus La protein: Sjogren 




syndrome type B antigen



SWISS-PROT: Q06265
Polymyositis/scleroderma




autoantigen 1



SWISS-PROT: Q01780
Polymyositis/scleroderma




autoantigen 2



SWISS-PROT: Q9Y2L1
Exosome complex exonuclease 




RRP44



SWISS-PROT: Q9NPD3
Exosome complex exonuclease 




RRP41



ENSP00000262489
Dhm1-like protein



a SWISS-PROT or




ENSEMBL accession




numbers are given at




http://srs.embl-




heidelberg.de:8000/srs5/




and




http://www.ensembl.org.









Novel Proteins









Novel proteins and




proteins with unclear




functions with sequence




similarities implicating




them in splicing/mRNA




processing




ENSP00000295270
Hypothetical protein
Similar to U5 snRNP 200 kDa


ENSP00000272417
CDNA FLJ13778 fis
Similar to U5 snRNP 200 kDa


ENSP00000301345
Hypothetical protein
Similar to U5 snRNP 220 kDa


TREMBL: Q9NUY0
CDNA FLJ11063 fis
Similar to arginine/serine-rich 4


SWISS-PROT: Q13523
Serine/threonine-protein kinase
Ser/Thr protein kinase family,




similar to S. pombe PRP4


ENSP00000296630
Hypothetical protein
RRM domain, bipartite NLS,




similar to arginine/serine-rich 11


ENSP00000266057
CDNA FLJ10998 fis
Similar to RNA lariat debranching




enzyme


ENSP00000273541
Hypothetical protein
Similar to Isy 1p, a potential splice




factor in yeast


XP_013029
Hypothetical protein
Similar to U2 snRNP A′


ENSP00000286032
Hypothetical protein
Similar to hnRNP A3


ENSP00000301786
Hypothetical protein
Similar to hnRNP U


ENSP000000301784
Hypothetical protein
Similar to hnRNP U


ENSP00000261832
Hypothetical protein
BASIC, basic domain



DKFZp434E2220
in HLH proteins of MYOD family,




PSP, proline-rich domain in spliceo-




some-associated proteins, zinc finger




CCHC, zinc knuckle


ENSP00000244367
CGI- 124 protein
Cyclophilin-type peptidyl-prolyl




cis-trans isomerase


ENSP00000215824
CYP-60
Cyclophilin-type peptidyl-prolyl




cis-trans isomerase


ENSP00000234288
PPIL3b
Cyclophilin-type peptidyl-prolyl




cis-trans isomerase


ENSP00000282972
Serologically defined
Cyclophilin-type peptidyl-prolyl



colon cancer antigen 10
cis-trans isomerase




bipartite NLS


SWISS-PROT: Q9UNP9
Cyclophilin E
Cyclophilin-type peptidyl-prolyl




cis-trans isomerase RRM domain


ENSP00000261308
KIAA0073 protein
Cyclophilin-type peptidyl-prolyl




cis-trans isomerase




G-protein beta WD-40 repeats


SWISS-PROT: Q92841
Probable RNA-dependent
DEAD/DEAH-box helicase



helicase p72



ENSP00000274514
RNA helicase
DEAD/DEAH-box helicase


ENSP00000242776
Hypothetical protein
Similar to nuclear RNA helicase,




DECD variant of DEAD-box




helicase family


SWISS-PROT: Q92499
DDX1
DEAD/DEAH-box helicase, SPRY




domain


SWISS-PROT: Q9NR30
DDX21
DEAD/DEAH-box helicase,




bipartite NLS


SWISS-PROT: Q9UJV9
DEAD-box protein
DEAD/DEAH-box



abstract homolog
helicase, zinc finger CCHC type


ENSP00000218971
DDX26
DEAD-box, von Willebrand factor




type A domain


SWISS-PROT: P38919
Eukaryotic initiation
DEAD-box helicase factor




4A-like NUK-34


ENSP00000297920
Hypothetical protein
Double-stranded



FLJ11307
RNA-binding domain (DsRBD)


ENSP00000263115
Hypothetical protein
G-patch domain


ENSP00000277477
Far upstream element
KH domain



(FUSE) binding protein 3



ENSP00000295749
KIAA 1604 protein
MIF4G, middle domain of eukaryotic




initiation factor 4G and MA3




domain, bipartite NLS


ENSP00000298643
PRO1777
PWI domain


SWISS-PROT: Q9Y580
RNA-binding protein 7
RRM domain


SWISS-PROT: O43251
RNA-binding protein 9
RRM domain


ENSP00000295971
Hypothetical protein
RRM domain



FLJ20273



ENSP00000266301
KIAA 1649 protein
RRM domain


SWISS-PROT: Q9Y388
Hypothetical protein
RRM domain



CGI-79.B



SWISS-PROT: Q02040
B-lymphocyte antigen
RRM domain



precursor



ENSP00000262632
Hypothetical 47.4 kDa
RRM domain,




ATP/GTP-binding site




motif A (P-loop)


ENSP00000293677
Hypothetical protein
RRM domain,




Bipartite NLS


SWISS-PROT: Q9BXP5
Arsenite-resistance protein 2
RRM domain, Bipartite NLS


ENSP00000220496
Hypothetical protein
RRM domain, DNAJ heat shock



FLJ10634
protein, bipartite NLS


TREMBL: O00425
Putative RNA-binding protein 
RRM domain, KH domain



KOC



ENSP00000262710
KIAA0670 protein
RRM domain, SAP domain


TREMBL: Q96SC6
OTT-MAL
RRM domain, SAP domain


ENSP00000295996
K1AA0332 protein
RRM domain, Surp domain




Bipartite NLS


ENSP00000199814
Hypothetical protein
RRM domain, Zinc



FLJ10290
finger C-x8-C-x5-C-x3-H type


SWISS-PROT: P98175
RNA-binding protein 10
RRM domain, C2H2 type zinc




finger, bipartite NLS


ENSP00000261972
Hypothetical protein S164
RRM domain, PWI domain, bipartite


(+ENSP00000261973)
(+N-terminal extension: CDNA:
NLS, Spectrin repeat



FLJ22454 fis, clone HRC09703)
(ENSP00000261973




encodes the N-terminal extension




of ENSP00000261972)


TREMBL: Q9UQ35
RNA-binding protein
RS domain


ENSP00000247001
F23858_1
Surp domain, G-patch domain


ENSP00000299951
Hypothetical protein
U1-like zinc finger, bipartite NLS


ENSP00000281372
HsKin17 protein
C2H2 zinc finger


TREMBL: Q96KR1
Putative Zinc finger protein
C2H2 zinc finger


ENSP00000239893
OPA-interacting protein OIP2
3′ exoribonuclease family


Novel proteins without




similarities implicating




them in splicing/mRNA




processing




SWISS-PROT: Q9C0J8
WDC146
G-protein beta WD-40 repeats


ENSP00000253952
Hypothetical 34.8 kDa protein
G-protein beta WD-40 repeats


ENSP00000263222
Hypothetical 57.5 kDa protein
G-protein beta WD-40 repeats


ENSP00000156471
K1AA0560 protein
ATP/GTP-binding site motif A




(P-loop)


SWISS-PROT: Q9UH06
Hypothetical 12.4 kDa protein
PHD-finger (C4HC3 zinc finger)


ENSP00000216252
BK223H9
belongs to the UPFO123




family of hypothetical proteins


ENSP00000260210
Hypothetical protein MGC13125
Bipartite NLS, ankyrin similarity


ENSP00000257181
Hypothetical protein FLJ14936
Bipartite NLS, similar to unknowns


ENSP00000290008
Hypothetical protein
Bipartite NLS


SWISS-PROT: Q9NZB2
C9orf10 protein
Bipartite NLS, similar to unknowns


ENSP00000247026
Hypothetical 66.4 kDa protein
Bipartite NLS


ENSP00000236273
GCIP-interacting protein p29
Bipartite NLS, similar to unknowns


ENSP00000292314
Hypothetical protein
Bipartite NLS, similar to unknowns


ENSP00000266923
C21orf70
Bipartite NLS, similar to unknowns


NSP00000221899
NY-REN-24 antigen
Bipartite NLS, Ezrin/radixin/moesin




family; similar to Drosophila cactin


SWISS-PROT: Q14331
FRG1 protein (FSHD region 
Bipartite NLS,



gene 1 protein)
Lipocalin-related protein and




Bos/Can/Equ allergen domain


SWISS-PROT: P42285
KIAA0052 protein
SKI2 helicase family


ENSP00000221413
CGI-46 protein
DnaB helicase family


ENSP00000222969
G10 protein homolog (EDG-2)
G10 protein family


ENSP00000279839
Adrenal gland protein AD-002
GTP-binding signal recognition




particle (SRP54) G-domain


ENSP00000278702
Similar to nuclear mitotic
Involucrin repeat, G-protein gamma



apparatus protein 1
subunit, DNA gyrase/topoisomerase




IV, subunit A, M protein repeat,




bZIP (Basic-leucine zipper)




transcription factor family


SWISS- PROT: Q92733
Proline-rich protein PRCC
Proline-rich extension


ENSP00000263905
KIAA1461 protein
PWWP domain, Methyl-CpG binding




domain


XP_089514
Hypothetical protein
Similar to nucleophosmin


ENSP00000258457
Hypothetical 25.9 kDa protein
Similar to Xenopus ashwin


TREMBL: Q8WYA6
Nuclear associated protein
Similar to Bos taurus P14


TREMBL: Q13769
Hypothetical protein
Similarity to intermediate filament




b [Dugesia japonica]


SWISS-PROT: Q9Y5B6
GC-rich sequence DNA-binding
Similar to C-TERMINAL OF



factor homolog
GCF/TCF9 and other putative 




transcription factors


SWISS-PROT: Q9Y224
Hypothetical protein CGI-99
Similarity to putative transcription




factors


ENSP00000216038
Hypothetical 55.2 kDa protein
Uncharacterized protein family




UPFOO27


ENSP00000289509
Hypothetical 80.5 kDa protein
Similar to unknowns


ENSP00000245838
Hypothetical protein L0C57187
Similar to unknowns


ENSP00000289996
Hypothetical protein
Similar to unknowns


ENSP00000252137
DiGeorge syndrome critical 
Similar to unknowns



region gene DGSI protein



ENSP00000256579
Hypothetical protein FLJ10330
Similar to unknowns


ENSP00000245651
C20orf158 protein
Similar to unknowns


SWISS-PROT: Q9BWJ5
Hypothetical protein MGC3133
Similar to unknowns


ENSP00000272091
Hypothetical protein XP_089191
Similar to unknowns


ENSP00000297526
KIAA144O protein
Similar to unknowns


ENSP00000271942
Hypothetical protein FLJ21919
Similar to unknowns


TREMBL: Q9BTU2
Hypothetical 31.5 kDa protein
Similar to unknowns


TREMBL: Q8WVN3
Hypothetical protein
Similar to unknowns


a SWISS-PROT or




ENSEMBL accession




numbers are given at




http://srs.embl-




heidelberg.de:8000 and




http://www.ensembl.org.




b Domains: RRM: RNA




recognition motive;




Bipartite NLS: Bipartite




Nuclear Localization




Signal; SPRY: SP1a/RY




anodine receptor SPRY




domain; G-patch: named




after seven highly




conserved glycines; KH:




hnRNP K homology




domain; PWI: proline-




tryptophan-isoleucine




motifs; SAP: SAF-A/B,




Acinus and PIAS motif;




RS: Arginine-Serine




repeats; Surp:




Suppressor-of-white-




apricot splicing regulator




domain.
















TABLE 3







Proteins Involved in Transcription, Translation,


and Other Functions









Acc. no. a
Name
Comments











SWISS-PROT: P16991
CCAAT-binding



transcription factor I



subunit A


ENSP00000271939
Interleukin enhancer



binding factor 2, 45 kD


TREMBL: O15043
Death associated



transcription factor 1


ENSP00000266071
Death associated



transcription factor-1



isoform b


SWISS-PROT: P16383
GC-rich sequence DNA



binding factor


SWISS-PROT: P78347
general transcription



factor II


ENSP00000228251
Cold shock domain



protein A


NP_005325
host cell factor CI


SWISS-PROT: P49848
Transcription initiation



factor TFIID 70 kD



subunit


SWISS-PROT: P12956
ATP-dependent DNA



helicase II, 70 kD



subunit


ENSP00000283131
SWI/SNF related, matrix



associated, actin



dependent regulator of



chromatin subfamily a,



member 6


SWISS-PROT: P30876
DNA-directed RNA



polymerase II 140 kD


SWISS-PROT: P24928
DNA-directed RNA



polymerase II largest



subunit


SWISS-PROT: P02261
Histone H2A-


SWISS-PROT: P20670
H2A histone family



member O


SWISS-PROT: Q93080
H2B histone family



several members



possible


SWISS-PROT: P09429
High-mobility group



protein 1


SWISS-PROT: O15347
High mobility group box 4


ENSP00000275182
Histone deacetylase 2


SWISS-PROT: Q16576
Histone acetyltransferase



type B subunit 2


SWISS-PROT: P23396
40S ribosomal protein S3


NP_000997
40S ribosomal protein



S3A


SWISS-PROT: P12750
40S ribosomal protein S4


SWISS-PROT: P22090
40S ribosomal protein



S4Y isoform


SWISS-PROT: P46782
40S ribosomal protein S5


SWISS-PROT: P23821
40S ribosomal protein S7


SWISS-PROT: P09058
40S ribosomal protein S8


SWISS-PROT: P46781
40S ribosomal protein S9


SWISS-PROT: P46783
40S ribosomal protein



S10


ENSP00000237131
40S ribosomal protein



S12


SWISS-PROT: Q02546
40S ribosomal protein



S13


SWISS-PROT: P11174
40S ribosomal protein



S15


SWISS-PROT: P39027
40S ribosomal protein



S15a


SWISS-PROT: P17008
40S ribosomal protein



S16


SWISS-PROT: P08708
40S ribosomal protein



S17


SWISS-PROT: P25232
40S ribosomal protein



S18


SWISS-PROT: P39019
40S ribosomal protein



S19


SWISS-PROT: P25111
40S ribosomal protein



S25


SWISS-PROT: P30054
40S ribosomal protein



S29


SWISS-PROT: Q05472
40S ribosomal protein



S30


SWISS-PROT: P04643
40S ribosomal protein



S11


SWISS-PROT: P46777
60S ribosomal protein L5


SWISS-PROT: P35268
60S ribosomal protein



L22


SWISS-PROT: P29316
60S ribosomal protein



L23a


SWISS-PROT: P12947
60S ribosomal protein



L31


TREMBL Q8WT0
Signal recognition



particle 9 kD


SWISS-PROT: P09132
Signal recognition



particle 19 kD


SWISS-PROT: Q9UHB9
Signal recognition



particle 68 kD


TREMBL: Q8WUK2
Signal recognition



particle 68 kD isoform


SWISS-PROT: Q76094
Signal recognition



particle 72 kD


SWISS-PROT: P04720
Elongation factor 1


SWISS-PROT: P12270
Nucleoprotein TPR


SWISS-PROT: P46940
Ras GTPase-activating-



like


ENSP00000268182
protein IQGAP1 (P195)


SWISS-PROT: P52292
Importin alpha-2 subunit


SWISS-PROT: O75909
Cyclin K


SWISS-PROT: P78396
Cyclin A1


SWISS-PROT: P09874
poly(ADP-



ribosyl)transferase


SWISS-PROT: O43823
A-kinase anchor protein 8


ENSP00000262971
PIAS1


ENSP00000296215
Smad nuclear-interacting



protein 1


ENSP00000234443
Protein kinase,



interferon-inducible



double stranded RNA



dependent activator;



protein activator of the



interferon-induced



protein kinase


ENSP00000300630
Ubiquitin


ENSP00000271238
Phosphatase 2A inhibitor


SWISS-PROT: P19338
Nucleolin


SWISS-PROT: P55081
Microfibrillar-associated



protein 1


SWISS-PROT: P11142
Heat shock cognate 71 kD



protein


ENSP00000286912
Dynein heavy chain


SWISS-PROT: P08670
Vimentin


ENSP00000243115
Tubulin, alpha


ENSP00000259925
Tubulin, beta 5


a SWISSPROT or


ENSEMBL accession


numbers are given.


(http://srs.embl-


heidelberg.de:8000/srs5/


and www.ensembl.org)
















TABLE 3





Transcription Factors


TFFACTOR sorted by molecular weight (SZ field)


Database: TFFACTOR


TRANSFAC database, binding factor information


Release 3.3, January 1998


E. Wingender, R. Knueppel, P. Dietze, H. Karas (GBF-Braunschweig)


2,285 entries


















1.
T01627
8.3
kDa; lin-32


2.
T02213
9.0
kDa; PC4 p9


3.
T01972
10.0
kDa; DMLP1


4.
T01852
10.5
kDa; HMG I(Y)


5.
T01980
10.5
kDa; HMG Y


6.
T01714
11.5
kDa; HOXA10 PL2


7.
T01851
11.5
kDa; HMG I


8.
T01859
11.8
kDa; HMGI-C


9.
T01860
11.8
kDa; HMGI-C


10.
T01322
12.1
kDa; ICER-Igamma


11.
T01324
12.1
kDa; ICER-IIgamma


12.
T01566
12.1
kDa; deltaMax


13.
T02230
12.1
kDa; TFIIA-S


14.
T02226
12.2
kDa; TFIIA-S


15.
T01630
12.3
kDa; Tal-2


16.
T01631
12.3
kDa; Tal-2


17.
T02180
12.5
kDa; SIII-p15


18.
T02224
12.5
kDa; TFIIA-gamma


19.
T02232
12.5
kDa; TFIIA-S


20.
T02269
12.5
kDa; SIII-p15


21.
T01263
12.9
kDa; HAP3


22.
T01809
13.0
kDa; Id3


23.
T00367
13.1
kDa; Id3


24.
T01811
13.1
kDa; Id3


25.
T02179
13.1
kDa; SIII-p18


26.
T02268
13.1
kDa; SIII-p18


27.
T01325
13.3
kDa; ATF-3deltaZIP


28.
T01319
13.4
kDa; ICER


29.
T01321
13.4
kDa; ICER-I


30.
T01323
13.4
kDa; ICER-II


31.
T02228
13.5
kDa; TFIIA (13.5 kDa subunit)


32.
T02150
13.9
kDa; SRB6


33.
T02117
14.3
kDa; TAF(II)18


34.
T02137
14.4
kDa; PC4


35.
T02138
14.4
kDa; PC4


36.
T01654
14.6
kDa; HEN1


37.
T00488
14.8
kDa; MATa1


38.
T01655
14.8
kDa; HEN1


39.
T01212
14.9
kDa; Id2


40.
T00404
15.0
kDa; Id2


41.
T01656
15.0
kDa; HEN2


42.
T01657
15.0
kDa; HEN2


43.
T01808
15.0
kDa; Id2


44.
T00441
15.4
kDa; KBP-1


45.
T00403
15.6
kDa; Id1


46.
T01420
15.6
kDa; LIP


47.
T01807
15.6
kDa; Id1


48.
T02274
15.6
kDa; Id1H′


49.
T00350
16.0
kDa; HAP3


50.
T01810
16.1
kDa; Id3/Heir-1


51.
T02151
16.1
kDa; SRB7


52.
T01801
16.2
kDa; Id1


53.
T01384
16.5
kDa; pX


54.
T01448
16.5
kDa; Tal-1beta


55.
T01436
16.6
kDa; MafF


56.
T01658
16.6
kDa; Id4


57.
T01600
16.8
kDa; CREMdeltaC-G


58.
T01120
17.0
kDa; MCBF


59.
T01650
17.0
kDa; HES-2


60.
T01060
17.1
kDa; MNB1b


61.
T00489
17.2
kDa; Max1


62.
T01591
17.3
kDa; P (short form)


63.
T01593
17.3
kDa; C1 (short form)


64.
T01301
17.4
kDa; E4


65.
T01606
17.4
kDa; Id1.25


66.
T01639
17.4
kDa; INO4


67.
T02311
17.4
kDa; CSE2


68.
T01434
17.5
kDa; MafK


69.
T01435
17.5
kDa; MafK


70.
T01622
17.6
kDa; ASH-3a


71.
T01745
17.6
kDa; HOXC6 (PRI)


72.
T01743
17.8
kDa; HOXC6 (PRI)


73.
T02249
17.8
kDa; Lmo1


74.
T01742
17.9
kDa; HOXC6


75.
T02116
17.9
kDa; TAF(II)20


76.
T01274
18.0
kDa; DBF-A


77.
T02254
18.0
kDa; PEBP2beta3


78.
T01437
18.1
kDa; MafG


79.
T00523
18.3
kDa; Myn


80.
T01567
18.3
kDa; Max2


81.
T02251
18.3
kDa; Lmo2


82.
T02250
18.4
kDa; Lmo2


83.
T01652
18.5
kDa; HES-5


84.
T02089
18.7
kDa; mat-Pc


85.
T01636
18.8
kDa; X-Twist


86.
T00127
19.0
kDa; CHOP-10


87.
T00224
19.0
kDa; EF1


88.
T00299
19.0
kDa; GADD 153


89.
T01206
19.0
kDa; EF1


90.
T02139
19.0
kDa; PC4


91.
T01651
19.1
kDa; HES-3


92.
T00197
19.3
kDa; Dr1


93.
T01687
19.3
kDa; Pcr1


94.
T00043
19.5
kDa; ARG RI


95.
T01644
19.9
kDa; E(spl)m5


96.
T01447
20.0
kDa; HEN1


97.
T02216
20.0
kDa; TFIIA-alpha/beta precursor (major)


98.
T02217
20.0
kDa; TFIIA-alpha/beta precursor (minor)


99.
T01646
20.3
kDa; E(spl)m8


100.
T00486
20.4
kDa; MATalpha1


101.
T01310
20.4
kDa; S-CREM


102.
T01313
20.6
kDa; ATF-3


103.
T01095
20.7
kDa; LRF-1


104.
T01612
20.7
kDa; Meso1


105.
T01645
20.7
kDa; E(spl)m7


106.
T01971
20.8
kDa; MLP


107.
T01623
20.9
kDa; ASH-3b


108.
T01637
20.9
kDa; EC2


109.
T02221
20.9
kDa; Bro


110.
T01275
21.0
kDa; mat-Mc


111.
T01635
21.2
kDa; M-Twist


112.
T01065
21.5
kDa; PEBP2beta2


113.
T02259
21.5
kDa; PEBP2beta


114.
T02126
21.6
kDa; TAF(II)30alpha


115.
T02309
21.6
kDa; MET28


116.
T01754
21.7
kDa; HOXD8


117.
T02118
21.7
kDa; TAF(II)30


118.
T01890
21.8
kDa; Brn-5(c7)


119.
T02222
21.8
kDa; Bgb


120.
T00274
22.0
kDa; Emc


121.
T02255
22.0
kDa; PEBP2beta1


122.
T02131
22.1
kDa; TAF(II)30beta


123.
T00799
22.4
kDa; TBP-1


124.
T00800
22.4
kDa; TBP-2


125.
T01621
22.4
kDa; ASH-1


126.
T00005
22.7
kDa; Ac


127.
T01813
22.7
kDa; Pax-3B


128.
T00616
22.8
kDa; NF-YB


129.
T02147
22.9
kDa; SRB2


130.
T01601
23.0
kDa; CREMdeltaC-F


131.
T02275
23.1
kDa; SUP


132.
T00216
23.3
kDa; C/EBPgamma


133.
T02114
23.3
kDa; TAF(II)28


134.
T01018
23.6
kDa; CAP


135.
T01569
23.8
kDa; Th1


136.
T00997
23.9
kDa; SRY


137.
T01735
23.9
kDa; HOXB7


138.
T00179
24.0
kDa; CUP2


139.
T01704
24.0
kDa; HOXA7


140.
T01734
24.0
kDa; HOXB7


141.
T01812
24.1
kDa; Pax-3A


142.
T01316
24.2
kDa; CREMgamma


143.
T00487
24.3
kDa; MATalpha2


144.
T01803
24.3
kDa; CREMalpha


145.
T00516
24.4
kDa; mtTF1


146.
T02061
24.4
kDa; K-2b


147.
T01987
24.5
kDa; SRY


148.
T01887
24.6
kDa; Brn-4


149.
T02211
24.6
kDa; BTEB2


150.
T01779
24.7
kDa; GLO


151.
T02025
24.7
kDa; C/EBPalpha(p30)


152.
T01059
24.8
kDa; MNB1a


153.
T01619
24.8
kDa; MASH-1


154.
T00087
25.0
kDa; CBF-A


155.
T00484
25.0
kDa; MASH-1


156.
T00520
25.0
kDa; Myf-4


157.
T01741
25.0
kDa; HOXC5


158.
T01736
25.1
kDa; HOXB7


159.
T00528
25.2
kDa; myogenin


160.
T01565
25.3
kDa; Mad


161.
T01733
25.3
kDa; HOXB6


162.
T00795
25.4
kDa; TBP


163.
T01315
25.4
kDa; CREMbeta


164.
T01778
25.4
kDa; GLO


165.
T02198
25.4
kDa; FosB/SF


166.
T00849
25.5
kDa; TRF


167.
T01314
25.5
kDa; CREMalpha


168.
T01732
25.5
kDa; HOXB6


169.
T02027
25.5
kDa; C/EBPalpha(p30)


170.
T02026
25.6
kDa; C/EBPalpha(p30)


171.
T01278
25.7
kDa; HOXA7


172.
T01533
25.7
kDa; myogenin


173.
T01620
25.7
kDa; MASH-1


174.
T01531
25.8
kDa; myogenin


175.
T00180
25.9
kDa; CYS3


176.
T01082
25.9
kDa; NRL


177.
T01438
26.1
kDa; NRL


178.
T01564
26.1
kDa; Mxi1


179.
T01740
26.2
kDa; HOXB9


180.
T01008
26.3
kDa; DEF A


181.
T01538
26.4
kDa; MRF4


182.
T01588
26.4
kDa; GL1


183.
T00967
26.5
kDa; E1A 12S protein


184.
T01729
26.5
kDa; HOXB4


185.
T00888
26.6
kDa; v-Fos


186.
T02039
26.6
kDa; HAC1


187.
T01746
26.7
kDa; HOXC6 (PRII)


188.
T01753
26.7
kDa; HOXD4


189.
T00633
26.8
kDa; N-Oct-Sb


190.
T00798
26.9
kDa; TBP


191.
T00923
26.9
kDa; Zta


192.
T01057
26.9
kDa; lin-31


193.
T01744
26.9
kDa; HOXC6 (PRII)


194.
T01747
26.9
kDa; HOXC6 (PRII)


195.
T00512
27.0
kDa; MRF4


196.
T00522
27.0
kDa; Myf-6


197.
T01537
27.0
kDa; MRF4


198.
T01777
27.0
kDa; GP


199.
T01255
27.1
kDa; DAT1


200.
T01539
27.1
kDa; MRF4


201.
T00171
27.2
kDa; C/EBPepsilon


202.
T02045
27.2
kDa; Flh


203.
T02210
27.2
kDa; BTEB


204.
T02212
27.2
kDa; BTEB


205.
T01752
27.3
kDa; HOXD4


206.
T01776
27.3
kDa; APETALA3


207.
T02046
27.3
kDa; Gsc


208.
T02060
27.3
kDa; K-2a


209.
T01484
27.4
kDa; Cdx-1


210.
T02044
27.4
kDa; Flh


211.
T02049
27.4
kDa; Gsc B


212.
T02132
27.4
kDa; TAF(II)30


213.
T02141
27.4
kDa; OCA-B


214.
T02256
27.4
kDa; AML1a


215.
T01515
27.5
kDa; Pur factor


216.
T01728
27.5
kDa; HOXB4


217.
T02069
27.5
kDa; Msx-1


218.
T01727
27.6
kDa; HOXB4


219.
T01737
27.6
kDa; HOXB8


220.
T02142
27.6
kDa; OCA-B


221.
T00485
27.7
kDa; MASH-2


222.
T01749
27.7
kDa; HOXC8


223.
T01726
27.8
kDa; HOXB4


224.
T00376
27.9
kDa; HOXD4


225.
T00347
28.0
kDa; HAP2


226.
T01370
28.0
kDa; p28 modulator


227.
T02047
28.0
kDa; Gsc


228.
T01534
28.2
kDa; Myf-5


229.
T01535
28.2
kDa; Myf-5


230.
T02074
28.2
kDa; Msx-2


231.
T02077
28.2
kDa; Msx-2


232.
T01090
28.3
kDa; TAF-1


233.
T01846
28.3
kDa; TCF-1D


234.
T02170
28.3
kDa; TFIIF-beta


235.
T00521
28.4
kDa; Myf-5


236.
T00583
28.4
kDa; C/EBPdelta


237.
T01536
28.4
kDa; Myf-5


238.
T01706
28.4
kDa; HOXA7


239.
T01986
28.4
kDa; SRY


240.
T01999
28.4
kDa; Cdx-1


241.
T02007
28.4
kDa; Dlx-1


242.
T02169
28.4
kDa; TFIIF-beta


243.
T02195
28.4
kDa; TBP


244.
T00109
28.6
kDa; C/EBPdelta


245.
T00949
28.6
kDa; Myf-5


246.
T01114
28.6
kDa; C/EBPdelta


247.
T01981
28.6
kDa; TCF-1F


248.
T00632
28.7
kDa; N-Oct-5a


249.
T00902
28.7
kDa; XBP-1


250.
T00926
28.7
kDa; SUM-1


251.
T01632
28.7
kDa; Lyl-1


252.
T01401
28.8
kDa; Spi-B


253.
T01592
28.8
kDa; C1 (long form)


254.
T01773
28.8
kDa; AG


255.
T02075
28.8
kDa; Msx-2


256.
T01880
28.9
kDa; Brn-3b


257.
T02076
28.9
kDa; Msx-2


258.
T00003
29.0
kDa; AS-C T3


259.
T01086
29.0
kDa; beta-1


260.
T01982
29.0
kDa; TCF-1G


261.
T02113
29.0
kDa; TAF(II)31


262.
T00871
29.1
kDa; USF


263.
T01116
29.1
kDa; SAP1


264.
T02099
29.1
kDa; Zen-2


265.
T00008
29.2
kDa; Adf-1


266.
T00160
29.2
kDa; CPC1


267.
T00377
29.2
kDa; HOXA5


268.
T00968
29.2
kDa; ATF-1


269.
T01072
29.2
kDa; TEF


270.
T01304
29.2
kDa; ATF-1


271.
T02105
29.2
kDa; C/EBPbeta(p34)


272.
T02125
29.3
kDa; TAF(II)40


273.
T00925
29.4
kDa; AMT1


274.
T01462
29.4
kDa; Fra-1


275.
T01702
29.4
kDa; HOXA5


276.
T01730
29.4
kDa; HOXB5


277.
T02050
29.4
kDa; Gtx


278.
T02090
29.4
kDa; Phox-2


279.
T01731
29.5
kDa; HOXB5


280.
T01648
29.6
kDa; HES-1


281.
T01649
29.7
kDa; HES-1


282.
T00349
29.8
kDa; HAP2


283.
T00292
29.9
kDa; Fra-1


284.
T01249
29.9
kDa; BUF1


285.
T00597
30.0
kDa; NF-kappaE2


286.
T01221
30.0
kDa; NF-kappaE2


287.
T01277
30.0
kDa; spE2F


288.
T01762
30.0
kDa; HOXD12


289.
T01775
30.0
kDa; APETALA1


290.
T02092
30.0
kDa; Prh


291.
T02225
30.0
kDa; TFIIA-L


292.
T01208
30.1
kDa; Fra-1


293.
T01290
30.1
kDa; MATalpha1


294.
T01872
30.1
kDa; Oct-4B


295.
T02172
30.1
kDa; TFIIF-beta


296.
T01000
30.2
kDa; TCF-1B


297.
T01633
30.2
kDa; Lyl-1


298.
T02091
30.2
kDa; Prh


299.
T00999
30.3
kDa; TCF-1A


300.
T01001
30.3
kDa; TCF-1C


301.
T01763
30.3
kDa; HOXD12


302.
T01317
30.4
kDa; CREMepsilon


303.
T02068
30.4
kDa; PU.1


304.
T02108
30.4
kDa; CREMtau1


305.
T02018
30.5
kDa; En-2


306.
T02070
30.5
kDa; Msx-1


307.
T00702
30.7
kDa; PU.1


308.
T02058
30.8
kDa; IPF1


309.
T02072
30.8
kDa; Msx-1


310.
T00845
30.9
kDa; Tra-1 (short form)


311.
T01474
30.9
kDa; Athb-1


312.
T01996
31.0
kDa; dJRA


313.
T02057
31.0
kDa; IPF1


314.
T02071
31.0
kDa; Msx-1


315.
T02073
31.0
kDa; Msx-1


316.
T00321
31.3
kDa; GCN4


317.
T00267
31.4
kDa; GATA-1


318.
T01426
31.4
kDa; HOXD8


319.
T00017
31.5
kDa; C/EBPbeta


320.
T00459
31.5
kDa; C/EBPbeta


321.
T02082
31.6
kDa; Otx2


322.
T02083
31.6
kDa; Otx2


323.
T02109
31.6
kDa; CREMtau2


324.
T00653
31.7
kDa; Oct-5


325.
T01720
31.7
kDa; HOXB1


326.
T00209
31.8
kDa; E1A 13S protein


327.
T01761
31.8
kDa; HOXD11


328.
T01389
31.9
kDa; LEF-1S


329.
T01475
31.9
kDa; Athb-2


330.
T01759
31.9
kDa; HOXD11


331.
T00961
32.0
kDa; ANF-2


332.
T01381
32.0
kDa; deltaCREB


333.
T01719
32.1
kDa; HOXB1


334.
T01816
32.1
kDa; Mab-18 (284 AA)


335.
T02174
32.1
kDa; TFIIF-beta


336.
T00815
32.2
kDa; TFIIA


337.
T02227
32.2
kDa; TFIIA (32 kDa subunit)


338.
T00524
32.3
kDa; MyoD


339.
T01093
32.4
kDa; CPRF-3


340.
T01764
32.4
kDa; HOXD13


341.
T00893
32.5
kDa; v-Jun


342.
T01532
32.5
kDa; myogenin


343.
T01893
32.6
kDa; TCFbeta1


344.
T02166
32.6
kDa; TFIIE-beta


345.
T01605
32.7
kDa; SGC1


346.
T01891
32.7
kDa; Brn-5


347.
T02111
32.7
kDa; TBP


348.
T00500
32.8
kDa; MCM1


349.
T00325
32.9
kDa; Pit-1


350.
T01172
32.9
kDa; Pit-1


351.
T01516
32.9
kDa; Pit-1b


352.
T01888
32.9
kDa; Brn-5(c2)


353.
T01128
33.0
kDa; MyoD


354.
T01551
33.0
kDa; MyoD


355.
T02163
33.0
kDa; TFIIE-beta


356.
T02238
33.0
kDa; TFIIE-beta


357.
T01889
33.1
kDa; Brn-5(c1)


358.
T01071
33.2
kDa; Hlf


359.
T01641
33.2
kDa; PHO80


360.
T01817
33.2
kDa; Mab-18 (296 AA)


361.
T02031
33.2
kDa; HSF24


362.
T02196
33.2
kDa; JunD


363.
T01716
33.3
kDa; HOXA11


364.
T01751
33.3
kDa; HOXD1


365.
T01876
33.3
kDa; Brn-3a


366.
T02304
33.4
kDa; Pur-1


367.
T00128
33.5
kDa; HOXA4


368.
T00874
33.5
kDa; USF


369.
T01760
33.5
kDa; HOXD11


370.
T02002
33.5
kDa; Cdx-2


371.
T01691
33.6
kDa; TTP


372.
T01847
33.6
kDa; TCF-1


373.
T01878
33.6
kDa; Brn-3a(s)


374.
T02003
33.6
kDa; Cdx-3


375.
T01063
33.7
kDa; PEBP2alphaA2


376.
T01718
33.8
kDa; HOXB1


377.
T01800
33.8
kDa; Tal-1


378.
T02020
33.8
kDa; En-2


379.
T00134
33.9
kDa; c-Jun


380.
T01078
33.9
kDa; GBF1


381.
T02188
33.9
kDa; TFIIH-p34


382.
T00615
34.0
kDa; NF-YA


383.
T01513
34.0
kDa; AEF-1


384.
T01836
34.0
kDa; Sox-2


385.
T00690
34.1
kDa; PHO4


386.
T01628
34.1
kDa; Ato


387.
T01750
34.1
kDa; HOXD1


388.
T01837
34.1
kDa; Sox-2


389.
T00526
34.2
kDa; MyoD


390.
T01241
34.2
kDa; INO2


391.
T01388
34.2
kDa; C/EBP


392.
T01675
34.2
kDa; Nkx-2.5


393.
T02019
34.2
kDa; En-2


394.
T02234
34.2
kDa; TFIIB


395.
T00790
34.3
kDa; Tal-1


396.
T00881
34.3
kDa; VBP


397.
T01453
34.3
kDa; v-Fos


398.
T01799
34.3
kDa; Tal-1


399.
T01976
34.3
kDa; c-Jun


400.
T02149
34.3
kDa; SRB5


401.
T02233
34.3
kDa; TFIIB


402.
T00183
34.4
kDa; DBP


403.
T01242
34.4
kDa; SNP1


404.
T02054
34.4
kDa; Hox11


405.
T02158
34.4
kDa; TFIIB


406.
T00519
34.5
kDa; Myf-3


407.
T00525
34.5
kDa; MyoD


408.
T00548
34.5
kDa; NF-AB


409.
T00707
34.5
kDa; PUF-I


410.
T01703
34.5
kDa; HOXA4


411.
T02014
34.5
kDa; En-1


412.
T00293
34.6
kDa; FRG Y1


413.
T02055
34.6
kDa; Hox11


414.
T00796
34.7
kDa; TBP


415.
T02009
34.7
kDa; Dlx-2


416.
T02160
34.7
kDa; TFIIB


417.
T00818
34.8
kDa; TFIIB


418.
T02159
34.8
kDa; TFIIB


419.
T00348
34.9
kDa; HAP2


420.
T00437
34.9
kDa; JunD


421.
T01826
34.9
kDa; Pax-8c


422.
T02197
34.9
kDa; JunD


423.
T00165
35.0
kDa; deltaCREB


424.
T00166
35.0
kDa; deltaCREB


425.
T00816
35.0
kDa; TFIIA


426.
T00846
35.0
kDa; TREB-1


427.
T01755
35.0
kDa; HOXD9


428.
T01938
35.0
kDa; IkappaB-alpha


429.
T02022
35.0
kDa; C/EBPbeta


430.
T01311
35.1
kDa; deltaCREB


431.
T01552
35.2
kDa; TFEC


432.
T01701
35.2
kDa; HOXA4


433.
T01939
35.2
kDa; IkappaB-alpha


434.
T01990
35.2
kDa; Fra-2


435.
T01991
35.2
kDa; Fra-2


436.
T02005
35.2
kDa; Dll


437.
T02194
35.2
kDa; TFIIH-KIN28


438.
T01881
35.3
kDa; Brn-3b


439.
T02199
35.3
kDa; Fra-2


440.
T00186
35.4
kDa; DbpB


441.
T00910
35.4
kDa; YB-1


442.
T01937
35.4
kDa; IkappaB-alpha


443.
T01978
35.4
kDa; JunD


444.
T02200
35.4
kDa; Fra-2


445.
T00421
35.5
kDa; IREBF-1


446.
T01433
35.5
kDa; MafB


447.
T02202
35.5
kDa; MafB


448.
T00950
35.6
kDa; IkappaB-alpha


449.
T01424
35.6
kDa; HOXD9


450.
T01681
35.6
kDa; PTFdelta


451.
T00107
35.7
kDa; C/EBPalpha


452.
T00133
35.7
kDa; c-Jun


453.
T00235
35.7
kDa; EFIA


454.
T01570
35.7
kDa; FlbD


455.
T00236
35.8
kDa; EFIA


456.
T00436
35.8
kDa; JunB


457.
T00691
35.8
kDa; Pit-1a


458.
T01439
35.8
kDa; kreisler


459.
T02187
35.8
kDa; TFIIH-MAT1


460.
T00131
35.9
kDa; c-Jun


461.
T01977
35.9
kDa; JunB


462.
T00132
36.0
kDa; c-Jun


463.
T00291
36.0
kDa; FosB


464.
T00538
36.0
kDa; NF-1


465.
T01696
36.0
kDa; HOXA1


466.
T00581
36.1
kDa; C/EBPbeta


467.
T01055
36.2
kDa; Slp1


468.
T01098
36.2
kDa; EmBP-1


469.
T01540
36.2
kDa; Nau


470.
T01992
36.2
kDa; abd-A


471.
T00110
36.5
kDa; CeMyoD


472.
T00423
36.5
kDa; IRF-1


473.
T01309
36.6
kDa; CREMtau


474.
T01589
36.6
kDa; MybSt1


475.
T01695
36.6
kDa; HOXA1


476.
T01919
36.6
kDa; CREMtau


477.
T02112
36.6
kDa; TBP


478.
T00163
36.7
kDa; CREB


479.
T00937
36.7
kDa; HBP-1a


480.
T00989
36.7
kDa; CREB


481.
T01602
36.7
kDa; CREMtaualpha


482.
T00938
36.8
kDa; HBP-1b


483.
T01970
36.8
kDa; Mec-3


484.
T00157
36.9
kDa; CP1B


485.
T01386
36.9
kDa; C/EBP


486.
T01392
36.9
kDa; GABP-beta2


487.
T01404
36.9
kDa; GABP-beta2


488.
T00164
37.0
kDa; CREB


489.
T00185
37.0
kDa; DbpA


490.
T00345
37.0
kDa; H


491.
T00547
37.0
kDa; NF-AB


492.
T01555
37.0
kDa; USF2


493.
T01892
37.0
kDa; Sprm-1


494.
T00424
37.1
kDa; IRF-1


495.
T00498
37.1
kDa; MBP-1 (2)


496.
T01076
37.1
kDa; Mec-3


497.
T02240
37.1
kDa; TFIIE-beta


498.
T00294
37.2
kDa; FRG Y2


499.
T01595
37.2
kDa; CBF-C


500.
T00422
37.3
kDa; IRF-1


501.
T02079
37.3
kDa; Otx1


502.
T01785
37.4
kDa; xMEF-2


503.
T02080
37.5
kDa; Otx1


504.
T00105
37.6
kDa; C/EBPalpha


505.
T01607
37.6
kDa; E2F-5


506.
T02081
37.6
kDa; Otx1


507.
T02184
37.6
kDa; TFIIH-cyclin H


508.
T00104
37.7
kDa; C/EBPalpha


509.
T00108
37.7
kDa; C/EBPalpha


510.
T00794
37.7
kDa; TBP


511.
T01050
37.7
kDa; HNF-3gamma


512.
T01677
37.7
kDa; LKLF


513.
T02201
37.7
kDa; c-Maf (short form)


514.
T02220
37.7
kDa; AML1DeltaN


515.
T01676
37.8
kDa; EKLF


516.
T02093
37.8
kDa; Ro


517.
T02155
37.8
kDa; SRB11


518.
T00677
37.9
kDa; Pax-1


519.
T01668
37.9
kDa; MATH-1


520.
T00651
38.0
kDa; Oct-4


521.
T00858
38.0
kDa; TTF-1


522.
T00859
38.0
kDa; TTF-1


523.
T00971
38.0
kDa; IkappaB-beta


524.
T01604
38.0
kDa; dCREB2-a


525.
T00004
38.1
kDa; Sc


526.
T01407
38.1
kDa; NRF-2gamma1


527.
T01757
38.4
kDa; HOXD10


528.
T02087
38.4
kDa; Pbx-1b


529.
T02088
38.4
kDa; Pbx-1b


530.
T00797
38.5
kDa; TBP


531.
T01303
38.5
kDa; CREB-2


532.
T01425
38.5
kDa; HOXD10


533.
T02098
38.5
kDa; TTF-1


534.
T00652
38.6
kDa; Oct-4A


535.
T00746
38.6
kDa; SGF-3


536.
T00856
38.6
kDa; TTF-1


537.
T00857
38.6
kDa; TTF-1


538.
T01012
38.6
kDa; xMEF-2


539.
T01629
38.6
kDa; MATH-2


540.
T01432
38.7
kDa; c-Maf


541.
T01957
38.7
kDa; Isl-1


542.
T00744
38.8
kDa; SGF-1


543.
T01079
38.8
kDa; GBF2


544.
T01430
38.9
kDa; v-Maf


545.
T01431
38.9
kDa; c-Maf (long form)


546.
T00125
39.0
kDa; c-Fos


547.
T00268
39.0
kDa; GABP


548.
T00304
39.0
kDa; GATA-1A


549.
T01017
39.0
kDa; CRE-BP2


550.
T01035
39.0
kDa; Isl-1


551.
T01956
39.0
kDa; Isl-1


552.
T02186
39.0
kDa; TFIIH-MO15


553.
T00819
39.1
kDa; TFIIB


554.
T02161
39.1
kDa; TFIIB


555.
T01653
39.2
kDa; Delilah


556.
T00917
39.3
kDa; Zen-1


557.
T01491
39.3
kDa; IRF-2


558.
T02301
39.3
kDa; CTF-7


559.
T02319
39.3
kDa; PEBP2alphaA/til-1(U)


560.
T00080
39.4
kDa; CBF1


561.
T01884
39.4
kDa; Brn-4


562.
T01885
39.4
kDa; Brn-4


563.
T01886
39.4
kDa; Brn-4


564.
T00425
39.5
kDa; IRF-2


565.
T00732
39.5
kDa; Ro


566.
T01625
39.7
kDa; NeuroD


567.
T02295
39.7
kDa; TFIIIA


568.
T02062
39.8
kDa; KN1


569.
T02312
39.8
kDa; GATA-1B


570.
T01898
39.9
kDa; I-POU


571.
T00154
40.0
kDa; CP1A


572.
T00200
40.0
kDa; DTF


573.
T00272
40.0
kDa; Eve


574.
T00399
40.0
kDa; IBF


575.
T00416
40.0
kDa; IkappaB-beta


576.
T00466
40.0
kDa; LF-A1


577.
T00700
40.0
kDa; PTF


578.
T00708
40.0
kDa; p40x


579.
T00863
40.0
kDa; Ubx


580.
T00868
40.0
kDa; URSF


581.
T01106
40.0
kDa; EBP40


582.
T01626
40.0
kDa; NeuroD


583.
T01674
40.0
kDa; BETA3


584.
T02015
40.0
kDa; En-1


585.
T01899
40.2
kDa; tI-POU


586.
T02032
40.2
kDa; HSF30


587.
T02276
40.2
kDa; ATBP


588.
T00782
40.3
kDa; TAF(II)55


589.
T01259
40.3
kDa; ARG RIII


590.
T02063
40.3
kDa; Knox3


591.
T01288
40.6
kDa; PHD1


592.
T01979
40.6
kDa; TCF-1E


593.
T00123
40.7
kDa; c-Fos


594.
T01395
40.7
kDa; HBP-1a(c14)


595.
T00122
40.8
kDa; c-Fos


596.
T01400
40.8
kDa; Ets-1 deltaVII


597.
T01698
40.8
kDa; HOXA2


598.
T01699
40.8
kDa; HOXA2


599.
T02205
40.8
kDa; c-Fos


600.
T00124
40.9
kDa; c-Fos


601.
T00083
41.0
kDa; CBF (2)


602.
T00088
41.0
kDa; CBF-B


603.
T00829
41.0
kDa; TGA1a


604.
T00924
41.0
kDa; CIIIB1


605.
T01700
41.0
kDa; HOXA2


606.
T02016
41.0
kDa; En-1


607.
T01080
41.1
kDa; GBF3


608.
T00769
41.2
kDa; Sry-beta


609.
T01391
41.3
kDa; GABP-beta1


610.
T01403
41.3
kDa; GABP-beta1


611.
T02241
41.3
kDa; PEBP2alphaB2


612.
T00265
41.4
kDa; Erg-1


613.
T01643
41.4
kDa; H


614.
T01715
41.4
kDa; HOXA10


615.
T02294
41.4
kDa; XFD-2


616.
T01440
41.6
kDa; NF-E2 p45


617.
T01441
41.6
kDa; NF-E2 p45


618.
T01452
41.6
kDa; v-Fos


619.
T01843
41.6
kDa; Sox-18


620.
T02231
41.6
kDa; TFIIA-L


621.
T01482
41.7
kDa; Exd


622.
T01825
41.7
kDa; Pax-8b


623.
T01286
41.8
kDa; Rox1


624.
T02052
41.8
kDa; CREB-2


625.
T02229
41.8
kDa; TFIIA-L


626.
T01373
42.0
kDa; CBTF


627.
T01822
42.0
kDa; Pax-2b


628.
T01968
42.0
kDa; LH-2


629.
T02024
42.0
kDa; Evx-1


630.
T00070
42.1
kDa; Pax-5


631.
T01692
42.1
kDa; T3R-beta1


632.
T01201
42.2
kDa; Pax-5


633.
T01382
42.3
kDa; CRE-BP2


634.
T01823
42.3
kDa; Pax-2


635.
T02298
42.3
kDa; NF-1A3


636.
T02021
42.4
kDa; Evx-1


637.
T01406
42.5
kDa; NRF-2beta1


638.
T02103
42.5
kDa; p53as


639.
T00243
42.6
kDa; EGR3


640.
T00305
42.6
kDa; GATA-1


641.
T01550
42.7
kDa; dDP


642.
T00026
42.8
kDa; Antp


643.
T00306
42.8
kDa; GATA-1


644.
T01877
42.8
kDa; Brn-3a(1)


645.
T01958
42.8
kDa; Lmx-1


646.
T02252
42.8
kDa; Ldb1


647.
T02097
42.9
kDa; STM


648.
T00135
43.0
kDa; c-Jun


649.
T00242
43.0
kDa; EGR2


650.
T00414
43.0
kDa; IkappaB-beta


651.
T00446
43.0
kDa; 43K protein


652.
T01096
43.0
kDa; GHF3


653.
T01380
43.0
kDa; CREB


654.
T01680
43.0
kDa; PTFgamma


655.
T01827
43.0
kDa; Pax-8d


656.
T01832
43.1
kDa; v-Qin


657.
T01842
43.1
kDa; WT1 I-del2


658.
T01429
43.2
kDa; Sox-5


659.
T02023
43.2
kDa; Evx-1


660.
T01722
43.5
kDa; HOXB3


661.
T01806
43.5
kDa; p53


662.
T01896
43.5
kDa; t-Pou2


663.
T01866
43.6
kDa; Oct-2.4


664.
T00671
43.7
kDa; p53


665.
T01456
43.7
kDa; ISGF-3gamma


666.
T01590
43.8
kDa; P (long form)


667.
T01965
43.8
kDa; Lim-3


668.
T02253
43.8
kDa; Ch-runtB2


669.
T01874
43.9
kDa; Oct-11


670.
T00877
44.0
kDa; USF


671.
T00878
44.0
kDa; USF2


672.
T01091
44.0
kDa; CPRF-1


673.
T01546
44.0
kDa; E2F-4


674.
T01942
44.0
kDa; IkappaB-gamma2


675.
T01963
44.0
kDa; Lim-3


676.
T01964
44.0
kDa; Lim-3


677.
T02115
44.0
kDa; USF2


678.
T00930
44.1
kDa; LEF-1


679.
T00802
44.2
kDa; TCF-1alpha


680.
T01723
44.3
kDa; HOXB3


681.
T01414
44.4
kDa; Net


682.
T01724
44.4
kDa; HOXB3


683.
T02185
44.4
kDa; TFIIH-p44


684.
T01051
44.5
kDa; XFD-1


685.
T01413
44.5
kDa; Net


686.
T01830
44.5
kDa; XFD-1′


687.
T01960
44.5
kDa; Lim-1


688.
T00278
44.6
kDa; delta factor


689.
T00162
44.7
kDa; CreA


690.
T00865
44.7
kDa; UCRBP


691.
T01841
44.7
kDa; WT1-del2


692.
T02128
44.7
kDa; SAP-1b


693.
T00678
44.8
kDa; Pax-2a


694.
T00915
44.8
kDa; YY1


695.
T00955
44.8
kDa; DSXF


696.
T01541
44.8
kDa; Esc1


697.
T01954
44.8
kDa; vHNF-1C


698.
T01959
44.8
kDa; Lim-1


699.
T01961
44.8
kDa; Lim-1


700.
T00250
44.9
kDa; Elk-1


701.
T01962
44.9
kDa; Lim-1


702.
T00051
45.0
kDa; ATF


703.
T00069
45.0
kDa; BrlA


704.
T00215
45.0
kDa; muEBP-C2


705.
T00527
45.0
kDa; MyoD


706.
T00563
45.0
kDa; NF-muE3


707.
T00834
45.0
kDa; TIN-1


708.
T00995
45.0
kDa; DBSF


709.
T01052
45.0
kDa; XFD-1+


710.
T01107
45.0
kDa; EBP45


711.
T01215
45.0
kDa; NF-muE3


712.
T01353
45.0
kDa; PPARbeta


713.
T01365
45.0
kDa; p45


714.
T02096
45.0
kDa; Scr


715.
T01548
45.1
kDa; DP-1


716.
T01549
45.1
kDa; DP-1


717.
T01834
45.1
kDa; Axial


718.
T01838
45.2
kDa; Sox-4


719.
T01850
45.2
kDa; DSP1


720.
T02193
45.2
kDa; TFIIH-CCL1


721.
T00656
45.3
kDa; Oct-6


722.
T00178
45.4
kDa; CTF-3


723.
T00969
45.5
kDa; Oct-6


724.
T01820
45.5
kDa; Gsb


725.
T02288
45.5
kDa; HFH-1


726.
T00445
45.6
kDa; Kni


727.
T01867
45.7
kDa; Oct-2.6


728.
T01075
45.8
kDa; lin-11


729.
T01239
45.8
kDa; CAD1


730.
T01921
45.9
kDa; Gfi-1


731.
T00141
46.0
kDa; c-Myc


732.
T00786
46.0
kDa; TAF-II


733.
T00836
46.0
kDa; T3R


734.
T00837
46.0
kDa; T3R


735.
T00838
46.0
kDa; T3R


736.
T00839
46.0
kDa; T3R


737.
T00840
46.0
kDa; T3R


738.
T00854
46.0
kDa; T3R


739.
T01385
46.0
kDa; CREB


740.
T00763
46.1
kDa; SRF


741.
T00149
46.2
kDa; COUP


742.
T01543
46.3
kDa; E2F-1


743.
T01915
46.3
kDa; NF-1X1


744.
T01409
46.4
kDa; p38erg


745.
T01265
46.5
kDa; MAC1


746.
T01647
46.5
kDa; Dpn


747.
T02279
46.5
kDa; ZNF174


748.
T01122
46.6
kDa; Pax-6


749.
T01481
46.6
kDa; Pbx-1a


750.
T02176
46.6
kDa; TFIIF-beta


751.
T00681
46.7
kDa; Pax-6


752.
T01967
46.7
kDa; LH-2


753.
T00737
46.8
kDa; SAP-1a


754.
T00841
46.8
kDa; T3R-alpha


755.
T01152
46.8
kDa; T3R-alpha1


756.
T01173
46.8
kDa; T3R-alpha


757.
T01342
46.8
kDa; T3R-alpha1


758.
T01351
46.8
kDa; T3R-alpha


759.
T01554
46.8
kDa; Mi


760.
T01683
46.8
kDa; PTFbeta


761.
T01928
46.8
kDa; Bcl-3


762.
T00295
46.9
kDa; Ftz


763.
T00630
46.9
kDa; N-Oct-3


764.
T01542
46.9
kDa; E2F-1


765.
T01553
46.9
kDa; Mi


766.
T01903
46.9
kDa; NF-1X


767.
T00029
47.0
kDa; AP-1


768.
T00045
47.0
kDa; ARP-1


769.
T00388
47.0
kDa; H1TF2


770.
T00442
47.0
kDa; 47-kDa CRE bind. prot.


771.
T00539
47.0
kDa; NF-1


772.
T01690
47.1
kDa; Elt-2


773.
T01873
47.1
kDa; N-Oct-3


774.
T00900
47.2
kDa; WT1 I-KTS


775.
T01524
47.2
kDa; N-Oct-3


776.
T01276
47.3
kDa; Sox-4


777.
T02321
47.3
kDa; SRE-ZBP


778.
T00552
47.4
kDa; NF-1B2


779.
T01526
47.4
kDa; Brachyury


780.
T01966
47.4
kDa; LH-2


781.
T01544
47.5
kDa; E2F-2


782.
T01840
47.5
kDa; WT1 I


783.
T02236
47.6
kDa; TFIIE


784.
T02237
47.6
kDa; TFIIE-alpha


785.
T02300
47.6
kDa; CTF-5


786.
T00882
47.8
kDa; VDR


787.
T01774
47.8
kDa; APETALA2


788.
T00177
47.9
kDa; CTF-2


789.
T00806
47.9
kDa; TEF-1


790.
T01124
47.9
kDa; TEF-1


791.
T01768
47.9
kDa; MEF-2C/delta32


792.
T00310
48.0
kDa; GATA-3


793.
T00439
48.0
kDa; KBF1


794.
T00568
48.0
kDa; NF-E1c


795.
T01213
48.0
kDa; KBF1


796.
T02156
48.0
kDa; Esc


797.
T02157
48.0
kDa; TFIIA


798.
T00035
48.1
kDa; AP-2


799.
T01824
48.1
kDa; Pax-8a


800.
T00402
48.2
kDa; ICSBP


801.
T01468
48.2
kDa; ZID


802.
T01469
48.2
kDa; Ik-1


803.
T01814
48.2
kDa; Pax-6/Pd-5a


804.
T01821
48.2
kDa; Gsbn


805.
T00885
48.3
kDa; VDR


806.
T01916
48.3
kDa; NF-1X2


807.
T02036
48.3
kDa; CRE-BP3


808.
T02038
48.3
kDa; ICSBP


809.
T00682
48.4
kDa; Pax[zf-a]


810.
T00716
48.5
kDa; RAR


811.
T01049
48.5
kDa; HNF-3B


812.
T00490
48.6
kDa; MAZ


813.
T02235
48.6
kDa; PEBP2alphaB1


814.
T02245
48.7
kDa; AML1b


815.
T00140
48.8
kDa; c-Myc


816.
T00371
48.8
kDa; HNF-3


817.
T00610
48.8
kDa; NF-1X


818.
T02303
48.8
kDa; Pur-1


819.
T00142
48.9
kDa; c-Myc


820.
T01828
48.9
kDa; Pax-8


821.
T01833
48.9
kDa; c-Qin


822.
T01839
48.9
kDa; WT1-KTS


823.
T02056
48.9
kDa; CRE-BP1


824.
T00106
49.0
kDa; C/EBP


825.
T00143
49.0
kDa; c-Myc


826.
T01599
49.0
kDa; LCR-F1


827.
T02165
49.0
kDa; TFIIE-alpha


828.
T01545
49.1
kDa; E2F-3


829.
T01869
49.1
kDa; Oct-2.8


830.
T01930
49.1
kDa; NF-kappaB2 (p49)


831.
T02306
49.1
kDa; GCMa


832.
T00554
49.2
kDa; NF-1C2


833.
T02037
49.3
kDa; ICSBP


834.
T01819
49.4
kDa; Pax-6


835.
T01870
49.4
kDa; Oct-2.1


836.
T00646
49.5
kDa; Oct-2.1


837.
T00996
49.5
kDa; SRY


838.
T01041
49.5
kDa; HSF


839.
T01445
49.5
kDa; N-Myc


840.
T01864
49.5
kDa; Oct-2.1


841.
T02162
49.5
kDa; TFIIE-alpha


842.
T00053
49.6
kDa; ATF-adelta


843.
T00767
49.7
kDa; Sry-delta


844.
T00952
49.7
kDa; AP-2


845.
T02030
49.7
kDa; Sd


846.
T02307
49.7
kDa; GCMa


847.
T01341
49.8
kDa; RAR-gamma2


848.
T00718
49.9
kDa; RAR


849.
T00033
50.0
kDa; AP-2


850.
T00034
50.0
kDa; AP-2


851.
T00037
50.0
kDa; AP-5


852.
T00201
50.0
kDa; DTF-1


853.
T00222
50.0
kDa; E4F


854.
T00380
50.0
kDa; H2RIIBP


855.
T00434
50.0
kDa; IUF-1


856.
T00435
50.0
kDa; JRF


857.
T00479
50.0
kDa; LyF-1


858.
T00567
50.0
kDa; NF-E1b


859.
T00719
50.0
kDa; RAR-alpha1


860.
T00733
50.0
kDa; RPF1


861.
T01465
50.0
kDa; TRF (2)


862.
T01923
50.0
kDa; NF-kappaB1


863.
T00668
50.1
kDa; Opaque-2


864.
T02053
50.1
kDa; HB24


865.
T01260
50.2
kDa; STD1


866.
T00111
50.3
kDa; c-Ets-1


867.
T00721
50.3
kDa; RAR-beta


868.
T01326
50.3
kDa; RAR-beta2


869.
T01330
50.3
kDa; RAR-gamma1


870.
T01338
50.3
kDa; RAR-beta2


871.
T01766
50.3
kDa; MEF-2C (465 AA form)


872.
T02040
50.3
kDa; c-Ets-1A


873.
T00112
50.4
kDa; c-Ets-1


874.
T00114
50.4
kDa; c-Ets-1 54


875.
T01769
50.4
kDa; MEF-2C


876.
T01689
50.5
kDa; Staf-50


877.
T02292
50.5
kDa; BF-2


878.
T00372
50.6
kDa; HNF-4


879.
T01056
50.6
kDa; slp2


880.
T01337
50.6
kDa; RAR-beta1


881.
T02144
50.6
kDa; ADA2


882.
T01335
50.7
kDa; RAR-alpha1


883.
T01253
50.8
kDa; PUB1


884.
T01340
50.8
kDa; RAR-gamma1


885.
T01345
50.8
kDa; RXR-alpha


886.
T02029
50.8
kDa; C/EBP


887.
T02051
50.8
kDa; HB24


888.
T01333
50.9
kDa; RXR-gamma


889.
T01336
50.9
kDa; RAR-alpha2


890.
T00396
51.0
kDa; Pax-7


891.
T00593
51.0
kDa; NF-kappaB1


892.
T01267
51.0
kDa; GAL80


893.
T01390
51.0
kDa; GABP-alpha


894.
T01408
51.0
kDa; Fli-1


895.
T01906
51.0
kDa; NF-1A5


896.
T02066
51.0
kDa; Fli-1


897.
T02067
51.0
kDa; Fli-1


898.
T00647
51.1
kDa; Oct-2


899.
T01815
51.1
kDa; Vab-3


900.
T02305
51.1
kDa; MAZi


901.
T00650
51.2
kDa; Oct-2


902.
T01331
51.2
kDa; RXR-alpha


903.
T01663
51.2
kDa; TR2-9


904.
T02283
51.2
kDa; Kox1


905.
T00079
51.3
kDa; Cad


906.
T00251
51.3
kDa; ELP


907.
T00648
51.3
kDa; Oct-2


908.
T01402
51.4
kDa; GABP-alpha


909.
T01428
51.4
kDa; E4BP4


910.
T01572
51.4
kDa; LSIRF-2


911.
T01831
51.5
kDa; BF-1


912.
T01895
51.5
kDa; Pou2


913.
T02145
51.5
kDa; GCN5


914.
T00764
51.6
kDa; SRF


915.
T01412
51.6
kDa; NF-EM5


916.
T01865
51.8
kDa; Oct-2.3


917.
T02246
51.8
kDa; AML1c


918.
T01046
51.9
kDa; HSF3


919.
T00266
52.0
kDa; Erg-2


920.
T00394
52.0
kDa; NF-kappaB2


921.
T00785
52.0
kDa; TAF-I


922.
T00899
52.0
kDa; WT1


923.
T01074
52.1
kDa; Ap


924.
T00851
52.2
kDa; T3R-beta


925.
T01882
52.3
kDa; Unc-86


926.
T02191
52.3
kDa; TFIIH-p50


927.
T00694
52.4
kDa; PPAR


928.
T00991
52.4
kDa; PPAR


929.
T01618
52.5
kDa; EBNA-2


930.
T00077
52.6
kDa; CACCC-binding factor


931.
T00853
52.7
kDa; T3R-beta1


932.
T01943
52.7
kDa; IkappaBR


933.
T02085
52.7
kDa; Elg


934.
T02135
52.7
kDa; TAF(I)48


935.
T01397
52.8
kDa; c-Ets-2


936.
T01951
52.8
kDa; HNF-1C


937.
T02297
52.8
kDa; NF-1A2


938.
T01352
52.9
kDa; PPARalpha


939.
T01868
52.9
kDa; Oct-2.7


940.
T02104
52.9
kDa; HSF1 (short)


941.
T00113
53.0
kDa; c-Ets-2


942.
T00679
53.0
kDa; Pax-3


943.
T00680
53.0
kDa; Pax-3


944.
T01357
53.0
kDa; RAR-gamma1


945.
T01417
53.0
kDa; tel


946.
T01662
53.0
kDa; TR2


947.
T00006
53.2
kDa; Ase


948.
T01010
53.2
kDa; RSRFC9


949.
T01066
53.3
kDa; runt


950.
T01339
53.3
kDa; RAR-beta3


951.
T00120
53.5
kDa; CF2-II


952.
T01009
53.6
kDa; RSRFC4


953.
T01044
53.6
kDa; HSF1


954.
T00505
53.7
kDa; MEF-2


955.
T01933
53.8
kDa; Cactus


956.
T02008
53.8
kDa; Ems


957.
T02129
53.8
kDa; p55erg


958.
T02130
53.8
kDa; p49erg


959.
T01200
53.9
kDa; Egr-1


960.
T02041
53.9
kDa; c-Ets-2A


961.
T02127
53.9
kDa; c-Ets-2B


962.
T00220
54.0
kDa; E2F


963.
T00221
54.0
kDa; E2F


964.
T00373
54.0
kDa; HNF-4


965.
T01354
54.1
kDa; PPARgamma


966.
T01771
54.1
kDa; MEF-2D


967.
T00894
54.3
kDa; Vmw65


968.
T01054
54.3
kDa; Fkh


969.
T01772
54.3
kDa; D-MEF2


970.
T00599
54.4
kDa; NF-1/L


971.
T01517
54.4
kDa; Twi


972.
T01571
54.4
kDa; IRF-3


973.
T00063
54.5
kDa; Bcd


974.
T00116
54.5
kDa; c-Ets-2 58-64


975.
T00167
54.5
kDa; CRE-BP1


976.
T02291
54.5
kDa; Croc


977.
T01905
54.6
kDa; NF-1A4


978.
T01713
54.7
kDa; HOXA10


979.
T01917
54.7
kDa; NF-1X3


980.
T02239
54.7
kDa; TFIIE-alpha


981.
T00301
54.8
kDa; GAGA factor


982.
T01005
54.8
kDa; MEF-2


983.
T01153
54.8
kDa; T3R-alpha2


984.
T00384
54.9
kDa; HSF


985.
T01525
54.9
kDa; HSF1


986.
T00115
55.0
kDa; c-Ets-1 68


987.
T00117
55.0
kDa; CF1


988.
T00314
55.0
kDa; GATA-3


989.
T01198
55.0
kDa; NRF-2


990.
T01199
55.0
kDa; NRF-2


991.
T01240
55.0
kDa; ABF1


992.
T01349
55.0
kDa; RXR-beta


993.
T01362
55.0
kDa; Hp55


994.
T01476
55.0
kDa; Abd-B


995.
T01343
55.1
kDa; T3R-alpha2


996.
T01910
55.1
kDa; NF-1B3


997.
T01918
55.1
kDa; NF-1C1


998.
T02281
55.1
kDa; AML3


999.
T01084
55.2
kDa; TEC1


1000.
T01875
55.4
kDa; Oct-2


1001.
T00175
55.5
kDa; CTF-1


1002.
T01901
55.5
kDa; PDM-2


1003.
T00176
55.6
kDa; CTF-1


1004.
T01616
55.7
kDa; RBP-Jkappa


1005.
T01062
55.8
kDa; PEBP2alphaA1


1006.
T00897
55.9
kDa; v-Rel


1007.
T01770
55.9
kDa; MEF-2D


1008.
T00307
56.0
kDa; GATA-2


1009.
T00509
56.0
kDa; MIG1


1010.
T00692
56.0
kDa; PO-B


1011.
T00993
56.0
kDa; hsp56


1012.
T01226
56.0
kDa; PO-B


1013.
T01904
56.0
kDa; NF-1A1.1


1014.
T02296
56.0
kDa; NF-1A1


1015.
T01853
56.1
kDa; SOX-9


1016.
T02308
56.1
kDa; GCMb


1017.
T01597
56.2
kDa; NF2d9


1018.
T02302
56.2
kDa; GCM


1019.
T01907
56.3
kDa; NF-1C1


1020.
T01784
56.4
kDa; MEF-2


1021.
T01603
56.5
kDa; dCREB-A


1022.
T00244
56.6
kDa; Egr-1


1023.
T01941
56.6
kDa; IkappaB-gamma1


1024.
T01308
56.8
kDa; CRE-BPa


1025.
T01334
56.9
kDa; RXR-beta


1026.
T00152
57.0
kDa; CP2


1027.
T00807
57.0
kDa; TEF-2


1028.
T00151
57.2
kDa; CP2


1029.
T01998
57.2
kDa; Cnc


1030.
T01042
57.3
kDa; HSF1 (long)


1031.
T01568
57.3
kDa; MYB.Ph3


1032.
T00956
57.4
kDa; DSXM


1033.
T02318
57.4
kDa; PEBP2alphaA/til-1


1034.
T00544
57.5
kDa; NF-1A1


1035.
T01088
57.7
kDa; ILF


1036.
T01273
57.9
kDa; TAF(II)60


1037.
T01950
57.9
kDa; HNF-1B


1038.
T00058
58.0
kDa; BAP


1039.
T00389
58.0
kDa; H2TF1


1040.
T00440
58.0
kDa; KBF2


1041.
T01364
58.0
kDa; p58


1042.
T02164
58.0
kDa; TFIIE


1043.
T01350
58.1
kDa; T3R-beta2


1044.
T00972
58.2
kDa; HSF2


1045.
T02168
58.3
kDa; TFIIF-alpha


1046.
T01953
58.4
kDa; vHNF-1B


1047.
T01617
58.5
kDa; RBP-Jkappa


1048.
T01909
58.6
kDa; NF-1B2


1049.
T02171
58.7
kDa; TFIIF-alpha


1050.
T02320
58.7
kDa; PEBP2alphaA/til-1 (Y)


1051.
T00358
59.0
kDa; HEF-1T


1052.
T00990
59.0
kDa; FKBP59


1053.
T01527
59.0
kDa; RORalpha1


1054.
T01897
59.0
kDa; Cf1a


1055.
T01523
59.1
kDa; p65delta


1056.
T01934
59.1
kDa; c-Rel


1057.
T00253
59.4
kDa; En


1058.
T01883
59.5
kDa; CEH-18


1059.
T00252
60.0
kDa; embryo DNA binding protein


1060.
T00448
60.0
kDa; 60K protein


1061.
T00553
60.0
kDa; NF-BA1


1062.
T00608
60.0
kDa; NF-W1


1063.
T00622
60.0
kDa; NHP-2


1064.
T00649
60.0
kDa; Oct-2


1065.
T00734
60.0
kDa; RVF


1066.
T00735
60.0
kDa; RVF


1067.
T00736
60.0
kDa; RVF


1068.
T00812
60.0
kDa; TFEB


1069.
T00884
60.0
kDa; VDR


1070.
T00906
60.0
kDa; XPF-1


1071.
T01133
60.0
kDa; TTF-2


1072.
T01195
60.0
kDa; NHP-2


1073.
T01196
60.0
kDa; NHP-2


1074.
T01489
60.0
kDa; RBP60


1075.
T01490
60.0
kDa; RBP60


1076.
T02167
60.0
kDa; TFIIE


1077.
T00594
60.2
kDa; RelA


1078.
T00595
60.2
kDa; RelA


1079.
T00964
60.2
kDa; Oct-2B


1080.
T01043
60.3
kDa; HSF2


1081.
T01932
60.3
kDa; RelB


1082.
T00676
60.6
kDa; Pap1+


1083.
T01614
60.6
kDa; Skn-1


1084.
T00684
60.8
kDa; PEA3


1085.
T00263
61.0
kDa; ER


1086.
T02154
61.2
kDa; SRB10


1087.
T00891
61.3
kDa; vHNF-1A


1088.
T00889
61.4
kDa; vHNF-1


1089.
T01955
61.5
kDa; vHNF-1


1090.
T00890
61.7
kDa; vHNF-1


1091.
T00918
61.8
kDa; Zeste


1092.
T02282
61.8
kDa; Glass


1093.
T00289
62.0
kDa; f-EBP


1094.
T00351
62.0
kDa; HAP4


1095.
T00449
62.0
kDa; 62K protein


1096.
T00604
62.0
kDa; NF-1/Red1


1097.
T00936
62.0
kDa; ENKTF-1


1098.
T01070
62.0
kDa; TREF2


1099.
T01399
62.0
kDa; TCF


1100.
T01931
62.0
kDa; RelB


1101.
T02183
62.0
kDa; TFIIH-p62


1102.
T01040
62.1
kDa; Olf-1


1103.
T01529
62.3
kDa; RORalpha3


1104.
T00329
62.5
kDa; Glass


1105.
T00551
62.6
kDa; NF-1B1


1106.
T01045
62.8
kDa; HSF2


1107.
T01997
62.8
kDa; dFRA


1108.
T00474
63.0
kDa; LSF


1109.
T00803
63.0
kDa; TCF-2alpha


1110.
T00862
63.0
kDa; UBP-1


1111.
T01246
63.0
kDa; TBF1


1112.
T01528
63.0
kDa; RORalpha2


1113.
T02134
63.0
kDa; TAF(I)63


1114.
T01894
63.1
kDa; pou[c]


1115.
T00689
63.4
kDa; PHO2


1116.
T01256
63.6
kDa; HCM1


1117.
T02248
63.6
kDa; StuAp


1118.
T00193
63.8
kDa; Dfd


1119.
T00095
64.0
kDa; CCAAT-binding factor


1120.
T00701
64.0
kDa; PTF1-beta


1121.
T01185
64.0
kDa; CCAAT-binding factor


1122.
T01186
64.0
kDa; CCAAT-binding factor


1123.
T01227
64.0
kDa; PTF1


1124.
T01254
64.3
kDa; PAB1


1125.
T02124
64.3
kDa; TAF(II)60


1126.
T01112
64.4
kDa; EBF


1127.
T02173
64.5
kDa; TFIIF-alpha


1128.
T01940
64.8
kDa; IkappaB-gamma


1129.
T00169
65.0
kDa; c-Rel


1130.
T00262
65.0
kDa; ER


1131.
T00392
65.0
kDa; H4TF-2


1132.
T00560
65.0
kDa; NF-E4


1133.
T00587
65.0
kDa; NF-kappaB


1134.
T00588
65.0
kDa; NF-kappaB


1135.
T00590
65.0
kDa; NF-kappaB


1136.
T01363
65.0
kDa; Hp65


1137.
T02247
65.0
kDa; Staf


1138.
T01900
65.2
kDa; PDM-1


1139.
T02266
65.2
kDa; PEBP2alphaA/Osf2


1140.
T01598
65.3
kDa; ECH


1141.
T01672
65.3
kDa; RFX5


1142.
T00699
65.5
kDa; Prd


1143.
T00049
66.0
kDa; ATF


1144.
T00062
66.0
kDa; BGP1


1145.
T00156
66.0
kDa; alpha-CP2a, alpha-CP2b


1146.
T01443
66.1
kDa; Nrf2


1147.
T00261
66.2
kDa; ER


1148.
T00463
66.3
kDa; Lc


1149.
T00674
66.4
kDa; E47


1150.
T00710
66.6
kDa; R


1151.
T00264
66.7
kDa; ER


1152.
T01154
66.8
kDa; c-Rel


1153.
T01415
66.8
kDa; pointedP1


1154.
T01615
66.9
kDa; Su(H)


1155.
T02204
66.9
kDa; Nrf2


1156.
T00258
67.0
kDa; ER


1157.
T00259
67.0
kDa; ER


1158.
T00672
67.0
kDa; p67


1159.
T00761
67.0
kDa; SRF


1160.
T00762
67.0
kDa; SRF


1161.
T00765
67.0
kDa; SRF


1162.
T01244
67.0
kDa; HSF


1163.
T02272
67.0
kDa; HEB1-p67


1164.
T01211
67.2
kDa; HNF-1


1165.
T00207
67.3
kDa; E47


1166.
T00368
67.3
kDa; HNF-1A


1167.
T01664
67.3
kDa; TR2-11


1168.
T00204
67.4
kDa; E12


1169.
T01113
67.5
kDa; Elf-1


1170.
T00675
67.7
kDa; E12


1171.
T01849
67.9
kDa; Ixr1


1172.
T02287
67.9
kDa; phiAP3


1173.
T00203
68.0
kDa; E1


1174.
T00791
68.0
kDa; TAR factor


1175.
T01245
68.0
kDa; Reb1p


1176.
T01374
68.0
kDa; URF


1177.
T02100
68.1
kDa; Zeste


1178.
T02064
68.2
kDa; Lab


1179.
T00168
68.5
kDa; c-Rel


1180.
T01292
68.6
kDa; RIM1


1181.
T00843
69.0
kDa; Ttk 69K


1182.
T01835
69.2
kDa; Whn


1183.
T01952
69.2
kDa; HNF-1


1184.
T01258
69.7
kDa; MSN4


1185.
T02078
69.7
kDa; Otd


1186.
T00068
70.0
kDa; BRF1


1187.
T00621
70.0
kDa; NHP-1


1188.
T01165
70.0
kDa; H16


1189.
T01193
70.0
kDa; NHP-1


1190.
T01194
70.0
kDa; NHP-1


1191.
T01787
70.0
kDa; E12


1192.
T01306
70.2
kDa; SKO1


1193.
T01250
70.3
kDa; BUF2


1194.
T02310
70.3
kDa; MET4


1195.
T01793
70.4
kDa; GE1


1196.
T00433
71.2
kDa; ITF-2


1197.
T00138
71.5
kDa; c-Myb


1198.
T02208
71.5
kDa; TAF(II)70-gamma


1199.
T01660
71.8
kDa; PR A


1200.
T00976
72.0
kDa; NFdeltaE3A


1201.
T00028
72.5
kDa; AP-1


1202.
T00137
72.5
kDa; c-Myb


1203.
T00139
72.5
kDa; c-Myb


1204.
T00783
72.7
kDa; TAF(II)70-alpha


1205.
T01497
72.9
kDa; ALF1A


1206.
T01503
72.9
kDa; HEB


1207.
T01679
72.9
kDa; PacC


1208.
T01789
72.9
kDa; SCBPgamma


1209.
T02190
72.9
kDa; TFIIH-p73


1210.
T00064
73.0
kDa; BmFTZ-F1


1211.
T00887
73.0
kDa; VETF


1212.
T01863
73.0
kDa; Oct-1C


1213.
T01087
73.3
kDa; Vp1


1214.
T01783
73.5
kDa; RLM1


1215.
T00750
73.6
kDa; Sim


1216.
T01251
73.7
kDa; PCT1


1217.
T01994
73.7
kDa; CAUP


1218.
T01034
73.9
kDa; Da


1219.
T00219
74.0
kDa; E2F


1220.
T00495
74.0
kDa; MBF-I


1221.
T01594
74.7
kDa; v-Myb/v-Ets


1222.
T00054
75.0
kDa; ATF-like


1223.
T00136
75.0
kDa; c-Myb


1224.
T00443
75.0
kDa; 75 kDa protein


1225.
T00662
75.0
kDa; Oct-2B


1226.
T01421
75.0
kDa; PTF1-alpha


1227.
T01264
75.4
kDa; HST


1228.
T01993
75.4
kDa; ARA


1229.
T00196
75.5
kDa; Dl


1230.
T01791
75.7
kDa; SCBPbeta


1231.
T01496
75.8
kDa; ALF1B


1232.
T01790
75.8
kDa; SCBPalpha


1233.
T01289
75.9
kDa; STE12


1234.
T00855
76.0
kDa; TSAP


1235.
T01031
76.0
kDa; Oct-1


1236.
T00641
76.5
kDa; Oct-1


1237.
T01669
76.5
kDa; RFX2


1238.
T01862
76.8
kDa; Oct-1B


1239.
T00386
76.9
kDa; HSTF


1240.
T01416
77.6
kDa; pointedP2


1241.
T01586
77.7
kDa; B-Myb


1242.
T01257
77.8
kDa; MSN2


1243.
T01945
77.8
kDa; NF-ATc


1244.
T02209
77.9
kDa; TAF(II)70-beta


1245.
T00772
78.0
kDa; STE12


1246.
T02148
78.5
kDa; SRB4


1247.
T01396
78.6
kDa; yan


1248.
T00065
78.8
kDa; B-Myb


1249.
T02322
78.8
kDa; BCL-6


1250.
T00922
79.1
kDa; Zmhox1a


1251.
T01587
79.1
kDa; B-Myb


1252.
T00315
79.3
kDa; GBF


1253.
T02122
79.3
kDa; TAF(II)80


1254.
T02146
79.3
kDa; ADA3


1255.
T01670
79.4
kDa; RFX3


1256.
T00644
79.5
kDa; Oct-1A


1257.
T01097
79.5
kDa; GT-2


1258.
T01975
79.9
kDa; RREB-1


1259.
T00211
80.0
kDa; EBNA-1


1260.
T01161
80.0
kDa; EBP-80


1261.
T01667
80.0
kDa; RFX2


1262.
T01856
80.7
kDa; SSRP1


1263.
T00754
81.0
kDa; Sp1


1264.
T01003
81.1
kDa; SSRP1


1265.
T01442
81.5
kDa; Nrf1


1266.
T01920
81.5
kDa; GR beta


1267.
T02203
81.5
kDa; Nrf1


1268.
T01848
81.7
kDa; Dm-SSRP1


1269.
T02278
81.7
kDa; SEM-4


1270.
T00056
82.0
kDa; BAF1


1271.
T00451
82.0
kDa; 77 + 82K protein


1272.
T01069
82.0
kDa; TREF1


1273.
T02175
82.2
kDa; TFIIF-alpha


1274.
T01661
82.4
kDa; PR A


1275.
T00172
82.8
kDa; CTCF


1276.
T02284
82.8
kDa; CTCF


1277.
T00383
83.0
kDa; HSF


1278.
T01573
83.0
kDa; STAT1beta


1279.
T02315
83.1
kDa; Rc


1280.
T01454
83.2
kDa; Hsp90


1281.
T01585
83.6
kDa; A-Myb


1282.
T02285
83.7
kDa; CTCF


1283.
T01794
84.0
kDa; INSAF


1284.
T00426
85.0
kDa; alpha-IRP


1285.
T00867
85.0
kDa; UHF-1


1286.
T01295
85.0
kDa; FTS


1287.
T01796
85.0
kDa; Arnt (774 AA form)


1288.
T01583
85.1
kDa; A-Myb


1289.
T01845
85.2
kDa; Sox-LZ


1290.
T01252
85.5
kDa; CDC10


1291.
T01584
85.5
kDa; A-Myb


1292.
T02084
85.6
kDa; Pb


1293.
T02219
85.6
kDa; Lz


1294.
T00337
85.7
kDa; GR alpha


1295.
T00698
85.7
kDa; PR


1296.
T00931
85.8
kDa; AmdR


1297.
T01576
85.9
kDa; STAT4


1298.
T00914
86.0
kDa; YPF1


1299.
T01582
86.0
kDa; A-Myb


1300.
T00335
86.1
kDa; GR


1301.
T01988
86.4
kDa; STAT


1302.
T00002
86.6
kDa; ACE2


1303.
T01346
86.6
kDa; Arnt


1304.
T00784
86.7
kDa; TAF(II)100


1305.
T01684
86.9
kDa; TEA1


1306.
T02182
86.9
kDa; TFIIH-p80


1307.
T01797
87.0
kDa; Arnt


1308.
T00208
87.1
kDa; E74A


1309.
T01575
87.2
kDa; STAT1


1310.
T01844
87.2
kDa; Sox-LZ


1311.
T02177
87.2
kDa; SIII-p110


1312.
T02178
87.2
kDa; SIII-p110


1313.
T01492
87.3
kDa; STAT1alpha


1314.
T01642
87.3
kDa; NUC-1


1315.
T01547
87.5
kDa; dE2F


1316.
T00455
88.0
kDa; Krox-24


1317.
T00929
88.0
kDa; PRDI-BF1


1318.
T01574
88.0
kDa; STAT3


1319.
T01493
88.1
kDa; STAT3


1320.
T00844
88.2
kDa; Ttk 88K


1321.
T00709
89.0
kDa; qa-1F


1322.
T01085
89.2
kDa; abaA


1323.
T02181
89.3
kDa; TFIIH-p90


1324.
T02189
89.8
kDa; TFIIH-p85


1325.
T00055
90.0
kDa; B‘’


1326.
T00369
90.0
kDa; HNF-1


1327.
T00387
90.0
kDa; H1TF1


1328.
T00638
90.0
kDa; NTF


1329.
T00944
90.0
kDa; STAT5B


1330.
T00992
90.0
kDa; Hsp90


1331.
T01272
90.0
kDa; TAF-90


1332.
T02243
90.0
kDa; TFIIF


1333.
T01013
90.6
kDa; SWI6


1334.
T01579
90.8
kDa; STAT5A


1335.
T01578
90.9
kDa; STAT5


1336.
T00320
91.0
kDa; GCF


1337.
T01247
91.0
kDa; UME6


1338.
T01795
91.7
kDa; AhR


1339.
T00725
92.1
kDa; REB1


1340.
T00715
92.5
kDa; RAP1


1341.
T01610
92.7
kDa; HIF-1alpha


1342.
T00385
93.3
kDa; HSTF


1343.
T01818
93.3
kDa; Ey


1344.
T01581
93.7
kDa; STAT6


1345.
T00333
94.0
kDa; GR


1346.
T01611
94.0
kDa; HIF-1beta


1347.
T02271
94.0
kDa; HEB1-p94


1348.
T00940
94.1
kDa; GRF-1


1349.
T01580
94.1
kDa; STAT6


1350.
T00322
94.3
kDa; GCR1


1351.
T00957
94.3
kDa; OBP


1352.
T00210
94.8
kDa; E74B


1353.
T00018
95.0
kDa; AhR


1354.
T00739
95.0
kDa; SBF-1


1355.
T00759
95.0
kDa; Sp1


1356.
T01230
95.0
kDa; Vav


1357.
T02133
95.3
kDa; TAF(I)110


1358.
T02192
95.3
kDa; TFIIH-SSL2/RAD25


1359.
T00768
95.4
kDa; Sry h-1


1360.
T02316
95.8
kDa; Blimp-1


1361.
T00453
96.0
kDa; 96K-protein


1362.
T00019
96.2
kDa; AhR


1363.
T00458
97.0
kDa; LAC9


1364.
T00779
97.0
kDa; TAF(II)125


1365.
T01494
97.9
kDa; STAT2


1366.
T00041
98.2
kDa; AR


1367.
T00042
98.2
kDa; AR


1368.
T00880
98.4
kDa; Vav


1369.
T01562
98.5
kDa; ADD1


1370.
T00697
98.7
kDa; PR


1371.
T00040
99.0
kDa; AR


1372.
T00302
99.0
kDa; GAL4


1373.
T00696
99.0
kDa; PR


1374.
T02121
99.3
kDa; TAF(II)110


1375.
T01929
99.7
kDa; NF-kappaB2 precursor


1376.
T00194
100.0
kDa; dioxin receptor


1377.
T00642
100.0
kDa; Oct-1


1378.
T00788
100.0
kDa; T-Ag


1379.
T01305
100.0
kDa; CBP100


1380.
T01927
100.6
kDa; NF-kappaB2 precursor


1381.
T01499
102.0
kDa; IL-6 RE-BP


1382.
T01666
103.7
kDa; RFX1


1383.
T01673
104.7
kDa; RFX1


1384.
T01109
105.0
kDa; TCF-1


1385.
T01925
105.4
kDa; NF-kappaB1 precursor


1386.
T01924
105.6
kDa; NF-kappaB1 precursor


1387.
T01486
106.1
kDa; p107


1388.
T00805
106.2
kDa; Tsh


1389.
T00774
106.3
kDa; su(Hw)


1390.
T00511
106.6
kDa; MR


1391.
T00513
106.9
kDa; MR


1392.
T00970
108.0
kDa; MEP-1


1393.
T00161
110.0
kDa; CPE binding protein


1394.
T00296
110.0
kDa; FTZ-F1


1395.
T00391
110.0
kDa; H4TF-1


1396.
T00420
110.0
kDa; IRBP


1397.
T01271
110.0
kDa; TAF(II)110


1398.
T00669
110.6
kDa; Ovo


1399.
T01558
111.1
kDa; SREBP-1c


1400.
T01163
111.4
kDa; PUT3


1401.
T02143
112.8
kDa; TIF1


1402.
T00428
113.0
kDa; ISGF-3


1403.
T01243
113.0
kDa; TSF3


1404.
T01455
113.0
kDa; ISGF-3alpha


1405.
T02034
113.4
kDa; SWI4


1406.
T01557
113.5
kDa; SREBP-1b


1407.
T00086
114.1
kDa; CBF (5)


1408.
T02314
114.2
kDa; BZP


1409.
T00502
115.0
kDa; MEB-1


1410.
T00503
115.0
kDa; MEB-1


1411.
T01946
115.6
kDa; NF-ATx


1412.
T01019
116.0
kDa; Elf-1


1413.
T02244
116.0
kDa; TFIIF


1414.
T02215
116.7
kDa; TIF1 (1051 AA form)


1415.
T00273
117.0
kDa; Evi-1


1416.
T00919
117.4
kDa; Zfh-1


1417.
T00330
118.0
kDa; GLI


1418.
T00270
120.0
kDa; ETF


1419.
T01379
120.0
kDa; 120-kDa CRE-binding protein


1420.
T01944
120.0
kDa; NF-ATp


1421.
T01948
120.0
kDa; NF-ATp


1422.
T01559
120.5
kDa; SREBP-1


1423.
T01270
120.7
kDa; TAF(II)145


1424.
T01556
121.6
kDa; SREBP-1a


1425.
T00842
122.8
kDa; Tra-1 (long form)


1426.
T01467
123.1
kDa; deltaEF1


1427.
T01694
123.1
kDa; NF-X1


1428.
T00835
123.2
kDa; TMF


1429.
T01688
123.3
kDa; STC


1430.
T01560
123.7
kDa; SREBP-2


1431.
T01561
123.7
kDa; SREBP-2


1432.
T00775
123.8
kDa; SWI4


1433.
T00625
124.1
kDa; AREB6


1434.
T01608
128.4
kDa; p130


1435.
T00879
130.0
kDa; vaccinia virus DNA-binding protein


1436.
T01367
133.0
kDa; E75A


1437.
T02120
138.5
kDa; TAF(II)150


1438.
T01077
140.0
kDa; c-abl


1439.
T02152
143.8
kDa; SRB8


1440.
T02042
144.3
kDa; Cux


1441.
T00778
147.0
kDa; TAF


1442.
T00382
150.0
kDa; HSE-binding protein


1443.
T00011
151.0
kDa; ADR1


1444.
T01368
152.0
kDa; E75B


1445.
T02153
160.0
kDa; SRB9


1446.
T01269
161.5
kDa; TAF(II)150


1447.
T02286
162.2
kDa; MTB-Zf


1448.
T00346
164.0
kDa; HAP1


1449.
T00100
164.4
kDa; CDP


1450.
T00401
170.0
kDa; ICP4


1451.
T01268
170.0
kDa; TAF(II)170


1452.
T00331
172.0
kDa; GLI3


1453.
T00366
180.0
kDa; HIP1


1454.
T01377
180.0
kDa; E2F-BF


1455.
T01682
180.0
kDa; PTFalpha


1456.
T01261
180.8
kDa; brahma


1457.
T02207
189.4
kDa; TAF(II)250Delta


1458.
T01949
190.0
kDa; NF-ATc3


1459.
T00473
200.0
kDa; LIT-1


1460.
T02206
212.7
kDa; CCG1


1461.
T00096
214.4
kDa; CCBF


1462.
T00781
214.7
kDa; TAF(II)250


1463.
T01038
220.0
kDa; TFIIF


1464.
T01378
220.0
kDa; E2F-I


1465.
T00822
230.0
kDa; TFIIE


1466.
T02262
230.0
kDa; TFIIH


1467.
T02119
232.5
kDa; TAF(II)250


1468.
T02004
233.6
kDa; Cut


1469.
T02317
243.7
kDa; Zn-15


1470.
T01427
264.1
kDa; p300


1471.
T02214
265.1
kDa; CBP


1472.
T01318
265.5
kDa; CBP


1473.
T02313
267.4
kDa; MIBP1


1474.
T00939
274.9
kDa; HIV-EP2


1475.
T00007
288.3
kDa; alphaA-CRYBP1


1476.
T00497
297.0
kDa; MBP-1 (1)


1477.
T00071
300.0
kDa; B-TFIID


1478.
T02107
300.0
kDa; PC5


1479.
T00048
305.7
kDa; ATBF1-B


1480.
T00920
332.1
kDa; Zfh-2


1481.
T00850
404.0
kDa; Ttx


1482.
T01665
404.5
kDa; ATBF1-A


1483.
T02140
500.0
kDa; PC2
















TABLE 4







Selected examples of RS-related proteins identified from the database searches,


sorted according to cluster assignment and functional association. 1
















Motifs
Name of


Functional
Entry
Cluster

(other
protein/


association
number
number
Species
than RS)
homolog















Splicing (RS-
3
2
Dm

SRM300


related



4
3
Ce

SWAP2



5
3
Dm

SWAP2



6
4
Hs

SWAP2



9
6
Hs

SIP1



23
7
Hs
RRM
RNPS1



35
7, 64
Dm
RRM
U1-70K



38
7, 64, 110,
Dm
RRM
U2AF-50




127, 131, 141



SWISS-PROT:



U2AF-65



P26368



SWISS-PROT:



9G8



Q16629



44
7, 64, 127, 141
Ce
RRM
U1-70K



76
21
Dm
SURP
SWAP1



89
28
Dm
KH-
SF1






RBD/ZNF



90
29
Dm
PWI
SRM16O



101
38
Dm

TRA



111
46
Ce
DEAD-
U5-100K






BOX



114
46
Dm
DEAD-
U5-100K






BOX



115
47
Ce
DEAD-
HRH1






BOX



116
47
Dm
S1-
HRH1






RBD/DEAH-






BOX



244
120
Dm
RRM
TRA2



SWISS-PROT:



U1 snRNP 70 kDa



P08621



SWISS-PROT:



U2AF 35 kDa



Q01081



SWISS-PROT:



U2AF 65 kDa



P26368



ENSP00000261905,



U5 snRNP 100 kDa



Q9BUQ8



SWISS-PROT:



SC35



Q01130



SWISS-PROT:



SRp20



P23152



SWISS-PROT:



SRp30C



Q13242



SWISS-PROT:



SRp54



Q05519



SWISS-PROT:



SRp55



Q13247



SWISS-PROT:



SF2



Q07955



SWISS-PROT:



DEAH-box protein 8



Q14562



SWISS-PROT:
hnRNP G



P38159



SWISS-PROT:



Serine/tbreonine-



Q13523



protein kinase



SWISS-PROT:



Hypothetical protein



Q9Y388



CGI-79.B



SWISS-PROT:



B-lymphocyte



Q02040



antigen precursor


3′-end processing
97
36
Ce

FIP1



98
36
Dm
FF
FIP1



119
50
Ce

CF-IM 68K



120
50
Dm

CF-IM 68K


Chrornatin-
108
44
Dm

CIR


associated



190
87
Hs
RRM
ACINUS



191
87
Dm
(RRM)
ACINUS



212
103
Dm
BROMO
GCN5


Transcription
11
6
Dm
PHD/ZNF/
SCAF1


(RNA pol II-



RING


associated



17
7
Hs

SCAF4



25
7, 17
Hs

SCAF10/SR-CYP



30
7, 17, 64, 127,
Dm
RRM
SCAF8





131



63
16
Hs

SCAF9



75
20
Ce

SRP129/SCAF11



82
25
Ce
ZNF/RING/
FCP1a






PHOS



99
36
Dm
WW
CA150



164
69
Ce
CYCLIN
CYCLIN L



165
69
Dm
CYCLIN
CYCLIN L



249
124
Dm

DSLF-P160/SPT5


Transcription
24
7, 17, 64, 127
Hs

LISCH


(other)



85
27
Hs

CACTIN1



87
27
Dm

CACTIN1



133
60
Dm
ZNF/RING
NF-







X1/SHUTTLECRAFT



208
100
Hs

BTF



291
137
Dm
PHD
ALHAMBRA


Kinases and
203
99
Hs
KIN
PRP4-RELATED


phosphatases




KINASE



204
99
Hs
KIN
CLK-2 KINASE



206
99
Dm
KIN
PITSLRE KINASE



207
99
Dm
KIN
CRK7 KINASE



320
148
Sc
RHOD
Ppz1p



324
152
Sc
PHOS
Mip1p/Cdc25p


Cell structure
168
72
Hs
B41
BAND 4 + 1-LIKE



169
72
Dm
B41
BAND 4 + 1-LIKE



235
114
Sc

Sla1p
















TABLE 5







Oligonucleotide sequences used for ChIP PCR


and Real Time PCR analysis.









Amplicon
Forward Primer
Reverse Primer





HIV LTR
ctgcatccggagtacttcaa
aaccagagaagacccagtaca



gaac
ggc



(SEQ ID NO 2)
(SEQ ID NO 3)


 


FFL
atgtatagatttgaagaaga
gataaatcgtatttgtcaatca



gctgtttct
gagtgct



(SEQ ID NO 4)
(SEQ ID NO 5)


 


gapdh
tactagcggttttacgggcg
tcgaacaggaggagcagagagc



(SEQ ID NO 6)
ga




(SEQ ID NO 7)


 


hsp70
gaagagtctggagagttctg
ccttttcccttctgagccaa



(SEQ ID NO 8)
(SEQ ID NO 9)


 


p21/CIP
tatatcagggccgcgctg
ggctccacaaggaactgacttc



(SEQ ID NO 10)
(SEQ ID NO 11)


 


cad
atcccgtggctccgcggac
gcaaactccactggaaccac



(SEQ ID NO 12)
(SEQ ID NO 13)


 


HLA-DRA
aacccttcccctagcaacag
ctagcacagggactccactta



at
tg



(SEQ ID NO 14)
(SEQ ID NO 15)










Antibodies used in the IP and ChIP assays.










Source
Catalog


Protein
(Company)
Number





GFP
Santa Cruz
sc-8334



Biotechnologies



 


RNA Polymerase II
Santa Cruz
sc-899


(N20)
Biotechnologies



 


CTD (8WG16)
Covance
MMS-126R


 


S5P-CTD (H14)
Covance
MMS134R


 


S2P-CTD (H5)
Covance
MMS-129R


 


HA
Covance
MMS-101P


 


CyclinT1
Santa Cruz
sc-10750



Biotechnologies



 


Normal Rabbit IgG
Upstate
12-370


 


HIV Tat
Covance
MMS-116P


 


Nucleolin
Santa Cruz
sc-13057

## Claims

1. A method of inhibiting replication of an immunodeficiency virus, the method comprising the steps of expressing in a cell a nucleic acid construct in an amount sufficient for inhibition of viral transcription, the construct comprising a first nucleic acid sequence encoding HIV-Tat activation domain linked to a second nucleic acid sequence encoding U2AF65, Sfl, 9G8, CstFl, or hnRNP A1.

2. A method of treating a subject infected with an immunodeficiency virus, the method comprising the steps of administering a nucleic acid construct in an amount sufficient for inhibition of viral transcription, the construct comprising a first nucleic acid sequence encoding HIV-Tat activation domain linked to a second nucleic acid sequence encoding U2AF65, Sfl, 9G8, CstFl, or hnRNP A1.

3. The method of claim 1, wherein the inhibition of transcription is at least 25%.

4. The method of claim 1, wherein the inhibition of transcription is at least 50%.

5. The method of claim 1, wherein the inhibition of transcription is at least 75%.

6. The method of claim 1, wherein the inhibition of transcription is at least 95%.

7. The method of claim 1, wherein the cell is a T-cell infected with HIV.

8. The method of claim 2, wherein the inhibition of viral transcription is at least 25%.

9. The method of claim 2, wherein the inhibition of viral transcription is at least 50%.

10. The method of claim 2, wherein the inhibition of viral transcription is at least 75%.

11. The method of claim 2, wherein the inhibition of viral transcription is at least 95%.

12. The method of claim 1, wherein the second nucleic acid sequence encodes U2AF65.

13. The method of claim 1, wherein the second nucleic acid sequence encodes Sfl.

14. The method of claim 1, wherein the second nucleic acid sequence encodes 9G8.

15. The method of claim 1, wherein the second nucleic acid sequence encodes CstF1.

16. The method of claim 1, wherein the second nucleic acid sequence encodes hnRNP A 1.

17. The method of claim 2, wherein the second nucleic acid sequence encodes U2AF65.

18. The method of claim 2, wherein the second nucleic acid sequence encodes Sfl.

19. The method of claim 2, wherein the second nucleic acid sequence encodes 9G8.

20. The method of claim 2, wherein the second nucleic acid sequence encodes CstF1.

21. The method of claim 2, wherein the second nucleic acid sequence encodes hnRNP A1.